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Abstract Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 historical and contemporary SPB PG1 isolates, obtained globally, between 1898 and 2021. We show that this pathogen existed in the 13th century, subsequently diversifying into 11 lineages and 38 genotypes with strong phylogeographic patterns. Following its discovery in 1896, it circulated across Europe until the 1970s, after which it was mostly reimported into Europe from South America, the Middle East, South Asia, and North Africa. Antimicrobial resistance recently emerged in various genotypes of SPB PG1, mostly through mutations of the quinolone-resistance-determining regions of gyrA and gyrB. This study provides an unprecedented insight into SPB PG1 and essential genomic tools for identifying and tracking this pathogen, thereby facilitating the global genomic surveillance of PTB.

The emergence of multidrug-resistant (MDR) Salmonella Enteritidis has highlighted the importance of regularly monitoring for the occurrence of antibiotic-resistant strains. The current study combined phenotyping analysis and whole-genome-sequencing (WGS) to investigate the associations between the antibiotic-resistant phenotypes (ARPs) and genetic characteristics determinants in 95 Salmonella Enteritidis isolates from retail meat and environmental samples in China (2014–2019). Phenotypic analyses revealed that 70 isolates (73.68%) were MDR with 12 distinct resistance patterns. Most MDR strains (81.43%) had NAL-AMP-FIS-STR ± TET profiles, showing a fluctuating trend from 2015 to 2019, likely influenced by tetracycline withdrawal management. WGS identified four types of mutations in the gyrA gene were associated with nalidixic acid resistance. The co-carrying of blaTEM, sul2 and aph(6)-Id/aph(3″)-Ib was likely mediated by an X1-type plasmid, corresponding to resistance against ampicillin, sulfisoxazole, and streptomycin. Combining phenotypic analyses and WGS data, the 31 sequenced strains were primarily divided into two clusters, with most epidemic resistant strains in the largest cluster A. Identical ARP patterns observed across different sample types, regions, and isolation years but clustering together in cluster A suggested potential cross-contamination within the retail chain. Cluster B exhibited more diverse resistance patterns and genetic characteristics. Notably, three isolates in cluster B require special mention: a monophasic strain resistant to eight antibiotics, a strain exhibiting highly heteroresistance, and a strain with additional exotoxin genes. These results highlight the importance of ongoing surveillance and the utility of WGS to track and understand antibiotic resistance in Salmonella Enteritidis.

Abstract Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-genome sequencing on 2,212 Chinese isolates and 1,739 publicly available genomes reveals the population structure and evolutionary history of the rough colony variants. Characterized by macro, red, dry, and rough (mrdar) colonies, these variants demonstrate enhanced biofilm formation at 28 °C and 37 °C compared to typical rdar colonies. The mrdar variants exhibit extensive multidrug resistance, with significantly higher resistance to at least five classes of antimicrobial agents compared to non-mrdar variants. This resistance is primarily conferred by an IncHI2 plasmid harboring 19 antimicrobial resistance genes. Phylogenomic analysis divides the global collections into six lineages. The majority of mrdar variants belong to sublineage L6.5, which originated from Chinese smooth colony strains and possibly emerged circa 1977. Among the mrdar variants, upregulation of the csgDEFG operons is observed, probably due to a distinct point mutation (−44G > T) in the csgD gene promoter. Pangenome and genome-wide association analyses identify 87 specific accessory genes and 72 distinct single nucleotide polymorphisms associated with the mrdar morphotype.

Abstract Background Salmonella, an important foodborne pathogen, was estimated to be responsible for 95.1 million cases and 50,771 deaths worldwide. Sixteen serovars were responsible for approximately 80% of Salmonella infections in humans in China, and infections caused by a few uncommon serovars have been reported in recent years, though not with S. Welikade. This study reports the first clinical case caused by S. Welikade in China and places Chinese S. Welikade isolates in the context of global isolates via genomic analysis. For comparison, S. Welikade isolates were also screened in the Chinese Local Surveillance System for Salmonella (CLSSS). The minimum inhibitory concentrations (MICs) of 28 antimicrobial agents were determined using the broth microdilution method. The isolates were sequenced on an Illumina platform to identify antimicrobial resistance genes, virulence genes, and phylogenetic relationships. Results The S. Welikade isolate (Sal097) was isolated from a two-year-old boy with acute gastroenteritis in 2021. Along with the other two isolates found in CLSSS, the three Chinese isolates were susceptible to all the examined antimicrobial agents, and their sequence types (STs) were ST5123 (n = 2) and ST3774 (n = 1). Single nucleotide polymorphism (SNP)-based phylogenetic analysis revealed that global S. Welikade strains can be divided into four groups, and these three Chinese isolates were assigned to B (n = 2; Sal097 and XXB1016) and C (n = 1; XXB700). In Group B, the two Chinese ST5123 isolates were closely clustered with three UK ST5123 isolates. In Group C, the Chinese isolate was closely related to the other 12 ST3774 isolates. The number of virulence genes in the S. Welikade isolates ranged from 59 to 152. The galF gene was only present in Group A, the pipB2 gene was only absent from Group A, the avrA gene was only absent from Group B, and the allB, sseK1, sspH2, STM0287, and tlde1 were found only within Group C and D isolates. There were 15 loci unique to the Sal097 isolate. Conclusion This study is the first to characterize and investigate clinical S. Welikade isolates in China. Responsible for a pediatric case of gastroenteritis in 2021, the clinical isolate harbored no antimicrobial resistance and belonged to phylogenetic Group B of global S. Welikade genomes.

ABSTRACT Salmonella enterica serovar Typhimurium is an important foodborne pathogen associated with human salmonellosis worldwide. A retrospective screening was performed to elucidate the prevalence, antimicrobial resistance, and phylogenomic characterization of this pathogen in Shanghai, China. S. Typhimurium isolates were selected from 2,211 serotyped Salmonella isolates collected during 2007–2019. Two hundred and seventy-seven S. Typhimurium isolates were detected in 15 of 16 districts in Shanghai. It was noted that 214 (77.3%) isolates were multi-drug resistant and 32 (11.6%) isolates were resistant to ciprofloxacin and 5 (1.8%) isolates were further resistant to ceftriaxone. Poisson generalized linear mixed model results showed that the multi-drug resistance (MDR) in 2017 and 2018 was significantly higher than that in 2010 (P＜0.05), highlighting an increase in the risk of MDR. Phylogenetic results showed that a global data set of 401 sequenced S. Typhimurium isolates was classified into four clones (ST36, ST313, ST19, and ST34), which appeared in international clonal dissemination. The ST34 isolates from China fell into two clades, ST34C1 and ST34C2, the latter of which might originate from Shanghai, and then expanded nationally, accompanied by extended-spectrum β-lactamase gene blaCTX-M-14 and a mutation in quinolone resistance-determining region of the gyrA 87 site. Furthermore, blaCTX-M-14 linking to ISEcp1 upstream and ΔIS903B downstream was found in IncI (Gamma)-like plasmids, and the plasmid conjugation contributed to its horizontal transmission. To our knowledge, it is the first report of the epidemiological and phylogenetic characterization for S. Typhimurium including the emerged clade ST34C2 in Shanghai, warranting the necessity of surveillance for this high-risk pathogen.IMPORTANCEOur study uncovered a widespread distribution of Salmonella enterica serovar Typhimurium isolates in Shanghai accompanied by the increase in antimicrobial resistance (AMR) especially MDR during a 10-year period, which filled in the gap about a long period of continuous monitoring of AMR in this pathogen in Shanghai. Meanwhile, we identified a new clade ST34C2 of S. Typhimurium with the acquisition of IncI (Gamma)-like plasmids mediated by extended-spectrum β-lactamase gene blaCTX-M-14 as well as gyrA 87 mutation, which had not been reported before. It was noted that IncI (Gamma)-like plasmids were reported in S. Typhimurium for the first time and conjugation could accelerate the spread of antimicrobial resistance gene blaCTX-M-14. These findings on the epidemic, antimicrobial resistance, and phylogenomic characterization for S. Typhimurium provide valuable insights into its potential risk to public health and also the basis for AMR prevention and control strategies in Shanghai in the future.

