Prevalence of Salmonella Isolates from Chicken and Pig Slaughterhouses and Emergence of Ciprofloxacin and Cefotaxime Co-Resistant S. enterica Serovar Indiana in Henan, China

Prevalence and characterization of ciprofloxacin-resistant Salmonella enterica spp. isolated from food animals during 2010-2023 in South Korea

We isolated 6,561 Salmonella strains from food animals, cattle (n = 217), pigs (n = 1526), chickens (n = 3942), and ducks (n = 876). Isolates were evaluated for antimicrobial sensitivity, mutations in quinolone resistance determination regions (QRDRs), and plasmid-mediated quinolone resistance (PMQR) genes. Clonal relationship and genetic diversity were assessed by multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Overall, 3.1% of isolates exhibited resistance to ciprofloxacin. Commonly identified mutations in QRDRs were S83F, D87N, and D87G in gyrA; T57S and S80I in parC; and L416F in parE. Furthermore, mutations differed by serotypes. In S. Albany, S83F mutation in gyrA and T57S in parC were prevalent, while in S. Kentucky, S83F and D87N in gyrA, T57S and S80I in parC; and in S. Indiana, S83F and D87G in gyrA, T57S and S80R in parC, and L416F in parE were common. Amongst PMQRs, qnrS was mainly observed in S. Albany, aac(6')-Ib-cr in S. Indiana, and qnrB1 in S. Albany. Among STs, ST198 S. Kentucky was predominant, followed by ST292 S. Albany and ST17 S. Indiana. Of 26 pulsotypes, KX1KA1 was mainly identified in S. Kentucky, AX1AA1 in S. Albany, and IX1IA1 in S. Indiana. Taken together, ciprofloxacin-resistant Salmonella can pose health hazards to humans and other animals.

Genomic and resistome analysis of Salmonella enterica isolates from retail markets in Yichun city, China

Nontyphoidal Salmonella (NTS) causes global outbreaks of foodborne disease. The main source of Salmonella for humans is animal-borne foods; however, the monitoring of Salmonella in the food chain via genomic platforms was limited in China. This study evaluated the prevalence, resistome, and virulome diversity of Salmonella strains identified from pork, retail environment, aquatic products, and poultry eggs of retail markets in Yichun city, Jiangxi province. The overall incidence of Salmonella was 9.4 %, with a higher contamination rate observed in pork at 13.5 %, followed by the retail environment at 7.69 %. The genomic analysis of the isolates revealed a total of fifteen distinct serovars, with serovar Enteritidis being the most prevalent (64.3 %). The phenotypic resistance analysis conducted by the broth microdilution method, revealed that 81.12 % of the isolates exhibited multidrug resistance (MDR), with high resistance to trimethoprim/sulphonamides (100 %), followed by tetracycline (99.3 %) and streptomycin (99.3 %). Genotypic analysis of antimicrobial resistance identified 80 antimicrobial-resistant genes (ARGs), with mdf(A), aph(3')-Ib, tet(A), dfrA12, floR, bla TEM-1B , qnrS3, and sul2, conferring resistance to different antimicrobial classes, being the predominant ARGs. Additionally, forty ESBL genes, particularly critical genes such as bla CTX-M and bla NDM-1, were also identified in Salmonella isolates. The IncR, IncFIB (K), and IncX1 plasmid replicons were widely prevalent and served as significant reservoirs of horizontally acquired foreign genes. Moreover, key virulence genes such as cdtB, lpf and sef were also detected, in addition to Salmonella pathogenicity islands SPI-1 and SPI-2. This study reveals the prevalence of multidrug-resistant and virulent strains of Salmonella serovars in the markets of Yichuan city, posing a risk of human infections. The gained knowledge provided essential baseline information that may be utilized for regular tracking of MDR Salmonella transmission in the food chain to minimize potential future outbreaks.

Genomic Characterization of a Plasmid-Free and Highly Drug-Resistant Salmonella enterica Serovar Indiana Isolate in China

The emergence of multi-drug resistant (MDR) Salmonella enterica serovar Indiana (S. Indiana) strains in China is commonly associated with the presence of one or more resistance plasmids harboring integrons pivotal in acquiring antimicrobial resistance (AMR). This study aims to elucidate the genetic makeup of this plasmid-free, highly drug-resistant S. Indiana S1467 strain. Genomic sequencing was performed using Illumina HiSeq 2500 sequencer and PacBio RS II System. Prodigal software predicted putative protein-coding sequences while BLASTP analysis was conducted. The S1467 genome comprises a circular 4,998,300 bp chromosome with an average GC content of 51.81%, encompassing 4709 open reading frames (ORFs). Fifty-four AMR genes were identified, conferring resistance across 16 AMR categories, aligning closely with the strain's antibiotic susceptibility profile. Genomic island prediction unveiled an approximately 51 kb genomic island housing a unique YeeVU toxin-antitoxin system (TAS), a rarity in Salmonella species. This suggests that the AMR gene cluster on the S1467 genomic island may stem from the integration of plasmids originating from other Enterobacteriaceae. This study contributes not only to the understanding of the genomic characteristics of a plasmid-free, highly drug-resistant S. Indiana strain but also sheds light on the intricate mechanisms underlying antimicrobial resistance. The implications of our findings extend to the broader context of horizontal gene transfer between bacterial species, emphasizing the need for continued surveillance and research to address the evolving challenges posed by drug-resistant pathogens.

Salmonella Infection in Pigs: Disease, Prevalence, and a Link between Swine and Human Health

Salmonella is one of the most spread foodborne pathogens worldwide, and Salmonella infections in humans still represent a global health burden. The main source of Salmonella infections in humans is represented by contaminated animal-derived foodstuffs, with pork products being one of the most important players. Salmonella infection in swine is critical not only because it is one of the main causes of economic losses in the pork industry, but also because pigs can be infected by several Salmonella serovars, potentially contaminating the pig meat production chain and thus posing a significant threat to public health globally. As of now, in Europe and in the United States, swine-related Salmonella serovars, e.g., Salmonella Typhimurium and its monophasic variant Salmonella enterica subsp. enterica 1,4,[5],12:i:-, are also frequently associated with human salmonellosis cases. Moreover, multiple outbreaks have been reported in the last few decades which were triggered by the consumption of Salmonella-contaminated pig meat. Throughout the years, changes and evolution across the pork industry may have acted as triggers for new issues and obstacles hindering Salmonella control along the food chain. Gathered evidence reinforces the importance of coordinating control measures and harmonizing monitoring programs for the efficient control of Salmonella in swine. This is necessary in order to manage outbreaks of clinical disease in pigs and also to protect pork consumers by controlling Salmonella subclinical carriage and shedding. This review provides an update on Salmonella infection in pigs, with insights on Salmonella ecology, focusing mainly on Salmonella Choleraesuis, S. Typhimurium, and S. 1,4,[5],12:i:-, and their correlation to human salmonellosis cases. An update on surveillance methods for epidemiological purposes of Salmonella infection in pigs and humans, in a "One Health" approach, will also be reported.

Is There a Shift in Salmonella Diversity Among Poultry in Northern India?

The present study was conducted to determine the serotype diversity of Salmonella among poultry in northern India. A total of 101 poultry droppings from 30 farms in the Jammu and Kashmir union territory were analyzed. Nineteen isolates of Salmonella were obtained, and these belonged to four serotypes: Salmonella enterica enterica serotype Kentucky (n = 3), Salmonella enterica enterica serotype Infantis (n = 5), Salmonella enterica enterica serotype Agona (n = 4), and Salmonella enterica enterica serotype Typhimurium (n= 7). The study has isolated some Salmonella serotypes that are infrequently reported in India. Some of the isolated serotypes are reported to be endemic for human nontyphoidal salmonellosis cases in the region. Whether this indicates a shift in the serotype pattern in poultry in the region needs to be investigated further. Nevertheless, the study clearly indicates the risk of foodborne salmonellosis associated with consumption of contaminated poultry and poultry products in the region.

