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The emergence and spread of plasmid-mediated tigecycline resistance genes have attracted extensive attention worldwide. We investigated the distribution of mobile tigecycline resistance genes in Salmonella genomes generated by both our laboratory and public bacterial genomes downloaded from the NCBI GenBank. The tet(X4)-positive strains were subjected to susceptibility testing and conjugation assays. The genetic features of the tet(X4)-bearing plasmid sequence were analyzed. Here, we report the identification of the plasmid-mediated tigecycline resistance gene tet(X4) in a conjugative plasmid of the Salmonella enterica serovar Llandoff strain SH16G3606, isolated from a man in China in 2016, the first reported serovar Llandoff in China as a novel sequence type ST8300. The tet(X4)-mediated resistance phenotype was successfully transferred from the Salmonella Llandoff strain into Escherichia coli J53, resulting in a 32-fold increase in the minimal inhibitory concentration of tigecycline. The tet(X4) gene was located between two copies of ISCR2 in the plasmid pSal21GXH-tetX4. To our knowledge, this is the first report of the plasmid-mediated tigecycline resistance gene tet(X4) in a Salmonella Llandoff strain isolated from a human stool sample in China. In addition, our findings demonstrated that a total of 171 isolates are carrying tet(X)-like genes distributed in 21 countries or areas across 6 continents, posing a serious threat to humans and public health. Overall, our timely discovery of the recent emergence of the tet(X4) gene in Salmonella isolates and other Enterobacteriaceae bacteria species supports the need for rapid surveillance to prevent the tet(X)-like gene from spreading.

Salmonella Enteritidis is an important foodborne pathogen with high prevalence of resistance to cephalosporins, imposing a serious threat to public health. Therefore, a total of 162 Salmonella Ente...

Multidrug-resistant Salmonella Enteritidis (S. Enteritidis) isolates have become a significant threat to public health, and fosfomycin has been proposed as one of the therapeutic antibiotics for serious infections by resistant pathogens. In this study, a total of 501 clinical S. Enteritidis isolates were screened and 14 (2.8%) isolates exhibited resistance to fosfomycin (MIC ≥ 1,024 μg/mL) as well as ceftriaxone (MIC ≥ 128 μg/mL). The fosA3 gene was identified in these 14 isolates. The fosA3 gene that co-transferred with blaCTX-M-55 was observed on the IncFII plasmids with sizes of ~ 78 (n = 7) or ~ 111 (n = 2) kbp in 9 transconjugants. The fosA3-bearing plasmid p12367A is 111,764 bp in length and possessed a typical IncFII backbone. A 7.6-kbp multidrug resistance region (MRR) was identified in p12367A, which was comprised of fosA3 and blaCTX-M-55 genes interspersed with ΔISEcp1 and three copies of IS26. Two typical antibiotic resistance determinants (IS26-orf3-orf2-orf1-fosA3-IS26 and IS26-orf477-blaCTX-M-55 -ΔISEcp1-IS26) shared one IS26 in the MRR. The genetic arrangement of the MRR may have resulted from the stepwise integration of IS26 mobile elements via homologous recombination. Horizontal transfer of IncFII plasmids might contribute to the dissemination of fosA3 and blaCTX-M-55 resistance genes in S. Enteritidis interspecies. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by epidemic IncFII plasmids bearing fosA3-blaCTX-M-55 .

In this study, we explored the prevalence of oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA) in staphylococcal food poisoning outbreak isolates and foodborne isolates, and then investigated their molecular characteristics, classical staphylococcal enterotoxins (SEs), and drug resistance. Eight (2.9%) of 275 isolates from food poisoning outbreaks and 7 (3.8%) of 184 isolates from retail foods were identified as OS-MRSA isolates. Among the 15 OS-MRSA isolates, the most frequently detected toxin genes were hld (100%), hla (93.3%), pvl (80.0%), and hlb (46.7%) followed by seg and seq (33.3%, each), hlg (26.7%), seb and hlgv (20.0%, each), sec, seh, sel, sep, and tst (13.3%, each), and sei, sem, sen, and seo (6.7%, each). None of isolates carried other tested virulence genes. The most frequently detected classical SEs were SEB and SEC (26.7%, each), followed by SEA and SEE (20.0%, each), and SED (6.7%). Resistance was most frequently observed in ampicillin, penicillin, and cefoxitin (100%, each), followed by trimethoprim/sulfamethoxazole (93.3%), erythromycin (73.3%), amoxicillin/clavulanic acid (46.7%), tetracyclines (26.7%), and ciprofloxacin (6.7%). All isolates were susceptible to other tested antibiotics. A dominant molecular type belonged to ST398-IVa-t034 (26.7%), followed by ST59-IVa-t437 (20.0%), ST88-III-t14340 and ST1-IVa-t114 (13.3%, each), and ST5-II-t002, ST630-t4549, ST5-II, and ST4495-t10738 (6.7%, each). Our findings indicated that OS-MRSA strains had a low prevalence rate among outbreak strains and foodborne strains, which frequently harbored SCCmec IVa, and carried a variety of toxin genes, and also expressed numerous classical SEs. In addition, all OS-MRSA isolates were susceptible to the majority of antibacterial agents except β-lactam. Our study is the first to report that OS-MRSA isolates are associated with food poisoning outbreaks worldwide.

Background At present, azithromycin has become an effective treatment for severe diarrhea caused by Enterotoxigenic Escherichia coli (ETEC) infection. However, enterobacteria have begun to develop resistance to azithromycin and have attracted attention in recent years. This study conducted to described the emergence of a high proportion of azithromycin-resistant ETEC serogroup O6 strains in Shanghai and to analyzed the mechanisms of azithromycin resistance. Results Strains from adult diarrhea patients with ETEC serogroup O6 infections were collected by Shanghai Diarrhea Surveillance Network and the Foodborne Surveillance Network from 2016 to 2018. We tested 30 isolates of ETEC O6 serogroup, 26 of which were resistant to azithromycin. Phylogenetic analysis revealed that these ETEC serogroup O6 strains have formed an independent dominant clone. S1-PFGE and southern blotting revealed the presence of the mphA gene on the 103 kb plasmid. Illumina and Nanopore sequencing and plasmid coverage analysis further confirmed that azithromycin-resistant strains carried a novel IncFII plasmid harboring mphA and blaTEM-1 resistance genes. Conclusions This is the first study to report a high proportion of azithromycin resistance in a particular ETEC serogroup due to a specific plasmid carrying mphA. Our findings indicate the rapid spread of azithromycin resistance, highlighting the urgency of stringent surveillance and control measure.

Purpose Carbapenem resistance is rarely reported in Salmonella Typhimurium, especially from a food origin. Here, we report a plasmid-mediated mobile carbapenem-resistant blaNDM-5 gene in Salmonella Typhimurium isolated from pork in Shanghai, China in 2016. Patients and methods In July 2016, the S. Typhimurium SH160 strain was recovered from minced pork meat purchased from a supermarket in Yangpu District, Shanghai, China. Antimicrobial susceptibility testing, multi-locus sequence typing, conjugation, S1-PFGE, southern hybridization, whole-genome sequencing and data analysis were performed. Results This isolate was found to be a ST34 strain and resistant to carbapenems, cephalosporins, and most other commonly used antibiotics. The blaNDM-5 gene was harbored by a 46161-bp IncX3 plasmid which was found to be transferable. The IncX3 plasmid contains a composite cassette, consisting of ISSwil-IS3000-ΔISAba125-IS5-blaNDM-5-bleMBL-trpF-dsbC-IS26-ctuA1-ΔumuD. In addition, this strain was found to harbor an additional 161706-bp IncHI2 plasmid which carries nine resistant genes, such as aadA1, aadA3, aph(3')-la, sul1, sul2, sul3, floR, cmlA and dfrA12. Conclusion We reported the S . Typhimurium with transferable IncX3 plasmid harboring blaNDM-5 gene from minced pork. We characterized the complete genetic features of the plasmid, which demonstrated the potential for spreading in different bacterial pathogens. Therefore, extensive surveillance and monitoring for carbapenem-resistant bacterium in the food chain and public health are urgently required.