ABSTRACT: Objectives: To investigate the resistance mechanism of a Salmonella Typhimurium (S. Typhimurium) isolated from a faecal sample of an infant, which exhibited concurrent resistance to ceftriaxone, ciprofloxacin and azithromycin. Methods: Antimicrobial susceptibility testing was performed by broth microdilution in two kinds of drug-sensitive plates. Antimicrobial resistance (AMR) genes were identified by whole genome sequencing and bioinformatics analysis. Genotyping of the strain was performed by multilocus sequence typing (MLST). Plasmid DNA was sequenced and analysed using plasmid bioinformatics tools. Results: The SH11G993 strain was resistant to 28 antibiotics and carried 54 AMR genes. MLST results showed that the strain belonged to a rare genotype. The plasmid profile and plasmid sequencing showed that the strain carried two resistance plasmids. The pSH11G993-1 carried 14 AMR genes (especially co-harboured blaCMY-2, mphA and ermB) and a variety of insertion sequences, belonging to the IncC. The pSH11G993-2 carried 3 AMR genes and 9 virulence genes, belonging to the IncFIB-FII, forming a novel resistance and virulence co-harbouring plasmid. Conclusions: Our findings highlight that continuously monitor the changes in antibiotic resistance patterns and research on the resistance mechanisms in potential human pathogens are imperative.

Abstract Lung segmentation is an essential step in a computer‐aided diagnosis system for chest radiographs. The lung parenchyma is first segmented in pulmonary computer‐aided diagnosis systems to remove the interference of non‐lung regions while increasing the effectiveness of the subsequent work. Nevertheless, most medical image segmentation methods nowadays use U‐Net and its variants. These variant networks perform poorly in segmentation to detect smaller structures and cannot accurately segment boundary regions. A multi‐interaction feature fusion network model based on Kiu‐Net is presented in this paper to address this problem. Specifically, U‐Net and Ki‐Net are first utilized to extract high‐level and detailed features of chest images, respectively. Then, cross‐residual fusion modules are employed in the network encoding stage to obtain complementary features from these two networks. Second, the global information module is introduced to guarantee the segmented region's integrity. Finally, in the network decoding stage, the multi‐interaction module is presented, which allows to interact with multiple kinds of information, such as global contextual information, branching features, and fused features, to obtain more practical information. The performance of the proposed model was assessed on both the Montgomery County (MC) and Shenzhen datasets, demonstrating its superiority over existing methods according to the experimental results.

A total of 265 Salmonella Enteritidis isolates collected from retail markets and children’s hospitals in Shanghai were used to investigate the prevalence and molecular epidemiology of plasmid-mediated fosfomycin resistance genes. Nine of the isolates—7 from the 146 (4.79%) retail chicken-related samples and 2 from the 119 (1.68%) samples from clinical children—were fosfomycin-resistant (FosR). The fosA3 gene was detected in all of the nine FosR isolates, which were located on Inc F-type (8/9, 88.9%) and unknown-type (1/9, 11.1%) transferable plasmids. In total, five plasmid types, namely Inc HI2 (1/9, 11.1%), Inc I1 (3/9, 33.3%), Inc X (8/9, 88.9%), Inc FIIs (9/9, 100%), and Inc FIB (9/9, 100%), were detected in these FosR isolates, which possessed five S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) profiles. The extended-spectrum β-lactamase determinant blaCTX-M-14 subtype was identified in one FosR S. Enteritidis isolate, which was located in a transferable unknown-type plasmid co-carrying fosA3 and tetR genes. Sequence homology analysis showed that this plasmid possessed high sequence similarity to previously reported blaCTX-M-14- and fosA3-positive plasmids from E. coli strains, implying that plasmids carrying the fosA3 gene might be disseminated among Enterobacterales. These findings highlight further challenges in the prevention and treatment of Enterobacteriaceae infections caused by plasmids containing fosA3.

Abstract Facial expression recognition technology has become a powerful tool for conveying human emotions and intentions and is widely used in areas such as assisted driving and intelligent medical care. Due to the limited computing power of current hardware devices and the real‐time requirements of application scenarios, this paper proposes a high‐performance and lightweight framework for real‐time facial expression recognition framework to solve the problem of real‐time completion of expression recognition tasks under low hardware costs. To address these issues, this paper first designs a RepVGG and mobileNetV2 dual‐channel structure in the feature extraction. It is then input into the MobileViT Block for global feature modelling. Finally, the position vector of the capsule network is used to replace the output of the global pooling, preserving the spatial relationship of the salient features and enhancing the classification effect. Compared with the mainstream facial expression recognition algorithm that cannot get good classification results under low complexity conditions, the model has a significant accuracy improvement while ensuring lightweight. With only 294.60M FLOPS and 0.95M parameters, it achieved an accuracy of 97.53% on the KDEF dataset and 85.56% on the RAF‐DB, demonstrating the advanced nature of the algorithm.

ABSTRACT Foodborne Salmonella infection remains a major public health concern worldwide. With rising antimicrobial resistance, genomic surveillance is key to tracking outbreaks and monitoring transmission, but there is no comprehensive national surveillance scheme for Salmonella involving humans, food, animals, and the environment in China. Moreover, the association between antimicrobial resistance and climate, social, and economic factors has rarely been investigated. Here, we use 1,962 Salmonella isolates collected from 22 Chinese provinces and add 6,035 publicly available genomes to build a Chinese local Salmonella genome database version 2 (CLSGDB v2) representing 30 Chinese provinces, covering 1905–2022. Using the CLSGDB v2, we mapped the landscape and spatiotemporal dynamics of antimicrobial resistance markers, virulome, and mobilome in Salmonella. We identified 317 mcr positive and 745 azithromycin resistance genes positive Salmonella isolates out of 7,997 isolates. We further uncovered the geographic distribution veil of mcr-1, fosA7, fosA3, mph(A), and bla CTX-M-55 genes in China, all of them resistant to the critically important antimicrobials including colistin, fosfomycin, azithromycin, and the third-generation cephalosporins. Interestingly, economic, climatic, and social factors can drive the rise of antimicrobial resistance was observed. Finally, we release the CLSGDB v2 as an open-access database and thus can assist surveillance studies tracking 164 Salmonella enterica serovars and 295 sequence types across the globe. The CLSGDB v2 is freely available at https://nmdc.cn/clsgdbv2. IMPORTANCE We established the largest Salmonella genome database from China and presented the landscape and spatiotemporal dynamics of antimicrobial resistance genes. We also found that economic, climatic, and social factors can drive the rise of antimicrobial resistance. The Chinese local Salmonella genome database version 2 was released as an open-access database (https://nmdc.cn/clsgdbv2) and thus can assist surveillance studies across the globe. This database will help inform interventions for AMR, food safety, and public health.

