Virulence and resistance genes profiles and clonal relationships of non-typhoidal food-borne Salmonella strains isolated in Tunisia by whole genome sequencing

Molecular Characteristics of Salmonella Spp. Responsible for Bloodstream Infections in a Tertiary Hospital in Nanjing, China, 2019-2021

Objective

To investigate the clinical and molecular characteristics of Salmonella spp. causing bloodstream infections (BSIs) in our hospital.

Methods

We studied 22 clinical Salmonella isolates from BSIs and 16 from non-BSIs, performing antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS). The analysis included serovars, antibiotic resistance genes (ARGs), virulence factors (VFs), sequence types (STs), plasmid replicons, and genetic relationships. We also assessed pathogenicity of the isolates causing BSIs through growth, biofilm formation, and anti-serum killing assays.

Results

WGS analysis identified 13 Salmonella serovars, with four responsible for BSIs. S. Enteritidis was the most prevalent serovar, involved in 19 (50.0%) cases. BSIs were caused by 17S. Enteritidis, two S. Typhimurium, two S. Munster and one S. Diguel. Of the 38 isolates, 27 (71.1%) exhibited high resistance to ampicillin, and 24 (63.2%) to ampicillin/sulbactam. Thirty-six types of ARGs were identified, with blaTEM-1B (n = 25, 65.8%) being the most frequent. Ten plasmid replicons were found; the combination of IncFIB(S)-IncFII(S)-IncX1 was the most common in S. Enteritidis (94.7%). Fifteen STs were identified, among which ST11 was the most prevalent and clonally disseminated, primarily responsible for BSIs. A total of 333 different VFs were detected, 177 of which were common across all strains. No significant differences were observed between the BSI and non-BSI isolates in terms of resistance rates, ARGs, plasmid replicons, and VFs, except for seven VFs. No strong pathogenicity was observed in the BSI-causing isolates.

Conclusion

BSIs were predominantly caused by clonally disseminated S. Enteritidis ST11, the majority of which carried multiple ARGs, VFs and plasmid replicons. This study provides the first data on clonally disseminated S. Enteritidis ST11 causing BSIs, highlighting the urgent need for enhanced infection control measures.

Antimicrobial resistance and genomic investigation of Salmonella isolated from retail foods in Guizhou, China

Introduction

Salmonella is a major foodborne pathogen worldwide that causes severe morbidity and mortality. It is mainly caused by consuming contaminated food, with retail food considered the primary source.

Methods

In Guizhou, China, 102 Salmonella strains isolated from 2016 to 2021 underwent phenotypic antimicrobial resistance testing and whole-genome sequencing (WGS) to understand Salmonella diversity, including serotypes, sequencing types (STs), antimicrobial genes, virulence genes, plasmid types, multi-locus sequence types (MLST), and core genome MLST (cgMLST).

Results and discussion

S.Typhimurium was the dominant serotype, and O:4(B) was the leading serogroup. The most prevalent genotype was ST40. Phenotypic antimicrobial resistance identified 66.7% of the sampled isolates as multi-drug resistant (MDR). S.Enteritidis (n = 7), S.Typhimurium (n = 1), S.Indiana (n = 1), S.Kentucky (n = 1), S.Uganda (n = 1), all of which were MDR, were resistant to Colistin. Resistance rates varied significantly across different strains and food types, particularly meat products exhibiting higher resistance. Notably, significant increases in resistance were observed from 2016 to 2021 for the following: ≥ 1 resistant (P = 0.001), MDR (P = 0.001), ampicillin (P = 0.001), tetracycline (P < 0.001), chloramphenicol (P = 0.030), and trimethoprim/sulfamethoxazole (P = 0.003). The marked escalation in drug resistance over the recent years, coupled with the varying resistance rates among food sources, underscores the growing public health concern. Our findings highlight the need for a coordinated approach to effectively monitor and respond to Salmonella infections in Guizhou, China.

