Prevalence, antimicrobial resistance and virulence genes characterization of nontyphoidal Salmonella isolated from retail chicken meat shops in Northern India

Immuno-PCR in the Analysis of Food Contaminants

Food safety is a significant issue of global concern. Consumer safety and government regulations drive the need for the accurate analysis of food contaminants, residues and other chemical constituents of concern. Traditional methods for the detection of food contaminants often present challenges, including lengthy processing times and food matrix interference; they often require expensive equipment, skilled personnel or have limitations in sensitivity or specificity. Developing novel analytical methods that are sensitive, specific, accurate and rapid is therefore crucial for ensuring food safety and the protection of consumers. The immuno-polymerase chain reaction (IPCR) method offers a promising solution in the analysis of food contaminants by combining the specificity of conventional immunological methods with the exponential sensitivity of PCR amplification. This review evaluates the current state of IPCR methods, describes a variety of existing IPCR formats and explores their application in the analysis of food contaminants, including pathogenic bacteria and their toxins, viruses, mycotoxins, allergens, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, phthalic acid esters, pesticides, antibiotics and other food contaminants. Depending on the type of analyte, either sandwich or competitive format IPCR methods are predominantly used. This review also examines limitations of current IPCR methods and explores potential advancements for future implementation in the field of food safety.

Antibiotic-Resistant Salmonella Enteritidis in Raw Chicken Meat of Dhaka City, Bangladesh

Foodborne zoonotic Salmonella is transmitted through contaminated meat, milk, and eggs. This study is aimed at investigating the antimicrobial resistance (AMR) profile of Salmonella Enteritidis isolated from raw chicken meat in Dhaka City, Bangladesh. Two hundred raw chicken meat samples were aseptically collected from 20 retail markets located in Dhaka City, and the isolated Salmonella species were identified based on their morphological, cultural, biochemical, and molecular characterization by polymerase chain reaction (PCR). The primer sets of the InvA and Enteritidis-specific STM3098 gene were used for the PCR detection of Salmonella species and S. Enteritidis, respectively. The isolates were then screened for AMR phenotypically and the presence of the tetracycline resistance (TetA) gene. The prevalence of Salmonella species and S. Enteritidis was 22.5% (n = 45/200) and 18.5% (n = 37/200), respectively. However, the prevalence was constant across all the sample markets (p > 0.05). Tetracycline, amoxicillin, and ampicillin resistance was phenotypically present in all isolates (100%). Furthermore, approximately 70%, 49%, and 30% of S. Enteritidis showed resistance against erythromycin, amoxicillin/clavulanic acid, and ciprofloxacin, respectively. However, S. Enteritidis were sensitive to gentamicin (86.5%), meropenem (64.9%), ciprofloxacin (62.2%), and ceftriaxone (59.5%). The TetA gene, which causes AMR against tetracycline, was shown to be present in all phenotypically resistant Salmonella species. Multiple antibiotic resistance index (MARI) ranged between 0.3 and 0.8. Overall, multidrug resistant (MDR) Salmonella Enteritidis emerged in the chicken meat along with the presence of a resistance gene that is a threat to human health. Therefore, action must be taken to stop the spread of AMR.

Genomic Differences in Antimicrobial Resistance and Virulence Among Key Salmonella Strains of Serogroups B and D1 in Brazilian Poultry

Salmonella is a significant threat to Brazilian poultry, causing economic losses and public health risks. This study analyzed 15 Salmonella isolates along with 45 retrieved complete genomes, including serovars Gallinarum, Pullorum, Enteritidis, Typhimurium, and Heidelberg. Biochemical characterization, antimicrobial susceptibility testing, whole-genome sequencing, and comparative genomics were performed. The studied strains exhibited high levels of antimicrobial resistance, particularly to tilmicosin, penicillin/novobiocin, nalidixic acid, and streptomycin. Genomic analysis revealed diverse virulence factors and antibiotic resistance genes (ARGs), with zoonotic strains showing higher virulence compared to avian-adapted strains. Multiple plasmid types carrying ARGs were identified, highlighting the potential for horizontal gene transfer. Pangenomic and phylogenomic analyses differentiated Salmonella strains from serogroup D1 from those from serogroup B. These findings emphasize the need for comprehensive surveillance and control measures to mitigate the impact of Salmonella on both animal and human health in Brazil.