The large plasmid carried class 1 integrons mediated multidrug resistance of foodborne Salmonella Indiana

Salmonella enterica serovar Indiana (S. Indiana) has aroused widespread concern as an important zoonotic pathogen. The molecular mechanism of multidrug resistance (MDR) in S. Indiana is not known and should be assessed. We aim to investigate the molecular mechanism of MDR and the importance of large plasmids carried class 1 integrons in the MDR of foodborne S. Indiana. Class 1 integrons in 48 S. Indiana isolates and 200 isolates of 7 other Salmonella serotypes were detected by polymerase chain reaction (PCR). To analyze the antimicrobial resistance genes (ARGs) of two S. Indiana isolates, designated S. Indiana 15 and S. Indiana 222, next-generation sequencing (NGS) was performed, and the resulting sequences were compared with the complete nucleotide sequences of S. Indiana D90 and S. Indiana C629. Comparative functional analysis was conducted between the intI1 (1,014 bp) of S. Indiana 222 and the intI1 (699 bp) of S. Indiana 15. Plasmid conjugation transfer analysis was performed to analyze the horizontal gene transfer of the integrons-related resistance genes with integron-positive and integron-negative Salmonella isolates. 64.58% of S. Indiana isolates carried class 1 integrons, which was significantly higher than that of other Salmonella serotypes (p < 0.001). The NGS results showed that the S. Indiana 15 and S. Indiana 222 isolates carried a large plasmid with a class 1 integron and multiple ARGs, similar to S. Indiana D90 and S. Indiana C629. Two integrases found in S. Indiana isolates belong to class 1 integrases and could integrate resistance genes into specific integration sites of the integrons. The conjugation frequency of intI1 (1,014 bp) was 6.08 × 10⁻⁵, which was significantly higher than that of intI1 (699 bp) (p < 0.01). The large plasmids carrying a class 1 integron and the number of ARGs were strongly correlated (p < 0.001). The conjugation frequency of integron-positive S. Indiana recipient isolates was significantly higher than that of integron-negative recipient isolates (p < 0.05). S. Indiana containing large plasmids carrying a class 1 integron more easily captured resistance genes from other bacteria (S. Enteritidis and S. Derby), which could be an important cause of the emerging pandemic of MDR clones.

Graphical abstract

Bacterial contamination of chicken meat in slaughterhouses and the associated risk factors: A nationwide study in Thailand

Slaughterhouses are a key source of bacterial contamination in poultry meat and products, which is a major health and economic concern for several public authorities. This study aimed to quantify the non-compliance of bacterial contamination on chicken meat sampled from slaughterhouses and identify risk factors associated with the contamination. A questionnaire survey of 569 chicken slaughterhouses was undertaken and 1,707 meat samples were collected to determine the level of bacterial contamination. The proportion of the non-compliance associated with aerobic plate count [APC] (24.6%), Staphylococcus aureus (6.3%), Enterococcus spp. (24.7%), coliforms (13.5%), Escherichia coli (33.3%), and Salmonella spp. (33.4%) based on the livestock authorities' criteria was determined. Our results highlighted that the scalding process without scalding water temperature control or improper scalding increased the risk of APC (odds ratio, OR = 4.84, 95% CI: 2.72-8.61), S. aureus (OR = 2.68, 95% CI: 1.29-5.55), Enterococcus spp. (OR = 3.38, 95% CI: 2.01-5.69), coliforms (OR = 3.01, 95% CI: 1.47-6.15), and E. coli (OR = 2.69, 95% CI: 1.58-4.56) contamination on meat samples. Meat from eviscerated carcasses was more likely to be non-compliance due to contamination by E. coli (OR = 1.96, 95% CI: 1.14-3.38). Furthermore, open or semi-closed system slaughterhouses (OR = 1.79, 95% CI: 1.23-2.60) and lack of equipment for specific slaughtering areas (OR = 1.65, 95% CI: 1.04-2.61) increased the likelihood of Salmonella spp. occurrence. This is the first study of factors influencing the non-compliance of meat samples across Thailand. Authorities can use the study findings to enhance food safety strategies at the national level.

Global Distribution of Extended Spectrum Cephalosporin and Carbapenem Resistance and Associated Resistance Markers in Escherichia coli of Swine Origin - A Systematic Review and Meta-Analysis

Third generation cephalosporins and carbapenems are considered critically important antimicrobials in human medicine. Food animals such as swine can act as reservoirs of antimicrobial resistance (AMR) genes/bacteria resistant to these antimicrobial classes, and potential dissemination of AMR genes or resistant bacteria from pigs to humans is an ongoing public health threat. The objectives of this systematic review and meta-analysis were to: (1) estimate global proportion and animal-level prevalence of swine E. coli phenotypically resistant to third generation cephalosporins (3GCs) and carbapenems at a country level; and (2) measure abundances and global distribution of the genetic mechanisms that confer resistance to these antimicrobial classes in these E. coli isolates. Articles from four databases (CAB Abstracts, PubMed/MEDLINE, PubAg, and Web of Science) were screened to extract relevant data. Overall, proportion of E. coli resistant to 3GCs was lower in Australia, Europe, and North America compared to Asian countries. Globally, <5% of all E. coli were carbapenem-resistant. Fecal carriage rates (animal-level prevalence) were consistently manifold higher as compared to pooled proportion of resistance in E. coli isolates. bla_CTX–M were the most common 3GC resistance genes globally, with the exception of North America where bla_CMY were the predominant 3GC resistance genes. There was not a single dominant bla_CTX–M gene subtype globally and several bla_CTX–M subtypes were dominant depending on the continent. A wide variety of carbapenem-resistance genes (bla_{NDM–, VIM–, IMP–, OXA–48}, _andKPC–) were identified to be circulating in pig populations globally, albeit at very-low frequencies. However, great statistical heterogeneity and a critical lack of metadata hinders the true estimation of prevalence of phenotypic and genotypic resistance to these antimicrobials. Comparatively frequent occurrence of 3GC resistance and emergence of carbapenem resistance in certain countries underline the urgent need for improved AMR surveillance in swine production systems in these countries.

Prevalence of Salmonella in Chinese Food Commodities: A Meta-Analysis

ABSTRACT

The objective of the present study was to analyze the prevalence of Salmonella in multiple food commodities in the People's Republic of China by performing a meta-analysis. Accordingly, we screened studies that examined the prevalence of Salmonella in PubMed, Embase, and Web of Science databases. Methodological quality assessment and heterogeneity analyses were performed for included studies. The prevalence rate with the 95% confidence interval (CI) was selected as the effect size. Subgroup analyses for each food type were conducted and then stratified by regions, food chain processing points, and seasons. In total, 49 studies were included in the meta-analysis, among them, 8 (16.3%) studies were deemed "high risk," 13 (26.5%) studies were "unclear risk," and 28 (57.2%) studies were "low risk." The overall prevalence rate of Salmonella was 20.0% (95% CI: 15.9 to 24.4). The prevalence rate of Salmonella in raw meat products was 23.6% (95% CI: 19.8 to 27.6), which was higher than that in aquatic products, 13.7% (95% CI: 3.1 to 29.9), milk products, 0.9% (95% CI: 0.0 to 3.9), frozen convenience foods, 6.5% (95% CI: 4.4 to 8.9), ready-to-eat foods, 2.0% (95% CI: 1.1 to 3.2), vegetables and fruits, 0.9% (95% CI: 0.0 to 5.2), and shell eggs, 4.2% (95% CI: 3.0 to 5.7). Subgroup analyses revealed that prevalence rates of Salmonella in raw meat products from abattoirs, 26.3% (95% CI: 17.4 to 36.3) and retail stores, 30.0% (95% CI: 24.6 to 35.8) were higher than those determined from farms, 10.2% (95% CI: 7.0 to 13.9); P < 0.05); however, no significant difference was observed in the prevalence of Salmonella stratified by different geographical regions or seasons (P > 0.05). On the basis of these findings, high levels of Salmonella contamination could be detected in raw meat products in China, and the prevalence rate of Salmonella in raw meat products from abattoirs and retail stores was high.

HIGHLIGHTS

Antimicrobial Resistance of Salmonella enteritidis and Salmonella typhimurium Isolated from Laying Hens, Table Eggs, and Humans with Respect to Antimicrobial Activity of Biosynthesized Silver Nanoparticles

Simple Summary

Salmonella enterica are common foodborne pathogens that cause gastrointestinal signs in a wide range of unrelated host species including poultry and humans. The overuse of antibiotics as therapeutic agents and growth promoters in the poultry industry has led to the emergence of multidrug-resistant (MDR) microorganisms. Thus, there is a need to find alternatives to conventional antibiotics. Recently, the biosynthesized silver nanoparticles (AgNPs) have shown an excellent antimicrobial activity. In this study, we investigated the antibacterial, antivirulent, and antiresistant activities of the biosynthesized AgNPs on the MDR and virulent S. enteritidis and S. typhimurium isolated from laying hens, table eggs, and humans. The obtained results indicated that AgNPs have the potential to be effective antimicrobial agents against MDR S. enteritidis and S. typhimurium and could be recommended for use in laying hen farms.

