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Purpose: Acute gastroenteritis caused by Salmonella spp. among children post a great threat for global public health. The increasing rate of drug-resistant Salmonella spp. has also become a challenging problem worldwide. In this study, the prevalence, serotypes, and antimicrobial characteristics of Salmonella isolated from children in Guangzhou, China, were investigated to provide supporting information for clinical treatment and prevention. Methods: Clinical data of children featured with gastroenteritis symptoms from 2018 to 2023 in Guangdong Women and Children Hospital were collected. The difference and fluctuation of antimicrobial resistance between serotypes and years were retrospectively analyzed. Results: A total of 1304 Salmonella isolates were cultural-confirmed. The overall positive rate of Salmonella isolated from stool samples was 22.0% (1304/5924). Salmonella infections occur mainly from June to September and the majority of infected children aged under 4 years. Serogroup B was the most common serogroup among Salmonella isolates (74.6%, 973/1304). The predominant serotypes of Salmonella isolates were Typhimurium (63.1%, 823/1304). Higher drug resistance rate of Salmonella spp. to ceftriaxone was observed in 2023. The drug resistance rates of Salmonella isolates to sulfamethoxazole/trimethoprim and ampicillin are at high level during the past 6 years. Notably, higher multi-drug resistance (MDR) rate was demonstrated in Salmonella Typhimurium compared with other serotypes. Conclusion: Salmonella Typhimurium was the most common serotype isolated from children in Guangzhou, China, and it may mainly account for the high drug resistance rate in Salmonella spp. to most of the antimicrobial profiles. For controlling the high drug resistance rate of Salmonella spp. continuous surveillance of drug resistance and appropriate use of antibiotics based on clinical and laboratory results are of great significance. [ABSTRACT FROM AUTHOR]

Salmonellosis is one of the important bacterial infectious diseases affecting the health of pigeons. Heretofore, the epidemiological characteristics of Salmonella in pigeon populations in China remain largely unclear. The present study investigated the antimicrobial resistance and genomic characteristics of Salmonella isolates in pigeons in different regions of China from 2022 to 2023. Thirty-two Salmonella isolates were collected and subjected to 24 different antimicrobial agents, representing nine categories. The results showed that these isolates were highly resistant to cefazolin (100%), gentamicin (100%), tobramycin (100%), and amikacin (100%). Three or more types of antimicrobial resistance were present in 90.62% of the isolates, indicating multidrug resistance. Furthermore, using whole genome sequencing technology, we analyzed the profiles of serotypes, multilocus sequence typing, virulence genes, antimicrobial resistance genes, and plasmid replicons and constructed phylogenetic genomics to determine the epidemiological correlation among these isolates. All strains belonged to Salmonella Typhimurium var. Copenhagen and exhibited five antimicrobial resistance genes and more than 150 Salmonella virulence genes. Moreover, each isolate contained both the IncFIB(S) and IncFII(S) plasmids. In addition, phylogenetic analysis showed that all isolates were very close to each other, and isolates from the same region clustered in the same branch. Overall, our findings provide the first evidence for the epidemiological characteristics of Salmonella in pigeons of China, highlighting the importance of preventing salmonellosis in pigeons. [ABSTRACT FROM AUTHOR]

Nontyphoidal Salmonella (NTS) is a cause of foodborne diarrheal diseases worldwide. Important emerging NTS serotypes that have spread as multidrug-resistant high-risk clones include S. Typhimurium monophasic variant and S. Kentucky. In this study, we isolated Salmonella in 5019 stool samples collected from patients with clinical diarrhea and 484 food samples. Antibiotic susceptibility testing and whole-genome sequencing were performed on positive strains. The detection rates of Salmonella among patients with diarrhea and food samples were 4.0% (200/5019) and 3.1% (15/484), respectively. These 215 Salmonella isolates comprised five main serotypes, namely S. Typhimurium monophasic variant, S. Typhimurium, S. London, S. Enteritidis, and S. Rissen, and were mainly resistant to ampicillin, tetracycline, chloramphenicol, and trimethoprim/sulfamethoxazole. The MDR rates of five major serotypes were 77.4%, 56.0%, 66.7%, 53.3%, and 80.0%, respectively. The most commonly acquired extended-spectrum β-lactamase-encoding genes were blaTEM−1B, blaOXA-10, and blaCTX-M-65. The S. Typhimurium monophasic variant strains from Jiaxing City belonged to a unique clone with broad antibiotic resistance. S. Kentucky isolates showed the highest drug resistance, and all were MDR strains. The discovery of high antibiotic resistance rates in this common foodborne pathogen is a growing concern; therefore, ongoing surveillance is crucial to effectively monitor this pathogen. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Kentucky ST198 has emerged as a global threat to humans. In this study, we aimed to characterize the prolonged carriage of ciprofloxacin-resistant and extended-spectrum β-lactamase (ESBL)-producing S. Kentucky ST198 in a single patient with inflammatory bowel disease (IBD). Methods: Three S. Kentucky strains were collected from a single patient with IBD on 11th January, 23rd January, and 8th February, 2022, respectively. Antimicrobial susceptibility testing, whole-genome sequencing, and phylogenetic analysis with 38 previously described Chinese S. Kentucky ST198 strains from patients and food were performed. Results: All three S. Kentucky isolates belonged to ST198. They carried identical 16 resistance genes, such as blaCTX-M-55, tet(A), and qnrS1, and had identical mutations within gyrA (S83F and D87N) and parC (S80I). Therefore, they exhibited identical multidrug-resistant profiles, including the clinically important antibiotics cephalosporins (ceftazidime and cefepime), fluoroquinolones (ciprofloxacin and levofloxacin), and third-generation tetracycline (tigecycline). Our three S. Kentucky strains were classified into the subclade ST198.2– 2, and were genetically identical (2– 6 SNPs) to each other. They exhibited a close genetic similarity (15– 20 SNPs) to the isolate NT-h3189 from a patient and AH19MCS1 from chicken meat in China, indicating a possible epidemiological link between these S. Kentucky ST198 isolates from the patients and chicken meat. Conclusion: Long-term colonization of ciprofloxacin-resistant and ESBL-producing S. Kentucky ST198 in a single patient is a matter of concern. Due to the potential transfer of S. Kentucky ST198 from food sources to humans, ongoing surveillance of this particular clone in animals, animal-derived food products, and humans should be strengthened. [ABSTRACT FROM AUTHOR]

Background: This study aimed to provide epidemiological features of Salmonella enterica serovar Rissen, determine antimicrobial susceptibility, virulence gene profiles, and describe the potential association of S. Rissen from different sources in China. Methods: During 2008– 2019, a total of non-repetitive 228 S. Rissen isolates were collected from human, animals and environment in China. The antimicrobial susceptibility test, screening of antimicrobial and virulence genes by PCR, and pulsed-field gel electrophoresis (PFGE) were performed. Results: Among the 154 isolates from human, the majority of the cases (80.5%) occurred in summer, and S. Rissen was mainly detected in people aged 21– 40 (37.7%) and 41– 60 (28.6%) years old, and 74 non-human source S. Rissen strains were identified, with pork being the most common source. About 93.4% isolates were resistant to at least one of the 12 tested antimicrobial agents, and high frequencies of resistance were observed for tetracyclines (91.2%), trimethoprim-sulfamethoxazole (74.1%) and ampicillin (67.5%). A total of 171 (75%) isolates were resistant to at least three categories of antimicrobials, and the most common resistance profile was Tetracycline(s)-β-Lactams-Sulfonamides. The resistance rates to chloramphenicol, quinolones and sulfafurazole were significantly higher in strains isolated from human compared to non-human source strains. Among these isolates, the β-Lactams resistance was mainly associated with gene blaTEM (54.7%), sulfonamide resistance with sul2 (45.7%) and sul3 (54.3%), tetracycline resistance with tetA (81.3%). All the isolates harbored virulence genes hilA, sopB, sciN, stn and ssrB, and most of them harbored ssaQ (98.7%), mgtC (98.7%) and invA (98.2%). The majority (91.7%) of S. Rissen isolates showed high similarity (> 80%) with each other in PFGE patterns and came from human, animals and environment. Conclusion: The high frequencies of multidrug resistance and probable clonal dissemination in this serovar call for the necessity of systematic surveillance on S. Rissen in China. [ABSTRACT FROM AUTHOR]

Salmonella enterica is a common pathogen in humans and animals that causes food poisoning and infection, threatening public health safety. We aimed to investigate the genome structure, drug resistance, virulence characteristics, and genetic relationship of a Salmonella strain isolated from patients with food poisoning. The pathogen strain 21A was collected from the feces of patients with food poisoning, and its minimum inhibitory concentration against commonly used antibiotics was determined using the strip test and Kirby-Bauer disk methods. Subsequently, WGS analysis was used to reveal the genome structural characteristics and the carrying status of resistance genes and virulence genes of strain 21A. In addition, an MLST-based minimum spanning tree and an SNP-based systematic spanning tree were constructed to investigate its genetic evolutionary characteristics. The strain 21A was identified by mass spectrometry as S. enterica, which was found to show resistance to ampicillin, piperacillin, sulbactam, levofloxacin, and ciprofloxacin. The WGS and bioinformatics analyses revealed this strain as Salmonella Enteritidis belonging to ST11, which is common in China, containing various resistance genes and significant virulence characteristics. Strain 21A was closely related to the SJTUF strains, a series strains from animal, food and clinical sources, as well as from Shanghai, China, which were located in the same evolutionary clade. According to the genetic makeup of strain 21A, the change G > A was found to be the most common variation. We have comprehensively analyzed the genomic characteristics, drug resistance phenotype, virulence phenotype, and genetic evolution relationship of S. Enteritidis strain 21A, which will contribute towards an in-depth understanding of the pathogenic mechanism of S. Enteritidis and the effective prevention and control of foodborne diseases. [ABSTRACT FROM AUTHOR]