Whole-Genome Sequencing Analysis of Non-Typhoidal Salmonella Isolated from Breeder Poultry Farm Sources in China, 2020-2021

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

Serotypes, Antimicrobial Resistance Profiles, and Virulence Factors of Salmonella Isolates in Chinese Edible Frogs (Hoplobatrachus rugulosus) Collected from Wet Markets in Hong Kong

Salmonella is an important agent of gastrointestinal disease in humans. While livestock, such as cattle, poultry, and pigs, are well-recognised animal reservoirs of Salmonella, there is a lack of data on Salmonella in edible frogs, even though frog meat is a popular food worldwide. In this study, 103 live edible Chinese frogs (Hoplobatrachus rugulosus) were collected from wet markets throughout Hong Kong. After euthanasia, faeces or cloacal swabs were examined for Salmonella. Overall, Salmonella spp. were isolated from 67 (65%, CI: 0.554-0.736) of the samples. The serotypes included S. Saintpaul (33%), S. Newport (24%), S. Bareilly (7%), S. Braenderup (4%), S. Hvittingfoss (4%), S. Stanley (10%), and S. Wandsworth (16%). Many isolates were phylogenetically related. A high number of genes encoding for resistance to clinically relevant antimicrobials, and a high number of virulence determinants, were identified. Antimicrobial susceptibility testing (AST) identified multidrug resistance (MDR) in 21% of the isolates. Resistance to ampicillin, ciprofloxacin, nalidixic acid, and tetracycline was common. These results demonstrate that a high percentage of live frogs sold for human consumption in wet markets are carriers of multidrug-resistant Salmonella. Public health recommendations for handling edible frogs should be considered, to mitigate the risk of Salmonella transmission to humans.

Microbiological analysis and characterization of Salmonella and ciprofloxacin-resistant Escherichia coli isolates recovered from retail fresh vegetables in Shaanxi Province, China

Fresh vegetables are closely associated with foodborne disease outbreaks; however, systematic analysis of the microbiological quality of fresh vegetables and molecular information on foodborne pathogens in fresh produce are poorly reported in China. Here, we evaluated the epidemiological prevalence of coliforms via the most probable number method and characterized Salmonella and ciprofloxacin-resistant (CIP^R) Escherichia coli isolates recovered from retail fresh vegetables in Shaanxi Province, China. Antimicrobial susceptibility testing, serotype determination, multilocus sequence typing (MLST), core genome multilocus sequence typing (cgMLST), antibiotic resistance encoding gene (ARG) annotation, virulence factor prediction, and functional classification were performed. Between October 2020 and September 2021, 576 samples (i.e., tomatoes, lettuces, spinaches, and cabbages) were found to be positive for coliforms, and the prevalence of coliforms showed a seasonal trend. Coliform counts of vegetables in supermarkets in Xi'an were significantly lower (P < 0.01) than that in other cities. The detection rates of Salmonella and CIP^RE. coli-positive vegetables were 1 % (6/576) and 0.7 % (4/576), respectively. All isolates exhibited resistance to ≥1 antibiotics, and 92.9 % (13/14) were multidrug-resistant. One extended spectrum β-lactamase (ESBL)-producing CIP^RE. coli isolate in spinach was resistant to not only three third-generation cephalosporins but also to two polymyxins. Among nine Salmonella isolates, five different serovars (S. Enteritidis, S. Indiana, monophasic variant of S. Typhimurium, S. Agona, and S. Gallinarum), four sequence types (STs; ST11, ST13, ST17, and ST34), and seven core genome STs (cgSTs) were identified. Five CIP^RE. coli strains were assigned to three serovars (O101:H4, O8:H18, and O11:H25), three STs (ST44, ST48, and ST457), and four cgSTs. Coexisting amino acid mutations of Thr57Ser/Ser80Arg in ParC and Ser83Phe/Asp87Gly in GyrA in quinolone resistance-determining regions (QRDRs) might be causes for nalidixic acid resistance. Eight definite virulence profiles in eight serovars were identified. Notably, cdtB and pltA only encoded typhoid toxins and were just detected from S. Typhoid isolates were also detected from S. Indiana and monophasic S. Typhimurium, which are closely associated with swine food chain were first detected in fresh vegetables. In conclusion, our findings suggest that coliform contamination on fresh vegetables is prevalent in this province. Most Salmonella and CIP^RE. coli isolates were phenotypically and genetically diverse and could resist multiple antibiotics by carrying multiple ARGs and virulence genes.