Characterization of novel mutations involved in the development of resistance to colistin in Salmonella isolates from retail pork in Shanghai, China

Salmonella is an important foodborne pathogen that poses a significant threat to food safety. This study aims to assess the prevalence, genomic features, and colistin-resistant mechanisms of Salmonella isolates collected from 118 retail pork samples from January 2021 to January 2022 in Shanghai, China. Overall, 46 (39.0 %, 46/118) Salmonella isolates were collected, which were identified as 12 serotypes by genomic analysis, including Salmonella Typhimurium (n = 17) and Salmonella London (n = 6). Antimicrobial resistance profiling revealed that the resistance rate of these isolates to colistin was 13.0 % (6/46), while 60.9 % (28/46) exhibited multidrug-resistant. It was found that there were 51 distinct antimicrobial resistance genes in these 46 isolates, which were predominantly associated with resistance to aminoglycosides, fluoroquinolones, and β-lactams. More importantly, among six colistin-resistant isolates, two isolates (Salmonella Schwarzengrund and Salmonella Indiana) were found to carry the mcr-1 gene. The mechanism of resistance in the remaining four colistin-resistant isolates was further studied, and it was found that there were nine amino acid substitutions in PmrAB. It was demonstrated by site-directed mutagenesis that novel substitutions G53W in PmrA and I83V in PmrB led to colistin resistance in Salmonella (MIC = 2 or 4 μg/mL). Analysis results by real-time quantitative PCR and mass spectrometry indicated that the mutants PmrAG53W and PmrBI83V displayed higher expression levels of the gene pmrE than in the parental strain. This upregulation resulted in an increase in the production of 4-amino-4-deoxy-l-arabinose (L-Ara4N) that modified lipid A, thereby conferring resistance to colistin. These findings demonstrated that there was a high prevalence of MDR Salmonella isolates in retail pork in Shanghai, and the substitution G53W in PmrA and I83V in PmrB were independent factors contributing to the development of resistance to colistin in Salmonella via modification of lipid A with L-Ara4N.

Systematic Review and Meta-Analysis on Prevalence and Antimicrobial Resistance Patterns of Important Foodborne Pathogens Isolated from Retail Chicken Meat and Associated Environments in India

The chicken value chain, a vital part of the global food supply, also represents a significant public health concern due to the risk of foodborne pathogens, particularly in low- and middle-income countries (LMICs) such as India. This systematic review and meta-analysis aimed to assess the prevalence of significant bacterial pathogens including Salmonella spp., Campylobacter spp., Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Clostridium perfringens, and Klebsiella pneumonia. in retail chicken meat and associated environments and the antimicrobial resistance based on the articles published between January 2010-December 2023. The research adhered to the guidelines in the 'Preferred Reporting Items for Systematic Review and Meta-Analysis' (PRISMA). Based on 90 included studies, S. aureus showed the highest pooled prevalence (56%; 95% CI: 38-74%), followed by E. coli (50%; 95% CI: 37-64%), C. perfringens (35%; 95% CI: 10-65%), and K. pneumoniae (21%; 95% CI: 7-38%). Salmonella spp. (95% CI: 11-26%) and Campylobacter spp. (95% CI: 11-27%) exhibited similar prevalence rates at 18%, while L. monocytogenes had the lowest prevalence at 13% (95% CI: 1-33%). A sensitivity analysis was subsequently conducted to assess the impact of influential studies, and the pooled prevalence of each pathogen was recalculated after removing these studies to ensure the robustness of the results. The pathogens, specifically Salmonella spp. and Campylobacter spp., displayed high levels of resistance to medically important antimicrobials (erythromycin, tetracycline, ciprofloxacin, colistin), a potential threat to human health. This study advocates for a collaborative and comprehensive approach, reflecting the multifaceted nature of the issue, and highlighting the importance of a holistic strategy to safeguard public health and maintain antibiotic effectiveness in the face of emerging challenges.

The genomic diversity and antimicrobial resistance of Non-typhoidal Salmonella in humans and food animals in Northern India

Introduction

Non-typhoidal Salmonella (NTS) serovars are the leading global cause of gastroenteritis and have established reservoirs in food animals.

Gap statement

Due to a lack of surveillance, there is limited information on the distribution of NTS serovars in India.

Aim

Here, we investigated the epidemiology, sequence types, serovar distribution, phylogenetic relatedness, and antimicrobial resistance patterns of NTS in humans and animals across a large geographic area in Northern India.