Abstract Multidrug-resistant (MDR) Salmonella has been a long-standing challenge in public health and food safety. The prevalence of MDR S. Enteritidis, especially isolated from humans, in China is significantly higher than those from the U.S. and other countries. A dataset of 197 S. Enteritidis genomes, including 16 sequenced clinical isolates from China and 181 downloaded genomes of human isolates from the U.S., Europe, and Africa, was analyzed for genomic diversity, virulence potential, and antimicrobial resistance (AMR). Phylogenomic analyses identified four major well-supported clades (I–IV). While AMR genotype in the majority of isolates in clades I and IV displayed as pan-susceptible, 81.8% (9/11) and 22.4% (13/58) of isolates in clades III and II were MDR, respectively. It is noted that 77% (10/13) of MDR isolates in clade II were from China. The most common antimicrobial resistance genes (ARGs) carried by the Chinese isolates were aph(3′)-IIa, bla CTX-M-55, and bla TEM-1B, whereas bla TEM-1B, sul1, sul2, drfA7, aph(3")-Ib/strA, and aph(6)-Id/strB were most often identified in those from Africa (clade III). Among the 14 plasmid types identified, IncX1 and IncFII(pHN7A8) were found exclusively in the Chinese MDR isolates, while IncQ1 was highly associated with the African MDR isolates. The spvRABCD virulence operon was present in 94.9% (187/197) of isolates tested and was highly associated with both the IncF (IncFII and IncFIB) plasmids. In addition, phylogenetic differences in distribution of Salmonella pathogenicity islands (SPIs), prophages and other accessory genes were also noted. Taken together, these findings provide new insights into the molecular mechanisms underpinning diversification of MDR S. Enteritidis.

ABSTRACT Typhoid fever, caused by Salmonella Typhi (S. Typhi), is a life-threatening disease, usually food-borne and commonly associated with international travel. The disease transmission remains endemic in many low- and middle-income countries, representing further hotspots for seeding new global outbreaks. China has historically been affected by typhoid fever, but the respective roles of local transmission and importation remain unknown. Here, we generated a nationwide map of the typhoid burden in China and investigated the associations between typhoid disease, climate and various socioeconomic parameters. To assess transmission dynamics, we sub-sampled S. Typhi isolated within China over five decades and sequenced their genomes. The resulting 705 new genomes, placed in context with 5,190 global isolates from 87 countries on six continents, led to the discovery of several predominant inland Chinese clones belonging to the clades 2.1/2.3/3.2/4.3. These clones were associated with multiple introductions from overseas, followed by local expansion. Notably, 4.3.1 isolates from eastern China were not genetically close to those from northwestern China but to the international isolates, indicating their association with international travel. Additional in vitro assays showed that 4.3.1 elaborated better intracellular survival, acid tolerance, and desiccation tolerance than other lineages, partially explaining its success. For the first time, we have probed typhoid transmission in China, finding local transmission and importation, which could guide the policy for typhoid control. IMPORTANCE Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi, resulting in a significant disease burden across developing countries. Historically, China was very much close to the global epicenter of typhoid, but the role of typhoid transmission within China and among epicenter remains overlooked in previous investigations. By using newly produced genomics on a national scale, we clarify the complex local and global transmission history of such a notorious disease agent in China spanning the most recent five decades, which largely undermines the global public health network.

Shigella sonnei is a major contributor to the global burden of dysenteric diarrhoea in developed countries. In this work, authors report a S. sonnei clone which has caused numerous waterborne shigellosis outbreaks in China from 2015 to 2020.

Abstract Invasive nontyphoidal Salmonella (iNTS) causes extraintestinal infections with ~15% case fatality in many countries. However, the mechanism by which iNTS emerged in China remains unaddressed. We conducted clinical investigations of iNTS infection with recurrent treatment failure, caused by underreported Salmonella enterica serovar Livingstone (SL). Genomic epidemiology demonstrated five clades in the SL population and suggested that the international animal feed trade was a likely vehicle for their introduction into China, as evidenced by multiple independent transmission incidents. Importantly, isolates from Clade‐5‐I‐a/b, predominant in China, showed an invasive nature in mice, chicken and zebrafish infection models. The antimicrobial susceptibility testing revealed most isolates (> 96%) in China are multidrug‐resistant (MDR). Overall, we offer exploiting genomics in uncovering international transmission led by the animal feed trade and highlight an emerging hypervirulent clade with increased resistance to frontline antibiotics.

ABSTRACT: Objectives: Since the gene encoding mobilised colistin resistance (mcr-1) was first reported in China in 2015, it has been reported in various Enterobacteriaceae worldwide. Escherichia coli, one of the main pathogens causing diarrhoea, is the most prevalent, clinically identified species carrying mcr-1. This study aimed to investigate the epidemiologic and genomic characteristics of mcr-1 in Escherichia coli from patients in Shanghai. Methods: Faecal samples were collected from hospitals in Shanghai between 2012 and 2015. Polymerase chain reaction was performed to detect mcr-1, and molecular characteristics of the mcr-1-positive E. coli was determined by antimicrobial susceptibility testing and whole-genome sequencing. Results: We detected 40 (3.9%) mcr-1-positive E. coli strains from faecal samples in clinical settings between 2012 and 2015 in Shanghai. Mcr-1 was detected in 4 types of E. coli, including atypical enteropathogenic E. coli (aEPEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), and enteroaggregative E. coli (EAEC). Most strains harbouring mcr-1 were isolated from children aged

Abstract. 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.

ABSTRACT Salmonella Weltevreden is an emerging pathogen associated with human diarrhea, and knowledge of the genomics and epidemiology of this serovar is still limited. In this study, we performed whole-genome sequencing of 96 S. Weltevreden isolates recovered from diarrheal patients and 62 isolates from food animals in China between 2006 and 2017. Together, with an additional 199 genome sequences of S. Weltevreden published in NCBI, we performed an analysis on all 357 S. Weltevreden genome sequences. Our results demonstrated that the majority of S. Weltevreden from diarrheal patients from China (97.92%, 94/96) and the other regions in the world (94.97%, 189/199) identified in this study were sequence type (ST) 365. The remaining types were ST3771 (n = 3), ST22 (n = 1), ST155 (n = 1), and ST684 (n = 1). In addition, ST365 was also widely recovered from animals, food, and environmental samples in different regions of the world. Phylogenetic analysis and pulsed-field gel electrophoresis (PFGE) revealed that S. Weltevreden from diarrheal patients was closely related to those recovered from food and environmental specimens. We also showed that S. Weltevreden did not exhibit severe antimicrobial resistance profiles, suggesting administering antibiotics is still effective for controlling the agent. Interestingly, we found that S. Weltevreden strains carried a number of virulence factor genes, and a 100.03-kb IncFII(S) type plasmid was widely distributed in S. Weltevreden strains. Elimination of this plasmid decreased the bacterial capacity to infect both Caco-2 cells and C57BL/6 mice, suggesting the importance of this plasmid for bacterial virulence. Our results contribute to the understanding of the epidemiology and virulence of S. Weltevreden. IMPORTANCE Salmonella Weltevreden is a pathogen associated with human diarrheal diseases found across the globe. However, knowledge of the genomics and epidemiology of this pathogen is still limited. In this study, we found S. Weltevreden sequence type (ST) 365 is commonly recovered from diarrheal patients in China and many other regions of the world, and there is no major difference between the Chinese isolates and the global isolates at the phylogenetic level. We also demonstrated that ST365 was widely recovered from animal, food, and environmental samples collected in different, global regions. Importantly, we discovered an IncFII(S) type plasmid commonly carried by S. Weltevreden strains of human, animal, and food origins, and this plasmid is likely to contribute to the bacterial pathogenesis. These findings enhance our understanding of the emergence of S. Weltevreden involved in diarrheal outbreaks and the global spread of S. Weltevreden strains.