Until 2015, polymyxin resistance was primarily attributed to chromosomal mutations. However, with the first report of mobile colistin resistance (mcr-1) in commensal Escherichia coli from food animals in China, the landscape has changed. To evaluate the presence of polymyxin resistance in Salmonella spp., a drop screening test for colistin and polymyxin B was carried out on 1156 isolates of non-human origin (animals, food, and the environment), received in Brazil, between 2016 and 2021. Subsequently, 210 isolates with resistant results in the drop test were subjected to the gold-standard test (broth microdilution) for both colistin and polymyxin B. Whole-genome sequencing (WGS) of 102 resistant isolates was performed for a comprehensive analysis of associated genes. Surprisingly, none of the isolates resistant to colistin in the drop test harbored any of the mcr variants (mcr-1 to mcr-10). WGS identified that the most common mutations were found in pmrA (n= 22; T89S) and pmrB (n = 24; M15T, G73S, V74I, I83A, A111V). Other resistance determinants were also detected, such as the aac(6′)-Iaa gene in 72 isolates, while others carried beta-lactamase genes (blaTEM-1 blaCTX-M-2, blaCMY-2). Additionally, genes associated with fluoroquinolone resistance (qnrB19, qnrS1, oqxA/B) were detected in 11 isolates. Colistin and polymyxin B resistance were identified among Salmonella from non-human sources, but not associated with the mcr genes. Furthermore, the already-described mutations associated with polymyxin resistance were detected in only a small number of isolates, underscoring the need to explore and characterize unknown genes that contribute to resistance. [ABSTRACT FROM AUTHOR]

Objective: Nontyphoidal Salmonella is a significant public health concern due to its ability to cause foodborne illnesses worldwide. This study aims to characterize the nontyphoidal Salmonella strains isolated from patients in China. Methods: A total of 19 nontyphoidal Salmonella strains were characterized through serovar identification, antimicrobial susceptibility testing (AST), biofilm formation assessment. Genetic relatedness was determined using pulsed-field gel electrophoresis (PFGE). WGS was employed to decipher the resistance mechanism and to contextualize the S. serovar Mbandaka strains among previously sequenced isolates in China. The biofilm associated mrkA gene was examined by PCR. Results: The predominant serovar identified was S. Enteritidis, followed by S. Mbandaka, S. Thompson, S. Livingston, S. Alachua, and S. Infantis. PFGE analysis indicated a notable genetic similarity among the S. Mbandaka isolates. Phylogenetic analysis suggested that these strains were likely derived from a single source that had persisted in China for over five years. One multidrug resistance (MDR) S. Enteritidis isolate carried a highly transferable IncB/O/K/Z plasmid with blaCTX-M-15. One S. Thompson strain, harboring the mrkABCDF operon in an IncX1 plasmid, isolated from cutaneous lesions, demonstrated robust biofilm formation. However, no mrkABCDF loci were detected in other strains. Conclusion: Our study emphasizes the importance of persisted surveillance and prompt response to Salmonella infections to protect public health. The dissemination of blaCTX-M-15-harboring IncB/O/K/Z plasmid and the spread of virulent mrkABCDF operon among Salmonella in China and other global regions warrant close monitoring. [ABSTRACT FROM AUTHOR]

Background Zoonotic infections, particularly those caused by non-typhoidal Salmonella (NTS), pose a significant disease burden. However, there is a notable lack of comprehensive and integrated studies employing the One Health approach to address Salmonella prevalence. In this study, we aimed to analyse NTS spatiotemporal prevalence, serovar distribution, and antimicrobial resistance (AMR) across China. Methods We conducted a systematic review and meta-analysis to understand the dynamics of NTS in a One Health context in China. We searched the CNKI, Wanfang, and PubMed databases for Chinese and English peer-reviewed articles published before 1 January 2022 dealing with Salmonella in the context of China. We examined the dynamic prevalence along the food chain, the risk of dominant serovars and the carriers’ regional contribution by principal component analysis, and the AMR burden before and after the ban on using antimicrobials as feed additives across five decades. We used the inverse variance index as an indicator of the inconsistency across studies, and we adopted the restricted maximum likelihood model due to high heterogeneity for analysis with a 95% confidence level for the pooled prevalence estimate. Results Based on 562 retrieved high-quality studies during 1967–2021, representing 5 052 496 samples overall and 80 536 positive samples for NTS isolates, the overall average prevalence was 7.35% (95% confidence interval (CI)=0.069–0.087), which was regionally relatively higher in northern China (8.19%; 95% CI=0.078–0.117) than in southern China (6.94%; 95% CI= 0.067–0.088). Poultry was the primary vehicle for serovars Enteritidis and Indiana (especially in the north), while swine and ruminants for Typhimurium and Derby were the first to highlight the regional livestock contribution to serovar prevalence. The overall AMR rate was 73.63% (95% CI=0.68– 0.99), decreasing after the ban on excessive use of feed-based antibiotics in livestock since 2020, with a relatively low resistance towards front-line and last-resort drugs. Conclusions Our study emphasises the importance of adopting a One Health framework to better understand the zoonotic nature of human NTS and highlights the dominant serovars on food contamination and human infection. The similarity in AMR patterns between poultry and human isolates further emphasises the integrated approach for evaluating disease burden and implementing targeted interventions. [ABSTRACT FROM AUTHOR]

Non-typhoidal salmonellosis is a dangerous foodborne disease that causes enormous economic loss and threatens public health worldwide. The consumption of food, especially poultry or poultry products, contaminated with non-typhoidal Salmonella (NTS) is the main cause of human salmonellosis. To date, no research has identified the molecular epidemiological characteristics of NTS strains isolated from breeder chicken farms in different provinces of China. In our study, we investigated the antimicrobial resistance, phylogenetic relationships, presence of antimicrobial resistance and virulence genes, and plasmids of NTS isolates recovered from breeder chicken farms in five provinces of China between 2020 and 2021 by using a whole-genome sequencing (WGS) approach and phenotypic methods. All sequenced isolates belonged to six serovars with seven sequence types. Nearly half of the isolates (44.87%) showed phenotypic resistance to at least three classes of antimicrobials. Salmonella enterica serotype Kentucky harbored more antimicrobial resistance genes than the others, which was highly consistent with phenotypic resistance. Furthermore, the carried rate of 104 out of 135 detected virulence genes was 100%. Overall, our WGS results highlight the need for the continuous monitoring of, and additional studies on, the antimicrobial resistance of NTS. [ABSTRACT FROM AUTHOR]

Simple Summary: Salmonella is an important pathogen, which causes a variety of animal salmonellosis and foodborne diseases in humans. In recent years, due to the abuse of antimicrobials, the rapid emergence of resistant Salmonella, especially extended spectrum β-lactamase-positive strains (ESBL-producers), has brought great challenges to animal industries and public health safety. The pathogenicity of Salmonella depends on a variety of virulence factors coded by genes in chromosomal pathogenicity islands (SPI) and plasmids. The antibiotic resistance and pathogenic potential of Salmonella have been studied extensively. However, there are gaps that still exist in our understanding of the relationship between resistance and virulence. In this study, we collected 117 Salmonella isolates from diseased chickens in Sichuan Province of China from 2019 to 2021, and investigated antimicrobial resistance (AMR) patterns, including extended spectrum β-lactamase (ESBL) resistance, the prevalence and con-translation of ESBL and virulence genes, and sequence type (ST) among these isolates. The Salmonella isolates showed different frequencies of resistance to antimicrobials, 41.03% of which were ESBL-producers. ESBL genes, such as blaCTX-M-55 (63.29%), blaOXA-31 (26.58%), blaCTX-M-65 (20.25%), and blaTEM-1 (18.99%), were detected. Moreover, the 117 isolates had 11 virulence genes, with frequencies ranging from 29.06% to 100%. There were associations between resistance to cephalosporins and the ESBL genes. The blaCTX-M-55 showed the largest effect on the resistance and there was also a significant association between the presence of most virulence genes and ESBL genes. All isolates were divided into 11 types. The co-transfer of ESBL and virulence genes was observed in the plasmid conjugation test. From this study, we can conclude that Salmonella isolates from chicken were common carriers of ESBLs and multiple virulence genes, and the horizontal transfer played a key role in the dissemination of antimicrobial resistance and pathogenesis. Importantly, the interaction of resistance and virulence factors reinforces the marked pathogenic potential of Salmonella. The aim of this study was to explore the association between antimicrobial resistance, ESBL genes, and virulence genes of Salmonella isolates. From 2019 to 2021, a total of 117 Salmonella isolates were obtained from symptomatic chickens in Sichuan Province, China. The strains were tested for antimicrobial resistance and the presence of ESBL according to the Clinical and Laboratory Standards Institute (CLSI) instructions. The presence of ESBL genes and genes for virulence was determined using Polymerase Chain Reaction (PCR). In addition, Multilocus Sequence Typing (MLST) was applied to confirm the molecular genotyping. Moreover, the mechanism of ESBL and virulence gene transfer and the relationships between the resistance phenotype, ESBL genes, and virulence genes were explored. The isolates exhibited different frequencies of resistance to antibiotics (resistance rates ranged from 21.37% to 97.44%), whereas 68.38% and 41.03% of isolates were multi-drug resistance (MDR) and ESBL-producers, respectively. In the PCR analysis, blaCTX-M was the most prevalent ESBL genotype (73.42%, 58/79), and blaCTX-M-55 showed the most significant effect on the resistance to cephalosporins as tested by logistic regression analysis. Isolates showed a high carriage rate of invA, avrA, sopB, sopE, ssaQ, spvR, spvB, spvC, stn, and bcfC (ranged from 51.28% to 100%). MLST analysis revealed that the 117 isolates were divided into 11 types, mainly ST92, ST11, and ST3717. Of 48 ESBL-producers, 21 transconjugants were successfully obtained by conjugation. Furthermore, ESBL and spv virulence genes were obtained simultaneously in 15 transconjugants. These results highlighted that Salmonella isolates were common carriers of ESBLs and multiple virulence genes. Horizontal transfer played a key role in disseminating antimicrobial resistance and pathogenesis. Therefore, it is necessary to continuously monitor the use of antimicrobials and the prevalence of AMR and virulence in Salmonella from food animals and to improve the antibiotic stewardship for salmonellosis. [ABSTRACT FROM AUTHOR]

A cross-sectional study was conducted to evaluate the risk factors associated with the Salmonella infection status of dairy herds in Henan and Hubei provinces, China. Herds were assigned a Salmonella status based on the isolation of Salmonella from fecal samples obtained from adult lactating dairy cows. Information on potential biosecurity risk factors was collected using a questionnaire template via a 15-min face-to-face interview with dairy cattle producers from May 2020 to March 2021. The questionnaire consisted of 23 questions across two broad categories of potential biosecurity risk factors: farm and biosecurity managemental factors. A total of 48 farms were surveyed. In all (100%, 48/48) of the surveyed farms, although sick animals were separated from healthy animals using fencing, there were no strict quarantine protocols for newly introduced animals. Mixed species rearing was practiced in 35.4% (17/48) of the farms. Feces were removed more than once a day in 45.8% (22/48) of the farms, whereas the remainder (54.2%, 26/48) only removed animal feces once a day. A total of 29.2% (14/48) of the farms were located < 2 km from other livestock farms. The use of personal protective equipment was consistently performed on all farms, with a majority of the workers on most farms (81.3%, 39/48) always disinfecting footwear before entering production areas. A significant association between Salmonella-positive status and the high frequency of the presence of wildlife (birds and rodents in sheds and feed storage places) was recorded (OR: 11.9, 95% CI: 1.7, 84.1, p = 0.013). Fortunately, no farms shared farm equipment with other farms. The study highlights the occurrence of wildlife as a risk factor for the presence of Salmonella in investigated dairy herds. There is a need to institute appropriate on-farm control measures for wild birds and rodents to control the potential spread of Salmonella in dairy production systems. [ABSTRACT FROM AUTHOR]