Abstract

Salmonella enterica is one of the most common causes of foodborne illness worldwide. Contaminated poultry products, especially meat and eggs are the main sources of human salmonellosis. Thus, the aim of the present study was to determine prevalence, antimicrobial resistance profiles, virulence, and resistance genes of Salmonella Enteritidis (S. enteritidis) and Salmonella Typhimurium (S. Typhimurium) isolated from laying hens, table eggs, and humans, in Sharkia Governorate, Egypt. The antimicrobial activity of Biosynthesized Silver Nanoparticles (AgNPs) was also evaluated. Salmonella spp. were found in 19.3% of tested samples with laying hens having the highest isolation rate (33.1%). S. Enteritidis) (5.8%), and S. Typhimurium (2.8%) were the dominant serotypes. All isolates were ampicillin resistant (100%); however, none of the isolates were meropenem resistant. Multidrug-resistant (MDR) was detected in 83.8% of the isolates with a multiple antibiotic resistance index of 0.21 to 0.57. Most isolates (81.1%) had at least three virulence genes (sopB, stn, and hilA) and none of the isolates harbored the pefA gene; four resistance genes (blaTEM, tetA, nfsA, and nfsB) were detected in 56.8% of the examined isolates. The AgNPs biosynthesized by Aspergillus niveus exhibit an absorption peak at 420 nm with an average size of 27 nm. AgNPs had a minimum inhibitory concentration of 5 µg/mL against S. enteritidis and S. typhimurium isolates and a minimum bactericidal concentration of 6 and 8 µg/mL against S. enteritidis and S. typhimurium isolates, respectively. The bacterial growth and gene expression of S. enteritidis and S. typhimurium isolates treated with AgNPs were gradually decreased as storage time was increased. In conclusion, this study indicates that S. enteritidis and S. typhimurium isolated from laying hens, table eggs, and humans exhibits resistance to multiple antimicrobial classes. The biosynthesized AgNPs showed potential antimicrobial activity against MDR S. enteritidis and S. typhimurium isolates. However, studies to assess the antimicrobial effectiveness of the biosynthesized AgNPs in laying hen farms are warranted.

Mutational Diversity in the Quinolone Resistance-Determining Regions of Type-II Topoisomerases of Salmonella Serovars

Quinolone resistance in bacterial pathogens has primarily been associated with mutations in the quinolone resistance-determining regions (QRDRs) of bacterial type-II topoisomerases, which are DNA gyrase and topoisomerase IV. Depending on the position and type of the mutation (s) in the QRDRs, bacteria either become partially or completely resistant to quinolone. QRDR mutations have been identified and characterized in Salmonella enterica isolates from around the globe, particularly during the last decade, and efforts have been made to understand the propensity of different serovars to carry such mutations. Because there is currently no thorough analysis of the available literature on QRDR mutations in different Salmonella serovars, this review aims to provide a comprehensive picture of the mutational diversity in QRDRs of Salmonella serovars, summarizing the literature related to both typhoidal and non-typhoidal Salmonella serovars with a special emphasis on recent findings. This review will also discuss plasmid-mediated quinolone-resistance determinants with respect to their additive or synergistic contributions with QRDR mutations in imparting elevated quinolone resistance. Finally, the review will assess the contribution of membrane transporter-mediated quinolone efflux to quinolone resistance in strains carrying QRDR mutations. This information should be helpful to guide the routine surveillance of foodborne Salmonella serovars, especially with respect to their spread across countries, as well as to improve laboratory diagnosis of quinolone-resistant Salmonella strains.

Cell-free supernatants produced by lactic acid bacteria reduce Salmonella population in vitro

The genus Salmonella is closely associated with foodborne outbreaks and animal diseases, and reports of antimicrobial resistance in Salmonella species are frequent. Several alternatives have been developed to control this pathogen, such as cell-free supernatants (CFS). Our objective here was to evaluate the use of lactic acid bacteria (LAB) CFS against Salmonella in vitro. Seventeen strains of LAB were used to produce CFS, and their antimicrobial activity was screened towards six strains of Salmonella. In addition, CFS were also pH-neutralized and/or boiled. Those with the best results were lyophilized. MICs of lyophilized CFS were 11.25-22.5 g l^-1. Freeze-dried CFS were also used to supplement swine and poultry feed (11.25 g kg^-1) and in vitro simulated digestion of both species was performed, with Salmonella contamination of 5×10⁶ and 2×10⁵ c.f.u. g^-1 of swine and poultry feed, respectively. In the antimicrobial screening, all acidic CFS were able to inhibit the growth of Salmonella. After pH neutralization, Lactobacillus acidophilus Llorente, Limosilactobacillus fermentum CCT 1629, Lactiplantibacillus plantarum PUCPR44, Limosilactobacillus reuteri BioGaia, Lacticaseibacillus rhamnosus ATCC 7469 and Pediococcus pentosaceus UM116 CFS were the only strains that partially maintained their antimicrobial activity and, therefore, were chosen for lyophilization. In the simulated swine digestion, Salmonella counts were reduced ≥1.78 log c.f.u. g^-1 in the digesta containing either of the CFS. In the chicken simulation, a significant reduction was obtained with all CFS used (average reduction of 0.59±0.01 log c.f.u. ml^-1). In general, the lyophilized CFS of L. fermentum CCT 1629, L. rhamnosus ATCC 7469 and L. acidophilus Llorente presented better antimicrobial activity. In conclusion, CFS show potential as feed additives to control Salmonella in animal production and may be an alternative to the use of antibiotics, minimizing problems related to antimicrobial resistance.

Antimicrobial Resistance Profiles and Genetic Typing of Salmonella Serovars from Chicken Embryos in China

Salmonella continues to be a major food and public health burden worldwide that can threaten human health via eating contaminated meats, particularly those originating from chicken. In this study, the antimicrobial resistance profiles, epidemiological characteristics of resistance genes, and pulsed field gel electrophoresis (PFGE-XbaI) typing of 120 non-Pullorum/Gallinarum Salmonella isolates recovered from chicken embryos in Henan province were determined. The antimicrobial resistant phenotypes and evaluation of the extended-spectrum beta-lactamases (ESBLs) producing strains of Salmonella were investigated by the Kirby-Bauer test and the double-disk synergy test. Additionally, 37 antimicrobial resistance genes encoding resistance to five different categories, including aminoglycosides, cephalosporins, sulphonamides, tetracyclines, and β-lactams, were examined by conventional PCR. However, genotyping analysis was conducted by macro-restriction using enzyme XbaI followed by the separation of the restricted DNA fragments by PFGE. The results of this study showed that the studied Salmonella strains were highly resistant to ampicillin (66.67%) and sulfisoxazole (66.67%), while they were all susceptible to meropenem, imipenem, colistin, and chloramphenicol. Additionally, 67.5% (81/120) of the studied strains were multidrug resistant, and 21.67% (26/120) were phenotypically confirmed as ESBLs positive. The statistical analysis showed that resistance depends on the serovars, and ESBLs positive strains showed more multi-resistance than ESBLs negative strains (p < 0.05). The genotypic antimicrobial resistance showed the detection of 14 among the 37 tested genes, and the concordance between genotypic and phenotypic antimicrobial resistance ranged from 0% to 100% depending on the serovars. However, the PFGE-XbaI typing results showed that the examined Salmonella strains were divided into 22 individual subtypes and were grouped in nine clusters, with similarity values ranging from 64.7% to 100%. From this study, we can conclude that the antimicrobial resistance of Salmonella serovars isolated from chicken embryos in Henan province was alarming, with rigorous multidrug resistance, which requires the urgent mitigation of the use of antimicrobial drugs in chicken hatcheries. Additionally, our results showed evidence of the presence of different PFGE patterns among the studied Salmonella serovars, suggesting the presence of different sources of contamination.

Genomic Investigation of Antimicrobial-Resistant Salmonella enterica Isolates From Dead Chick Embryos in China

Salmonella spp. is recognized as an important zoonotic pathogen. The emergence of antimicrobial resistance in Salmonella enterica poses a great public health concern worldwide. While the knowledge on the incidence and the characterization of different S. enterica serovars causing chick embryo death remains obscure in China. In this study, we obtained 45 S. enterica isolates from 2,139 dead chick embryo samples collected from 28 breeding chicken hatcheries in Henan province. The antimicrobial susceptibility assay was performed by the broth microdilution method and the results showed that 31/45 (68.8%) isolates were multidrug-resistant (≥3 antimicrobial classes). Besides the highest resistance rate was observed in the aminoglycoside class, all the isolates were susceptible to chloramphenicol, azithromycin, and imipenem. Furthermore, genomic characterization revealed that S. Enteritidis (33.33%; 15/45) was a frequent serovar that harbored a higher number of virulence factors compared to other serovars. Importantly, genes encoding β-lactamases were identified in three serovars (Thompson, Enteritidis, and Kottbus), whereas plasmid-mediated quinolone resistance genes (qnrB4) were detected in certain isolates of S. Thompson and the two S. Kottbus isolates. All the examined isolates harbored the typical virulence factors from Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2). Additionally, a correlation analysis between the antimicrobial resistance genes, phenotype, and plasmids was conducted among Salmonella isolates. It showed strong positive correlations (r < 0.6) between the different antimicrobial-resistant genes belonging to certain antimicrobial classes. Besides, IncF plasmid showed a strong negative correlation (r > −0.6) with IncHI2 and IncHI2A plasmids. Together, our study demonstrated antimicrobial-resistant S. enterica circulating in breeding chicken hatcheries in Henan province, highlighting the advanced approach, by using genomic characterization and statistical analysis, in conducting the routine monitoring of the emerging antimicrobial-resistant pathogens. Our findings also proposed that the day-old breeder chicks trading could be one of the potential pathways for the dissemination of multidrug-resistant S. enterica serovars.