Infection caused by invasive Salmonella occurs when Salmonella bacteria, which normally cause diarrhea, enter the bloodstream and spread through the body. We report the dramatic increase in florfenicol-resistant invasive non-typhoidal Salmonella (iNTS) in China between 2007 and 2016. Of the 186 iNTS strains isolated during the study period, 34 were florfenicol resistant, most of which harbored known resistance genes. Florfenicol is exclusively used in veterinary medicine in China, but now florfenicol-resistant iNTS is found in clinical patients. This finding indicates that antimicrobial resistance produced in veterinary medicine can be transmitted to humans, which poses a severe threat to public health.

Purpose Human infections caused by invasive non-typhoidal Salmonella (iNTS) are highly prevalent worldwide. However, data for such infections in China are scarce. This study reports the epidemiology of iNTS in China. Methods INTS isolates were recovered from blood and other clinical specimens collected during 2007-2016 across five provinces (Shanghai, Xinjiang, Fujian, Guangxi, and Chongqing) in China. Antimicrobial susceptibility was performed using the agar dilution method and molecular epidemiology was performed using standard microbiological techniques. Results A total of 178 iNTS isolates were recovered from approximately 9700 patient specimens during 2007-2016. The predominant serovars were Salmonella Enteritidis (57/178, 32%), Salmonella Choleraesuis (47/178, 26.4%), and Salmonella Typhimurium (24/178, 13.5%). Up to 50 isolates (28.1%) were from patients who were ≤1 year of age, while 28 (15.7%) were from patients who were ≥60 years. Among these isolates, high rates of resistance to nalidixic acid (114/178, 64%), sulfisoxazole (59%), ciprofloxacin (15.2%), and cefotaxime (8.4%) were found. Moreover, 53.4% (95/178) exhibited multidrug resistance, and 3.9% (7/178) showed co-resistance to third-generation cephalosporins and ciprofloxacin. Steadily increasing numbers of nalidixic acid, cefotaxime, and ciprofloxacin-resistant isolates, but decreasing numbers of multidrug resistance isolates were detected during the study period. Detection of quinolone genes in 114 nalidixic acid-resistant isolates showed that 58.3% (67/114) harbored plasmid-mediated quinolone resistance (PMQR) genes [aac(6´)-Ib-cr, qnrA, qnrB, oqxAB, qepA, qnrS, and qnrD] and 98.2% (112/114) exhibited mutations in quinolone resistance determining regions [gyrA, parC, and parE]. Furthermore, we detected beta-lactamases genes in the ceftriaxone-resistant isolates. The most common were blaTEM-1 (93.3%), followed by blaCTX-M-55 (40%), blaCMY-2 (33.3%), and blaOXA-1 (33.3%). Finally, a range of pulsed-field gel electrophoresis patterns were detected among the Salmonella Enteritidis and Salmonella Typhimurium isolates. Conclusion High rates of multidrug resistance and steadily increasing cefotaxime and ciprofloxacin-resistant iNTS could pose a significant challenge for the effective treatment of salmonellosis in China.

Background Shigella spp., facultative anaerobic bacilli of the family Enterobacteriaceae, are one of the most common causes of diarrheal diseases in human worldwide which have become a significant public health burden. So, we aimed to analyze the antimicrobial phenotypes and to elucidate the molecular mechanisms underlying resistance to cephalosporins and fluoroquinolones in Shigella isolates from patients with diarrhea in Shanxi Province. Results During 2006–2016, we isolated a total of 474 Shigella strains (including 337 S. flexneri and 137 S. sonnei). The isolates showed high rates of resistance to traditional antimicrobials, and 26, 18.1 and 3.0% of them exhibited resistance to cephalosporins, fluoroquinolones and co-resistance to cephalosporins and fluoroquinolones, respectively. Notably, 91.1% of these isolates, including 22 isolates that showed an ACTSuT profile, exhibited multidrug resistance (MDR). The resistance rates to cephalosporins in S. sonnei isolates were higher than those in S. flexneri. Conversely, the resistance rates to fluoroquinolones were considerably higher in S. flexneri isolates. Among the 123 cephalosporins-resistant isolates, the most common extended-spectrum beta-lactamase gene was blaTEM-1, followed by blaCTX-M, blaOXA-1, and blaSHV-12. Six subtypes of blaCTX-M were identified, blaCTX-M-14 (n = 36) and blaCTX-M-55 (n = 26) were found to be dominant. Of all the 86 isolates with resistance to fluoroquinolones and having at least one mutation (Ser83Leu, His211Tyr, or Asp87Gly) in the the quinolone resistance-determining regions of gyrA, 79 also had mutation of parC (Ser80Ile), whereas 7 contained plasmid-mediated quinolone resistance genes including qnrA, qnrB, qnrS, and aac(60)-Ib-cr. Furthermore, pulsed-field gel electrophoresis analysis (PFGE) showed a considerable genetic diversity in S. flexneri isolates. However, the S. sonnei isolates had a high genetic similarity. Conclusions Coexistence of diverse resistance genes causing the emergence and transmission of MDR might render the treatment of shigellosis difficult. Therefore, continuous surveillance might be needed to understand the actual disease burden and provide guidance for shigellosis. Electronic supplementary material The online version of this article (10.1186/s12866-019-1495-6) contains supplementary material, which is available to authorized users.

Metals are widely used in animal feed for their growth-stimulating and antimicrobial effects, yet their use may potentially promote the proliferation of antibiotic resistance through co-selection. We studied the prevalence and associations of metal, antibiotic, and disinfectant resistances of 300 Salmonella Typhimurium isolates from pig meat, pig manure, chicken meat, poultry manure, and human stool from Sichuan, China. Seventy four percent of the 300 Salmonella Typhimurium isolates were considered resistant to Cu, almost 50% to Zn and Cr, over 25% to Mn and Cd, and almost 10% to Co. Most of the isolates carried at least one heavy metal resistance gene (HMRG). The Cr-Zn-Cd-resistance gene czcD was carried by 254 isolates and the Cu-resistance genes pcoR and pcoC by 196 and 179 isolates, respectively. Most of the isolates were resistant to at least one antibiotic and almost 80% were multidrug-resistant. The prevalence of resistance to six antibiotics was higher among the pig meat and manure isolates than among other isolates, and that of streptomycin and ampicillin were highest among the pig meat isolates and that of ciprofloxacin and ofloxacin among the pig manure isolates. From 55 to 79% of the isolates were considered resistant to disinfectants triclosan, trichloroisocyanuric acid, or benzalkonium chloride. The metal resistances and HMRGs were associated with resistance to antibiotics and disinfectants. Especially, Cu-resistance genes were associated with resistance to several antibiotics and disinfectants. The transfer of the Cr-Zn-Cd-resistance gene czcD, Cu-resistance gene pcoC, and Co-Ni-resistance gene cnrA into Escherichia coli and the increased Cu-resistance of the transconjugants implied that the resistance genes were located on conjugative plasmids. Thus, the excessive use of metals and disinfectants as feed additives and in animal care may have the potential to promote antibiotic resistance through co-selection and maintain and promote antibiotic resistance even in the absence of antibiotics.