Salmonella 4,[5],12:i:-, a monophasic variant of S. Typhimurium, has become a global serovar causing animal and human infections since its first emergence in the late 1980's. Several previous studies showed the increasing prevalence of S. 4,[5],12:i:-in China, most of which were from swine with multidrug resistance (MDR) profiles. However, the molecular characteristic and evolution of S. 4,[5],12:i:- in the same swine farm are still unknown. In this study, a total of 54 S. enterica strains were isolated from different fattening pigs aged 1, 3, and 6 months, most of which belonged to S. 4,[5],12:i:-. Whole-genome sequencing revealed that all 45 S. 4,[5],12:i:- strains belonged to ST34 and were further divided into two different ribosomal STs and nine different core-genome STs. Phylogenetic analysis of 286 S. 4,[5],12:i:- strains in China, including 241 from the EnteroBase Salmonella database, revealed the genetic diversity of S. 4,[5],12:i:- and indicated that S. 4,[5],12:i:- in this swine farm might have multiple origins. Three different IncHI2 plasmids carrying various resistance genes were characterized by nanopore sequencing and could be conjugated to Escherichia coli. The colistin resistance gene mcr-1 and ESBLs gene blaCTX-M-14 were co-located on the chromosome of one strain. The dynamic changes in antimicrobial resistance regions and transferability of IncHI2 plasmids, as well as the chromosomal location of resistance genes, facilitated the diversity of the antimicrobial resistance characteristics in S. 4,[5],12:i:-. Since the swine farm is regarded as the important reservoir of MDR S. 4,[5],12:i:-, the prevalence and evolution of S. 4,[5],12:i:- from swine farms to pig products and humans should be continually monitored. [ABSTRACT FROM AUTHOR]

Introduction: Salmonella is a ubiquitous foodborne pathogen and mainly transmitted to human farm-to-fork chain through contaminated foods of animal origin. Methods: In this study, we investigated the serotypes, antimicrobial resistance and virulence of Salmonella from China. Results: A total of 617 Salmonella isolates were collected from 4 major food animal species across 23 provi nces in China from 2015-2021. Highest Salmonella prevalence were observed in Guangdong (44.4%) and Sandong (23.7%). Chickens (43.0%) was shown to be the major source of Salmonella contamination, followed by pigs (34.5%) and ducks (18.5%). The number of Salmonella increased significantly from 5.51% to 27.23% during 2015-2020. S. Derby (17.3%), S. Enteritidis (13.1%) and S. Typhimurium (11.4%) were the most common serotypes among 41 serotypes identifiedin this study. Antibiotic susceptibility testing showing that the majority of the Salmonella isolates were resistant to neomycin (99.7%), tetracycline (98.1%), ampicillin (97.4%), sulfadiazine/trimethoprim (97.1%), nalidixic acid (89.1%), doxycycline (83.1%), ceftria xone (70.3%), spectinomycin (67.7%), florfenicol (60.0%), cefotaxime (52.0%) and lomefloxacin (59.8%). The rates of resistance to multiple antibiotics in S. Derby and S.Typhimurium were higher than that in S. Enteritidis. However, the rate of resistance to fosfomycin were observed from higher to lower by S. Derby, S. Enteritidis, and S. Typhimurium. Biofilm formation ability analysis found that 88.49%of the Salmonella were able to produce biofilms, of which 236 Salmonella isolates were strong biofilm producer. Among the 26 types of antibiotics resistance genes (ARGs) were identified in this study, 4 ARGs (tetB,sul2,aadA2, and aph(3')-IIa) were highly prevalent. In addition, 5 β-lactam resistance genes (blaTEM, blaSHV, blaCMY-2, blaCTX-M, and blaOXA) and 7 quinolone resistance genes (oqxA, oqxB, qnrB, qnrC, qnrD, qnrS, and qeqA) were detected among these isolates. 12 out of 17 virulence genes selected in this study were commonly presented in the chromosomes of tested isolate, with a detection rate of over 80%, including misL, spiA, stn, pagC, iroN, fim, msgA, sopB, prgH, sitC, ttrC, spaN. Discussion: This study provided a systematical updating on surveillance on prevalence of Salmonella from food animals in China, shedding the light on continued vigilance for Salmonella in food animals. [ABSTRACT FROM AUTHOR]

Salmonella enterica is considered a significant threat to the global poultry industry and public health. In recent decades, antimicrobial resistance in Salmonella enterica has attracted increasing concern throughout the world. However, limited information is available on Salmonella enterica among different breeds of breeder chickens. Thus, this study aimed to compare the prevalence, serotype distribution, emergence of extended-spectrum beta-lactamases (ESBLs), antimicrobial resistance, and genetic resistance mechanisms in Salmonella enterica among different breeds of breeder chickens. A total of 693 samples (dead embryos, cloacal swabs, water, feed, environmental swabs, and meconium of newly hatched chicks) were selected and cultured for Salmonella from four breeder chicken farms in Shandong province, China, representing one imported and three native breeds, and the isolates were further serotyped. Of the Salmonella isolates, susceptibility to 11 antimicrobials of 5 classes, ESBL screening, and the presence of 21 antimicrobial resistance genes were determined in the present study. Overall, 94 (13.6%) isolates were recovered, which were divided into 3 serotypes (Salmonella Pullorum (n = 36), Salmonella Thompson (n = 32), and Salmonella Enteritidis (n = 26)). The results showed that the prevalence of Salmonella enterica isolates from the imported breeds was higher compared with the three domestic breeds. Eight of the ninety-four isolates were ESBL-positive strains, which were recovered from a domestic breed chicken farm. These eight ESBL-producing isolates were serotyped to Pullorum. Surprisingly, Salmonella Enteritidis (S. enteritidis) and S. pullorum were simultaneously isolated from a single dead embryo observed among one native breed. Meanwhile, among the Salmonella isolates, 53.2% (50/94) were multidrug-resistant strains, and 44.7% (42/94) of the isolates presented resistance to at least five antibiotics. Nearly all of the isolates (97.9%, 92/94) were resistant to at least one antimicrobial; one isolate of S. Thompson was resistant to seven antimicrobial agents belonging to four different classes. The carriage rate of three resistance genes (tetA, tetB, and sul1) among isolates from the imported breeds (87%, 70%, and 65.2%) was higher than that in those from domestic breeds (35.2%, 36.6, and 14.1%). To our knowledge, this is the first report of ESBLs-producing Salmonella isolated from a Chinese native breed of breeder chickens. Our results also highlight that a high prevalence of multidrug-resistant Salmonella enterica contamination is widespread among different breeds of breeder chickens, which is a major risk of food-borne diseases and public health. [ABSTRACT FROM AUTHOR]

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Objective: Non-typhoidal Salmonella (NTS) is a major cause of human salmonellosis globally. Food animals are major NTS reservoirs. An increase in antimicrobial resistance (AMR) in foodborne NTS has led to clinical treatment failures. Here, to examine the prevalence and perform characterization of foodborne NTS with AMR in China, we tested the antimicrobial susceptibility of 1,256 NTS isolates cultured from retail foods in 2020 in China. Methods: The antimicrobial susceptibility of 26 antimicrobial agents representing 12 classes was evaluated with the broth-microdilution method; the presence of ten mcr genes was screened with multi-PCR. The complete closed genomes of mcr-gene-carrying isolates were generated by hybrid assembly through whole genome sequencing on both the PacBio and Illumina platforms. Genomic features and genetic environments of the mcr-1 gene were analysed. Results: The overall drug resistance rate was 92.28%, and the multi-drug resistance (MDR) rate was 76.53%. A total of 341 AMR profiles were determined, and resistance was highest to nalidixic acid (63.38%). Among 887 NTS isolates with MDR, 232 showed co-resistance to cefotaxime and ciprofloxacin, and 25 were resistant to ten classes of antimicrobial agents. The resistance of NTS isolated from different regions varied. Isolates from raw chicken sources most frequently showed resistance. Four NTS carried the mcr-1 gene and represented four different serotypes. Four mcr-1 gene-bearing plasmids from the four Salmonella isolates were classified into two replicon types (IncI2 and IncHI2A). Two mcr-1 genes in IncI2 type plasmids were found to be located between a PAP2 family protein-encoding gene and a relaxaseencoding gene, whereas the other two mcr-1 gene structures in IncHI2A type plasmids showed variations in the presence of insertion sequences. Conclusion: Our data demonstrated severe AMR among foodborne NTS isolated from food in China, thus highlighting the importance of antimicrobial susceptibility surveillance to decrease the spread of AMR, particularly to critical drugs in human medicine. [ABSTRACT FROM AUTHOR]

Food contamination by Salmonella can lead to serious foodborne diseases that constantly threaten public health. Innovative and effective strategies are needed to control foodborne pathogenic contamination since the incidence of foodborne diseases has increased gradually. In the present study, two broad-spectrum phages named Salmonella phage PSE-D1 and Salmonella phage PST-H1 were isolated from sewage in China. Phages PSE-D1 and PST-H1 were obtained by enrichment with Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) CVCC1806 and Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) CVCC3384, respectively. They were able to lyse Salmonella, E. coli and K. pneumoniae and exhibited broad host range. Further study demonstrated that PSE-D1 and PST-H1 showed high pH and thermal tolerances. Phage PSE-D1 belongs to the Jiaodavirus genus, Tevenvirinae subfamily, while phage PST-H1 belongs to the Jerseyvirus genus, Guernseyvirinae subfamily according to morphology and phylogeny. The results of genome analysis showed that PSE-D1 and PST-H1 lack virulence and drug-resistance genes. The effects of PSE-D1 and PST-H1 on controlling S. Enteritidis CVCC1806 and S. Typhimurium CVCC3384 contamination in three kinds of foods (eggshells, sausages and milk) were further investigated, respectively. Our results showed that, compared to phage-free groups, PSE-D1 and PST-H1 inhibited the growth of their host strain significantly. A significant reduction of host bacteria titers (1.5 and 1.9 log10 CFU/sample, p < 0.001) on eggshells was observed under PSE-D1 and PST-H1 treatments, respectively. Furthermore, administration of PSE-D1 and PST-H1 decreased the counts of bacteria by 1.1 and 1.2 log10 CFU/cm2 (p < 0.001) in sausages as well as 1.5 and 1.8 log10 CFU/mL (p < 0.001) in milk, respectively. Interesting, the bacteriostasis efficacy of both phages exhibited more significantly at 4 °C than that at 28 °C in eggshells and milk and sausages. In sum, the purpose of our research was evaluating the counteracting effect of phage PSE-D1 and PST-H1 on the spread of Salmonella on contaminated foods products. Our results suggested that these two phage-based biocontrol treatments are promising strategies for controlling pathogenic Salmonella contaminated food. [ABSTRACT FROM AUTHOR]