Fluoroquinolone resistance in non-typhoidal Salmonella enterica isolated from slaughtered pigs in Thailand

Introduction. The emergence and spread of non-typhoidal Salmonella enterica (NTS) serovars resistant to fluoroquinolones and third- and higher-generation cephalosporins is a matter of great concern. Antimicrobial-resistant NTS is increasingly being discovered in humans, animals, food animals, food products, and agricultural environments. Pigs are considered a major reservoir of antimicrobial-resistant Salmonella spp.Hypothesis/Gap Statement. Fluoroquinolone-resistant Salmonella spp. warrant further surveillance and characterization for a better understanding of the bacteria isolated from animals.Aim. NTS isolated from pork from slaughterhouses across Thailand were characterized in terms of their serovars; resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems; and antimicrobial resistance genes.Methodology. A total of 387 NTS isolates, collected from slaughtered pigs in ten provinces across Thailand between 2014 and 2015, were characterized based on their serovars, antimicrobial resistance genes, and susceptibility to fluoroquinolones, third-generation cephalosporins, and carbapenems.Results. Among all NTS isolates, S. enterica serovar Rissen was predominant. Antimicrobial resistance was exhibited in 93/387 isolates (24 %). Although 24 (6.2 %) isolates were susceptible to all the tested antimicrobials, they were found to possess β-lactamase genes, such as bla _TEM, bla _SHV, or bla _CTX-M. Mobilized colistin-resistant genes (mcr) and resistance to colistin were not observed in any tested isolate. Carbapenem resistance was detected in ten isolates (10.7 %); however, bla _KPC, bla _NDM, bla _OXA-48-like, and bla _IMP were not present. Among the 93 antimicrobial-resistant isolates, 87.1 % showed fluoroquinolone resistance with the quinolone resistance gene (qnrS) combined with topoisomerase genes parC (T57S) or gyrA (S83E/Y and D124E/G) substitutions, or topoisomerase gene substitutions alone.Conclusion. We found high fluoroquinolone resistance rates among the NTS isolates from pigs from slaughterhouses. The fluoroquinolone resistance mechanism in NTS was associated with the combination of qnrS and substitutions in gyrA, parC, or both. To prevent the transmission of antimicrobial-resistant NTS between animals and humans, continuous monitoring, surveillance, and regulation of Salmonella in the pork supply chain are pivotal.

Genomic Investigation of Salmonella Isolates Recovered From a Pig Slaughtering Process in Hangzhou, China

The pig industry is the principal source of meat products in China, and the presence of pathogens in pig-borne meat is a crucial threat to public health. Salmonella is the major pathogen associated with pig-borne diseases. However, route surveillance by genomic platforms along the food chain is still limited in China. Here, we conducted a study to evaluate the dynamic prevalence of Salmonella in a pig slaughtering process in Hangzhou, Zhejiang Province, China. Fifty-five of 226 (24.37%) samples were positive for Salmonella; from them, 78 different isolates were selected and subjected to whole genome sequencing followed by bioinformatics analyses to determine serovar distribution, MLST patterns, antimicrobial resistance genes, plasmid replicons, and virulence factors. Moreover, phenotypic antimicrobial resistance was performed using the broth dilution method against 14 antimicrobial agents belonging to 10 antimicrobial classes. Our results showed that samples collected from the dehairing area (66.66%) and the splitting area (57.14%) were the most contaminated. Phenotypic antimicrobial resistance classified 67 of 78 isolates (85.90%) as having multidrug resistance (MDR), while the highest resistance was observed in tetracycline (85.90%; 67/78) followed by ampicillin (84.62%; 66/78), chloramphenicol (71.80%; 56/78), and nalidixic acid (61.54%; 48/78). Additionally, serovar prediction showed the dominance of Salmonella Typhimurium ST19 (51.28%; 40/78) among the 78 studied isolates, while plasmid prediction reported the dominance of IncHI2A_1 (20.51%; 16/78), followed by IncX1_1 (17.95%; 14/78) and IncHI2_1 (11.54%; 9/78). Virulence factor prediction showed the detection of cdtB gene encoding typhoid toxins in two Salmonella Goldcoast ST358 and one Salmonella Typhimurium ST19, while one isolate of Salmonella London ST155 was positive for genes encoding for the siderophore “yersiniabactin” and the gene senB encoding for enterotoxin production. From this study, we conclude that pig slaughterhouses are critical points for the dissemination of virulent and multidrug-resistant Salmonella isolates along the food chain which require the implementation of management systems to control the critical points. Moreover, there is an urgent need for the implementation of the whole genome sequencing platform to monitor the emergence of virulent and multidrug-resistant clones along the food chain.

Characterization of Salmonella Isolates Recovered from Stages of the Processing Lines at Four Broiler Processing Plants in Trinidad and Tobago

This cross-sectional study determined the prevalence, characteristics, and risk factors for contamination of chicken with Salmonella at four operating broiler processing plants in Trinidad. Standard methods were used to isolate and characterize the Salmonella isolates. The overall prevalence of Salmonella at the four processing plants was 27.0% (107/396). The whole carcass enrichment (WCE) method yielded a statistically significantly (p = 0.0014) higher frequency of isolation (53.9%; 97/180) than the whole carcass rinse (35.0%; 63/180) and neck skin methods (42.2%; 38/90). S. enterica serotypes Enteritidis, Javiana, and Infantis were the predominant serotypes isolated accounting for 20.8%, 16.7% and 12.5%, respectively, of the serotyped isolates. Risk factors included the use of over 100 contract farmers (OR 4.4), pre-chiller (OR 2.3), addition of chlorine to chiller (OR 3.2), slaughtering sick broilers (OR 4.4), and flocks with >50% mortality. Multi-drug resistance was detected in 12.3% (14/114) of the isolates of Salmonella. Resistance was high to kanamycin (85.7%) and doxycycline (74.6%) but low to amoxicillin-clavulanic acid (2.4%) and sulphamethoxazole-trimethoprim (0.8%). The occurrence of resistant Salmonella in chickens processed at commercial broiler processing plants has implications for salmonellosis and therapeutic failure in consumers of improperly cooked contaminated chickens from these plants in the country.

Prevalence and genomic investigation of Salmonella isolates recovered from animal food-chain in Xinjiang, China

Salmonella is a major foodborne pathogen worldwide, causing serious cases of morbidity and mortality due to the consumption of contaminated foods. Animal-borne foods were considered the main source of transferring Salmonella to humans; however, route surveillance by genomic platforms along the food-chain is limited in China. Here, we proceeded to the application of whole genome sequencing in the epidemiological analysis of Salmonella isolated along the food-chain in Xinjiang, China. A total of 2408 samples were collected from farms, slaughterhouses, and markets, and subjected to the isolation of Salmonella strains. 314 (13.04%) of the samples were positive for Salmonella. Phenotypic antimicrobial resistance was conducted by the broth dilution method using 14 antimicrobial agents belonging to ten classes for all 314 isolates. A selection of representative 103 isolates was subjected to whole-genome sequencing for understanding the Salmonella diversity, including serovars, antimicrobial and virulence genes, plasmid types, multi-locus sequence types, and allelic types. We found that S. Agona was the dominant serovar and O:4(B) was the dominant serogroup. The dominant genotype was ST13 and each serovar has a unique MLST pattern. Plasmids prediction reported Col(MGD2)_1 and Col(Ye4449)_1 as the dominant plasmids, in addition to the detection of IncFII(S)_1 and IncFIB(S)_1 carried by all S. Enteritidis isolates. Importantly, virulence genes prediction showed the presence of cdtB gene encoding typhoid toxins, spv genes, and pef gene cluster encoding fimbriae in the genomes of S. Indiana and S. Enteritidis. Phenotypic antimicrobial resistance identified 92.04% of the sampled isolates as multi-drug resistance (MDR), with high resistance to tetracycline (78.03%; 245/314), amoxicillin/ clavulanic acid (75.80%; 238/314), and ampicillin (70.70%; 222/314). Together, we firstly reported the prevalence of MDR Salmonella isolates harboring critical virulence factors transmission via animal-borne food-chain in Xinjiang, hence route surveillance by whole-genome sequencing platform could facilitate recognition and project early warning for the emerging MDR clones along the food-chain.