Salmonellosis represents a growing threat to global public health. Salmonella enterica remains the leading cause of bacterial foodborne diseases in China. Salmonella enterica serovar Rissen (S. Rissen) has been recognized as one of the emerging serovars among humans in different countries worldwide. However, knowledge on the prevalence of S. Rissen in China is largely lacking. To address essential epidemiological information for S. Rissen in China, a total of 1,182 S. Rissen isolates recovered from samples across the food chain were collected from 16 provinces or province-level cities between 1995 and 2019. Risk factors due to the consumption of animal-derived food products were also analyzed. We found S. Rissen is widely distributed, especially in the Eastern and Southern parts of China, and there is an increasing frequency in recent years as evidenced by the greater number of isolates recovered in 2016, 2017, and 2018. Interestingly, the majority of S. Rissen isolates recovered in this study were from human samples (63.4%; 749/1182), remarkably, 58.4% (438/749) were from asymptomatic carriers. We obtained most of the S. Rissen isolates from humans from Guangxi (59.5%; 446/749) and Shanghai (29.5%; 221/749). Among 302 human diarrheal isolates (40.3%; 302/749), we found 44.6% (139/311) of S. Rissen in children with diarrhea (age below 10 years old). This is of clinical significance as diarrhea is one of the crucial causes of child mortality globally and our findings here highlighted the importance of Salmonella infections in Chinese children. Additionally, S. Rissen isolates were also found to be associated with pork and poultry products in China. This study projected the most updated national-wide study of S. Rissen isolates obtained from different sources in China over the past two decades. Continued surveillance is warranted to further monitor this emerging serovar in China and elsewhere over the world.

Background Salmonella Wandsworth is a rare serotype of Salmonella. This study analyzed the genotyping, genome structure, and molecular biological functions of Salmonella Wandsworth based on the results of multilocus sequence typing and next‐generation sequencing genome assembly analysis. Methods Serological typing was performed using the slide‐agglutination method. The micro broth dilution method was used to test antibiotic susceptibility. Multilocus sequence typing (MLST) was used to perform the homology analysis, while the second‐generation sequencing genome analysis was used to analyze the whole genome of the bacteria. Results Salmonella Wandsworth is Group Q Salmonella. The MLST of this strain was ST1498. Salmonella Wandsworth was sensitive to antibiotics, such as ceftriaxone, imipenem, chloramphenicol, and colistin, but was resistant to ampicillin, cefalotin, gentamicin, and ciprofloxacin. The second‐generation sequencing results showed that the genome sequence length of the bacteria was 5109457bp. Annotated COG library analysis generated 3,746 corresponding genes. After the comparison with the KEGG library, 1,340 genes, which participate in 19 types of metabolic pathways, were obtained. A total of 249 pathogenic factors and 2 disease islands were predicted. 2 CRISPR sites and 8 Cas sites were predicted. It can be seen from the evolutionary tree that Salmonella Wandsworth MLST1498 and Paratyphi B str.SPB7 are gathered together. We identified one resistance gene, namely, aac(6’)‐Iaa accounting for aminoglycoside resistance. Conclusion Salmonella Wandsworth isolated in this study is Salmonella group Q. Consequently, it is necessary to strengthen the understanding of clinical infections of Salmonella Wandsworth and carry out continuous monitoring and research., Salmonella Wandsworth is a rare serotype of Salmonella. Based on genome sequences, We employed the alignment and assembly‐free (AAF) method to construct a genomic evolutionary tree.

Salmonella is the primary cause of community-acquired foodborne infections, so its resistance to antimicrobials, such as aminoglycosides, is a public health issue. Of concern, aminoglycoside resistance in Salmonella is increasing rapidly. Here, we performed a retrospective study evaluating the prevalence of Salmonella harboring armA-mediated aminoglycoside resistance in community-acquired infections and in food or environmental sources. The prevalence rates of armA-harboring Salmonella strains were 1.1/1,000 (13/12,095) and 8.7/1,000 (32/3,687) in outpatient and food/environmental isolates, respectively. All the armA-harboring Salmonella strains were resistant to multiple drugs, including fluoroquinolone and/or extended-spectrum cephalosporins, and most (34/45) belonged to serovar Indiana. The armA gene of these strains were all carried on plasmids, which spanned five replicon types with IncHI2 being the dominant plasmid type. All the armA-carrying plasmids were transferable into Escherichia coli and Acinetobacter baumannii recipients. The conjugation experiment results revealed that the armA-harboring S. Indiana strains had a relatively higher ability to acquire armA-carrying plasmids. The low similarity of their pulsed field gel electrophoresis patterns indicates that the armA-harboring Salmonella strains were unlikely to have originated from a single epidemic clone, suggesting broad armA spread. Furthermore, the genetic backgrounds of armA-harboring Salmonella strains isolated from outpatients exhibited higher similarity to those isolated from poultry than to those isolated from swine, suggesting that poultry consumption maybe an infection source. These findings highlight an urgent need to monitor the prevalence and transmission of armA-harboring Salmonella, especially S. Indiana, to better understand the potential public health threat and prevent the further spread of these strains.

The emergence of extended-spectrum &beta, lactamase-producing Salmonella enterica serovar Enteritidis (ESBL-SE) in humans and foods has gained global attention. In particular, CTX-M-type ESBL-SE are increasingly being detected from various sample types. The aim of this study was to comprehensively analyze the epidemiology and characteristics of blaCTX-M-55-carrying ESBL-SE isolates of clinical origin in Shanghai, China. A total of 292 S. Enteritidis isolates were recovered from the feces and blood of outpatients and inpatients between 2006 and 2014. Overall, there was a high frequency of cefotaxime-resistant isolates (97.3%), which was significantly higher (p &lt, 0.01) than that of isolates resistant to the other tested antibiotics. All S. Enteritidis isolates exhibited resistance to &ge, 1 antibiotic, and 98.0% were multidrug resistant. A total of 233 isolates were identified as ESBL-SE, 166 of which were CTX-M type. Six subtypes of CTX-M-encoding genes were detected, among which blaCTX-M-55 (91.6%, 152/166) was the most prevalent genotype. There was high genetic similarity among blaCTX-M-55-positive ESBL-SE. The blaCTX-M-55 gene in the ESBL-SE donor strains could be easily transferred into Enterobacteriaceae recipient strains. This study highlights that CTX-M-55 should be considered an important surveillance target in Shanghai, China. Cephalosporins, especially cefotaxime, must be used with caution in empirical treatment for Salmonella infections.

Salmonella spp. are recognized as important foodborne pathogens globally. Salmonella enterica serovar Rissen is one of the important Salmonella serovars linked with swine products in numerous countries and can transmit to humans by food chain contamination. Worldwide emerging S. Rissen is considered as one of the most common pathogens to cause human salmonellosis. The objective of this study was to determine the antimicrobial resistance properties and patterns of Salmonella Rissen isolates obtained from humans, animals, animal-derived food products, and the environment in China. Between 2016 and 2019, a total of 311 S. Rissen isolates from different provinces or province-level cities in China were included here. Bacterial isolates were characterized by serotyping and antimicrobial susceptibility testing. Minimum inhibitory concentration (MIC) values of 14 clinically relevant antimicrobials were obtained by broth microdilution method. S. Rissen isolates from humans were found dominant (67%, 208/311). S. Rissen isolates obtained from human patients were mostly found with diarrhea. Other S. Rissen isolates were acquired from food (22%, 69/311), animals (8%, 25/311), and the environment (3%, 9/311). Most of the isolates were resistant to tetracycline, trimethoprim-sulfamethoxazole, chloramphenicol, streptomycin, sulfisoxazole, and ampicillin. The S. Rissen isolates showed susceptibility against ceftriaxone, ceftiofur, gentamicin, nalidixic acid, ciprofloxacin, and azithromycin. In total, 92% of the S. Rissen isolates were multidrug-resistant and ASSuT (27%), ACT (25%), ACSSuT (22%), ACSSuTAmc (11%), and ACSSuTFox (7%) patterns were among the most prevalent antibiotic resistance patterns found in this study. The widespread dissemination of antimicrobial resistance could have emerged from misuse of antimicrobial agents in animal husbandry in China. These findings could be useful for rational antimicrobial usage against Salmonella Rissen infections.