Salmonella are widely distributed foodborne pathogens and are often associated with food animal products. Colistin resistance mediated by mcr-1 is an increasing threat; however, data on the characteristics of mcr-1-harboring Salmonella among retail foods are still lacking. In this study, retail meats from 24 supermarkets and eggs from nine markets in Qingdao city were investigated to determine the presence and genomic characteristics of mcr-1-harboring Salmonella. We found the retail meats and eggs were highly contaminated by Salmonella, with detection rates of 17.5% (31/177) and 12.3% (16/130), respectively. A total of 76 Salmonella isolates were obtained in this study, and 77.6% showed multidrug resistance (MDR). The MDR proportion of egg isolates (97.5%) was significantly higher than that in meat isolates (55.6%) (p < 0.05). The most prevalent Salmonella serotypes were Typhimurium (56.6%) and Enteritidis (17.1%). Of the 76 Salmonella isolates, 40 possessed mcr-1. All 40 mcr-1-positive isolates were ST34 S. Typhimurium and were from eggs of eight brands. Different mcr-1-harboring isolates existed in the same egg, and some isolates from different egg samples or brands showed clonal relationships. The mcr-1 was located on similar IncHI2/HI2A MDR non-conjugative plasmids lacking transfer region, resulting in the failure of conjugation. The phylogenetic tree using genome sequences showed that the mcr-1-positive isolates from eggs clustered together with mcr-1-positive isolates from chicken and humans in China, revealing that mcr-1-positive egg-borne Salmonella might be derived from chicken and could potentially trigger outbreaks in humans. The high occurrence of mcr-1-harboring Salmonella in fresh eggs is alarming, and there is an urgent need to monitor mcr-1-harboring Salmonella in retail meats and eggs. We report for the first time the role of retail eggs in disseminating mcr-1-positive Salmonella and the risk of transmission of these MDR pathogens from retail food to humans should be evaluated comprehensively. [ABSTRACT FROM AUTHOR]

Salmonella is an important foodborne pathogen that poses a significant threat to food safety. This study aims to assess the prevalence, genomic features, and colistin-resistant mechanisms of Salmonella isolates collected from 118 retail pork samples from January 2021 to January 2022 in Shanghai, China. Overall, 46 (39.0 %, 46/118) Salmonella isolates were collected, which were identified as 12 serotypes by genomic analysis, including Salmonella Typhimurium (n = 17) and Salmonella London (n = 6). Antimicrobial resistance profiling revealed that the resistance rate of these isolates to colistin was 13.0 % (6/46), while 60.9 % (28/46) exhibited multidrug-resistant. It was found that there were 51 distinct antimicrobial resistance genes in these 46 isolates, which were predominantly associated with resistance to aminoglycosides, fluoroquinolones, and β-lactams. More importantly, among six colistin-resistant isolates, two isolates (Salmonella Schwarzengrund and Salmonella Indiana) were found to carry the mcr-1 gene. The mechanism of resistance in the remaining four colistin-resistant isolates was further studied, and it was found that there were nine amino acid substitutions in PmrAB. It was demonstrated by site-directed mutagenesis that novel substitutions G53W in PmrA and I83V in PmrB led to colistin resistance in Salmonella (MIC = 2 or 4 μg/mL). Analysis results by real-time quantitative PCR and mass spectrometry indicated that the mutants PmrA G53W and PmrB I83V displayed higher expression levels of the gene pmrE than in the parental strain. This upregulation resulted in an increase in the production of 4-amino-4-deoxy-l-arabinose (L-Ara4N) that modified lipid A, thereby conferring resistance to colistin. These findings demonstrated that there was a high prevalence of MDR Salmonella isolates in retail pork in Shanghai, and the substitution G53W in PmrA and I83V in PmrB were independent factors contributing to the development of resistance to colistin in Salmonella via modification of lipid A with L-Ara4N., Competing Interests: Declaration of competing interest The work described has not been published previously except in the form of a preprint, an abstract, a published lecture, academic thesis or registered report. The article is not under consideration for publication elsewhere. The article's publication is approved by all authors and tacitly or explicitly by the responsible authorities where the work was carried out. If accepted, the article will not be published elsewhere in the same form, in English or in any other language, including electronically without the written consent of the copyright-holder. All authors believe that the manuscript represents honest work, and can verify the validity of the results reported. This article does not contain any studies related to human or animal subjects performed by any of the authors. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Salmonella is one of the most common foodborne pathogens. Antimicrobial-resistant Salmonella isolates, especially those resistant to colistin, pose a significant threat to public health worldwide. However, data about the prevalence of mcr-positive Salmonella in animals was few and the dissemination of mcr-positive Salmonella from animals to food, especially eggs, has not been fully addressed. The role of houseflies in the Salmonella transmission has also not been clarified. Here, we analyzed the prevalence and resistance characteristics of mcr-positive Salmonella in 1707 samples of animals (commercial laying hens, broilers, waterfowls and swine), eggs and flies from 23 farms in four cities of China between July 2021 and October 2022. Pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) analyses of Salmonella from different sources were further performed. Among animals, waterfowls had the highest isolation rate of Salmonella (18.1 %, 35/193), followed by swine (6.1 %, 23/377), laying hens (4.2 %, 21/505) and broilers (1.4 %, 7/489). Two of the 53 flies (3.8 %) carried Salmonella. The detection rate of Salmonella in eggs from farms was 26.7 %. All mcr-1-positive Salmonella isolates were S. 1,4,[5],12:i:- and were only found in hens (0.2 %) and eggs (11.1 %). PFGE and WGS analyses showed that the mcr-1-positive S. 1,4,[5],12:i:- from commercial laying hens and eggs in the same farm had no single nucleotide polymorphism (SNP) variation, indicating that the mcr-1-positive S. 1,4,[5],12:i:- in eggs were derived from hens. The phylogenomic analysis also showed that the mcr-1-positive S. 1,4,[5],12:i:- isolates from hens and eggs were closely related to previously reported mcr-1-positive Salmonella from human in China, further confirming that such mcr-1-positive Salmonella in animals could transmit to humans via the food chain. Furthermore, the bla CTX-M-1G -positive S. Kentucky isolates from broiler and flies in the same farm had a limited number of variations (5-7 SNPs), proving the clonal transmission of Salmonella between broilers and flies. The S. Kentucky isolates carrying bla CTX-M-1G from broilers were also closely related to the S. Kentucky isolates from chicken meats and humans. Our findings suggest that Salmonella including those carrying mcr-1 in animals could transmit to eggs/meats and potentially trigger human infections. The houseflies can play an important role in the Salmonella transmission within farms. Salmonella carrying mcr in animals and animal products should be monitored regularly and control measures are urgently needed to reduce the dissemination of such pathogens., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Objective: To explore the genomic epidemiological characteristics of Salmonella in fruits, vegetables, and irrigation water in China., Methods: A total of 410 samples of fruits, vegetables and irrigation water were collected from Hubei and Shaanxi Provinces from June to December 2022. Salmonella strains were detected and identified referenced in the United States Food and drug administration&apos;s bacteriological analytical manual. The antimicrobial susceptibility to 17 antibiotics in 9 classes was assessed by broth microdilution, and the serotype and antibiotic resistance genes(ARG) were predicted by whole genome sequencing technology., Results: In total, 29 strains of Salmonella were collected. There were 3 strains isolated from fruits and vegetables, 25 from irrigation water, and 1 from soil fertilizers. The detection rate in irrigation water(22.32%) was higher than that in fruits, vegetables(1.46%), and soil fertilizers(1.08%). The individual detection rate(13.01%) was higher than the large-scale monitoring point detection rate(4.03%). Based on the analysis of the whole genome sequencing, a total of 19 serotypes were identified, with S. Thompson being the most frequently detected serotype(24.14%).31.0% of isolates showed resistance to the tested drugs and showed the highest resistance to cotrimoxazole, tetracycline, ampicillin.24.1% were multi-drug resistant strains and were resistant to 14 kinds of antimicrobial compounds belonging to 8 categories. Moreover, based on the whole-genome sequence analysis of antibiotic resistance genes, it was found that the carriage rate of aminoglycoside ARGs was 100%, and the carriage rates of other ARGs were folate pathway antagonists, fosfomycins, tetracyclines, phenicols, sulfonamids, quinolones, beta-lactam, macrolids and rifamycins were 31.03%, 27.59%, 27.59%, 27.59%, 24.14%, 20.69%, 6.90%, and 6.90%, respectively. Over 30% of the strains carried more than 6 antibiotic resistance genes., Conclusion: Salmonellas were detected in fruits, vegetables, irrigation water and soil fertilizer in Hubei and Shaanxi Provinces. The strains isolated from irrigation water exhibiting a diverse range of serotypes and carrying numerous antibiotic resistance genes. More intensive efforts should be made on the monitoring of Salmonella and its antibiotic resistance in irrigation water.

Salmonella is a foodborne zoonotic pathogen that threatens food safety and public health. However, few people have conducted long-term and systematic studies on Salmonella contamination in food in Yantai City. In order to investigate the situation of Salmonella contamination in food and improve the ability of early warning and control of foodborne diseases, a total of 3420 samples from 20 categories were collected from 13 monitoring points in Yantai City, from 2010 to 2023. The difference in detection rate and bacterial strain of different monitoring points, different types, and different sources of samples was compared. Of the 3420 samples, 80 were positive with a detection rate of 2.34%. Salmonella detection rates were significantly different for samples collected at different monitoring sites. Salmonella was detected only in meat and meat products and catering food, and none of the other types were detected. The detection rate of Salmonella was higher in raw animal meat and raw poultry. Samples collected at the market stage had the highest detection rate (5.81%), and there was a significant difference in detection rate between samples from different sources (χ 2 = 36.93, p < 0.05). Eighty-one strains of Salmonella were detected out of 3420 samples (2 different strains were detected in 1 positive sample). The serological test identified 8 groups and 27 serotypes. The dominant serum groups were group B 30.86% (25/81), group E1 23.46% (19/81), and group D 16.05% (13/81). The main dominant serotypes were Salmonella give 17.28% (14/81), Salmonella enteritidis 16.05% (13/81), and Salmonella derby 13.58% (11/81). Meat and meat products and catering food were the main food products contaminated with Salmonella . The resulting secondary contamination is the hidden threat of foodborne diseases and should be given sufficient attention.

Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Objectives: To reconstruct the genomic epidemiology and evolution of MDR Salmonella Indiana in China.Methods: A total of 108 Salmonella Indiana strains were collected from humans and livestock in China. All isolates were subjected to WGS and antimicrobial susceptibility testing. Phylogenetic relationships and evolutionary analyses were conducted using WGS data from this study and the NCBI database.Results: Almost all 108 Salmonella Indiana strains displayed the MDR phenotype. Importantly, 84 isolates possessed concurrent resistance to ciprofloxacin and cefotaxime. WGS analysis revealed that class 1 integrons on the chromosome and IncHI2 plasmids were the key vectors responsible for multiple antibiotic resistance gene (ARG) [including ESBL and plasmid-mediated quinolone resistance (PMQR) genes] transmission among Salmonella Indiana. The 108 Salmonella Indiana dataset displayed a relatively large core genome and ST17 was the predominant ST. Moreover, the global ST17 Salmonella Indiana strains could be divided into five distinct lineages, each of which was significantly associated with a geographical distribution. Genomic analysis revealed multiple antimicrobial resistance determinants and QRDR mutations in Chinese lineages, which almost did not occur in other global lineages. Using molecular clock analysis, we hypothesized that ST17 isolates have existed since 1956 and underwent a major population expansion from the 1980s to the 2000s and the genetic diversity started to decrease around 2011, probably due to geographical barriers, antimicrobial selective pressure and MDR, favouring the establishment of this prevalent multiple antibiotic-resistant lineage and local epidemics.Conclusions: This study revealed that adaptation to antimicrobial pressure was possibly pivotal in the recent evolutionary trajectory for the clonal spread of ST17 Salmonella Indiana in China. [ABSTRACT FROM AUTHOR]

Salmonella enterica serotype Indiana (S. Indiana) in Chinese poultry meat has aroused widespread concern because of its high prevalence and strong antimicrobial resistance. In consideration of the relationship in our previous study between S. Indiana and co-resistance to ciprofloxacin and cefotaxime (CIP-CTX), which were the first-line drug which were used in Salmonella infection in clinical, the antimicrobial resistance (AMR) of 224 CIP-CTX co-resistant S. Indiana isolated from retail chicken samples in China were investigated, with the aim of characterizing the AMR profiles and related resistance mechanisms to ciprofloxacin and cefotaxime among these CIPCTX co-resistant S. Indiana isolates, all of which showed multi-drug-resistant (MDR) phenotypes. GyrA (S83F and D87N/G) with ParC (T57S and S80R) were the dominant amino acid substitution types, with oqxA, oqxB, and aac (6')-Ibcr identified as common plasmid-mediated quinolone resistance (PMQR)-encoding genes. Five blaCTX-M gene subtypes were identified with blaCTX-M-65 ranking at the top. Equally important, we obtained one isolate CFSA664 harboring the mcr-1 gene was ESBL producer with co-resistance to nine in ten classes of tested drugs inclduing colistin. A single circular chromosome and 3 circular plasmids were found in its genome. Among the 26 AMR genes identified, 24 were located on plasmid pCFSA664-1, including three ESBL genes, while plasmid pCFSA664-3 owning only the mcr-1 gene and sharing the same backbone structure with plasmids from Enterobacteriaceae. No insertion sequences were found near the mcr-1 gene but a relaxase-encoding gene in the flank, which could transfer into E. coli J53 at a relatively high frequency. S. Indiana in this study exhibited highly drug-resistant phenotypes, contributing to the acceleration of the dissemination and emergence of this pathogen among different sources. Surveillance and a One Health strategy are needed to limit the emergence of S. Indiana along the food chain. [ABSTRACT FROM AUTHOR]

[Display omitted] • Salmonella epidemiological and genome characteristics differ across the type of supply mode. • Frozen supply mode Salmonella have high resistance and harbor many resistance and virulence genes. • Identified a genetic relationship between S. Enteritidis in frozen chicken and clinical isolates. • The narZ gene, linked to anaerobic respiration, is a key Salmonella gene in frozen supply mode chains. Salmonella is a foodborne pathogen that causes salmonellosis, of which retail chicken meat is a major source. However, the prevalence of Salmonella in different retail chicken supply modes and the threat posed to consumers remains unclear. The prevalence, serotype distribution, antibiotic resistance, and genomic characteristics of Salmonella in three supply modes of retail chicken (live poultry, frozen, and chilled) were investigated using whole-genome sequencing (WGS) and machine learning (ML). In this study, 480 retail chicken samples from live poultry, frozen, and chilled supply modes in Guangzhou from 2020 to 2021, as well as 253 Salmonella isolates (total isolation rate = 53.1 %), were collected. The prevalence of isolates in the live poultry mode (67.5 %, 81/120) was statistically higher than in the frozen (50.0 %, 120/240) and chilled (43.3 %, 52/120) (P < 0.05) modes. Serotype identification showed significant differences in the serotype distribution of Salmonella in different supply modes. S. Enteritis (46.7 %) and S. Indiana (14.2 %) were predominant in the frozen mode. S. Agona (23.5 %) and S. Saintpaul (13.6 %) were predominant in live poultry, while S. Enteritis (40.4 %) and S. Kentucky (17.3 %) were predominant in chilled mode. Antibiotic testing showed that frozen mode isolates were more resistant; the multidrug-resistant (MDR) rate of isolates in the frozen mode reached 91.8 %, significantly higher than in the chilled (86.5 %) and live (74.1 %) (P < 0.05) modes. WGS was performed on 155 top serotypes (S. Enteritidis, S. Kentucky, S. Indiana, and S. Agona). The antibiotic resistance gene analysis showed that the abundance and carrying rate of antibiotic resistance genes of Salmonella in the frozen mode (54 types, 16.1 %) were significantly higher than in other modes (live poultry: 36 types, 9.4 %, P < 0.05; chilled: 31 types, 11.6 %). The bla NDM-1 and bla NDM-9 genes encoding carbapenem resistance were found in frozen mode isolates on a complex transposon consisting of Tn AS3 -IS 26. Virulence factors and plasmid replicons were abundant in the studied frozen mode isolates. In addition, single nucleotide polymorphism (SNP) phylogenetic tree results showed that in the frozen supply mode, the S. Enteritidis clonal clade continued to contaminate retail chicken meat and was homologous to S. Enteritidis strains found in farm chicken embryos, slaughterhouse chicken carcasses, and patients from hospitals in China (SNP 0 = 10). Notably, the pan-genome-based ML model showed that characteristic genes in frozen and live poultry isolates differed. The narZ gene was a key characteristic gene in frozen isolates, encoding nitrate reductase, relating to anaerobic bacterial growth. The ydgJ gene is a key characteristic gene in the live mode and encodes an oxidoreductase related to oxidative function in bacteria. The high prevalence of live poultry mode Salmonella and the transmission of frozen mode MDR Salmonella in this study pose serious risks to food safety and public health, emphasizing the importance of improving disinfection and cold storage measures to reduce Salmonella contamination and transmission. In conclusion, the continued surveillance of Salmonella across different supply models and the development of an epidemiological surveillance system based on WGS is necessary. [ABSTRACT FROM AUTHOR]

Salmonella enterica subspecies enterica serovar abortus equi (S. Abortus equi) is the most common cause of abortion in mares. It has recently been found to cause abortion in donkeys more frequently in China. A novel virulent bacteriophage vB_SabS_Sds2 (hereafter designated as Sds2) was isolated from the feces of donkeys using a S. Abortus equi strain as a host. Phage Sds2 had an isometric polyhedral head and an uncontracted long tail, belonging to the Tequintavirus, Markadamsvirinae, Demerecviridae, Caudovirales. The genome of phage Sds2 was 114,770 bp, with a GC content of 40.26%. The genome contained 160 open reading frames (ORFs), and no ORFs were associated with pathogenicity, drug resistance, or lysogenization by sequence analysis. Both genome annotation and phylogenetic analysis indicated that phage Sds2 was highly similar to T5-like bacteriophages. Phage Sds2 could lyse 100% (30/30) of S. Abortus equi strains, 25.3% (24/95) of other serotypes of Salmonella strains, and 27.6% (8/29) of Escherichia coli strains using the double-layer agar plate method. The in vitro test showed that phage Sds2 had high bactericidal activity against S. Abortus equi at a wide range of MOIs. The in vivo test indicated that phage Sds2 had an inhibitory effect on abortion in mice challenged with S. Abortus equi. In general, phage Sds2 is a novel lytic phage with a wide host range and has the potential to prevent abortion caused by S. Abortus equi. [ABSTRACT FROM AUTHOR]

Pullorum disease and fowl typhoid are among the most significant poultry diseases worldwide. However, the global burden of these diseases remains unknown. Most importantly, the parameters contributing to the prevalence of Salmonella Gallinarum variants are not well documented. Therefore, in this study, we present a systematic review and meta-analysis of the global prevalence of Salmonella Gallinarum during 1945–2021. In total, 201 studies were identified for qualitative analysis (>900 million samples). The meta-analysis was subjected to over 183 screened studies. The global prevalence of S. Gallinarum (percentage of positive samples in total samples) was 8.54% (95% CI: 8.43–8.65) and showed a V-shaped recovery over time. Pullorum disease is most common in Asia, particularly in eastern China. Further investigations on chicken origin samples revealed significant differences in S. Gallinarum prevalence by gender, breed, raising mode, economic use, and growth stage, indicating a critical role of vertical transmission. Together, this study offered an updated, evidence-based dataset and knowledge regarding S. Gallinarum epidemics, which might significantly impact decision-making policy with targeted interventions. Measurement(s) S. Gallinarum positive samples Technology Type(s) Serological test • Molecular method (PCR) • Plate culture and identification • Biochemical test Factor Type(s) biovar • time • geographic sampling site • reservoir of bacteria • chicken breed • raising mode • economic use • growth stage • gender Sample Characteristic - Organism Animal Sample Characteristic - Location world [ABSTRACT FROM AUTHOR]