Salmonella prevalence and persistence in industrialized poultry slaughterhouses

Salmonella contamination sources and transmission routes were studied in 5 Belgian poultry slaughterhouses. Samples from the slaughter and cutting line after cleaning and disinfection were collected, as well as neck skin samples and thighs during slaughter of the first flock. In total, 680 swab and water samples were taken from the slaughter line before slaughter. In all slaughterhouses, Salmonella was notwithstanding cleaning and disinfection still isolated from the slaughter line before start of activities. The prevalence of Salmonella in the plucking area was 10.4% (38/365) (hanging area: 5.0%, scalding tank: 5.8%, plucking machine: 17.0%); in the evisceration room, 1.5% (2/138); and in the cutting area, 2.0% (3/149). No Salmonella (0/28) was found in samples from the chilling line. On neck skin samples taken from the various lines, Salmonella prevalence was 16.1% (48/299) after plucking, 16.0% (48/300) after evisceration, 23.3% (70/300) after chilling; on thighs, prevalence was 10.0% (24/240). Nine Salmonella serotypes were identified of which Salmonella Infantis was the most common serovar (53.8%), especially in slaughterhouse A. Two contamination causes were identified; first, although all flocks had an official Salmonella negative status, this was in one case incorrect and led to an enormous contamination of the neck skins of the flock and the slaughterline (i.e., cooling water). Second, molecular typing revealed cross-contamination from flocks slaughtered 1 d before sampling. Salmonella was apparently not always eliminated by the cleaning and disinfection process and able to contaminate the carcasses of the first slaughtered flock. In conclusion, the results of this study provided practical insights for poultry production to further improve their Salmonella control, for example, Salmonella status determination closer to the slaughter date, to adapt cleaning and disinfection protocols especially for critical machinery and better hygienic designed equipment.

Characterization of integrons and antimicrobial resistance in Salmonella from broilers in Shandong, China

Salmonella spp. are one of the most important foodborne bacterial pathogens in human beings and animals. This study aimed to analyze the prevalence and characterization of Salmonella from broilers in Shandong, China. A total of 67 Salmonella were recovered from 600 rectal swabs collected from 3 large-scale intensive broiler farms (67/600, 11.2%) between May and October 2018. Among Salmonella isolates, the most common serovars were S. enteritidis and S. typhimurium. The highest occurrence of resistance observed was for polymyxin (100%), followed by ampicillin (68.7%). The multidrug-resistant Salmonella isolation rate was observed to be 53.7%. Four β-lactamase genes were detected among the isolates, and all the isolates carried blaTEM (67/67, 100%), followed by blaOXA (19/67, 28.4%), blaCTX-M (17/67, 25.4%), and blaPSE (7/67, 10.4%). Four plasmid-mediated quinolone resistance gene were detected among the isolates; the prevalent resistance genes was aac(6')-Ib-cr (18/67, 26.9%), followed by oqxB (9/67, 13.4%), qnrB (6/67, 9.0%), and qnrD (1/67, 1.5%). The prevalent rate of mcr-1 was 6.0% (4/67). Class 1 integrons were detected in 26.9% of these isolates and contained 7 groups of resistance gene cassettes. Multilocus sequence typing analysis revealed 7 sequence types, and ST11 was the most frequent sequence types. This study indicated that reduction of Salmonella and strict control on the use of antibiotics in more than 5,000 million broilers in Shandong are the vitally important measures to keep public health.

Prevalence and antimicrobial resistance of Salmonella enterica subspecies enterica serovar Enteritidis isolated from broiler chickens in Shandong Province, China, 2013-2018

Salmonella is a major zoonotic foodborne pathogen that persists on poultry farms worldwide. The present study aimed to survey the prevalence of Salmonella and antimicrobial resistance of Salmonella enterica serovar Enteritidis (S. Enteritidis) recovered from broiler chickens in Shandong Province, China. A total of 280 Salmonella isolates were identified from 923 broiler chicken samples between 2013 and 2018. Among the isolates, S. Enteritidis (n = 128, 45.7%) was the predominant serovar, and high antimicrobial resistance rates to piperacillin (PIP) (n = 123, 96.1%), ampicillin (AM) (n = 122, 95.3%), nitrofurantoin (FT) (n = 106, 96.1%), and tetracycline (TE) (n = 93, 72.7%) were observed in S. Enteritidis. A total of 96 (75.0%) S. Enteritidis isolates presented with multidrug resistance, the most frequent of which were the combination of AM, PIP, TE, and FT. Resistance to fluoroquinolone tended to increase during 2013 to 2018. Our findings provide important and updated information about the baseline antimicrobial-resistant data for food safety and a risk assessment of S. Enteritidis from broiler chickens in Shandong Province and will be helpful for future surveillance activities to ensure the safety of the chicken supply.

Antibiotic resistance in Salmonella spp. isolated from poultry: A global overview

Salmonella enterica is the most important foodborne pathogen, and it is often associated with the contamination of poultry products. Annually, Salmonella causes around 93 million cases of gastroenteritis and 155,000 deaths worldwide. Antimicrobial therapy is the first choice of treatment for this bacterial infection; however, antimicrobial resistance has become a problem due to the misuse of antibiotics both in human medicine and animal production. It has been predicted that by 2050, antibiotic-resistant pathogens will cause around 10 million deaths worldwide, and the WHO has suggested the need to usher in the post-antibiotic era. The purpose of this review is to discuss and update the status of Salmonella antibiotic resistance, in particular, its prevalence, serotypes, and antibiotic resistance patterns in response to critical antimicrobials used in human medicine and the poultry industry. Based on our review, the median prevalence values of Salmonella in broiler chickens, raw chicken meat, and in eggs and egg-laying hens were 40.5% ( interquartile range [IQR] 11.5-58.2%), 30% (IQR 20-43.5%), and 40% (IQR 14.2-51.5%), respectively. The most common serotype was Salmonella Enteritidis, followed by Salmonella Typhimurium. The highest antibiotic resistance levels within the poultry production chain were found for nalidixic acid and ampicillin. These findings highlight the need for government entities, poultry researchers, and producers to find ways to reduce the impact of antibiotic use in poultry, focusing especially on active surveillance and finding alternatives to antibiotics.

Epidemiological Study on Prevalence, Serovar Diversity, Multidrug Resistance, and CTX-M-Type Extended-Spectrum β-Lactamases of Salmonella spp. from Patients with Diarrhea, Food of Animal Origin, and Pets in Several Provinces of China

A total of 2,283 Salmonella isolates were recovered from 18,334 samples, including samples from patients with diarrhea, food of animal origin, and pets, across 5 provinces of China. The highest prevalence of Salmonella spp. was detected in chicken meats (39.3%, 486/1,237). Fifteen serogroups and 66 serovars were identified, with Salmonella enterica serovars Typhimurium and Enteritidis being the most dominant. Most (85.5%, 1,952/2,283) isolates exhibited resistance to ≥1 antimicrobial, and 56.4% were multidrug resistant (MDR). A total of 222 isolates harbored extended-spectrum β-lactamases (ESBLs), and 200 of these were of the CTX-M type and were mostly detected in isolates from chicken meat and turtle fecal samples. Overall, eight blaCTX-M genes were identified, with blaCTX-M-65, blaCTX-M-123, blaCTX-M-14, blaCTX-M-79, and blaCTX-M-130 being the most prevalent. In total, 166 of the 222 ESBL-producing isolates had amino acid substitutions in GyrA (S83Y, S83F, D87G, D87N, and D87Y) and ParC (S80I), while the plasmid-mediated quinolone resistance (PMQR)-encoding genes oqxA, oqxB, qepA, qnrB, and qnrS were detected in almost all isolates. Of the 15 sequence types (STs) identified in the 222 ESBLs, ST17, ST11, ST34, and ST26 ranked among the top 5 in number of isolates. Our study revealed considerable serovar diversity and a high prevalence of the co-occurrence of MDR determinants, including CTX-M-type ESBLs, quinolone resistance-determining region (QRDR) mutations, and PMQR genes. This is the first report of CTX-M-130 Salmonella spp. from patients with diarrhea and QRDR mutations from turtle fecal samples. Our study emphasizes the importance of actions, both in health care settings and in the veterinary medicine sector, to control the dissemination of MDR, especially the CTX-M-type ESBL-harboring Salmonella isolates.