ABSTRACT The two-component system (TCS) is one of the primary pathways by which bacteria adapt to environmental stresses such as antibiotics. This study aimed to systematically explore the role of TCSs in the development of multidrug resistance (MDR) in Salmonella enterica serovar Enteritidis. Twenty-six in-frame deletion mutants of TCSs were generated from S. Enteritidis SJTUF12367 (the wild type [WT]). Antimicrobial susceptibility tests with these mutants revealed that 10 TCSs were involved in the development of antibiotic resistance in S. Enteritidis. In these 10 pairs of TCSs, functional defects in CpxAR, PhoPQ, and GlnGL in various S. Enteritidis isolates led to a frequent decrease in MIC values against at least three classes of clinically important antibiotics, including cephalosporins and quinolones, which indicated the importance of these TCSs to the formation of MDR. Interaction network analysis via STRING revealed that the genes cpxA, cpxR, phoP, and phoQ played important roles in the direct interaction with global regulatory genes and the relevant genes of efflux pumps and outer membrane porins. Quantitative reverse transcription-PCR analysis further demonstrated that the increased susceptibility to cephalosporins and quinolones in ΔphoP and ΔcpxR mutant cells was accompanied by increased expression of membrane porin genes (ompC, ompD, and ompF) and reduced expression of efflux pump genes (acrA, macB, and mdtK), as well as an adverse transcription of the global regulatory genes (ramA and crp). These results indicated that CpxAR and PhoPQ played an important role in the development of MDR in S. Enteritidis through regulation of cell membrane permeability and efflux pump activity. IMPORTANCE S. Enteritidis is a predominant Salmonella serotype that causes human salmonellosis and frequently exhibits high-level resistance to commonly used antibiotics, including cephalosporins and quinolones. Although TCSs are known as regulators for bacterial adaptation to stressful conditions, which modulates β-lactam resistance in Vibrio parahaemolyticus and colistin resistance in Salmonella enterica serovar Typhimurium, there is little knowledge of their functional mechanisms underlying the development of antibiotic resistance in S. Enteritidis. Here, we systematically identified the TCS elements in S. Enteritidis SJTUF12367, revealed that the three TCSs CpxAR, PhoPQ, and GlnGL were crucial for the MDR formation in S. Enteritidis, and preliminarily illustrated the regulatory functions of CpxAR and PhoPQ for antimicrobial resistance genes. Our work provides the basis to understand the important TCSs that regulate formation of antibiotic resistance in S. Enteritidis.

Salmonella enterica subsp. enterica serovar Typhimurium (S. typhimurium) is an important zoonotic pathogen with important public health significance. To understand S. typhimurium’s epidemiological characteristics in China, multi-locus sequence typing, biofilm-forming ability, antimicrobial susceptibility testing, and resistant genes of isolates from different regions and sources (human, food) were investigated. Among them, ST34 accounted for 82.4% (243/295), with ST19 ranking second (15.9%; 47/295). ST34 exhibited higher resistance levels than ST19 (p < 0.05). All colistin, carbapenem, and ciprofloxacin-resistant strains were ST34, as were most cephalosporin-resistant strains (88.9%; 32/36). Overall, 91.4% (222/243) ST34 isolates were shown to have multidrug resistance (MDR), while 53.2% (25/47) ST19 isolates were (p < 0.05). Notably, 97.8% (45/46) of the MDR-ACSSuT (resistance to Ampicillin, Chloramphenicol, Streptomycin, Sulfamethoxazole, and Tetracycline) isolates were ST34, among which 69.6% (32/46) of ST34 isolates were of human origin, while 30.4% (14/46) were derived from food (p < 0.05). Moreover, 88.48% (215/243) ST34 showed moderate to strong biofilm-forming ability compared with 10.9% (5/46) ST19 isolates (p < 0.01). This study revealed the emergence of high-level antibiotic resistance S. typhimurium ST34 with strong biofilm-forming ability, posing concerns for public health safety.

Sleep, as the basis for regular body functioning, can affect human health. Poor sleep conditions can lead to various physical ailments, such as poor immunity, memory loss, slow cognitive development, and cardiovascular diseases. Along the increasing stress in society comes with a growing surge in conditions associated with sleep disorders. Studies have shown that sleep stages are essential for the body’s memory, immune system, and brain functioning. Therefore, automatic sleep stage classification is of great medical practice importance as a basis for monitoring sleep conditions. Although previous research into the classification of sleep stages has been promising, several challenges remain to be addressed: (1) The EEG signal is a non-smooth signal with harrowing feature extraction and high requirements for model accuracy. (2) Some existing network models suffer from overfitting and gradient descent. (3) Correlation between long time sequences is challenging to capture. This paper proposes NAMRTNet, a deep model architecture based on the original single-channel EEG signal to address these challenges. The model uses a modified ResNet network to extract features from sub-epochs of individual epochs, a lightweight attention mechanism normalization-based attention module (NAM) to suppress insignificant features, and a temporal convolutional network (TCN) network to capture dependencies between features of long time series. The recognition rate of 20-fold cross-validation with the NAMRTNet model for Fpz-cz channel data in the public sleep dataset Sleep-EDF was 86.2%. The experimental results demonstrate the network’s superiority in this paper, surpassing some state-of-the-art techniques in different evaluation metrics. Furthermore, the total time to train the network was 5.1 h, which was much less than the training time of other models.