Methodology

We collected stool samples from patients with diarrhea who presented to 14 laboratories in Chandigarh and from five states in India (Punjab, Haryana, Uttarakhand, Himachal Pradesh, and Rajasthan). We sequenced the genomes and analyzed 117 NTS organisms isolated from humans and animals. Minimum inhibitory concentrations (MICs) were estimated using a Vitek2 system.

Results

The prevalence of NTS in participants presenting to our study with diarrhea was 1.28 %, affecting all age groups. All NTS caused moderate to severe diarrhea. We found a high diversity of serovars with considerable serovar and sequence types (STs) overlap and phylogenetic closeness between isolates from human infections and food animals. We report serovars such as S. Agona, S. Bareilly, S. Kentucky, S. Saintpaul, and S. Virchow, causing human infections from north India for the first time. Among the different food-producing animals, pigs appeared to be a key source of human infections. Twenty-eight percent (28 %) of the NTS isolates were multi-drug resistant (MDR), and human isolates showed a higher proportion of resistance. A higher level of contamination of meat samples in our study (8.4 %) potentially suggests a close association of NTS serovars with the food chain and high transmission risk in north India.

Conclusions

This study provides information on AMR genes and plasmid replicons associated with different serovars and highlights the role of food animals in AMR dissemination in our region.

Contribution of veterinary sector to antimicrobial resistance in One Health compendium: an insight from available Indian evidence

The application of antibiotics in the poultry and veterinary sectors is very common practice in India. Owing to the seriousness of antimicrobial resistance (AMR), the present study has illustrated the overall scenario of AMR in the poultry and veterinary sectors in India through an in-depth scoping review and key informant interview (KII). In the poultry sector, most of the studies reviewed have reported resistant bacteria isolated from chicken meat, eggs, cloacal swabs, and fecal samples, and only a few have reported the presence of resistant bacteria in and around the environment of poultry farms. The major resistant bacteria that have been reported are E. coli, Salmonella spp., S. aureus, Campylobacter jejuni, and K. pneumoniae. These bacterial isolates exhibited resistance to various antibiotics, such as azithromycin (21.43%), tetracycline (11.30-100%), chloramphenicol (4.76-100%), erythromycin (75-83.33%), ciprofloxacin (5.7-100%), gentamicin (17-100%), amikacin (4.76%), cotrimoxazole (42.2-60%), trimethoprim (89.4%), ceftriaxone (80%), and cefotaxime (14.29-70%). Like the poultry sector, different antibiotics are also used for treating clinical and subclinical bovine mastitis, which is one of the major problems plaguing the dairy sector. Several AMR bacterial strains, such as E. coli, Staphylococcus aureus, S. epidermidis, and Klebsiella pneumoniae, have been reported by many researchers and showed resistance against tetracycline (74%), oxytetracycline (47.37%), ciprofloxacin (51%), streptomycin (57.89%), cephalosporin (100%), and trimethoprim (70%). The KIIs have revealed several reasons behind these AMR scenarios, of which the growing need for the production of food animals and their products with inadequate infrastructure and a lack of proper knowledge on farm management among the farmers are the major ones. Though several government legislations and policies have been laid down, proper implementation of these policies, strict surveillance on antibiotic application in the poultry and veterinary sectors, awareness generation among farmers, and infrastructure development can help minimize the development and transmission of AMR bacteria within and from these sectors.

Prevalence, Molecular Detection, and Antimicrobial Resistance of Salmonella Isolates from Poultry Farms across Central Ethiopia: A Cross-Sectional Study in Urban and Peri-Urban Areas

A cross-sectional study was conducted to assess the prevalence, molecular detection, and antimicrobial resistance of Salmonella isolates within 162 poultry farms in selected urban and peri-urban areas of central Ethiopia. A total of 1515 samples, including cloacal swabs (n = 763), fresh fecal droppings (n = 188), litter (n = 188), feed (n = 188), and water (n = 188), were bacteriologically tested. The molecular detection of some culture-positive isolates was performed via polymerase chain reaction (PCR) by targeting spy and sdfl genes for Salmonella Typhimurium and Salmonella Enteritidis, respectively. Risk factors for the occurrence of the bacterial isolates were assessed. Antimicrobial susceptibility testing of PCR-confirmed Salmonella isolates was conducted using 12 antibiotics. In this study, it was observed that 50.6% of the farms were positive for Salmonella. The overall sample-level prevalence of Salmonella was 14.4%. Among the analyzed risk factors, the type of production, breed, and sample type demonstrated a statistically significant association (p < 0.05) with the bacteriological prevalence of Salmonella. The PCR test disclosed that 45.5% (15/33) and 23.3% (10/43) of the isolates were positive for genes of Salmonella Typhimurium and Salmonella Enteritidis, respectively. The antimicrobial susceptibility test disclosed multi-drug resistance to ten of the tested antibiotics that belong to different classes. Substantial isolation of Salmonella Typhimurium and Salmonella Enteritidis in poultry and on poultry farms, along with the existence of multi-drug resistant isolates, poses an alarming risk of zoonotic and food safety issues. Hence, routine flock testing, farm surveillance, biosecurity intervention, stringent antimicrobial use regulations, and policy support for the sector are highly needed.