Salmonella is composed of a wide variety of serovars, causing human self-limited gastrointestinal illnesses or invasive infections. Invasive non-typhoidal Salmonella (iNTS) is well documented, with high mortality for children and immunocompromised adults in sub-Saharan Africa and has recently been reported in Southeast Asia. However, iNTS in China remains unknown. In May 2019, a case of invasive infection caused by Salmonella enterica serovar Uzaramo (S. Uzaramo) was reported for the first time in China. Phylogenomic analysis was performed by genomic sequencing the available contextualized isolates, which separated the two Chinese strains into different sublineages. Both phenotypic and genomic characterization demonstrated that the S. Uzaramo isolates showed in general low antimicrobial resistance potential, except one isolated from lake-water in China. Additional comparative genomic analysis and Caenorhabditis elegans killing assays suggested a unique combination of virulence factors, including typhoid toxin and tcf fimbrial adhesin, which might play a role in the invasive infection. This study highlights that the transparency of global surveillance genomic data could accelerate understanding of virulence and antimicrobial resistance makeup of a previously unknown threat.

Human infections caused by Salmonella Newport generally lead to gastrointestinal diseases. These infections are normally self-limiting; however, in certain cases, broad-spectrum antimicrobials are prescribed for the treatment. The Chinese National Foodborne Disease Surveillance Network has reported a gradual increase in the incidence of multidrug-resistant S. Newport infections in humans. After careful evaluation of the dynamic relationship among the clinical findings, the age group, and the genomic sequence data, it was found that young patients represented the major group with persistent diarrhea, whereas adults were either asymptomatic or diarrheic. Furthermore, all these strains contained multiple acquired antimicrobial resistance determinants, which limited the use of antimicrobials for human patients of all age groups. This analysis of the laboratory-confirmed cases, coupled with genetic analysis of the corresponding pathogen, revealed that antimicrobial treatment of persistent infections by S. Newport in infants and toddlers, and in asymptomatic or diarrheic adults, may not be successful. If the antimicrobials must be prescribed at all, they must be used with caution because of the presence of multiple acquired antimicrobial resistance determinants in such strains., Salmonella enterica serovar Newport (S. Newport) infections are gradually on the rise in China from the last decade. For humans’ infections, S. Newport has been ranked among the top five serovars responsible for persistent infections, globally. A total of 290 S. Newport strains with their relevant clinical metadata were analyzed, and the strains were subjected to whole-genome sequence analysis. Among these, 62.4% (n = 181) were from diarrheic patients and 28.9% (n = 84) were from asymptomatic individuals (including adults and youngsters) while 8.6% (n = 25) were from cases of persistent diarrhea in infants (28%, n = 7) and toddlers (72%, n = 18). The association between the sequence types (STs) and the variations in the clinical presentation was statistically significant (P = 0.0432), with ST46 causing diarrhea or representing asymptomatic patients and ST31 or ST68 causing persistent diarrhea. Genomic analysis revealed that the highest proportion of the isolates (98.5%, n = 279), primarily from patients with or without diarrhea rather than from asymptomatic individuals, carried antimicrobial resistance determinants corresponding to the aminoglycosides and beta-lactams, highlighting the need for cautionary usage of antimicrobials in such patients. These findings also suggest that cases of nontyphoidal Salmonella infection with symptoms of acute diarrhea or persistent diarrhea caused by S. Newport should be handled with caution, due to the high chance of development of an antimicrobial resistance phenotype that might lead to therapeutic failures. Together, S. Newport ST31 and ST46, which have the highest frequency of carriage of multidrug resistance, are potentially responsible for antimicrobial-resistant diarrhea/persistent diarrhea in infants and children, while adult humans are more likely to be (asymptomatic) carriers of the S. Newport strains. IMPORTANCE Human infections caused by Salmonella Newport generally lead to gastrointestinal diseases. These infections are normally self-limiting; however, in certain cases, broad-spectrum antimicrobials are prescribed for the treatment. The Chinese National Foodborne Disease Surveillance Network has reported a gradual increase in the incidence of multidrug-resistant S. Newport infections in humans. After careful evaluation of the dynamic relationship among the clinical findings, the age group, and the genomic sequence data, it was found that young patients represented the major group with persistent diarrhea, whereas adults were either asymptomatic or diarrheic. Furthermore, all these strains contained multiple acquired antimicrobial resistance determinants, which limited the use of antimicrobials for human patients of all age groups. This analysis of the laboratory-confirmed cases, coupled with genetic analysis of the corresponding pathogen, revealed that antimicrobial treatment of persistent infections by S. Newport in infants and toddlers, and in asymptomatic or diarrheic adults, may not be successful. If the antimicrobials must be prescribed at all, they must be used with caution because of the presence of multiple acquired antimicrobial resistance determinants in such strains.

In this study, we investigated the pattern of antimicrobial resistance in Salmonella enterica serotype Enteritidis isolates in Shanghai, China from 2005 to 2014. We found the first isolates with resistance to the fourth-generation cephalosporin cefepime starting in 2010. Furthermore, we analyzed the epidemic characteristics and mechanisms of underlying cefepime resistance in S. Enteritidis isolates found from 2010. In total, 38 of 2,914 (1.30%) isolates were identified as cefepime-resistant S. Enteritidis (CRSE) isolates by Kirby-Bauer disk diffusion. Two isolates were from animal derived food sources; 36 isolates were from fecal samples of human patients with salmonellosis. Antimicrobial susceptibility testing using the agar dilution method revealed that all CRSE isolates showed additional resistances at least to ceftazidime, cefotaxime, and ampicillin. Additionally, pulsed-field gel electrophoresis (PFGE) profiles indicated that 89.47% of CRSE isolates also displayed similar PFGE patterns. Five types of β-lactamase genes, bla CTX-M (100.00%, 38/38), bla SHV (65.79%, 25/38), bla TEM (52.63%, 20/38), bla ACC (18.42%, 7/38), and bla PSE (5.26%, 2/38) were detected by PCR and sequencing. Among bla CTX-M genes, bla CTX-M-55 was the dominant type (84.21%, 32/38). Conjugation and transformation experiments along with plasmid replicon typing revealed that bla CTX-M-55 was located on plasmids of various replicon types with sizes ranging from 76.8 to 138.9 kb. Plasmid sequence analysis also showed that the bla CTX-M-55 gene was mobilized mainly by the ISEcp1-bla CTX-M-55-ORF477 transposition unit and had its own ISEcp1-based promoter, which accelerated the expression and transmission of bla CTX-M-55. Analysis of whole genome sequences (Illumina) of one selected transformant SH12G706-C showed high similarity of the bla CTX-M-55 carrying plasmid with the IncI1 plasmid backbone p628-CTX-M of Klebsiella pneumoniae detected in 2010 in China. The present study demonstrated that the bla CTX-M-55 gene mobilized by ISEcp1- bla CTX-M-55-ORF477 was the main feature shared by CRSE isolates and seems to play an important role for transmission of cefepime resistance. The number of CRSE isolates is rising annually, and the strong dissemination ability of ISEcp1-bla CTX-M-55-ORF477-harboring plasmids among different species represents an important threat to the therapeutic effectiveness of cefepime.