ABSTRACT Salmonella enterica serovar Indiana (S. Indiana) is an extremely expanded foodborne pathogen in China in recent years. This study aimed to elucidate the national prevalence and phylogenomic characterization of this pathogen in China. Among 5, 287 serotyped Salmonella isolates collected during 2002 to 2018, 466 S. Indiana isolates were found in 15 provinces, and 407 were identified to be ST17, and the rest were ST2040. Among 407 ST17 isolates, 372 (91.4%) were multidrug resistant, and 366 (89.9%) were resistant to ciprofloxacin, 235 (57.7%) were further resistant to ceftriaxone. Phylogenomic analysis revealed that ST17 isolates were classified into four clades (I, II, III and IV), which appeared in international clonal dissemination. ST17 isolates from China fell into Clade IV with part of isolates from the United Kingdom, the United States, South Korea, and Thailand, suggesting their close genetic relationship. Mutations in quinolone resistance-determining regions (QRDR) of GyrA and ParC, and plasmid-mediated quinolone resistance (PMQR) genes aac(6′)-Ib-cr, oqxAB, and qnrS as well as extended spectrum β-lactamases (ESBL) genes blaCTX-M, blaOXA, and blaTEM in isolates from Clade IV were much higher than those from other three clades. Various blaCTX-M subtypes (blaCTX-M-65, blaCTX-M-55, blaCTX-M-27, blaCTX-M-14, and blaCTX-M-123) with ISEcp1, IS903B, ISVsa5, and IS1R were found in ST17 isolates, especially Tn1721 containing ΔISEcp1-blaCTX-M-27-IS903B in P1-like bacteriophage plasmids. These findings on the prevalent and genomic characterization for the S. Indiana multidrug-resistant ST17 clone in China, which have not been reported yet, provide valuable insights into the potential risk of this high-resistant clone. IMPORTANCE Fluoroquinolones and cephalosporins are the primary choices for severe salmonellosis treatment. S. Indiana has become one of the most prevalent serovars in breeding poultry and poultry meats in China in recent years. ST17 was recognized as the leading epidemiological importance in S. Indiana because of its high-level resistance to the most of common antibiotics, including ciprofloxacin and ceftriaxone. However, the prevalence and phylogenomic characterization of ST17 isolates are unclear. Here, we did a retrospective screening on a large scale for S. Indiana in China, and performed its phylogenomic analysis. It was found that ST17 isolates had extensive spread in 15 provinces of China and became a multidrug-resistant clone. The international spread of the ST17 isolates was observed among several countries, especially China, the United Kingdom, and the United States. Our study emphasized the importance of surveillance of a high-resistant S. Indiana ST17 clone to combat its threat to public health.

Mono-allelic loss-of-function variants in ARFGEF1 have recently caused a developmental delay, intellectual disability, and epilepsy, with varying clinical expressivity. However, given the clinical heterogeneity and low-penetrance mutations of ARFGEF1-related neurodevelopmental disorder, the robustness of the gene-disease association requires additional evidence. In this study, five novel heterozygous ARFGEF1 variants were identified in five unrelated pediatric patients with neurodevelopmental disorders, including one missense change (c.3539T>G), two canonical splice site variants (c.917-1G>T, c.2850+2T>A), and two frameshift (c.2923_c.2924delCT, c.4951delG) mutations resulting in truncation of ARFGEF1. The pathogenic/likely pathogenic variants presented here will be highly beneficial to patients undergoing genetic testing in the future by providing an expanded reference list of disease-causing variants.

Salmonella enterica resistant to colistin, third-generation cephalosporins (3GCs), and fluoroquinolones (FQs) has been deemed a high-priority pathogen by the World Health Organization (WHO). The objective of this study was to characterize 11 mcr-1-harboring Salmonella enterica serovar Typhimurium isolates from raw pork and ready-to-eat (RTE) pork products in Guangzhou, China. All isolates were multi-drug resistant and contained 6–24 antibiotic-resistant genes. The mcr-1 gene was localized in the most conserved structure (mcr-1-orf ) in eight isolates and in mobile structure (ISApl1-mcr-1-orf ) in three isolates. One raw pork isolate SH16SF0850, co-harbored mcr-1, blaCTX−M−14, and oqxAB genes. One isolate 17Sal008 carried mcr-1, blaCTX−M−14, qnrS2, and oqxAB genes located on a 298,622 bp IncHI2 plasmid pSal008, which was obtained from an RTE pork product for the first time. The pSal008 was closely related to a plasmid in an S. typhimurium isolate from a 1-year-old diarrheal outpatient in China and was found to be transferable to Escherichia coli J53 by conjugation. Genome sequence comparisons by core-genome Multi Locus Sequence Typing (cgMLST) based on all S. typhimurium isolates from China inferred highly probably epidemiological links between selected pork isolates and no possible epidemiologically links between RTE pork isolate 17Sal008 and other isolates. Our findings indicate that raw pork and pork products are potential reservoirs of mcr-1-harboring S. typhimurium and highlight the necessity for continuous monitoring of colistin, 3GCs, and FQs resistant S. typhimurium from different origins.

Abstract 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.

Objective The aims of this study were to investigate the antibiotic resistance, disinfectant resistance and their associations in 302 Salmonella enterica Typhimurium (S. Typhimurium) isolates from retail meats, food animals and humans. Methods Antibiotic susceptibility testing was performed according to the Kirby-Bauer disk diffusion method. The minimal inhibitory concentrations (MICs) of disinfectants were determined by broth microdilution method, and disinfectant resistance genes were detected by polymerase chain reaction (PCR) amplification. Results Antibiotic susceptibility testing demonstrated that 96.03% (290/302) of S. Typhimurium isolates were resistant to at least one antibiotic and 79.80% (241/302) were multidrug resistant (MDR). Tested isolates showed the highest resistance to streptomycin (78.81%, 238/302), followed by compound sulphonamides (78.15%, 236/302), tetracycline (75.50%, 228/302) and ampicillin (71.85%, 217/302). All isolates were sensitive to cefepime and imipenem. The resistance of S. Typhimurium from food to compound sulphonamides, tetracycline, ampicillin, nalidixic acid, and gentamicin were significantly higher than those from human and animal origin (P1 024 mg/L, respectively. In addition, the frequency of resistance to PVP-I, BC and TCS was observed significantly higher in food and animal isolates than human isolates (P

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 < 0.05). 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.

Problems such as complex image backgrounds, low image quality, diverse text forms, and similar or common character layouts in different script categories in natural scenes pose great challenges to scene script identification. This paper proposes a new Res2Net-based improved script identification method, namely FAS-Res2Net. In the feature extraction part, the feature pyramid network (FPN) module is introduced, which is beneficial to aggregate the geometric feature information extracted by the shallow network and the semantic feature information extracted by the deep network. Integrating the Adaptive Spatial Feature Fusion (ASFF) module is beneficial to obtain local feature information for optimal weight fusion. In addition, the global feature information of the image is extracted by introducing the swin transformer coding block, which makes the extracted feature information more abundant. In the classification part, the convolutional classifier is used to replace the traditional Linear classification, and the classification confidence of each category is output, which improves the identification efficiency. The improved algorithm achieved identification rates of 94.7% and 96.0% on public script identification datasets SIW-13 and CVSI-2015, respectively, which verified the superiority of the method.