Diversity of Serotype, Genotype, and Antibiotic Susceptibility of Salmonella Prevalent in Pickled Ready-to-Eat Meat

Pickled ready-to-eat meat (PRTEM) is a meat product that is treated with various seasonings and then cooked. PRTEM is a popular food consumed mostly in China and some Asian countries. Since this food is considered 'ready to eat', once it is contaminated by foodborne pathogens such as Salmonella, the prospect for significant morbidity, mortality, and immeasurable economic losses can occur. Here we investigated the prevalence and concentration of Salmonella in 107 PRTEM samples collected from Shaanxi, China during 2015-2016. Furthermore, we analyzed the serotype, antibiotic susceptibility, and presence of antibiotic resistance genes and amino acid mutations in 219 Salmonella isolates, followed by subtyping of 115 representative isolates. The average detection rate of Salmonella-positive PRTEM was 58.9%, and the average most probable number (MPN) of Salmonella in positive samples was 2.27 logMPN per gram of sample (range: 2.10-2.43). Ten serotypes were identified from the 219 Salmonella isolates, with S. Thompson (37.9%) and S. Indiana (20.5%) being predominant. The remaining serotypes were S. Typhi (7.8%), S. Typhimurium (7.3%), S. Mbandaka (6.9%), S. Albany (6.4%), S. Blockley (5.5%), S. Infantis (4.1%), S. Escanaba (3.2%), and S. Dusseldorf (0.5%). All isolates were resistant to ceftiofur (100%), while most of them were resistant to ciprofloxacin (99.1%), amoxicillin-clavulanic acid (97.7%), trimethoprim-sulfamethoxazole (96.4%), ampicillin (92.3%), sulfisoxazole (92.2%), tetracyclines (90.4%), and nalidixic acid (90.4%), respectively. A single mutation of Ser83Phe (27.1%) and double mutations of Ser83Phe-Asp87Gly (25.9%) in GyrA were detected in 85 isolates, whereas mutations of Thr57Ser (63.9%) and Ser80Arg (36.1%) in ParC were detected in 122 isolates. qnrB, oqxAB, aac(6')-Ib, and qnrA were present in 50 (22.8%), 48 (21.9%), 26 (11.9%), and 1 (0.5%) isolate(s), respectively. Pulse field gel electrophoresis results revealed that those isolates recovered from the same type of PRTEM or the same sampling place shared identical or similar DNA profiles, antibiotic resistance phenotypes, and even plasmid-mediated quinolone resistance encoding genes. The findings indicate that Salmonella is commonly prevalent in PRTEMs at high concentrations in Shaanxi, China. More attention should be paid to the processing and storage of this ready-to-eat food to prevent bacterial contamination and foodborne outbreaks.

Prevalence, Bacterial Load, and Antimicrobial Resistance of Salmonella Serovars Isolated From Retail Meat and Meat Products in China

Salmonella remains the leading cause of reported bacterial foodborne disease in China. Meat products are recognized as one of the major sources of human salmonellosis; however, there is a lack of comprehensive, quantitative data concerning Salmonella contamination of these foods. Therefore, the objectives of this study were to investigate the prevalence, bacterial load, and antimicrobial resistance profiles of various Salmonella serovars in retail meat across the whole of China. Between July 2011 and June 2016, a total of 807 retail meat samples were collected, covering most provincial capitals in China. Overall, 159 (19.7%) samples tested positive for Salmonella. The highest contamination rate occurred in pork (37.3%, n = 287), followed by beef (16.1%, n = 161), mutton (10.9%, n = 92), dumplings (6.6%, n = 212), and smoked pork (3.6%, n = 55). Most probable number (MPN) analysis revealed that contamination was mainly in the range of 0.3–10 MPN/g among those samples testing positive using this method (n = 83), with eight samples exceeding 110 MPN/g. Among the 456 Salmonella enterica subsp. enterica isolates obtained in this study, 29 serovars and 33 multilocus sequence typing patterns were identified, with S. Derby, S. Typhimurium, S. London, S. Rissen, S. 1,4,[5],12:i:-, S. Weltevreden, and S. Enteritidis being the most prevalent. Among the 218 non-duplicate isolates, 181 (83.0%) were resistant to at least one class of antimicrobials and 128 (58.7%) were resistant to at least three classes. High rates of resistance were observed for tetracycline (65.6%), ampicillin (45.4%), trimethoprim-sulfamethoxazole (40.8%), streptomycin (40.4%), and nalidixic acid (35.8%), with the seven most prevalent serovars, except S. Weltevreden, showing higher rates of resistance and multidrug resistance compared with the less dominant serovars. Of note, all S. Indiana isolates exhibited resistance to extended-spectrum cephalosporins (including ceftriaxone and cefepime), ciprofloxacin, and multiple other classes of antibiotics. Further, two S. 1,4,[5],12:i:- isolates showed resistance to imipenem. This study provides systematic and comprehensive data on the prevalence and antimicrobial resistance profiles of various Salmonella serovars isolated from meat products in China, indicating their potential risk to public health.

Antibiotic Resistance Profiles of Salmonella Recovered From Finishing Pigs and Slaughter Facilities in Henan, China

With the increase in commercial pig farming, there is a simultaneous increase in the use of antibiotics for prophylaxis as well as therapeutics in China. In this study, we evaluated the prevalence and resistance diversity of salmonellae isolated from feces of asymptomatic, live and slaughtered pigs. We analyzed 1,732 pig fecal samples collected over 8 months, at Henan province of China. The salmonellae were isolated and identified by PCR. They were serotyped using commercial antisera and assayed for the MIC of 16 antibiotics by broth microdilution method. The average prevalence of Salmonella was 19.4% (95% CI: 17.6–21.4). Large farms (herd size ≥1,000) were found to have a higher prevalence as compared to the small- and medium-scale farms (p < 0.0001). The prevalence of salmonellae in samples collected from the farms [11.77% (95% CI: 10.1–13.6)] and from the slaughterhouse [45.23% (95% CI: 40.3–50.30)] was statistically different (p < 0.0001). Uncommon serovars of Salmonella such as Agama and common serovars such as Derby and Typhimurium were isolated. High resistance (>80%) was recorded toward ciprofloxacin (100%), tetracycline (99.4%), doxycycline (97%), sulfamethoxazole (85.8%), ampicillin (81.6%), and amoxicillin (80.4%). Multidrug resistance (MDR) to four, five, and seven classes of antibiotics was recorded to be approximately 25% in the most prevalent serovar like Derby. We conclude that the presence of alarmingly high resistance, toward the critical antibiotics such as fluoroquinolones and beta-lactams, in large swine farms in China, should draw public attention. These results highlight the need for continued antibiotic stewardship programs for judicious use of critical antibiotics in animal health as well as for producing safe pork.

Characterization of the emerging multidrug-resistant Salmonella enterica serovar Indiana strains in China

Emergence of multidrug-resistant (MDR) Salmonella enterica serovar Indiana (S. Indiana), a dominant Salmonella serovar in China, has raised global awareness because the MDR S. Indiana also was rapidly emerged in other countries recently. To improve our understanding of underlying MDR mechanism and evolution of this emerging zoonotic pathogen, here we examined the standard ATCC51959 strain together with 19 diverse and representative Chinese S. Indiana strains by performing comprehensive microbiological, molecular, and comparative genomics analyses. The findings from S1-PFGE, plasmid origin analysis and Southern blotting suggested the MDR phenotype in the majority of isolates was associated with large integron-carrying plasmids. Interestingly, further in-depth analyses of two recently isolated, plasmid-free MDR S. Indiana revealed a long chromosomal class I integron (7.8 kb) that is not linked to the Salmonella Genome Island 1 (SGI1), which is rare. This unique chromosomal integron shares extremely high similarity to that identified in a MDR E. coli plasmid pLM6771 with respect to both genomic organization and sequence identity. Taken together, both plasmid and chromosomal integron I exist in the examined MDR S. Indiana strains. This timely study represents a significant step toward the understanding of molecular basis of the emerging MDR S. Indiana.

Prevalence and Antimicrobial Resistance of Salmonella in Pork, Chicken, and Duck from Retail Markets of China

Salmonella is one of the most important foodborne pathogens associated with animal and human diseases. In this study, 672 samples of fresh meat (pork, 347; chicken, 196; and duck, 129) were collected from retail markets in different provinces of China from 2010 to 2014. We identified 10 different serotypes among 80 Salmonella isolates, whereas 12 isolates were nonmotile precluding conventional identification of complete serotype. Among these 92 isolates, Salmonella enterica serovar Derby (n = 21) was the most prevalent serotype, followed by Salmonella Enteritidis (n = 17), Salmonella Typhimurium (n = 15), Salmonella Indiana (n = 9), Salmonella Agona (n = 7), and Salmonella Assinie (n = 5). Antimicrobial resistance testing for 18 antimicrobial agents revealed that all 92 isolates were resistant to at least 1 antimicrobial agent, and 39 different resistance profiles were identified. The highest resistance was to trimethoprim-sulfamethoxazole (n = 87), followed by tetracycline (n = 51), carbenicillin (n = 38), amoxicillin/A.clav (n = 30), and piperacillin (n = 24). Our results demonstrated that meats presented a potential public health risk, thereby underlining the necessity for local regulatory enforcement agencies in China to monitor salmonellosis.