New Delhi metallo-β-lactamase-13 (NDM-13) is an NDM variant that was first identified in 2015 and has not been detected in Salmonella species prior to this study. Here we describe the first identification of a Salmonella Rissen strain SR33 carrying blaNDM-13. The aim of this study was to molecularly characterize SR33's antimicrobial resistance and virulence features as well as investigate the genetic environment of blaNDM-13. The Salmonella Rissen SR33 strain was isolated from a patient with fever and diarrhea. SR33 belonged to ST469, and it was found to be multidrug-resistant (MDR) and to carry many virulence genes. Phylogenetic analysis showed that SR33 shared a close relationship with most of the Chinese S. Rissen ST469 strains. blaNDM-13 was located in a transmissible IncI1 plasmid pNDM13-SR33. Sequence analysis of blaNDM-13-positive genomes downloaded from GenBank revealed that a genetic context (ΔISAba125-blaNDM-13-bleMBL-trpF) and a hybrid promoter (consisting of -35 sequences provided by ISAbal25 and -10 sequences) were conserved. ISAbal25 was truncated by IS1294 in three plasmids carrying blaNDM-13, including pNDM13-SR33. To our knowledge, this is the first report of blaNDM-13 carried by Salmonella. The emergence of blaNDM-13 in a clinical MDR S. Rissen ST469 strain highlights the critical need for monitoring and controlling the dissemination of blaNDM-13. bla NDM-13 carried by a transmissible IncI1 plasmid may result in an increased risk of blaNDM-13 transmission. IS1294 may be involved in the movement of blaNDM-13. [ABSTRACT FROM AUTHOR]

Salmonella is a major zoonotic pathogen, which usually contaminates food resulting in salmonellosis in humans. Exploring the characteristics and origins of Salmonella is essential in formulating prevention and control measures for Salmonella infection. We used slide agglutination, antimicrobial susceptibility testing, and whole-genome sequencing to analyze and compare Salmonella's phenotype, genotyping diversity, and genetic relatedness from livestock meat and diarrhea patients in Hanzhong, China, from 2018 to 2020. Totally 216 Salmonella enterica isolates were screened from frozen whole chicken carcasses (44.3%, 70/158), frozen raw ground pork (36.2%, 59/163), and diarrhea patients (4.4%, 87/1964). Salmonella Typhimurium was the dominant serotype. Notably, compared with other sources, isolates obtained from frozen whole chicken carcasses showed significant resistance to third-generation cephalosporin and fluoroquinolones (p < 0.05). All strains were assigned into 36 sequence types (STs) and two novel STs, and an excellent consistency was observed between ST and serotype. Genomic data revealed that extended-spectrum b-lactamase genes were responsible for third-generation cephalosporin resistance in 52 Salmonella strains, and the most predominant resistance determinant was blaCTXM. Furthermore, of the 60 ciprofloxacin-resistant isolates, five single-base mutations in quinolone resistancedetermining regions were identified in gyrA or parC, and the plasmid-mediated quinolone resistance gene aac(6')Ib-cr was most often detected. The cgMLST clusters show that five clusters among four serotypes (including S. Typhimurium, S. London, S. Derby, and S. Agona) cover samples from diarrhea patients and livestock meat pathway isolate, indicating a possibility of cross-host transmission. In conclusion, the livestock meat isolates have a higher level of resistance than diarrhea patients' isolates and could be an essential source of human Salmonella infection. [ABSTRACT FROM AUTHOR]

Background: Salmonella is a leading foodborne and zoonotic pathogen, and is widely distributed in different nodes of the pork supply chain. In recent years, the increasing prevalence of antimicrobial resistant Salmonella poses a threat to global public health. The purpose of this study is to the prevalence of antimicrobial resistant Salmonella in pig slaughterhouses in Hubei Province in China, and explore the effect of using lytic bacteriophages fighting against antimicrobial resistant Salmonella. Results: We collected a total of 1289 samples including anal swabs of pigs (862/1289), environmental swabs (204/1289), carcass surface swabs (36/1289) and environmental agar plates (187/1289) from eleven slaughterhouses in seven cities in Hubei Province and recovered 106 Salmonella isolates. Antimicrobial susceptibility testing revealed that these isolates showed a high rate of antimicrobial resistance; over 99.06% (105/106) of them were multidrug resistant. To combat these drug resistant Salmonella, we isolated 37 lytic phages using 106 isolates as indicator bacteria. One of them, designated ph 2–2, which belonged to the Myoviridae family, displayed good capacity to kill Salmonella under different adverse conditions (exposure to different temperatures, pHs, UV, and/or 75% ethanol) and had a wide lytic spectrum. Evaluation in mouse models showed that ph 2–2 was safe and saved 80% (administrated by gavage) and 100% (administrated through intraperitoneal injection) mice from infections caused by Salmonella Typhimurium. Conclusions: The data presented herein demonstrated that Salmonella contamination remains a problem in some pig slaughter houses in China and Salmonella isolates recovered in slaughter houses displayed a high rate of antimicrobial resistance. In addition, broad-spectrum lytic bacteriophages may represent a good candidate for the development of anti-antimicrobial resistant Salmonella agents. [ABSTRACT FROM AUTHOR]

Salmonella enterica is not only the most common pathogen of poultry and poultryderived products but is also a significant foodborne pathogen. In recent years, many S. enterica isolates have exhibited multi-drug resistance, which places huge pressure on global economy and health. Since phages are an attractive alternative to biocontrol pathogens, we isolated a total of 15 Salmonella phages from sewage effluent, sediment, and chicken manure. The GRNsp1, GRNsp3, GRNsp6, GRNsp21, GRNsp27, GRNsp30, GRNsp50, and GRNsp51 phages exhibited a wide host range against S. enterica serovars Enteritidis and Typhimurium in vitro. In particular, GRNsp51 exerted highly efficient lytic effects against a large proportion of S. Enteritidis and S. Typhimurium strains isolated from different regions of China. Meanwhile, GRNsp8 expanded the host range of GRNsp6 and GRNsp51. Based on their host ranges and lytic capacities, GRNsp6, GRNssp8, and GRNsp51 were selected for further investigation. Morphology, one-step growth curves, and stability assays revealed that GRNsp6, GRNsp8, and GRNsp51 all belong to the Caudovirales order and display relatively short latency periods with broad pH and thermal stability. Genomic analysis indicated that the genomes of these three phages contained no genes related to virulence, antibiotic resistance, or lysogeny. In addition, we tested the effectiveness of a cocktail composed of these three phages against S. Enteritidis in a chicken model. Treatment with the oral phage cocktail 24 h before or alongside Salmonella challenge significantly reduced colonization of the intestinal tract and decreased the mRNA expression of IL-6, IFN-g, and IL-1b in the duodenum. Together, these findings indicate that a cocktail of the GRNsp6, GRNsp8, and GRNsp51 phages could serve as an effective antimicrobial therapeutic agent against multidrug-resistant Salmonella in animal production to mitigate infections by multiple zoonotic Salmonella species. [ABSTRACT FROM AUTHOR]

Simple Summary: Non-typhoid Salmonella is the general term of Salmonella other than typhoid and paratyphoid, which often causes foodborne gastroenteritis in humans, but some serotypes have been proved to be pathogenic to poultry. Salmonella Enterica and Salmonella Typhimurium are the common serotypes pathogenic to poultry and have been systematically studied, but other serotypes have rarely been studied. During Salmonella surveillance in farms, we discovered by chance that Salmonella Thompson, a common non-typhoid Salmonella, is also pathogenic to avian embryos. Therefore, this study aimed to explore antimicrobial resistance and pathogenicity of clinical S. Thompson. Firstly, we found that the core-genome multilocus sequence typing of 14 clinical S. Thompson was consistent with two strains of S. Thompson from humans in China. Secondly, the antimicrobial resistance gene analysis demonstrated that all strains carried the polymyxin resistance gene mcr-9, which had not appeared resistance phenotype. Meanwhile, many essential virulence genes were also found in each S. Thompson isolate. Finally, the bacterial inoculation experiment revealed that clinical S. Thompson was highly pathogenic to newborn chicks after yolk sac inoculation. This study suggests that Salmonella Thompson can circulate between humans and poultry farms and transmit drug resistance genes and demonstrated that Salmonella Thompson is highly pathogenic to chicks and should be guarded against in the hatching stage of poultry farms. Salmonella Thompson, an important foodborne pathogen, is rarely found to be pathogenic to poultry. Accidentally, S. Thompson was found to be pathogenic to embryos of white feather broiler at a poultry farm in China. Therefore, this study aimed to explore antimicrobial resistance and pathogenicity of clinical S. Thompson isolated from dead poultry embryos. The phylogenetic tree based on 16S rRNA and seven housekeeping genes showed that the 14 clinical S. Thompson were closely related. The core-genome multilocus sequence typing of 14 clinical S. Thompson based on whole-genome sequencing was cgST-12774, consistent with the only two strains of S. Thompson from humans in China as reported in the NCBI database. The antimicrobial resistance gene analysis demonstrated that all strains carried aac(6′)-Iaa and the polymyxin resistance gene mcr-9. Antimicrobial sensitivity tests for 18 antibiotics showed that S. Thompson isolates displayed resistance against streptomycin (100%), ampicillin (35.7%), and doxycycline (14.3%), but sensitivity to polymyxin B, proving that the mcr-9 gene had not appeared resistance phenotype. Virulence genes Salmonella pathogenicity island (SPI) SPI1-5, type I fimbriae gene (fimA), flagellar assembly genes (bcfC, flhD, fliA, fliC, fljB, flgK, and lpfC), and other virulence genes (iroN, pagC, and cigR) were found in each S. Thompson isolate. Additionally, the bacterial inoculation experiment with 1-day-old chicks revealed that clinical S. Thompson was highly pathogenic to newborn chicks after yolk sac inoculation. This study highlighted that the S. Thompson isolated from poultry embryos and the S. Thompson causing human foodborne diarrhea in some parts of China belong to the same cgMLST typology (cgST-12774) and showed the pathogenicity of this clinical S. Thompson to chicks. [ABSTRACT FROM AUTHOR]