With the rapid emergence of plasmid-mediated colistin resistance gene mcr-1, the increased resistance of Salmonella has attracted extensive attention. This study reports on 11 multidrug-resistant Salmonella enterica serovar Typhimurium strains harboring mcr-1 in China. They all presented resistance to colistin, and additionally, one that was isolated from a child’s stool sample was also resistant to ceftriaxone and azithromycin. We screened 1454 strains of Salmonella for mcr-1 gene through PCR, and these strains are all preserved in our laboratory. Antimicrobial sensitivity analysis was carried out for the screened mcr-1 positive strains. Genetic polymorphism analysis of S. Typhimurium was performed by using the Pulsed-Field Gel Electrophoresis (PFGE). The plasmids harboring mcr-1 were identified by S1-PFGE and southern blotting. Plasmid conjugation assays were used to analyze the transferability of colistin resistance. The plasmids harboring mcr-1 were characterized by sequencing and bioinformatic analysis. Eleven S. Typhimurium strains harboring mcr-1 with colistin resistance (MICs 4μg/ml) were detected, which were isolated from children and pig offal in China. All of them were multidrug-resistant strains. PFGE results revealed that the strains isolated from different samples or locations have identical genotypes. S1-PFGE and southern blotting experiments showed that three plasmids of different sizes (33, 60, and 250 kb) all carried the mcr-1 gene. The plasmid conjugation assays revealed that Salmonella acquired mcr-1 harboring plasmids by horizontal transfer. Sequencing and plasmid type analysis revealed that these plasmids were types IncX4, IncI2, and IncHI2. Among them, IncX4 and IncI2 plasmids had extremely similar backbones and contained one resistant gene mcr-1. IncHI2 plasmid contained multiple resistant genes including blaCTX–M, oqxB, sul, aph, aadA, and blaTEM. We identified 11 mcr-1 harboring S. Typhimurium strains in China and described their characteristics. Our findings indicate that the mcr-1 gene can effectively spread among intestinal bacteria by horizontal transfer of three types of plasmids. Moreover, the IncHI2 plasmid can also mediate the transfer of other drug resistance genes. These results reveal that constant surveillance of mcr-1 harboring S Typhimurium is imperative to prevent the spread of colistin resistance.

Soil organic matter (SOM), as the greatest carbon storage in the terrestrial environment, is inextricably related to the global carbon cycle and global climate change. Accurate estimation and mapping of SOM content are crucial for guiding agricultural output and management, as well as controlling the climate issue. Traditional chemical analysis is unable to satisfy the dynamic estimation of SOM due to its low timeliness. Remote and proximal sensing have significant advantages in terms of ease of use, estimation accuracy, and geographical resolution. In this study, we developed a framework based on machine learning to estimate SOM with high accuracy and resolution using Fourier mid-infrared attenuation total reflectance spectroscopy (FTIR-ATR), Sentinel-2 images, and DEM derivatives. This framework’s performance was evaluated on a regional scale using 245 soil samples from northeast China. Results indicated that the calibration size could be shrunk to 50% while achieving a fair prediction performance for SOM content. The Lasso, partial least squares (PLS), support vector regression (SVR), and convolutional neural networks (CNN) performed well in predicting SOM from FTIR-ATR spectra, and the performance was enhanced further by using Sentinel-2 images and DEM derivates. The PLS, SVR, and CNN models created SOM maps with higher spatial resolution and variation than the Kriging approach. The PLS and SVR models provided enough variety and were more realistic in the local SOM map, making them usable at the field scale, and the suggested framework took a fresh look at high-resolution SOM mapping.

Multimodal biometric authentication method can conquer the defects of the unimodal biometric authentication technology. In this paper, we design and develop an efficient Android-based multimodal biometric authentication system with face and voice. Considering the hardware performance restriction of the smart terminal, including the random access memory (RAM), central processing unit (CPU) and graphics processor unit (GPU), etc., which cannot efficiently accomplish the tasks of storing and quickly processing the large amount of data, a face detection method is introduced to efficiently discard the redundant background of the image and reduce the unnecessary information. Furthermore, an improved local binary pattern (LBP) coding method is presented to improve the robustness of the extracted face feature. We also improve the conventional endpoint detection technology, i.e. the voice activity detection (VAD) method, which can efficiently increase the detection accuracy of the voice mute and transition information and boost the voice matching effectiveness. To boost the authentication accuracy and effectiveness, we present an adaptive fusion strategy which organically integrates the merits of the face and voice biometrics simultaneously. The cross-validation experiments with public databases demonstrate encouraging authentication performances compared with some state-of-the-art methods. Extensive testing experiments on Android-based smart terminal show that the developed multimodal biometric authentication system achieves perfect authentication effect and can efficiently content the practical requirements.

Abstract 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

Abstract 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 bla TEM-1, followed by bla CTX-M, bla OXA-1, and bla SHV-12. Six subtypes of bla CTX-M were identified, bla CTX-M-14 (n = 36) and bla CTX-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.

Background: Colistin resistance mediated by mcr-1-harbouring plasmids is an emerging threat in Enterobacteriaceae, like Salmonella. Based on its major contribution to the diarrhoea burden, the epidemic state and threat of mcr-1-harbouring Salmonella in community-acquired infections should be estimated. Methods: This retrospective study analysed the mcr-1 gene incidence in Salmonella strains collected from a surveillance on diarrhoeal outpatients in Shanghai Municipality, China, 2006–2016. Molecular characteristics of the mcr-1-positive strains and their plasmids were determined by genome sequencing. The transfer abilities of these plasmids were measured with various conjugation strains, species, and serotypes. Findings: Among the 12,053 Salmonella isolates, 37 mcr-1-harbouring strains, in which 35 were serovar Typhimurium, were detected first in 2012 and with increasing frequency after 2015. Most patients infected with mcr-1-harbouring strains were aged

Handwritten signatures have traditionally been used as a common form of recognition and authentication in tasks such as financial transactions and document authentication. However, there are few studies on minority languages such as Uyghur and Kazakh used in Xinjiang, China, and no available public dataset for these scripts, which are widely used in banking and other fields. Therefore, this paper addresses this problem by constructing a dataset containing Uyghur, Kazakh, and Han languages and presents an automatic handwritten signature recognition approach based on Uyghur, Kazakh, Han, and public datasets. In the paper, a handwritten signature recognition method that combines local maximum occurrence features (LOMO) and histogram of orientated gradients (HOG) features was proposed. LOMO features use a sliding window to represent the local features of the signature image. The high-dimensional features formed by the combination of these methods are dimensionally reduced by principal component analysis (PCA). The classification is performed using k-nearest neighbors (k-NN), and it is compared with the random forest method. The proposed method achieved a recognition rate of 98.4% using a diverse signature database compared with existing methods. It shows that the method was effective and can be applied to large datasets of mixed, multilingual signatures.

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.

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.

Scene text detection task aims to precisely localize text in natural environments. At present, the application scenarios of text detection topics have gradually shifted from plain document text to more complex natural scenarios. Objects with similar texture and text morphology in the complex background noise of natural scene images are prone to false recall and difficult to detect multi-scale texts, a multi-directional scene Uyghur text detection model based on fine-grained feature representation and spatial feature fusion is proposed, and feature extraction and feature fusion are improved to enhance the network’s ability to represent multi-scale features. In this method, the multiple groups of 3 × 3 convolutional feature groups that are connected like the hierarchical residual to build a residual network for feature extraction, which captures the feature details and increases the receptive field of the network to adapt to multi-scale text and long glued dimensional font detection and suppress false positives of text-like objects. Secondly, an adaptive multi-level feature map fusion strategy is adopted to overcome the inconsistency of information in multi-scale feature map fusion. The proposed model achieves 93.94% and 84.92% F-measure on the self-built Uyghur dataset and the ICDAR2015 dataset, respectively, which improves the accuracy of Uyghur text detection and suppresses false positives.