Salmonella enterica Newport (S. Newport), with phylogenetic diversity feature, contributes to significant public health concerns. Our previous study suggested that S. Newport from multiple animal-borne routes, with distinct antibiotic resistant pattern, might transmit to human. However, their genetic information was lacking. As a complement to the earlier finding, we investigate the relationship between each other among the hosts, sources, genotype and antibiotic resistance in S. Newport. We used the multilocus sequence typing (MLST) in conjunction with minimum inhibitory concentration of 16 antibiotics of globally sampled 1842 S. Newport strains, including 282 newly contributed Chinese strains, to evaluate this association. Our analysis reveals that sequence types (STs) are significantly associated with different host sources, including livestock (ST45), birds (ST5), contaminated water and soil (ST118), reptiles (ST46) and seafood (ST31). Importantly, ST45 contained most of (344/553) the multi-drug resistance (MDR) strains, which were believed to be responsible for human MDR bacterial infections. Chinese isolates were detected to form two unique lineages of avian (ST808 group) and freshwater animal (ST2364 group) origin. Taken together, genotyping information of S. Newport could serve to improve Salmonella source-originated diagnostics and guide better selection of antibiotic therapy against Salmonella infections.

In this study, 205 Salmonella enterica serovar Corvallis strains were obtained from humans and foods from Guangdong, Guangxi, and Shanghai in China from 2009 to 2017 to assess drug resistance and molecular epidemiology. These isolates displayed high rates of resistance to sulfisoxazole (94.15%) and tetracycline (77.56%). Surprisingly, the rate of resistance to ciprofloxacin reached 21.46%. Moreover, 63.9% of the strains displayed multidrug resistance. Detection of quinolone genes showed that 97.56% of the strains had single mutations (T57S) in parC. The plasmid-mediated quinolone resistance (PMQR) genes qnrS, aac(6')-Ib-cr, and qnrB, were also detected. The extended spectrum β-lactamase (ESBLS) gene that was most common among the isolates was blaTEM-1 (18.05%). These S. Corvallis isolates are the first to date, that have been reported to possess blaCTX-M-55 or blaNDM-5. Additionally, 95.61% of isolates were biofilm producers. The streptomycin resistance rate was higher in strong biofilm producers (87.50%) than in moderate (37.93%) and weak (26.49%) biofilm producers. Pulsed-field gel electrophoresis (PFGE) showed that some strains from different sources had the same genotype. These isolates may be transmitted to humans through food and therefore the monitoring of these isolates should be strengthened in China.

Salmonella producing β-lactamases has spread rapidly worldwide and poses a serious threat to human and animal health. In this study, we characterized 220 ceftriaxone (CRO)-resistant isolates identified among 3153 Salmonella from humans, animals, food, and water collected in Shanghai, China. They were assessed for antimicrobial susceptibility, phenotypic identification of extended-spectrum β-lactamases (ESBLs), and β-lactamase genes and integrons. CRO resistance in Salmonella increased from 5.0% in 2011 to 8.4% in 2013. Salmonella Enteritidis (45.5%), Salmonella Typhimurium (20.9%) from humans, and Salmonella Indiana (14.5%) from poultry represented the majority of the CRO-resistant isolates. Many isolates were also resistant to other antimicrobials, including nalidixic acid (84.5%), sulfisoxazole (70.5%), and tetracycline (61.8%). Resistance to ciprofloxacin was also found in 33.6% of the isolates. Most isolates (98.2%) were confirmed as ESBL producers. Resistance genes such as blaCTX-M, blaTEM, and blaOXA were detected in 207 (94.1%), 99 (45%), and 53 (24.1%) isolates, respectively. Three types of integron I and one type of integron II were identified in 13 (5.9%) and 2 (0.9%) isolates, respectively. The integrons encompassed 10 different genes: dfrA1/12/17/25, aadA1/2/5, sat2, orfF, and ybeA. Our study underscores concern for increasing CRO resistance, and highlights the widespread ESBL genes in Salmonella enterica.

Disease caused by nontyphoidal serotypes of Salmonella enterica is the leading cause of foodborne illness worldwide. Many serotypes have also developed resistance to antimicrobials commonly used for the treatment of salmonellosis. Here we analyze 179 ciprofloxacin-resistant isolates identified among 3680 Salmonella isolated from humans, food, animals, and water collected in Shanghai, China. They were assessed for antimicrobial susceptibility, plasmid-mediated quinolone resistance (PMQR) determinants, and mutations in quinolone resistance determination regions (QRDRs); genetic relatedness was examined using PFGE. Ciprofloxacin resistance in Salmonella increased from 2.3% in 2006 to 5.9% in 2012. Multidrug resistance was common, and most carried mutations in QRDR (97.2%) and PMQR determinants (71.5%). Mutations frequently included changes in gyrA: Ser83Phe (53.6%) and Asp87Asn (35.8%), and in parC: Thr57Ser (53.1%) and Ser80Arg (44.1%). Mutations in parC and parE without changes in gyrA were identified in S. Derby and most S. Thompson. Among PMQR determinants, aac(6')-Ib-cr (62.0%) and oqxA/oqxB (33.5%/33.0%) were most common, and conferred resistance without target mutations in five S. Typhimurium isolates. PFGE analysis revealed that S. Typhimurium, isolated from pork and aquatic products, and S. Indiana, isolated from chicken, were highly similar to isolates from humans, suggesting these products be the major source of ciprofloxacin-resistant infections. Our findings highlight the important role QRDRs and PMQR play in ciprofloxacin resistance of Salmonella, and reveal the potential sources of the pathogen associated with human infections.

We characterized antibiotic resistance profiles, antibiotic resistance-associated genes, and pulsed-field gel electrophoresis (PFGE) patterns of 145 Salmonella enterica serotype Typhimurium isolates from human infections and retail foods that were possibly responsible for salmonellosis outbreaks from 2008 to 2012 in Shanghai, China. Resistance to at least three antibiotics was found in 66.7% of chicken isolates, 76.5% of duck isolates, 77.8% of pork isolates, and 80.5% of human isolates. Seven antibiotic resistance phenotypes were detected in chicken isolates, 16 in pork isolates, 17 in duck isolates, and 50 in human isolates. No significant difference (p 0.05) was found between Salmonella isolates derived from human salmonellosis and from retail foods in terms of the percent resistance of ampicillin, amoxicillin/clavulanic acid, ceftiofur, ceftriaxone, nalidixic acid, chloramphenicol, gentamicin, kanamycin, streptomycin, tetracycline, sulfisoxazole, and sulfamethoxazole/trimethoprim. PFGE using XbaI and BlnI showed that some Salmonella isolates recovered from human infections and retail foods had same or highly similar genetic profile. Same or similar antibiotic resistance profiles, antibiotic resistance associated genes (i.e., qnrA, qnrB, qnrS, aac(6')-Ib, and oqxAB), gene cassettes (i.e., aadA2, dfrA12-aadA2, and aadA1), and mutations were detected in those isolates that exhibited high genetic similarities. These findings highlighted the frequent presence of Salmonella Typhimurium in retail chicken, pork, duck, and humans.