Salmonella is a major zoonotic pathogen, which usually contaminates food resulting in salmonellosis in humans. Exploring the characteristics and origins of Salmonella is essential in formulating prevention and control measures for Salmonella infection. We used slide agglutination, antimicrobial susceptibility testing, and whole-genome sequencing to analyze and compare Salmonella 's phenotype, genotyping diversity, and genetic relatedness from livestock meat and diarrhea patients in Hanzhong, China, from 2018 to 2020. Totally 216 Salmonella enterica isolates were screened from frozen whole chicken carcasses (44.3%, 70/158), frozen raw ground pork (36.2%, 59/163), and diarrhea patients (4.4%, 87/1964). Salmonella Typhimurium was the dominant serotype. Notably, compared with other sources, isolates obtained from frozen whole chicken carcasses showed significant resistance to third-generation cephalosporin and fluoroquinolones (p < 0.05). All strains were assigned into 36 sequence types (STs) and two novel STs, and an excellent consistency was observed between ST and serotype. Genomic data revealed that extended-spectrum β-lactamase genes were responsible for third-generation cephalosporin resistance in 52 Salmonella strains, and the most predominant resistance determinant was bla CTX–M. Furthermore, of the 60 ciprofloxacin-resistant isolates, five single-base mutations in quinolone resistance-determining regions were identified in gyrA or parC , and the plasmid-mediated quinolone resistance gene aac(6')Ib-cr was most often detected. The cgMLST clusters show that five clusters among four serotypes (including S. Typhimurium, S. London, S. Derby, and S. Agona) cover samples from diarrhea patients and livestock meat pathway isolate, indicating a possibility of cross-host transmission. In conclusion, the livestock meat isolates have a higher level of resistance than diarrhea patients' isolates and could be an essential source of human Salmonella infection. [ABSTRACT FROM AUTHOR]

Nontyphoidal Salmonella (NTS) in children remains a growing burden on public health and often causes children to be hospitalized with diarrheic symptoms. In this work, 260 strains of human Salmonella isolated from Jilin, China were characterized by serotypes and antimicrobial resistance using whole genome sequencing (WGS). The most prevalent serotype was Salmonella enteritidis (47.3%), followed by S. I 4,[5],12:i:- (33.1%), and Salmonella Typhimurium (7.3%). Furthermore, the consistency between resistance phenotype and genotype was confirmed. Similarly, strains harbored bla TEM −1 B and tetA genes were detected, which verified the level of resistant phenotype in β-lactams and tetracyclines. The presence of a single mutation in parC, gyrA , and qnrS1 genes corresponding to quinolones was also observed. In our work, multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) were found to have a high resolution to molecular traceability, and the combination of both was conducive to practical application in an actual situation. Taking all of this into account, we suggested that the comprehensive surveillance of Salmonella infection in children should be carried out to monitor antimicrobial-resistant trends from various sources and to alert on outbreaks of foodborne diseases to protect public health. [ABSTRACT FROM AUTHOR]

On September 21, 2019, the Shenzhen and Dongguan Centers for Disease Control and Prevention received notification of a large cluster of suspected gastroenteritis involving primarily children who sought medical care at hospitals throughout two adjacent cities in China, Shenzhen, and Dongguan. A joint outbreak response was promptly initiated across jurisdictions in a concerted effort between clinical microbiologists, epidemiologists, and public health scientists. Concurrently, multiplex PCRs were used for rapid laboratory diagnosis of suspected cases; epidemiological investigations were conducted to identify the outbreak source, complemented by near real-time multicenter whole-genome analyses completed within 34 h. Epidemiological evidence indicated that all patients had consumed egg sandwiches served on September 20 as snacks to children and staff at a nursery in Dongguan, located near Shenzhen. Salmonella Enteritidis was isolated from case-patients, food handlers, kitchenware, and sandwiches with kitchen-made mayonnaise. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis demonstrated a well-supported cluster with pairwise distances of ≤1 SNP between genomes for outbreak-associated isolates, providing the definitive link between all samples. In comparison with historical isolates from the same geographical region, the minimum pairwise distance was >14 SNPs, suggesting a non-local outbreak source. Genomic source tracing revealed the possible transmission dynamics of a S. Enteritidis clone throughout a multi-provincial egg distribution network. The efficiency and scale with which multidisciplinary and integrated approaches were coordinated in this foodborne disease outbreak response was unprecedented in China, leading to the timely intervention of a large cross-jurisdiction Salmonella outbreak. [ABSTRACT FROM AUTHOR]

Background: Bacteria-mediated cancer immunotherapy (BCI) robustly stimulates the immune system and represses angiogenesis, but tumor recurrence and metastasis commonly occur after BCI. The natural product Ilex kudingcha C. J Tseng enriched with ursolic acid has anti-cancer activity and could potentially augment the therapeutic effects of BCI. The objective of the present study was to determine potential additive effects of these modalities. Methods: We investigated the anti-cancer activity of KDCE (Kudingcha extract) combined with S.t△ppGpp in the mice colon cancer models. Results: In the present study, KDCE combined with S.t△ppGpp BCI improved antitumor therapeutic efficacy compared to S.t△ppGpp or KDCE alone. KDCE did not prolong bacterial tumor-colonizing time, but enhanced the antiangiogenic effect of S.t△ppGpp by downregulatingVEGFR2. We speculated that KDCE-induced VEGFR2 downregulation is associated with FAK/MMP9/STAT3 axis but not AKT or ERK. Conclusions: Ursolic acid-enriched KDCE enhances the antitumor activity of BCI, which could be mediated by VEGFR2 downregulation and subsequent suppression of angiogenesis. Therefore, combination therapy with S.t△ppGpp and KDCE is a potential cancer therapeutic strategy. [ABSTRACT FROM AUTHOR]

Objectives: To investigate the prevalence and molecular characteristics of fosA3 and fosA7 among Salmonella isolates.Methods: Five hundred and fifty-one Salmonella isolates collected from food animals in China during 2016-19 were screened for fos genes. The drug resistance, serovars, clonal relationships and genetic environments of fosA were compared between fosA7- and fosA3-positive Salmonella.Results: A relatively high prevalence of fosA7 (9.26%) and fosA3 (6.53%) was identified. fosA3 was associated with high-level fosfomycin resistance (≥512 mg/L), while fosA7 conferred relatively low-level resistance that was independent of the presence of glucose-6-phosphate. Additionally, fosA7 could facilitate Salmonella survival under oxidative stress. Both fosA3 and fosA7 were found in diverse serovars and STs, but segregated into distinct groups. The fosA3-positive Salmonella Typhimurium/Salmonella Indiana strains showed close genetic relationships, while fosA7-positive Salmonella Meleagridis/Salmonella Agona/Salmonella Derby showed a relatively high degree of whole-genome sequence heterogeneity. fosA3 was located on conjugative IncHI2 plasmids or chromosomes, while fosA7 was strictly chromosomal. Furthermore, two strains carried large chromosomal fosA7 regions within genomic islands. The fosA3 and fosA7 contigs from our isolates and the NCBI could be segregated into four primary and distinct genomic backbones. IS26 and the antibiotic resistance genes (ARGs) blaCTX-M, blaTEM-1B and rmtB were frequently adjacent to fosA3, while fosA7-carrying contigs generally lacked mobile elements and ARGs.Conclusions: fosA3 and fosA7 were the primary factors contributing to reduced fosfomycin susceptibility, to different degrees, in these Salmonella isolates. The distinct distributions and molecular characteristics of fosA7 and fosA3 indicated that their origin and evolution in Salmonella were most likely distinct. [ABSTRACT FROM AUTHOR]

Salmonella is a group of bacteria that constitutes the leading cause of diarrheal diseases, posing a great disease burden worldwide. There are numerous pathways for zoonotic Salmonella transmission to humans; however, the role of companion animals in spreading these bacteria is largely underestimated in China. We aimed to investigate the prevalence of Salmonella in pet dogs and cats in Hangzhou, China, and characterize the antimicrobial resistance profile and genetic features of these pet-derived pathogens. In total, 137 fecal samples of pets were collected from an animal hospital in Hangzhou in 2018. The prevalence of Salmonella was 5.8% (8/137) in pets, with 9.3% (5/54) of cats and 3.6% (3/83) of dogs being Salmonella positive. By whole-genome sequencing (WGS), in silico serotyping, and multilocus sequence typing (MLST), 26 pet-derived Salmonella isolates were identified as Salmonella Dublin (ST10, n = 22) and Salmonella Typhimurium (ST19, n = 4). All of the isolates were identified as being multidrug-resistant (MDR), by conducting antimicrobial susceptibility testing under both aerobic and anaerobic conditions. The antibiotics of the most prevalent resistance were streptomycin (100%), cotrimoxazole (100%), tetracycline (96.20%), and ceftriaxone (92.30%). Versatile antimicrobial-resistant genes were identified, including floR (phenicol-resistant gene), blaCTX-M-15, and blaCTX-M-55 (extended-spectrum beta-lactamase genes). A total of 11 incompatible (Inc) plasmids were identified, with IncA/C2, IncFII(S), and IncX1 being the most predominant among Salmonella Dublin, and IncFIB(S), IncFII(S), IncI1, and IncQ1 being the most prevailing among Salmonella Typhimurium. Our study applied WGS to characterize pet-derived Salmonella in China, showing the presence of MDR Salmonella in pet dogs and cats with a high diversity of ARGs and plasmids. These data indicate a necessity for the regular surveillance of pet-derived pathogens to mitigate zoonotic diseases. [ABSTRACT FROM AUTHOR]

Salmonella as a foodborne pathogen, has a very important impact on human health. This study characterized the serotype, plasmid replicon, MLST typing, resistance phenotype and resistance gene of 282 strains of Salmonella isolated from the environment, animals, foods, and patients in China. These strains are classified into four sources: poultry farms (39/282), animals (30/282), foods (164/282), and hospitals (49/282) their resistance to ciprofloxacin, levofloxacin and ceftazidime is gradually increasing. Among them, ST11, ST19 and ST314 are dominant ST types; Salmonella enteritidis, Salmonella typhimurium and Kentucky Salmonella enteritidis serotypes are the dominant serotypes. This study conducted a comprehensive molecular epidemiological investigation of Salmonella from the unique perspective of Onehealth. It was revealed that the mcr-1 carried by Salmonella mainly relies on the horizontal transfer of Inc I2 and Inc Q plasmids. And a novel integron variable region cassette arrangement pattern aadA2-aadA23-catB3-tet(B)-dfrA12-eptB has emerged in Salmonella strains. More noteworthy is the outbreak of bla TEM-148 subtype in Salmonella from food sources, in which the Inc HI plasmid played an important role., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Salmonella is a zoonotic pathogen posing a serious risk to the farming industry and public health due to food animals serving as reservoirs for future contamination and spread of Salmonella. The present study is designed to monitor the contamination status of Salmonella in duck farms and the main control points during breeding. 160 strains of duck-derived Salmonella were isolated from the 736 samples (cloacal swabs, feces, water, feed, soil, air and dead duck embryos) collected in southwest Shandong Province and the province's surrounding area. The percentage of Salmonella-positive samples collected was 21.74 % (160/736), and the greatest prevalence from duck embryo samples (40.00 %, 36/90). These Salmonella were classified into 23 serotypes depending on their O and H antigens, in which S. Typhimurium (30.15 %), S. Kottbus (13.97 %) and S. Enteritidis (10.29 %) were the prevailing serotypes. Subsequently, the molecular subtyping was done. Clustered regularly interspaced short palindromic repeats (CRISPR) analysis showed that 41 strains of S. Typhimurium and 14 strains of S. Enteritidis were classified into 13 and 3 genotypes, respectively. 19 S. Kottbus isolates from different sources featured ST1546, ST198, ST321, and ST1690 by multilocus sequence typing (MLST) analysis, among which ST1546 belongs to S. Kottbus was a new ST. The minimum spanning tree analysis based on the two CRISPR loci and seven MLST loci from all S. Typhimurium, S. Enteritidis and S. Kottbus isolates revealed that duck embryos, feed and water were key control points to the spread of Salmonella along the breeding chain. Meanwhile, the emergence of S. Kottbus in duck flocks was considered a potential public health hazard., Competing Interests: Declaration of competing interest All authors declare no conflict of interest., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