Plasmid Composition, Antimicrobial Resistance and Virulence Genes Profiles of Ciprofloxacin- and Third-Generation Cephalosporin-Resistant Foodborne Salmonella enterica Isolates from Russia

Salmonella enterica is an important foodborne pathogen worldwide. Ciprofloxacin and extended-spectrum cephalosporins are the common first-line antimicrobial drugs for the treatment of salmonellosis, antimicrobial resistance genes for which are mostly transferred via plasmids. The goal of this work was to perform genomic analysis of plasmids from foodborne S. enterica isolates obtained in Russia based on whole-genome sequencing. In the current study, 11 multidrug-resistant samples isolated in 2021 from 8 regions of Russia were selected based on their resistance to ciprofloxacin and third-generation cephalosporins (CIP-3rd). Whole-genome short-read sequencing (WGS) was performed for all isolates; the samples belonged to five different sequence types (ST32, ST469, ST11, ST142, and ST548) which had different profiles of antimicrobial resistance (AMR) and virulence genes. We have performed additional long-read sequencing of four representative S. enterica isolates, which showed that they carried pESI-like megaplasmids of 202-280 kb length harboring extended-spectrum β-lactamase genes, fluoroquinolone, tetracycline, and aminoglycosides resistance genes, as well as several virulence determinants. We believe that the WGS data obtained will greatly facilitate further studies of foodborne S. enterica isolates epidemiology in terms of their self-transmissible plasmid composition that mediated antimicrobial resistance and virulence determinants conferring selective advantages of this important bacterial pathogen.

Biochemical and molecular mechanisms of antibiotic resistance in Salmonella spp

Salmonella is a diverse Gram-negative bacterium that represents the major disease burden worldwide. According to WHO, Salmonella is one of the fourth global causes of diarrhoeal disease. Antibiotic resistance is a worldwide health concern, and Salmonella spp. is one of the microorganisms that can evade the toxicity of antimicrobials via antibiotic resistance. This review aims to deliver in-depth knowledge of the molecular mechanisms and the underlying biochemical alterations perceived in antibiotic resistance in Salmonella. This information will help understand and mitigate the impact of antibiotic-resistant bacteria on humans and contribute to the state-of-the-art research developing newer and more potent antibiotics.

Study of Virulence Genes, Antimicrobial Resistance, and Genetic Relatedness of Foodborne Salmonella Isolates from Tunisia

ABSTRACT

Nontyphoidal Salmonella strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibility testing of a collection of Salmonella isolates (n = 54) recovered from poultry and bivalve molluscs was performed. The study also investigated profiling of virulence and resistance genes as well as phylogenetic relationships through pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella isolates. Salmonella intestinal infection A (siiA), Salmonella outer protein (sopB and sopE), putative 4-hydroxybutyrate coenzyme A transferase (cat2), Salmonella atypical fimbria C (safC), and Salmonella Enteritidis fimbria B (sefB) were present in most (83.32 to 100%) of the isolates, whereas the remaining tested genes (Salmonella plasmid virulence [spvC and spvB]), and the sopE gene, were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%), and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin-clavulanic acid (14.8%), trimethoprim-sulfamethoxazole (9.3%), and ciprofloxacin (5.5%). The results indicate that the Salmonella Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confer a selective advantage for the evolution of these bacteria and represent an alarming problem for global public health. The genetic study via PFGE and ERIC-PCR showed the high diversity of the clonal origins of these bacteria and the sources of contamination and revealed the great capacity of Salmonella to diversify within food-producing animals.