Salmonella enterica serovar Indiana has become a widely prevalent non-typhoidal serovar in China in recent years. To improve the understanding of antimicrobial resistance and genetic bias in this emerging pathogen, a total of 214 S. Indiana isolates from foods, patients, and the environments in China from 2007 to 2016 were characterized for antimicrobial susceptibility, antimicrobial resistance-determining factors, and molecular typing. It was found that 208 (97.2%) exhibited resistance to ciprofloxacin, and 102 (47.7%) isolates to ceftriaxone. Ciprofloxacin resistance increased from 82.4% in 2007–2008 to 100.0% in 2015–2016. Ceftriaxone resistance increased from 29.4% in 2007–2008 to 47.1% in 2015–2016. In particular, the proportion of multidrug-resistant (MDR) S. Indiana isolates increased from 64.7% in 2007–2008 to 91.4% in 2015–2016. Mutations in the quinolone resistance determining region (QRDR) (gyrA and parC), plasmid-mediated quinolone resistance (PMQR) genes [aac(6’)-Ib-cr, oqxAB, qnrA, qnrS, qnrB and qepA], extended-spectrum beta-lactamase (ESBL) genes (blaOXA, blaCTX-M, blaTEM, blaCMY and blaVEB), and class I integrons were identified in these S. Indiana isolates, along with transposon units of ΔISEcp1-blaCTX-M-65-IS903B, ISEcp1-ISVsa5-blaCTX-M-14-IS903B, and ISEcp1-blaCTX-M-55/15-Δorf477. To our knowledge, the ESBL gene blaVEB was identified in Salmonella for the first time. Diverse plasmid types (IncHI2, IncN, IncA/C, IncFIB, IncI1 and IncFII) were identified in these isolates, among which IncHI2-type plasmid (49.1%) was the most common type in S. Indiana. Multilocus sequence typing (MLST) showed a single ST17 in S. Indiana. Pulsed-field gel electrophoresis (PFGE) results showed that there was a genotypic diversity, and some clones might have existed in S. Indiana between patients and foods for several years. These findings suggested that the frequent emergence of S. Indiana isolates with resistance to ciprofloxacin and ceftriaxone would pose a huge threat to food safety and public health.

Salmonella enterica serotype Derby is among the three most common serotypes of nontyphoidal Salmonella isolated from patients with diarrhea in China. In this study, 133 Salmonella Derby isolates from human patients (n = 74) and foods of animal origin (n = 59) in Shanghai, China, between September 2013 and December 2014, were selected to study its phenotypic characteristics and genetic diversity. The isolates were subjected to antimicrobial susceptibility testing, plasmid replicon typing, virulence profile determination, and molecular subtyping by pulsed-field gel electrophoresis (PFGE). Isolates were frequently resistant to tetracycline (87.22%), sulfisoxazole (74.44%), and streptomycin (62.41%), and a low frequency of resistance was found toward ofloxacin (3.01%), ceftazidime (2.26%), and cefepime (1.50%); in addition, 93 (69.92%) isolates were multidrug resistant. The most common plasmid incompatibility replicon types were the IncF family (FIA, 51.31%; FIC, 27.82%; and FIB, 21.80%) and IncP types (35.34%): these plasmid types may be associated with the spread of antibiotic resistance and virulence genes. All isolates were positive for the Salmonella pathogenicity island (SPI) gene avrA and the fimbrial gene bcfC from among the 10 virulence genes detected, and most of them carried ssaQ (99.25%), mgtC (97.74%), siiD (98.50%), sopB (97.74%), and sopE (96.99%). PFGE showed 68 patterns in nine main clusters at an 85% similarity threshold. Most of the isolates from different sources possessed the same fingerprints or molecular profiles in each cluster, which strongly suggests the possibility that foods of animal origin, especially pork, serve as an important source for human infection. Moreover, this diversity may suggest strains originating from multiple clones. Therefore, surveillance on this serotype should be strengthened to prevent transmission of Salmonella Derby from foods of animal origin, especially pork, to humans.

Human adenovirus F (HAdV-F) is one of the major causative species detected in acute gastroenteritis in children worldwide. HAdV-F is composed of serotypes 40 and 41. Most studies have reported the prevalence of HAdV-41 and focused on its epidemiologic characteristics. In this study, seventeen samples were identified as HAdV-41 out of 273 fecal specimens from children with acute diarrhea in Shanghai. Five isolates were isolated and subjected to whole genome sequencing and analysis to characterize the genetic variation and evolution. Full genome analysis revealed low genetic variation (99.07–99.92% identity) among the isolates, and InDels are observed in the E2A gene and the hexon gene compared to the reference strain NIVD103. Phylogenetic analysis showed that all isolates mainly formed two genome-type clusters but with incongruence in the trees of whole genomes and individual genes. The recombination breakpoints of the five isolates were inferred by the Recombination Detection Program (RDP) and varied in the number and location of the recombination events, indicating different evolution origins. Overall, our study highlights the genetic diversity of HAdV-41 isolates circulating in Shanghai, which may have evolved from inter-strain recombination.

Objectives With the wide use of heavy metals as feed additives in animal production, little attention has been paid to heavy metal resistance in pathogenic bacteria. This study was performed to investigate the presence of heavy metal resistance genes (HMRGs) in Escherichia coli and Salmonella isolates and its correlation with disinfectant resistance genes (DRGs) and antibiotic resistance genes (ARGs). Methods HMRGs of 178 E. coli and 294 Salmonella isolated from chicken broiler farms and retail meat were detected by PCR. Minimum inhibitory concentrations (MICs) of heavy metals were determined by the broth microdilution method. The complete genome of E. coli E308, which had indications of multidrug resistance, was recovered and assembled using third-generation sequencing. Results The frequency of different HMRGs in E. coli and Salmonella ranged from 0.60–77.0% and 0.30–87.1%, respectively. MICs of heavy metals for E. coli and Salmonella ranged widely from ≤12.5 mg/L to 1600 mg/L. Moreover, HMRGs (zntA, arsB, merA, pcoR, pcoA, pcoC and chrA) were found to be significantly associated with one or more DRGs [sugE(c), emrE, mdfA, ydgE/ydgF, qacF, sugE(p) and qacEΔ1] and ARGs (sul1, sul2, sul3, tetA, tetB, tetC, blaTEM, blaSHV and blaCTX) (P Conclusion This study demonstrated that HMRGs are widely present in E. coli and Salmonella isolated from chicken farms and retail meat. The association between HMRGs with DRGs and ARGs may lead to co-resistance to heavy metals and other antimicrobial agents.

Background Internalins are surface proteins that are utilized by Listeria monocytogenes to facilitate its invasion into human intestinal epithelial cells. The expression of a full-length InlA is one of essential virulence factors for L. monocytogenes to cross the intestinal barrier in order to invade epithelial cells. Results In this study, the gene sequences of inlA in 120 L. monocytogenes isolates from food (n = 107) and humans (n = 13) were analyzed. Premature stop codon (PMSC) mutations in inlA were identified in 51 isolates (50 from food and 1 from human). Six mutation types of PMSCs were identified. Among the 51 isolates with PMSCs in inlA, there were 44 serogroup 1/2c, 3c isolates from food, of which seven belonged to serogroups 1/2a, 3a. A total of 153,382 SNPs in 2247 core genes from 42 genomes were identified and used to construct a phylogenetic tree. Serotype 1/2c isolates with inlA PMSC mutations were grouped together. Cell culture studies on 21 isolates showed that the invasion to Caco-2 cells was significantly reduced among isolates with inlA PMSC mutations compared to those without PMSC mutations (P

Although spice extracts are well known to exhibit antibacterial properties, there is lack of a comprehensive evaluation of the antibacterial effect of spices against antibiotic-resistant bacteria. In the present study, ethanolic extracts from a total of 67 spices were comprehensively investigated for their in vitro antibacterial activities by agar well diffusion against two common food-borne bacteria, Staphylococcus aureus and Salmonella enteritidis, with multi-drug resistance. Results showed that S. aureus was generally more sensitive to spice extracts than S. enteritidis. Of the 67 spice extracts, 38 exhibited antibacterial activity against drug-resistant S. aureus, while only four samples were effective on drug-resistant S. enteritidis. In addition, 11 spice extracts with inhibition zones greater than 15 mm were further verified for their broad-spectrum antibacterial properties using another 10 drug-resistant S. aureus strains. It was found that five spice extracts, including galangal, fructus galangae, cinnamon, yellow mustard seed, and rosemary, exhibited the highest antibacterial capacity. Further cytotoxicity of these 11 spices was determined and LC50 values were found to be more than 100 &mu, g/mL except for galangal, rosemary, and sage, whose LC50 values were 9.32 &plusmn, 0.83, 19.77 &plusmn, 2.17, and 50.54 &plusmn, 2.57, respectively. Moreover, the antioxidant activities (ferric-reducing antioxidant power (FRAP) and trolox equivalent antioxidant capacity (TEAC) values) and total phenolic content (TPC) of spice extracts were determined to establish possible correlations with the antibacterial activity. Although the antibacterial effect was positively correlated with the antioxidant activities and TPC, the correlation was weak (r &lt, 0.5), indicating that the antibacterial activity could also be attributed to other components besides antioxidant polyphenols in the tested spice extracts. In conclusion, dietary spices are good natural sources of antibacterial agents to fight against antibiotic-resistant bacteria, with potential applications as natural food preservatives and natural alternatives to antibiotics in animal feeding.