Tic disorders (TDs) are a series of childhood neuropsychiatric disorders characterized by involuntary motor and/or vocal tics and commonly comorbid with several other psychopathological and/or behavioral disorders (e.g., attention deficit hyperactivity disorder and obsessive–compulsive disorder), which indeed aggravate clinical symptoms and complicate diagnosis and treatment. Micro-RNAs (miRNAs) derived from small extracellular vesicles (sEVs) have been recognized as novel circulating biomarkers of disease. To identify specific miRNAs derived from plasma sEVs for TDs’ diagnosis and prognosis, we used official EV isolation and purification methods to characterize the plasma-derived EV miRNAs from children with different types of TDs. Nanoparticle tracking analysis, transmission electron microscopy, and immunoblot analysis of EV surface markers were applied to confirm the features and quality of sEVs. The RNA sequencing (RNA-seq) approach was adapted to identify novel circulating sEVs-derived miRNAs with altered expression levels in paired comparisons of TDs versus healthy controls (HCs), transient tic disorder (TTD) versus chronic motor or vocal tic disorder (CTD), and TTD versus Tourette Syndrome (TS). GO term and KEGG pathway were performed for functional analysis and the receiver operator curve analysis was followed to test the diagnosis efficacy of differentially expressed miRNAs (DEMs) derived from plasma sEVs among paired groups, namely, TDs versus HCs, TTD versus CTD, and TTD versus TS. As a result, 10 miRNAs (hsa-let-7a, hsa-let-7b, hsa-let-7c, hsa-let-7e, hsa-let-7f, hsa-miR-25-3p, hsa-miR-29a-3p, hsa-miR-30b-5p, hsa-miR-125b-5p, and hsa-miR-1469) have demonstrated a significantly different expression signature in the TDs group compared to HCs with excellent area under curve (AUC) values of 0.99, 0.973, 0.997, 1, 0.99, 0.997, 0.987, 0.993, 0.977, and 0.997, respectively, and the diagnostic efficacy of miRNAs was also estimated for discriminating TTD from CTD or TS. In our research, we finally obtained several potential sEVs-derived miRNA biomarkers to assess the diagnosis and prognosis of TDs.

Diarrhoea remains a major cause of childhood morbidity and mortality worldwide. This study aimed to monitor the aetiology of acute diarrhoea in children in Shanghai. Paediatric outpatients with acute diarrhoea were enrolled in the study from Jan 2015 to Dec 2018. Faecal samples were collected for testing. Enteric bacteria were identified and typed by culture and serotyping, respectively. Enteric viruses were identified by real-time PCR. Enteric pathogens were identified in 1572 (58.4%) of the 2692 enrolled children with acute diarrhoea. Viruses were detected more frequently than bacteria (41.3% versus 25.0%). Nontyphoidal Salmonella spp. (NTS) was the most common (10.3%) bacteria isolated, followed by enteropathogenic Escherichia coli (EPEC) (6.5%), enteroaggregative Escherichia coli (EAEC) (6.2%), Campylobacter spp. (3.6%), enterotoxigenic Escherichia coli (ETEC) (1.1%), Shigella spp. (0.2%), and enterohemorrhagic Escherichia coli (EHEC) (0.1%). Rotavirus was the most common (16.0%) virus detected, followed by norovirus (15.5%), adenovirus (7.2%), sapovirus (3.0%) and astrovirus (2.7%). Rotavirus, norovirus and NTS were the major pathogens responsible for diarrhoea in Shanghainese children. Improving uptake of the rotavirus vaccine and strengthening foodborne-pathogen prevention will aid in reducing the burden of diarrhoeal disease in children in Shanghai.

ABSTRACT 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, blaCTX–M (100.00%, 38/38), blaSHV (65.79%, 25/38), blaTEM (52.63%, 20/38), blaACC (18.42%, 7/38), and blaPSE (5.26%, 2/38) were detected by PCR and sequencing. Among blaCTX–M genes, blaCTX–M–55 was the dominant type (84.21%, 32/38). Conjugation and transformation experiments along with plasmid replicon typing revealed that blaCTX–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 blaCTX–M–55 gene was mobilized mainly by the ISEcp1-blaCTX–M–55-ORF477 transposition unit and had its own ISEcp1-based promoter, which accelerated the expression and transmission of blaCTX–M–55. Analysis of whole genome sequences (Illumina) of one selected transformant SH12G706-C showed high similarity of the blaCTX–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 blaCTX–M–55 gene mobilized by ISEcp1- blaCTX–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-blaCTX–M–55-ORF477-harboring plasmids among different species represents an important threat to the therapeutic effectiveness of cefepime.

The rapid emergence of multidrug resistant Salmonella is a global public-health concern as outbreaks in recent years have mostly been caused by multidrug resistant strains. Here, we evaluated an outbreak in China caused by multidrug resistant Salmonella enterica serovar Typhimurium (S. Typhimurium) by employing an epidemiological and laboratory investigation using conventional methods and whole genome sequencing (WGS). Eleven of the 12 people who participated in a banquet showed gastrointestinal symptoms, and 8S. Typhimurium strains were recovered. Isolated outbreak strains showed multidrug resistance (MDR), and decreased susceptibility to ciprofloxacin, a first-line drug recommended by WHO for clinical treatment of intestinal infections. Antimicrobial resistance (AMR) gene analysis indicated that the MDR phenotype of these outbreak strains may be due to the presence of a number of AMR genes, including the blaOXA-1 and blaTEM-1 β-lactamase genes, which are often plasmid-borne and easily transferred. Further virulence gene analysis indicated that these outbreak strains also carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2) and many adhesion-related virulence genes. Cluster analysis based on pulse-field gel electrophoresis data and phylogenetic analysis based on WGS revealed that the outbreak clone was closely related to and thus probably derived from local strains. This outbreak caused by multidrug resistant S. Typhimurium highlights the need for government improved strategies for the prevention and control of Salmonella infections.

The rapid and accurate acquisition of rice growth variables using unmanned aerial system (UAS) is useful for assessing rice growth and variable fertilization in precision agriculture. In this study, rice plant height (PH), leaf area index (LAI), aboveground biomass (AGB), and nitrogen nutrient index (NNI) were obtained for different growth periods in field experiments with different nitrogen (N) treatments from 2019–2020. Known spectral indices derived from the visible and NIR images and key rice growth variables measured in the field at different growth periods were used to build a prediction model using the random forest (RF) algorithm. The results showed that the different N fertilizer applications resulted in significant differences in rice growth variables; the correlation coefficients of PH and LAI with visible-near infrared (V-NIR) images at different growth periods were larger than those with visible (V) images while the reverse was true for AGB and NNI. RF models for estimating key rice growth variables were established using V-NIR images and V images, and the results were validated with an R2 value greater than 0.8 for all growth stages. The accuracy of the RF model established from V images was slightly higher than that established from V-NIR images. The RF models were further tested using V images from 2019: R2 values of 0.75, 0.75, 0.72, and 0.68 and RMSE values of 11.68, 1.58, 3.74, and 0.13 were achieved for PH, LAI, AGB, and NNI, respectively, demonstrating that RGB UAS achieved the same performance as multispectral UAS for monitoring rice growth.