Prevalence, antibiotic resistance, virulence genes and molecular characteristics of Salmonella isolated from ducks and wild geese in China

Salmonella is a major foodborne pathogen and the cause of significant morbidity and mortality via consumption of contaminated meat and meat-products. The prevalence of Salmonella in ducks and wild geese in China are poorly characterized and these sources represent a potential pool that could be transferred to farm-reared fowl. In this study, we isolated 335 (18.3%) Salmonella from 1830 samples and identified 24 serotypes and most prevalent were Salmonella Indiana, Salmonella Kentucky and Salmonella Typhimurium. Whole genome sequencing revealed the presence of the dominant sequence types ST17, ST198 and ST19 for these three serotypes, respectively. In addition, these isolates were most likely clonally spread across different regions while S. Kentucky also crossed the species barrier. The majority of the Salmonella isolates possessed β-lactam and fluoroquinolone resistance and these were consistent with antibiotic resistance gene profiles. We also identified 8 plasmid replicon types and all isolates possessed virulence genes and the numbers were greatest for S. Enteritidis and S. Typhimurium isolates. This study provides novel insights concerning the epidemiology of Salmonella in ducks and wild geese and provides basic data for public health screening and management.

Salmonella enterica serovars linked with poultry in India: antibiotic resistance profiles and carriage of virulence genes

Salmonella is an important poultry pathogen with zoonotic potential. Being a foodborne pathogen, Salmonella-contaminated poultry products can act as the major source of infection in humans. In India, limited studies have addressed the diversity of Salmonella strains of poultry origin. This study represented 26 strains belonging to Salmonella serovars Typhimurium, Infantis, Virchow, Kentucky, and Agona. The strains were tested for resistance to 14 different antimicrobial agents using the Kirby-Bauer disk-diffusion assay. The presence of the invA, hilA, agfA, lpfA, sopE, and spvC virulence genes was assessed by polymerase chain reaction (PCR), and the genetic diversity was assessed by Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR). The highest resistance to tetracycline (n = 17; 65.38%) followed by nalidixic acid (n = 16; 61.53%) was detected among the strains. Among the strains (n = 17) phenotypically resistant to tetracycline, 94% (n = 16) were also positive for the tetA gene. Based on the presence of virulence genes, the strains were characterized into three virulence profiles (PI, P2, and P3). Among the investigated virulence genes, invA, hilA, agfA, and lpfA were present in all strains. The sopE gene was mostly associated with serovars Virchow (n = 3; 100%) and Typhimurium (n = 8; 80%), whereas spvC gene was exclusive for two Typhimurium strains that lacked sopE gene. ERIC-PCR profiling indicated clusters correlating their serovar, geographical, and farm origins. These results demonstrate that Salmonella isolates with a wide genetic range, antibiotic resistance, and virulence characteristics can colonize poultry. The presence of such strains is crucial for both food safety and public health.

Prevalence of Antimicrobial Resistance in Escherichia coli and Salmonella Species Isolates from Chickens in Live Bird Markets and Boot Swabs from Layer Farms in Timor-Leste