Salmonella enterica serovar Typhimurium is one of the most important serovars among nontyphoidal Salmonella. The inappropriate and over usage of antimicrobials in clinical and animal husbandry has increased the prevalence of antimicrobial-resistant Salmonella Typhimurium (S. Typhimurium). Diverse mobile genetic elements (MGEs) such as plasmids, insertion sequences and integrons also have a crucial role in the rapid dissemination of multidrug resistance (MDR) bacteria. This study aimed to screen and analyze the genetic environment of MGEs carried by S. Typhimurium, and to clarify the multidrug resistance dissemination mechanism in S. Typhimurium. The results showed that, out of 255 S. Typhimurium isolates, 62 isolates, were screened out for the presence of IncHI2 plasmid by PCR amplification, of which 61 isolates were carrying both IS26 and class 1 integron. All the 61 isolates were resistant to at least one antimicrobial and 58 were MDR. The correlation between plasmids and antimicrobial resistance components was determined by conjugation, antimicrobial susceptibility test, PCR-based replicon typing (PBRT) and S1-PFGE experiment. The results of PBRT revealed that 15 transconjugants harboring two kinds of plasmid incompatibility groups including HI2 and I1. Further, S1-PFGE validated the presence of HI2 plasmid in 13 and I1 plasmid in 2 transconjugants, which was about 200–300 kb and 80–100 kb in size, respectively. Whole genome sequencing revealed that no significant difference (P > 0.05) was found at the number of antimicrobial resistance gene categories among 15 donor isolates, and ST34 was the predominant sequence type. Phylogenetic analysis based on the complete plasmid sequences revealed 15 IncHI2 plasmids in this study clustered in two different clades and clustered together with other IncHI2 plasmids isolated from China, suggesting that the prevalence and dissemination of IncHI2 plasmids from diverse sources and regions. Four kinds of IS elements-class 1 integron arrangement patterns were identified in the 15 conjugative IncHI2-plasmids, of which three patterns were characterized to be complex IS26-class 1 integron arrangement and the other one was IS256-class 1 integron arrangement. Overall, these results suggested that IncHI2 was one of the major plasmid lineages presented in the MDR S. Typhimurium strains. Furthermore, the presence of complex IS elements-class 1 integrons and resistance genes co-located on IncHI2 plasmids contributed to the prevalence and rapid dissemination of multidrug resistance genes in Salmonella.

A total of 120 Listeria monocytog enes isolates (107 from foods and 13 from humans) in Shanghai, China, were characterized by serogroup typing and virulence genes detection with PCR, antimicrobial susceptibility testing, and molecular subtyping using pulsed-field Gel Electrophoresis (PFGE). Isolates belonged to three L. monocytogenes serogroups, 1/2c, 3c (n = 47, 39.1%) was the most prevalent, followed by 1/2a, 3a (n = 44, 36.7%) and 1/2b, 3b, 7 (n = 29, 24.2%). Although the isolates were all susceptible to most antibiotics tested, 13 isolates were resistant to ceftriaxone and seven to tetracycline. None of the isolates were resistant to multiple antibiotics. The tet (M) genes were detected among tetracycline-resistant isolates. The isolates all harbored virulence genes hly , prfA , plcA , plcB , inlA , inlB , inlI ; 116 isolates (96.7%) were positive for inlC ; 78 (65.0%) for inlG ; 119 (99.2%) for inlJ ; 8 (6.67%) for llsX . A total of 74 distinct patterns were generated for the 119 isolates tested using Apa I and Asc I with Pulsed Field Gel Electrophoresis (PFGE). Three clinical isolates shared the same PFGE patterns with retail meet (chicken, duck, and beef) isolates. These findings indicated that food of animal origin likely serve as a major vehicle in transmitting human listeriosis in Shanghai. Active surveillance for L. monocytogenes is needed for better understanding the epidemiology of the pathogen, and for effective control and prevention of human listeriosis.

Salmonella Typhimurium is one of the most common Salmonella serovars and possesses many variants. The detection of this pathogen and its variants is imperative to trace the source of infection, to explore the transmission, and to prevent the spread of disease. A PCR assay was used and primers were designed against the gene STM4495 specific for S. Typhimurium, and oafA, fliC, and fljB encoding the O5, H1 and H2 antigens of S. Typhimurium. A novel multiplex PCR method was developed to detect S. Typhimurium and its variants, including Copenhagen, 1,4,12:-:1,2, 1,4,[5],12:i:- and 1,4,5,12:-:-. The detection limit of this method was found to be as low as 1.1pg/PCR for S. Typhimurium DNA template. S. Typhimurium and its variants were detected rapidly and accurately. Of 2350 isolates, 294 strains of S. Typhimurium, 13 strains of 1,4,[5],12:i:- and 1 strain of Copenhagen variant, were identified, consistent with serological testing. Thus, this multiplex PCR assay complements the serological method and enhances detection accuracy. All 1,4,[5],12:i:- strains were identified as ST34 by MLST analysis, which carried multidrug resistances. The expansion of multidrug-resistant S. Typhimurium variant strains must be controlled to limit further transmission from animal food to humans.

BACKGROUND Campylobacter is a major cause of bacterial gastroenteritis worldwide. Young children represent a particular age group affected by Campylobacter infection because of their limited diets and weak immune systems. METHODS In this study, a total of 110 Campylobacter (80 Campylobacter jejuni and 30 Campylobacter coli) isolated from children younger than 5 years of age with diarrhea in Shanghai, China in 2011 were examined for their genetic relationship and antimicrobial susceptibility. The presence of virulence genes and its association with invasion potential in Caco-2 cell were also determined. RESULTS Multilocus sequence typing revealed 62 sequence types (STs) under 14 clonal complexes from C. jejuni and 15 STs under 2 clonal complexes from C. coli. High resistance rates among the 110 isolates were observed to nalidixic acid (88.2%), ciprofloxacin (87.3%) and tetracycline (87.3%), followed by ampicillin (30.9%), gentamicin (28.2%), clindamycin (21.8%), erythromycin (21.8%) and chloramphenicol (8.2%). Compared with that of C. jejuni (32.5%), a larger proportion of C. coli (83.3%) were resistant to multiple antimicrobials, including 16 isolates of ST-828 complex resistant to 6 antimicrobials: ciprofloxacin, clindamycin, erythromycin, gentamicin, nalidixic acid and tetracycline. Furthermore, 57 Campylobacter isolates were selected based on their distinct STs and the presence of virulence genes to determine their abilities to adhere to and invade Caco-2 cells. The level of invasion varied widely among isolates and had relatively weak correlation with the genotype data. CONCLUSION Our findings provided baseline data on Campylobacter among young children. Active surveillance of Campylobacter is needed to better understand the epidemiology and antimicrobial resistance trends of this significant pathogen to help control and protect young children from such infections.