HIGHLIGHTS

Salmonella Yoruba: a rare serotype revealed through genomic sequencing along the farm-to-fork continuum of an intensive poultry farm in KwaZulu-Natal, South Africa

Salmonella enterica is a zoonotic pathogen of worldwide public health importance. We characterised Salmonella isolates from poultry along the farm-to-fork continuum using whole genome sequencing (WGS) and bioinformatics analysis. Three multilocus sequence types (MLSTs), i.e., ST15 (1.9%), ST152 (5.9%) and ST1316 (92.2%) and three serotypes, i.e., S. Heidelberg (1.9%), Kentucky (5.9%) and Yoruba (92.2%) were detected. The rare serotype, S. Yoruba, was detected among the farm and abattoir isolates and contained resistance and virulence determinants. Resistome analysis revealed the presence of the aac(6')-Iaa gene associated with aminoglycoside resistance, a single point mutation in the parC gene associated with fluoroquinolone and quinolone resistance, and a single isolate contained the fosA7 gene responsible for fosfomycin resistance. No antibiotic resistance genes (ARGs) were identified for isolates phenotypically non-susceptible to azithromycin, cephalosporins, chloramphenicol and nitrofurantoin and resistance was thought to be attributable to other resistance mechanisms. The fully susceptible profiles observed for the wastewater isolates suggest that the poultry environment may receive antibiotic-resistant strains and resistance determinants from poultry with the potential of becoming a pathway of Salmonella transmission along the continuum. Six plasmids were identified and were only carried by 92.2% of the S. Yoruba isolates in varying combinations. Four plasmids were common to all S. Yoruba isolates along the continuum; isolates from the litter and faeces on the farm contained two additional plasmids. Ten Salmonella pathogenicity islands (SPIs) and 177 virulence genes were identified; some were serotype-specific. Phylogenetic analysis of S. Heidelberg and Kentucky showed that isolates were related to animal and human isolates from other countries. Phylogenetic analysis among the S. Yoruba isolates revealed four clades based on the isolate sources along the farm-to-fork continuum. Although the transmission of Salmonella strains along the farm-to-fork continuum was not evident, pathogenic, resistant Salmonella present in the poultry production chain poses a food safety risk. WGS analysis can provide important information on the spread, resistance, pathogenicity, and epidemiology of isolates and new, rare or emerging Salmonella strains to develop intervention strategies to improve food safety.

A Public Health Insight into Salmonella in Poultry in Africa: A Review of the Past Decade: 2010-2020

Poultry is a cheap source of animal protein and constituent of diets in Africa. Poultry can serve as a reservoir for Salmonella and cause food-borne infections in humans. This review describes Salmonella contamination of food, poultry, and the farming environment, antimicrobial resistance profiles, and serotypes of Salmonella, as well as the farming systems, antimicrobial use (AMU), hygiene, and husbandry conditions used to rear poultry in Africa. Using the PRISMA (preferred reporting items for systematic reviews and meta-analysis) guidelines, PubMed, Science Direct, and Web of Science databases were searched using a set of predefined keywords. Full-length research articles in English were examined for the period 2010-2020 and relevant information extracted for the narrative synthesis. Of the articles that met the inclusion criteria, 63.1% were conducted on farms and among households, while 36.9% were undertaken at government-controlled laboratories, which quarantine imported birds, processing plants, and retail outlets. The farming systems were intensive, semi-intensive, and extensive. AMU was described in 11.5% of the studies and varied within and across countries. Multidrug-resistant (MDR) Salmonella isolates were detected in 30 studies and the prevalence ranged from 12.1% in Zimbabwe to 100% in Egypt, Ethiopia, Nigeria, Senegal, and South Africa. A total of 226 different Salmonella serotypes were reported. Twenty-four (19.7%) of the studies reported food-borne Salmonella contamination in eggs, poultry, and poultry products at retail outlets and processing plants. The apparent extensive use of antimicrobials and circulation of MDR Salmonella isolates of various serotypes in Africa is a concern. It is important to implement stricter biosecurity measures on farms, regulate the use of antimicrobials and implement surveillance systems, in addition to food safety measures to monitor the quality of poultry and poultry products for human consumption.