This study examined the prevalence and antibiotic resistance pattern of blaCTX-M extended-spectrum β-lactamase positive Salmonella species isolated from a hospital in Weifang. Salmonella strains were isolated from hospitalized patients from January 2018 to April 2023. Whole-genome sequencing was performed by Illumina platform. CTX-M-producing Salmonella were identified by Comprehensive Antibiotic Research Database (CARD). Strain susceptibility to six antimicrobial agents was assessed by BD Phoenix™ M50 System. MLST analysis confirmed sequence types and additionally, serotypes were determined by SeqSero2. Genetic environments of blaCTX-M genes were analyzed by Isfinder and BLASTn. Single nucleotide polymorphisms were used to construct a phylogenetic tree to analyze homology. A total of 34 CTX-M-producing Salmonella were detected. The most prevalent serotype was Salmonella enterica subsp. enterica 1,4,[5],12:i:- (14/34, 41.18%), belonging to ST34, followed by Salmonella Enteritidis (10/34, 29.41%), belonging to ST11. The highest resistance rate was detected to ampicillin (97.06%), followed by ceftriaxone (94.12%) and ceftazidime (58.83%). In CTX-M-producing Salmonella five types of blaCTX-M genes were identified, the most prevalent was blaCTX-M-55 (47.06%, 16/34), followed by blaCTX-M-14, blaCTX-M-65, blaCTX-M-125, and blaCTX-M-27 at 26.47% (9/34), 11.77% (4/34), 8.82% (3/34), and 5.88% (2/34), respectively. Apart from blaCTX-M, 40 antibiotic resistance genes were also detected, conveying resistance to multiple drugs and the most frequent genes were namely, mcr-1.1, aph(6)-Id, aph(3″)-Ib, oqxAB, qnrB6, qnrS1. According to genetic environment analysis, the insertion sequence ISEcp1 was prevalent upstream of the blaCTX-M gene. Our study demonstrates that multiple resistance genes are carried by clinical isolates of Salmonella spp. however, the dominant ESBL genotype is CTX-M-55, that is associated with ISEcp1.

Chlorine disinfectants have been widely used in the poultry supply chain but this exposure can also result in the development of bacterial tolerance to chlorine and this is often linked to antibiotic cross-resistance. The objectives of this study were to investigate sodium hypochlorite (NaClO) tolerance of Salmonella isolated from poultry supply chains and evaluate cross-resistance. We collected 172 Salmonella isolates from poultry farms, slaughter houses and retail markets in China during 2019–2020. We found that S. Enteritidis, S. Kentucky, and S. Typhimurium constituted > 80% of our Salmonella isolates. Overall, 68% of Salmonella isolates were resistant to > 3 antibiotics and S. Kentucky displayed a significantly (p > 0.05) higher frequency (93.2%) of multidrug resistance than the other serovars. Tolerance to chlorine at MIC > 256 mg/L was detected in 93.6% of isolates (161/172) and tolerant isolates displayed higher decimal reduction times (D value) and less ultrastructural damage than did the suspectable strains under chlorine stress. Spearman analysis indicated significant positive correlations between chlorine tolerance (evaluated by the OD method) and antibiotic resistance (p < 0.05) to ceftiofur, tetracycline, ciprofloxacin and florfenicol and this was most likely due to efflux pump over-expression. The most frequently detected chlorine resistance gene was qacE Δ 1 (83.1%, n = 143) and we found a positive correlation between its presence and MIC levels (r = 0.66, p < 0.0001). Besides, we found weak correlations between chlorine-tolerance and antibiotic resistance genes. Our study indicated that chlorine disinfectants most likely played an important role in the emergence of chlorine tolerance and spread of antibiotic resistance and therefore does not completely control the risk of food-borne disease. The issue of disinfectant resistance should be examined in more detail at the level of the poultry production chain. [ABSTRACT FROM AUTHOR]

NDM-1-producing multidrug-resistant Proteus mirabilis brings formidable clinical challenges. We report a nosocomial outbreak of carbapenem-resistant P. mirabilis in China. Six P. mirabilis strains collected in the same ward showed close phylogenetic relatedness, indicating clonal expansion. Illumina and MinION sequencing revealed that three isolates harbored a novel Salmonella genomic island 1 carrying a bla NDM–1 gene (SGI1-1NDM), while three other isolates showed elevated carbapenem resistance and carried a similar SGI1 but with two bla NDM–1 gene copies (SGI1-2NDM). Four new single nucleotide mutations were present in the genomes of the two- bla NDM–1-harboring isolates, indicating later emergence of the SGI1-2NDM structure. Passage experiments indicated that both SGI variants were stably persistent in this clone without bla NDM–1 copy number changes. This study characterizes two novel bla NDM–1-harboring SGI1 variants in P. mirabilis and provides a new insight into resistance gene copy number variation in bacteria. [ABSTRACT FROM AUTHOR]

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This study aimed to investigate the prevalence of fosfomycin fosA7 in Salmonella enterica isolates from food animals and retail meat products in China and the impact of fosA7 on bacterial fitness. A total of 360 Salmonella isolates collected from 11 provinces and cities in China were detected for fosA7. All fosA7 -positive Salmonella isolates were determined minimum inhibitory concentrations (MICs) and sequenced by Illumina Hiseq. The fosA7 gene of S. Derby isolate HA2-WA5 was knocked out. The full length of fosA7 was cloned into vector pBR322 and then transformed into various hosts. MICs of fosfomycin, growth curves, stability, and fitness of fosA7 were evaluated. The fosA7 gene was identified in S. Derby (ST40, n = 30) and S. Reading (ST1628, n = 5). MICs to fosfomycin of 35 fosA7 -positive isolates were 1 to 32 mg/L. All fosA7 were located on chromosomes of Salmonella. The deletion of fosA7 in HA2-WA5 decreased fosfomycin MIC by 16-fold and slightly affected its fitness. The acquisition of plasmid-borne fosA7 enhanced MICs of fosfomycin in Salmonella (1,024-fold) and Escherichia coli (16-fold). The recombinant plasmid pBR322- fosA7 was stable in Salmonella Typhimurium, S. Pullorum, S. Derby, and E. coli , except for Salmonella Enteritidis, and barely affected on the growth of them but significantly increased biological fitness in Salmonella. The spread of specific Salmonella serovars such as S. Derby ST40 will facilitate the dissemination of fosA7. fosA7 can confer high-level fosfomycin resistance and enhance bacterial fitness in Salmonella if transferred on plasmids; thus, it has the potential to be a reservoir of the mobilized fosfomycin resistance gene. [ABSTRACT FROM AUTHOR]

Pig is usually the carrier of Salmonella and Staphylococcus aureus, and can transmit the bacteria along the pork production chain to cause severe public health problems. In this study, we investigated the prevalence of Salmonella and S. aureus in fattening pigs in Hubei Province, China. The overall prevalence of Salmonella in rectal swab among 896 samples from 22 farms was 17.30%, and that of S. aureus in nasal swab among 814 samples from 20 farms was 28.26%. Antimicrobial resistance (AMR) analysis showed that 95.33% of the Salmonella strains exhibited resistance to more than three classes of antimicrobial agents tested. The highest resistance proportions were for chloramphenicol (100%), sulfamethoxazole/trimethoprim (SXT) (100%), and tetracycline (TET) (93.46%), while the lowest proportions were for cefotaxime (37.38%), gentamicin (GEN) (34.58%), and ciprofloxacin (24.30%). On the other hand, 98.42% of the S. aureus strains were resistant to more than three classes of antimicrobial agents tested. The most common resistance among the S. aureus strains was against SXT (100.00%), followed by TET (98.43%), erythromycin (91.34%), and clindamycin (91.34%), while the lowest frequent resistances were against GEN (34.65%) and oxacillin (16.54%). The prevalence and AMR of Salmonella and S. aureus exhibited an obvious diversity among different pig farms. Our results provided the epidemiological data for risk analysis of foodborne bacteria and AMR in pig farms. [ABSTRACT FROM AUTHOR]

Although knowledge of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system has been applied in many research areas, comprehensive studies of this system in Salmonella , particularly in analysis of antibiotic resistance, have not been reported. In this work, 75 Salmonella isolates obtained from broilers or broilers products were characterized to determine their antimicrobial susceptibilities, antibiotic resistance gene profiles, and CRISPR array diversities, and genotyping was explored. In total, 80.00% (60/75) of the strains were multidrug resistant, and the main pattern observed in the isolates was CN-AZM-AMP-AMC-CAZ-CIP-ATM-TE-SXT-FOS-C. The resistance genes of streptomycin (aadA), phenicol (floR-like and catB3-like), β-lactams (bla TEM, bla OXA, and bla CTX), tetracycline [ tet(A)-like ], and sulfonamides (sul1 and sul2) appeared at higher frequencies among the corresponding resistant isolates. Subsequently, we analyzed the CRISPR arrays and found 517 unique spacer sequences and 31 unique direct repeat sequences. Based on the CRISPR spacer sequences, we developed a novel typing method, CRISPR locus three spacer sequences typing (CLTSST), to help identify sources of Salmonella outbreaks especially correlated with epidemiological data. Compared with multi-locus sequence typing (MLST), conventional CRISPR typing (CCT), and CRISPR locus spacer pair typing (CLSPT), discrimination using CLTSST was weaker than that using CCT but stronger than that using MLST and CLSPT. In addition, we also found that there were no close correlations between CRISPR loci and antibiotics but had close correlations between CRISPR loci and antibiotic resistance genes in Salmonella isolates. [ABSTRACT FROM AUTHOR]

Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004–2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella ; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China. [ABSTRACT FROM AUTHOR]