Salmonellosis is an important global foodborne disease, and Salmonella isolates that are resistant to a wide variety of antibiotics have become a major public health concern. The aim of this study was to investigate the distribution and transmission of mphA gene in azithromycin-resistant Salmonella isolates and characterize the plasmid bearing mphA. In this study, the azithromycin resistance was shown in 15 Salmonella enterica serovar Indiana (S. Indiana) isolates from chicken, duck and humans with concurrent resistance to ciprofloxacin and ceftriaxone, two of which were resistant to all antibiotics tested except colistin and imipenem. MLST and PFGE results suggested that these 15 isolates were closely related in phylogeny. The azithromycin resistance gene (mphA), extended-spectrum beta-lactamase (ESBL)-encoding genes (blaCTX-M-65, blaCTX-M-14 and blaCTX-M-15) and plasmid-mediated quinolone resistance (PMQR) genes [oqxAB, qepA, qnrA and aac(6′)-Ib-cr] with mutations in the quinolone resistance determining region (QRDR) (gyrA and parC) were identified in these S. Indiana isolates. Plasmid conjugation and transformation were performed in these 15 isolates. The co-existence of the mphA gene with oqxAB-blaCTX-M-65 was observed on the IncHI2 plasmid with a size of~240 kbp in 7 transformants, and these 7 transformants exhibited the resistance to azithromycin (MIC from 32 μg/mL to 64 μg/mL) and ceftriaxone (MIC≥ 256 μg/mL). The complete sequence of an IncHI2 type plasmid, p13520, was determined. An approximately 80-kbp of multidrug resistance region (MRR) comprising 29 antimicrobial resistance genes (ARGs) including mphA, oqxAB, blaCTX-M-65, fosA3 and rmtB interspersed with different insertion sequences (ISs) (IS26, ISAba1, IS91, IS1006 and IS903B) was located on the plasmid. The typical IS26-mphA-mrx-mphR-IS6100 transposable structure was identified in the IncHI2 plasmid of nine transformants via genome sequencing and PCR mapping, which suggested that azithromycin resistance in S. Indiana was probably due to the dissemination of the IncHI2 plasmid carrying the mphA-mrx-mphR cluster. This study highlighted the emergence of S. Indiana isolates with concurrent resistance to azithromycin, ciprofloxacin and ceftriaxone in humans and retail foods in China. This is likely due to the co-existence of mphA, oqxAB and blaCTX-M-65 carried by the IncHI2 plasmid. These findings emphasized the importance of ongoing surveillance for the prevalence and transmission of the p13520-like plasmid in S. Indiana, so as to better understand the potential threat to public health.

This study aimed to trace the transmission source of Salmonella enterica serovar Typhimurium and Salmonella enterica serovar Enteritidis strains associated with enteric infections in Shanghainese children, and understand the molecular mechanism of resistance to third-generation cephalosporins and ciprofloxacin.The profiles of pulsed-field gel electrophoresis (PFGE) were compared among the isolates from children, animal, and environment. Antimicrobial susceptibility was determined using the minimal inhibitory concentrations and Kirby-Bauer disk diffusion method. Extended-spectrum β-lactamase (ESBL) producing isolates mediated by resistance genes were identified using polymerase chain reaction and sequencing.Based on PFGE patterns, 49 (33.1%) of 148 human Salmonella Typhimurium isolates located in the dominant PFGE clusters were genetically related to the isolates from poultry source, environment water, aquatic products, and reptiles, whereas 97 (97.0%) of 100 human Salmonella Enteritidis isolates were genetically related to isolates from poultry and water. The rates of resistance to ceftriaxone among clinical Salmonella Typhimurium and Salmonella Enteritidis isolates were 42.0% and 14.2%, respectively. Besides, 35.1% of Salmonella Typhimurium isolates displayed resistance to ciprofloxacin; 64.9% of Salmonella Typhimurium isolates and 97.0% of Salmonella Enteritidis isolates displayed reduced susceptibility to ciprofloxacin. Of 64 ESBL/AmpC-producing strains, CTX-M, TEM, DHA, and CMY were detected at frequencies of 86.0%, 62.5%, 7.8%, 3.1%, and 3.1%, respectively.The transmission sources of Salmonella Typhimurium and Salmonella Enteritidis infections in Shanghainese children were diverse. The high prevalence of resistance to third-generation cephalosporins and ciprofloxacin mediated by multiple molecular mechanisms needs continuous monitoring and intervention.

An extreme learning machine (ELM) is a novel training method for single-hidden layer feedforward neural networks (SLFNs) in which the hidden nodes are randomly assigned and fixed without iterative tuning. ELMs have earned widespread global interest due to their fast learning speed, satisfactory generalization ability and ease of implementation. In this paper, we extend this theory to hypercomplex space and attempt to simultaneously consider multisource information using a hypercomplex representation. To illustrate the performance of the proposed hypercomplex extreme learning machine (HELM), we have applied this scheme to the task of multispectral palmprint recognition. Images from different spectral bands are utilized to construct the hypercomplex space. Extensive experiments conducted on the PolyU and CASIA multispectral databases demonstrate that the HELM scheme can achieve competitive results. The source code together with datasets involved in this paper can be available for free download at https://figshare.com/s/01aef7d48840afab9d6d.

A growing number of cancer deaths draws attractions in the areas of bioinformatics worldwide. It is worth noting that cancer microarray data is composed of tens of thousands of genes, but there are only a few dozens of genes that are really relative to cancers. Thus, it is particularly import to pick out the relevant genes by means of microarray data analysis. Gene selection and classification techniques capture the essence of cancer mechanism and represent a suite of the refreshing cancer cure. In the paper, we summarize 4 types of cancer microarrays which show up in reference providing their attributes and download websites. Furthermore, we also review most extensively studied gene selection and classification techniques. Meanwhile, comparison and analysis on accuracies of gene selection and classification methods in view of remarkably influential algorithms are outlined with unique and randomized algorithms. Thus, the most correlative cancer genes are selected, Leukemia and Colon cancer as typical representatives are listed in the survey. From the microcosmic perspectives, these emerging techniques are considerably conductive to solve the dimensional curse of cancer microarray data applied in the treatment of cancer.

Diverse mobile genetic elements (MGEs) including plasmids, insertion sequences, and integrons play an important role in the occurrence and spread of multidrug resistance (MDR) in bacteria. It was found in previous studies that IS26 and class 1 integrons integrated on plasmids to speed the dissemination of antibiotic-resistance genes in Salmonella. It is aimed to figure out the patterns of specific genetic arrangements between IS26 and class 1 integrons located in plasmids in MDR Salmonella in this study. A total of 74 plasmid-harboring Salmonella isolates were screened for the presence of IS26 by PCR amplification, and 39 were IS26-positive. Among them, 37 isolates were resistant to at least one antibiotic. The thirty-seven antibiotic-resistant isolates were further involved in PCR detection of class 1 integrons and variable regions, and all were positive for class 1 integrons. Six IS26-class 1 integron arrangements with IS26 inserted into the upstream or downstream of class 1 integrons were characterized. Eight combinations of these IS26-class 1 integron arrangements were identified among 31 antibiotic-resistant isolates. Multidrug-resistance plasmids of the IncHI2 incompatibility group were dominant, which all belonged to ST3 by plasmid double locus sequence typing. These 21 IncHI2-positive isolates harbored six complex IS26-class 1 integron arrangement patterns. Conjugation assays and Southern blot hybridizations confirmed that conjugative multidrug-resistance IncHI2 plasmids harbored the different complex IS26-class 1 integron arrangements. The conjugation frequency of IncHI2 plasmids transferring alone was 10−5-10−6, reflecting that different complex IS26-class 1 integron arrangement patterns didn't significantly affect conjugation frequency (P > 0.05). These data suggested that class 1 integrons represent the hot spot for IS26 insertion, forming diverse MDR loci. And ST3-IncHI2 was the major plasmid lineage contributing to the horizontal transfer of composite IS26-class 1 integron MDR elements in Salmonella.