TetR-Type Regulator Lp_2642 Positively Regulates Plantaricin EF Production Based on Genome-Wide Transcriptome Sequencing of Lactiplantibacillus plantarum 163

Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plantaricin EF biosynthesis and enhanced plantaricin EF production. Its production was 17.30 mg/L in 163 (Lp_2642), which was 1.29-fold higher than that of the original strain. The regulation mechanism demonstrated that Lp_2642 can bind to three sites of plnA promoter, which enhances its transcription and expression, thereby increasing plantaricin EF production. Amino acids Asn-100, Asn-64, and Thr-69 may play a key role in the binding of Lp_2642. These results provide a novel strategy for mass production of plantaricin EF, which facilitates its large-scale production and application in the agriculture and food industries as a preservative.

Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces

Background

Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database.

Results

Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes.

Conclusions

Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-021-00476-8.

Antimicrobial resistance genes, virulence markers and prophage sequences in Salmonella enterica serovar Enteritidis isolated in Tunisia using whole genome sequencing

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Antimcrobial resistance genes, virulence factors and prophage sequences were studied in WGS of 45 Salmonella Enteritidis from different sources.

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WGS is most powerful tool for determining genomic variation in S. Enteritidis.

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Two major lineages of S. Enteritidis were detected in Tunisia.

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Missense mutations identified in virulence genes were mostly detected in lineage B.

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Salmon118970_sal3 and RE_2010 phages were detected in lineage A and lineage B, respectively.

Salmonella Enteritidis causes a major public health problem in the world. Whole genome sequencing can give us a lot of information not only about the phylogenetic relatedness of these bacteria but also in antimicrobial resistance and virulence gene predictions. In this study, we analyzed the whole genome data of 45 S. Enteritidis isolates recovered in Tunisia from different origins, human, animal, and foodborne samples. Two major lineages (A and B) were detected based on 802 SNPs differences. Among these SNPs, 493 missense SNPs were identified. A total of 349 orthologue genes mutated by one or two missense SNPs were classified in 22 functional groups with the prevalence of carbohydrate transport and metabolism group. A good correlation between genotypic antibiotic resistance profiles and phenotypic analysis were observed. Only resistant isolates carried the respective molecular resistant determinants. The investigation of virulence markers showed the distribution of 11 Salmonella pathogenicity islands (SPI) out of 23 previously described. The SPI-1 and SPI-2 genes encoding type III secretion systems were highly conserved in all isolates except one. In addition, the virulence plasmid genes were present in all isolates except two. We showed the presence of two fimbrial operons sef and ste previously considered to be specific for typhoidal Salmonella. Our collection of S. Enteritidis reveal a diversity among prophage profiles. SNPs analysis showed that missense mutations identified in fimbriae and in SPI-1 and SPI-2 genes were mostly detected in lineage B.

In conclusion, WGS is a powerful application to study functional genomic determinants of S. Enteritidis such as antimicrobial resistance genes, virulence markers and prophage sequences. Further studies are needed to predict the impact of the missenses SNPs that can affect the protein functions associated with pathogenicity.

Comparative Whole-Genome Analysis of Russian Foodborne Multidrug-Resistant Salmonella Infantis Isolates

Non-typhoidal Salmonella infections remain a significant public health problem worldwide. In this study, we present the first detailed genomic analysis report based on short-read (Illumina) whole-genome sequencing (WGS) of 45 multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Infantis isolates from poultry and meat product samples obtained in Russia during 2018-2020, and long-read (MinION) WGS of five more representative isolates. We sought to determine whether foodborne S. Infantis have acquired new characteristics, traits, and dynamics in MDR growth in recent years. All sequenced isolates belonged to the sequence type ST32 and more than the half of isolates was characterized by six similar antimicrobial susceptibility profiles, most of which corresponded well with the antimicrobial resistance determinants to aminoglycosides, sulphonamides, tetracycline, and chloramphenicol revealed in silico. Some of the isolates were characterized by the presence of several types of plasmids simultaneously. Plasmid typing using WGS revealed Col440I, ColpVC, ColRNAI, IncFIB, IncFII, IncX1, IncHI2, IncHI2A, and IncN replicons. The identified virulence genes for 45 whole genomes of S. Infantis were similar and included 129 genes encoding structural components of the cell, factors responsible for successful invasion of the host, and secreted products. These data will be a valuable contribution to further comparative genomics of S. Infantis circulating in Russia, as well as to epidemiological surveillance of foodborne Salmonella isolates and investigations of Salmonella outbreaks.