Characteristics of third-generation cephalosporin-resistant Salmonella from retail chicken meat produced by integrated broiler operations

Integrated broiler operations, which control and operate vertically through all phases of the chicken industry, have applied biosecurity and sanitation practices, housing technologies, feeding regimens, and antibiotic applications in different ways to improve food safety. The objective of this study was to compare the prevalence and antimicrobial resistance profiles of Salmonella isolates recovered from 6 different integrated broiler operations and to analyze the characteristics of extended-spectrum β-lactamase (ESBL)- and plasmid-mediated AmpC β-lactamase (pAmpC)-producing Salmonella isolates. Among 336 chicken meat samples, 57 were observed to be positive for Salmonella. However, the prevalence varied from 6.8% to 45.8% in chicken meat, indicating variations in Salmonella occurrence among the operations. Salmonella Albany was the dominant serovar, followed by Salmonella Virchow. In the antimicrobial resistance test, nalidixic acid-resistant isolates were the most prevalent (73.7%), followed by isolates resistant to ampicillin (49.1%) and tetracycline (42.1%). Among 14 third-generation cephalosporin-resistant isolates, 9 (64.3%) ESBL/pAmpC-producing isolates were only obtained from 2 operations: blaCTX-M-15 (n = 7) and blaCTX-M-79 (n = 1) for ESBL genes and blaCMY-2 (n = 1) for pAmpC. All ESBL/pAmpC-positive isolates exhibited high minimum inhibitory concentrations (≥128 μg/mL) of most cephalosporins and showed multidrug resistance. The transfer of ESBL/pAmpC genes was confirmed in transconjugants, which had the same genes and similar resistance patterns as those of the donor. Our findings suggest that Salmonella with resistance to third-generation cephalosporins can now be found in association with integrated broiler operations, providing data to support the development of monitoring and prevention programs for the development and spread of antimicrobial resistance in integrated broiler operations.

Inhibitory Effects of Antimicrobial Peptide JH-3 on Salmonella enterica Serovar Typhimurium Strain CVCC541 Infection-Induced Inflammatory Cytokine Release and Apoptosis in RAW264.7 Cells

The antibiotic resistance of Salmonella has become increasingly serious due to the increased use of antibiotics, and antimicrobial peptides have been considered as an ideal antibiotic alternative. Salmonella can induce macrophage apoptosis and thus further damage the immune system. The antimicrobial peptide JH-3 has been shown to have a satisfactory anti-Salmonella effect in previous research, but its mechanism of action remains unknown. In this study, the effects of JH-3 on macrophages infected with Salmonella Typhimurium CVCC541 were evaluated at the cellular level. The results showed that JH-3 significantly alleviated the damage to macrophages caused by S. Typhi infection, reduced the release of lactic dehydrogenase (LDH), and killed the bacteria in macrophages. In addition, JH-3 decreased the phosphorylation level of p65 and the expression and secretion of interleukin 2 (IL-2), IL-6, and tumor necrosis factor-α (TNF-α) by inhibiting the activation of the mitogen-activated protein kinase (MAPK) (p38) signaling pathway and alleviating the cellular inflammatory response. From confocal laser scanning microscopy and flow cytometry assays, JH-3 was observed to inhibit the release of cytochrome c in the cytoplasm; the expression of TNF-αR2, caspase-9, and caspase-8; to further weaken caspase-3 activation; and to reduce the S.-Typhi-induced apoptosis of macrophages. In summary, the mechanism by which JH-3 inhibits Salmonella infection was systematically explored at the cellular level, laying the foundation for the development and utilization of JH-3 as a therapeutic alternative to antibiotics.

Non-typhoidal Salmonella in the Pig Production Chain: A Comprehensive Analysis of Its Impact on Human Health

Salmonellosis remains one of the most frequent foodborne zoonosis, constituting a worldwide major public health concern. The most frequent sources of human infections are food products of animal origin, being pork meat one of the most relevant. Currently, particular pig food production well-adapted and persistent Salmonella enterica serotypes (e.g., Salmonella Typhimurium, Salmonella 1,4,[5],12:i:-, Salmonella Derby and Salmonella Rissen) are frequently reported associated with human infections in diverse industrialized countries. The dissemination of those clinically-relevant Salmonella serotypes/clones has been related to the intensification of pig production chain and to an increase in the international trade of pigs and pork meat. Those changes that occurred over the years along the food chain may act as food chain drivers leading to new problems and challenges, compromising the successful control of Salmonella. Among those, the emergence of antibiotic resistance in non-typhoidal Salmonella associated with antimicrobials use in the pig production chain is of special concern for public health. The transmission of pig-related multidrug-resistant Salmonella serotypes, clones and/or genetic elements carrying clinically-relevant antibiotic resistance genes, frequently associated with metal tolerance genes, from pigs and pork meat to humans, has been reported and highlights the contribution of different drivers to the antibiotic resistance burden. Gathered data strengthen the need for global mandatory interventions and strategies for effective Salmonella control and surveillance across the pig production chain. The purpose of this review was to provide an overview of the role of pig and pork meat in human salmonellosis at a global scale, highlighting the main factors contributing to the persistence and dissemination of clinically-relevant pig-related Salmonella serotypes and clones.

Highly Prevalent Multidrug-Resistant Salmonella From Chicken and Pork Meat at Retail Markets in Guangdong, China

This study aimed to investigate the prevalence, serotype distribution, and antibiotic resistance, and to characterize the extended spectrum β-lactamases (ESBLs) producing Salmonella isolates from chicken and pork meats from retail markets in Guangdong province, China. A total of 903 retail meat samples (475 chicken and 428 pork meats) were obtained from six cities (Guangzhou, Shenzhen, Heyuan, Shaoguan, Foshan, and Yunfu) of Guangdong province between May 2016 and April 2017. High levels of Salmonella contamination were detected in chicken (302/475, 63.6%) and pork (313/428, 73.1%). Thirty-eight serotypes were identified in 615 detected Salmonella, and the serotypes varied greatly between chicken and pork samples. Agona (55/302, 18.2%), Corvallis (45/302, 14.9%), Kentucky (38/302, 12.6%), Mbandaka (32/302, 10.6%) was the dominant serotypes in chicken samples. However, Typhimurium (78/313, 24.9%), Rissen (67/313, 24.1%), Derby (66/313, 21.1%), and London (48, 15.3%) were the most common in pork samples. High rates of antibiotic resistance were found to sulfisoxazole (468/615, 76.1%), tetracycline (463/615, 75.3%), ampicillin (295/615, 48.0%), and ofloxacin (275/615, 44.7%). Notably, antimicrobial susceptibility tests identified resistance to polymyxin B (12/615, 2.0%) and imipenem (3/615, 0.5%). Multidrug-resistance (MDR) was detected in Salmonella isolated from chicken (245/302, 81.1%) and pork (229/313, 73.2%). The resistance rate of different Salmonella serotypes varied widely. Especially, isolates such as Typhimurium, Agona, Corvallis and Kentucky exhibited highly resistance to antibiotics. The MDR rate of Salmonella isolates from chicken was significantly higher than that from pork isolates (P < 0.05). Twenty-one Salmonella isolates were identified as ESBLs-producing, covering six Salmonella serotypes and displaying different pulse field gel electrophoresis (PFGE) genotypes. Bla_OXA-1 was the dominant ESBLs gene (9/21, 42.9%), followed by bla_CTX-M-55 (5/21, 23.8%). This study indicated that Salmonella was widespread in chicken and pork from retail markets in Guangdong province and the isolates showed high multidrug-resistance, especially the known multidrug-resistant Salmonella serotypes. Therefore, it is important to focus on Salmonella serotypes and strengthen the long-term monitoring of MDR Salmonella serotypes in animal-derived foods.