Abstract Background Among 2179 Salmonella isolates obtained during national surveillance for salmonellosis in China from 2005 to 2013, we identified 46 non-H2S-producing strains originating from different sources. Methods The isolates were characterized in terms of antibiotic resistance and genetic variability by pulsed-field gel electrophoresis and multilocus sequence typing. Mutation in the phs operon, which may account for the non-H2S-producing phenotype of the isolated Salmonella strains, was performed in this study. Results Among isolated non-H2S-producing Salmonella strains, more than 50% were recovered from diarrhea patients, of which H2S-negative S. Gallinarum, S. Typhimurium, S. Choleraesuis and S. Paratyphi A isolates constituted 76%. H2S-negative isolates exhibited a high rate of resistance to ticarcillin, ampicillin, and tetracycline, and eight of them had the multidrug resistance phenotype. Most H2S-negative Salmonella isolates had similar pulsed-field gel electrophoresis profiles and the same sequence type as H2S-positive strains, indicating a close origin, but carried mutations in the phsA gene, which may account for the non-H2S-producing phenotype. Conclusions Our data indicate that multiple H2S-negative strains have emerged and persist in China, emphasizing the necessity to implement efficient surveillance measures for controlling dissemination of these atypical Salmonella strains.

Rapid quantification of soil organic matter (SOM) is a great challenge for the health assessment and fertility management of agricultural soil. Laser-induced breakdown spectroscopy (LIBS) with appropriate modeling algorithms is an alternative tool for this measurement. However, the current calibration strategy limits the prediction performance of the LIBS technique. In this study, 563 soil samples from Hetao Irrigation District in China were collected; the LIBS spectra of the soils were recorded in the wavenumber range of 288–950 nm with a resolution of 0.116 nm; a self-adaptive partial least squares regression model (SAM–PLSR) was employed to explore optimal model parameters for SOM prediction; and calibration parameters including sample selection for the calibration database, sample numbers and sample location sites were optimized. The results showed that the sample capacity around 60–80, rather than all of the samples in the soil library database, was selected for calibration from a spectral similarity re-ordered database regarding unknown samples; the model produced excellent predictions, with R2 = 0.92, RPD = 3.53 and RMSEP = 1.03 g kg−1. Both the soil variances of the target property and the spectra similarity of the soil background were the key factors for the calibration model, and the small sample set led to poor predictions due to the low variances of the target property, while negative effects were observed for the large sample set due to strong interferences from the soil background. Therefore, the specific unknown sample depended strategy, i.e., self-adaptive modelling, could be applied for fast SOM sensing using LIBS for soils in varied scales with improved robustness and accuracy.

As a research hotspot in the field of natural language processing (NLP), sentiment analysis can be roughly divided into explicit sentiment analysis and implicit sentiment analysis. However, due to the lack of obvious emotion words in the implicit sentiment analysis task and because the sentiment polarity contained in implicit sentiment words is not easily accurately identified by existing text-processing methods, the implicit sentiment analysis task is one of the most difficult tasks in sentiment analysis. This paper proposes a new preprocessing method for implicit sentiment text classification; this method is named Text To Picture (TTP) in this paper. TTP highlights the sentiment differences between different sentiment polarities in Chinese implicit sentiment text with the help of deep learning by converting original text data into word frequency maps. The differences between sentiment polarities are used as sentiment clues to improve the performance of the Chinese implicit sentiment text classification task. It does this by transforming the original text data into a word frequency map in order to highlight the differences between the sentiment polarities expressed in the implicit sentiment text. We conducted experimental tests on two common datasets (SMP2019, EWECT), and the results show that the accuracy of our method is significantly improved compared with that of the competitor’s. On the SMP2019 dataset, the accuracy-improvement range was 4.55–7.06%. On the EWECT dataset, the accuracy was improved by 1.81–3.95%. In conclusion, the new preprocessing method for implicit sentiment text classification proposed in this paper can achieve better classification results.

Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) are foodborne pathogens that cause hemolytic uremic syndrome and fatal infant diarrhea, respectively, but the characterization of these bacteria from imported food in China are unknown. A total of 1577 food samples from various countries during 2015–2021 were screened for STEC and EPEC, and the obtained isolates were tested for antimicrobial resistance and whole genome sequencing analysis was performed. The prevalence of STEC and EPEC was 1.01% (16/1577) and 0.51% (8/1577), respectively. Antimicrobial resistances to tetracycline (8%), chloramphenicol (8%), ampicillin (4%), ceftazidime (4%), cefotaxime (4%), and trimethoprim-sulfamethoxazole (4%) were observed. The antimicrobial resistance phenotypes corresponded with genotypes for most strains, and some resistance genes were related to mobile genetic elements. All 16 STEC isolates were eae negative, two solely contained stx1 (stx1a or stx1c), 12 merely carried stx2 (stx2a, stx2d, or stx2e), and two had both stx1 and stx2 (stx1c + stx2b, stx1a + stx2a + stx2c). Although they were eae negative, several STEC isolates carried other adherence factors, such as iha (5/16), sab (1/16), and lpfA (8/16), and belonged to serotypes (O130:H11, O8:H19, and O100:H30) or STs (ST297, ST360), which have caused human infections. All the eight EPEC isolates were atypical EPEC; six serotypes and seven STs were found, and clinically relevant EPEC serotypes O26:H11, O103:H2, and O145:H28 were identified. Two STEC/ETEC (enterotoxigenic E. coli) hybrids and one EPEC/ETEC hybrid were observed, since they harbored sta1 and/or stb. The results revealed that food can act as a reservoir of STEC/EPEC with pathogenic potential, and had the potential ability to transfer antibiotic resistance and virulence genes.

Abstract 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.

We sequenced 25 isolates of phenotypically multidrug-resistant Salmonella Indiana (n = 11), Typhimurium (n = 8), and Enteritidis (n = 6) using both MinION long-read [SQK-LSK109 and flow cell (R9.4.1)] and MiSeq short-read (Nextera XT and MiSeq Reagent Kit v2) sequencing technologies to determine the advantages of each approach in terms of the characteristics of genome structure, antimicrobial resistance (AMR), virulence potential, whole-genome phylogeny, and pan-genome. The MinION reads were base-called in real-time using MinKnow 3.4.8 integrated with Guppy 3.0.7. The long-read-only assembly, Illumina-only assembly, and hybrid assembly pipelines of Unicycler 0.4.8 were used to generate the MinION, MiSeq, and hybrid assemblies, respectively. The MinION assemblies were highly contiguous compared to the MiSeq assemblies but lacked accuracy, a deficiency that was mitigated by adding the MiSeq short reads through the Unicycler hybrid assembly which corrected erroneous single nucleotide polymorphisms (SNPs). The MinION assemblies provided similar predictions of AMR and virulence potential compared to the MiSeq and hybrid assemblies, although they produced more total false negatives of AMR genotypes, primarily due to failure in identifying tetracycline resistance genes in 11 of the 19 MinION assemblies of tetracycline-resistant isolates. The MinION assemblies displayed a large genetic distance from their corresponding MiSeq and hybrid assemblies on the whole-genome phylogenetic tree, indicating that the lower read accuracy of MinION sequencing caused incorrect clustering. The pan-genome of the MinION assemblies contained significantly more accessory genes and less core genes compared to the MiSeq and hybrid assemblies, suggesting that although these assemblies were more contiguous, their sequencing errors reduced accurate genome annotations. Our research demonstrates that MinION sequencing by itself provides an efficient assessment of the genome structure, antimicrobial resistance, and virulence potential of Salmonella; however, it is not sufficient for whole-genome phylogenetic and pan-genome analyses. MinION in combination with MiSeq facilitated the most accurate genomic analyses.