Global Spread and Molecular Characterization of CTX-M-Producing Salmonella Typhimurium Isolates

This study aimed to determine the global prevalence and molecular characterization of CTX-M-producing Salmonella Typhimurium isolates. A total of 330 (15.2%, 330/21779) bla_CTX-M-positive S. Typhimurium were obtained from the public databases in July 2021. Thirteen variants were found in the 330 members of the bla_CTX-M group, and bla_CTX-M-9 (26.4%, 88/330) was the most prevalent. The majority of bla_CTX-M-positive S. Typhimurium were obtained from humans (59.7%, 197/330) and animals (31.5%, 104/330). The number of bla_CTX-M-positive S. Typhimurium increased annually (p < 0.0001). These isolates were primarily found from China, the United Kingdom, Australia, the USA, and Germany. In addition, these isolates possessed 14 distinct sequence types (ST), and three predominated: ST34 (42.7%, 141/330), ST19 (37.0%, 122/330), and ST313 (10.3%, 34/330). The majority of ST34 S. Typhimurium isolates were distributed in China and mainly from swine. However, the majority of ST19 were distributed in the United Kingdom and Australia. Analysis of contigs showed that the major type of bla_CTX-M-carrying plasmid was identified as IncI plasmid (52.9%, 27/51) and IncHI2 plasmid (17.6%, 9/51) in 51 bla_CTX-M-positive S. Typhimurium isolates. In addition, WGS analysis further revealed that bla_CTX-M co-existed with nine antibiotic-resistant genes with a detection rate over 50%, conferring resistance to five classes of antimicrobials. The 154 virulence genes were detected among these isolates, of which 107 virulence genes were highly common. This study revealed that China has been severely contaminated by bla_CTX-M-positive S. Typhimurium isolates, these isolates possessed numerous ARGs and virulence genes, and highlighted that continued vigilance for bla_CTX-M-positive S. Typhimurium in animals and humans is urgently needed.

Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004-2019

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

Tracking Salmonella enterica by whole genome sequencing of isolates recovered from broiler chickens in a poultry production system

Salmonella enterica is a major cause of foodborne diseases, and is also an important pathogenic bacterium in poultry industry. Whole genome sequencing (WGS) has become a crucial molecular typing technology used for the surveillance of the pathogenic bacteria. In the present study, we adopted WGS for tracking transmission of S. enterica in the production chain of broiler chickens. A total of 74 S. enterica strains were isolated from the different steps of breeding and slaughtering in a large production enterprise in Sichuan Province, China. The isolation rate of Salmonella was the highest in procedure of defeathering (50.0%) and evisceration (36.7%). Serotype identification showed that 74 Salmonella isolates included 7 serotypes, among which Mbandaka accounted for the highest proportions (35.1%). WGS revealed that 74 strains belonged to 7 different sequence types (STs), as well as 7 different ribosomal STs and 35 core genome STs. cgMLST-based Minimum Spanning Trees and phylogenetic tree based on the SNPs indicated that three serotypes, Mbandaka, Indiana and Kentucky, could be clonally transmitted between broiler farm and slaughterhouse. Heterogeneous resistant phenotypes and genotypes were found in two serotypes, Indiana and Kentucky. Our study indicated WGS in an accurate tool for molecular typing of S. enterica. Routine surveillance of S. enterica in the production chain of broiler chickens is needed.