Serovar-Specific Polymerase Chain Reaction for Detection of Salmonella enterica Serovar Indiana

Salmonella enterica serovar Indiana (S. Indiana) is a newly emerging pathogen with high levels of drug resistance. It has become one of the most common Salmonella serovars in China with a worldwide distribution, posing significant public health concerns. Detection of S. Indiana by traditional bacteriological methods is time-consuming and laborious, which prevents timely surveillance and effective control of the pathogen. In this study, comparative genomics was used to identify an A7P63_13850 gene that is uniquely present in S. Indiana, but not in other Salmonella serovars or any non-Salmonella bacteria. Then, a polymerase chain reaction (PCR) assay targeting this serovar-specific gene was established for specific detection of S. Indiana. The detection limit of this method is 10 pg per reaction for bacterial genomic DNA, being equivalent to 100 colony-forming units (CFU) per reaction. The established PCR amplifies all S. Indiana strains (n = 56), but none of other Salmonella serovars (n = 146) and non-Salmonella species (n = 14). The assay established in this study was also used to detect clinical samples from poultry, showed a positivity of 14.7% (23/156) for S. Indiana, which were verified by bacteriological methods. The highly sensitive and serovar-specific PCR for S. Indiana established in this study is suitable and convenient for detection of S. Indiana which aids in surveillance and control of the pathogen.

Sensitive and rapid detection of Salmonella enterica serovar Indiana by cross-priming amplification

Salmonella enterica serovar Indiana (S. Indiana) was the most frequently reported foodborne pathogen, which has a broad host range including poultry, swine, and humans. Traditional methods used for the detection of S. Indiana from contaminated food products are time-consuming and labor-intensive. Therefore, rapid detection methods with high sensitivity and specificity are vitally important to prevent the spread of S. Indiana. In this study, we developed a nearly instrument-free, simple molecular method which incorporates cross-priming amplification (CPA) combined with a nucleic acid detection strip (NADS) for sensitive detection of S. Indiana. A set of CPA primers was designed based on S. Indiana specific nucleotide sequences and the specificity of CPA-NADS was tested against 42 bacterial strains. The results showed that this method was highly specific for detection of S. Indiana. The sensitivity of CPA-NADS was evaluated and compared with that of the serovar-specific PCR method and the real-time PCR method. The limit of detection of the CPA method was 8.997 fg/μL for genomic DNA and 6.2 × 10¹ CFU/mL for bacteria in pure culture. An application of the CPA assay was conducted with 90 inoculated specimens by S. Indiana. The accuracy of CPA-NADS was consistent with the results of the traditional culture-based methods in inoculated specimens. This method showed a higher sensitivity than the serovar-specific PCR method did and was more convenient to perform. In conclusion, we demonstrated that the CPA-NADS system offers high specificity, sensitivity, rapidity, and a simple detection tool for screening S. Indiana.

Antimicrobial Resistance in Nontyphoidal Salmonella

Non-typhoidal Salmonella is the most common foodborne bacterial pathogen in most countries. It is widely present in food animal species, and therefore blocking its transmission through the food supply is a prominent focus of food safety activities worldwide. Antibiotic resistance in non-typhoidal Salmonella arises in large part because of antibiotic use in animal husbandry. Tracking resistance in Salmonella is required to design targeted interventions to contain or diminish resistance and refine use practices in production. Many countries have established systems to monitor antibiotic resistance in Salmonella and other bacteria, the earliest ones appearing the Europe and the US. In this chapter, we compare recent Salmonella antibiotic susceptibility data from Europe and the US. In addition, we summarize the state of known resistance genes that have been identified in the genus. The advent of routine whole genome sequencing has made it possible to conduct genomic surveillance of resistance based on DNA sequences alone. This points to a new model of surveillance in the future that will provide more definitive information on the sources of resistant Salmonella, the specific types of resistance genes involved, and information on how resistance spreads.

Distribution of Salmonella Enteritidis in internal organs and variation of cecum microbiota in chicken after oral challenge

The aim study was to explore the distribution of Salmonella Enteritidis (S. enteritidis) in internal organs and variation of cecum microbiota in newly hatched chicken after oral challenge during a 21-day period. The quantities of S. enteritidis DNA in different internal organs (heart, liver, spleen, stomach, pancreas, small intestine, blood and cecum contents) were determined by real-time fluorescent quantitative polymerase chain reaction (FQ-PCR). The result showed that all of the above-mentioned samples were positive at 12 h post inoculation (PI) after oral challenge. The highest copy numbers of S. enteritidis in all tissue were heart and liver, with about 2 × 10² to 6 × 10⁶ copies of DNA target sequences/0.5 g. The copy number of S. enteritidis in the stomach was only lower than the heart and liver. The blood at 8 d PI, the pancreas at 10 d PI, the heart at 14 d PI and the stomach at 17 d PI didn't have a positive result. However, the liver, spleen, cecum contents and small intestine were all positive during the 21-day period. The cecum contents at 0 d PI, 4 d PI and 10 d PI from the control group and experiment group were collected for bacterial 16 S rRNA sequencing targeting the V3-V4 hypervariable region. The result showed that at the 0 d PI, the main cecum microbiota ingredient of the two-day old chicken was Enterobacteriaceae (Proteobacteria) and the other microbiology species were fewer. At the 10 d PI, the microbiota ingredient of cecum became abundant and stable mainly including the families Ruminococcaceae (Firmicutes), Enterobacteriaceae (Proteobacteria), Lachnospiraceae (Firmicutes) and clostridiacaea (Firmicutes) both of the two group, suggesting Salmonella infection with 2-day old chicken might not significantly change cecum microbiota community. The study indicated the major organs, which carried numerous S. enteritidis, providing a significantly guideline for salmonella detection in poultry and revealed the main microbiota ingredient of chicken cecum.

Salmonella Species' Persistence and Their High Level of Antimicrobial Resistance in Flooded Man-Made Rivers in China

Man-made rivers, owing to proximity to human habitats, facilitate transmission of salmonellosis to humans. To determine the contamination situation by Salmonella in flooded man-made rivers and thereafter the exposure risk to public health, we investigated the prevalence of Salmonella species and their antimicrobial resistance in such rivers, as well as the relationship between the incidence of local infectious diarrhea cases and the number of Salmonella isolates from patients. After a heavy flood, 95 isolates of 13 Salmonella serotypes were isolated from 80 river water samples. The two most prevalent serotypes were Typhimurium and Derby. Eight Salmonella serotypes were newly detected after the flood. Overall, 50 isolates were resistant to ampicillin and/or cefotaxime and carried at least bla_TEM. Twelve isolates of serotypes Typhimurium, Derby, Rissen, and Indiana were extended-spectrum β-lactamase (ESBL) producing and carried at least one of bla_OXA and bla_CTX-M-like genes. Twelve isolates of serotypes Typhimurium, Derby, Agona, Rissen, and Indiana were resistant to ciprofloxacin and had gyrA mutations. Isolates of Typhimurium, Derby, and Indiana were concurrently ciprofloxacin resistant and ESBL producing. Pulsed-field gel electrophoresis illustrates the circulation of two dominant clones of Salmonella Typhimurium isolates among patients, river, and food. High prevalence of various highly pathogenic and antimicrobial-resistant Salmonella serotypes shows that man-made rivers are prone to heavy contamination with Salmonella, and as a result put public health at greater risk.

Comparative Study on Antibiotic Resistance and DNA Profiles of Salmonella enterica Serovar Typhimurium Isolated from Humans, Retail Foods, and the Environment in Shanghai, China

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

Antibiogram and genetic diversity of Salmonella enterica with zoonotic potential isolated from morbid native chickens and pigeons in Egypt

AIMS

This study investigated the possible role of Fayoumi chickens and pigeons in the transmission of multidrug resistant (MDR) Salmonella with zoonotic potential.

METHODS AND RESULTS

Morbid Fayoumi chickens (70) and pigeons (30) were examined to detect the prevalence and antibiotic resistance of Salmonella and to detect and sequence sodC-1 gene as a zoonotic and phylogenetic marker. Salmonella isolates were detected in 14·3 and 20% of the examined Fayoumi chickens and pigeons, respectively. Salomonella subspecies salamae (43·8%) and S. subspecies enterica serovar Bukuru (31·3%) were the most prevalent isolates. All tested Salmonella isolates were MDR to at least five classes of antibiotics. S. salamae and S. Bukuru isolates that carried bla_TEM , qnrS, aadA2 and floR genes expressed phenotypic resistance to cefotaxime, ciprofloxacin, streptomycin and chloramphenicol, respectively. The aacC gene was detected in one of each S. salamae and S. Bukuru isolate, although only the S. Bukuru isolate showed phenotypic resistance to gentamicin. The sequence analysis of the sodC-1 gene from Salmonella isolates showed clear inter- and intra-subspecies phylogenetic segregation.

CONCLUSIONS

Fayoumi chickens and pigeons could act as reservoirs of MDR Salmonella.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the possible emergence of Salmonella subspecies salamae with zoonotic potential.