The rapid emergence of antimicrobial resistance is a global concern, and high levels of resistance have been detected in chicken populations worldwide. The purpose of this study was to determine the prevalence of antimicrobial resistance in Escherichia coli and Salmonella spp. isolated from healthy chickens in Timor-Leste. Through a cross-sectional study, cloacal swabs and boot swabs were collected from 25 live bird markets and two layer farms respectively. E. coli and Salmonella spp. from these samples were tested for susceptibility to six antimicrobials using a disk diffusion test, and a subset was tested for susceptibility to 27 antimicrobials using broth-based microdilution. E. coli and Salmonella spp. isolates showed the highest resistance towards either tetracycline or ampicillin on the disk diffusion test. E. coli from layer farms (odds ratio:5.2; 95%CI 2.0-13.1) and broilers (odds ratio:18.1; 95%CI 5.3-61.2) were more likely to be multi-drug resistant than those from local chickens. Based on the broth-based microdilution test, resistance to antimicrobials in the Timor-Leste Antimicrobial Guidelines for humans were low, except for resistance to ciprofloxacin in Salmonella spp. (47.1%). Colistin resistance in E. coli was 6.6%. Although this study shows that antimicrobial resistance in chickens was generally low in Timor-Leste, there should be ongoing monitoring in commercial chickens as industry growth might be accompanied with increased antimicrobial use.

Prevalence and antibiotic resistance of Salmonella in organic and non-organic chickens on the Eastern Shore of Maryland, USA

Introduction

Salmonella infections have been intensely increasing and becoming a universal public health crisis. This study investigated the prevalence of Salmonella in organic and non-organic chickens and the antimicrobial resistance profiles and virulence genes (invA, pagC, and spvC) in recovered Salmonella isolates.

Methods

Whole chicken carcasses [organic (n = 240) and non-organic (n = 240)] were obtained monthly for 1 year (n = 480) from a retail store on the Eastern Shore of Maryland. Salmonella isolation and identification were conducted by following the whole carcass enrichment method recommended by USDA-FSIS. Confirmed Salmonella isolates (organic n = 76; non-organic n = 137) were serotyped and tested for antibiotic susceptibility and virulence genes using standard methods.

Results

Forty-nine percent (237/480) of the carcasses were positive for Salmonella. Organic and non-organic positivity rates were 37.1 and 61.8%, respectively. A significantly higher Salmonella contamination was observed in non-organic chickens (p < 0.05). The most common serovars were Salmonella Kentucky (47%), S. Infantis (35%), S. Enteritidis (6%), S. Typhimurium (5%), and S. Blockley (4%). Isolates were frequently resistant to at least one antibiotic (91.24%) or multidrug resistant (45.54%). Resistance was observed to tetracycline (82.8%), minocycline (42.3%), nitrofurantoin (40.3%), cefazolin (38.3%), ampicillin (32.1%), and ceftriaxone (26%). All isolates were susceptible to fluoroquinolone, carbapenem, and glycylcycline. The majority of isolates (99.1%) possessed at least one of three virulence genes of concern and 4.2% tested positive for all three. Ninety-five, 89, and 6.6% of isolates contained invA, pagC, and spvC genes, respectively. The spvC gene was not detected in serovars recovered from organic chickens though 92% and 82% of isolates were positive for invA and pagC. The frequency of Salmonella recovered from non-organic chickens possessing invA, pagC, and spvC genes were 97.1, 89.8, and 10.2%, respectively. Detection of invA and pagC genes showed no significant difference (p > 0.05) between organic and non-organic chickens but a significantly higher spvC gene (p < 0.05) was detected in non-organic chickens due to the majority of S. Enteritidis (92.3%) exclusively recovered from non-organic chicken carried spvC gene.

Discussion

This study reveals a high prevalence of Salmonella in both organic and non-organic chickens, which exhibit resistance to vital antibiotics and carry virulence genes, thereby creating a potential risk of salmonellosis.

Resistance and Virulence Surveillance in Escherichia coli Isolated from Commercial Meat Samples: A One Health Approach

Escherichia coli is a key indicator of food hygiene, and its monitoring in meat samples points to the potential presence of antimicrobial-resistant strains capable of causing infections in humans, encompassing resistance profiles categorized as serious threats by the Centers for Disease Control and Prevention (CDC), such as Extended-Spectrum Beta-Lactamase (ESBL)-a problem with consequences for animal, human, and environmental health. The objective of the present work was to isolate and characterize ESBL-producing E. coli strains from poultry, pork, and beef meat samples, with a characterization of their virulence and antimicrobial resistance profiles. A total of 450 meat samples (150 chicken, 150 beef, and 150 pork) were obtained from supermarkets and subsequently cultured in medium supplemented with cefotaxime. The isolated colonies were characterized biochemically, followed by antibiogram testing using the disk diffusion technique. Further classification involved biofilm formation and the presence of antimicrobial resistance genes (blaCTX-M, AmpC-type, mcr-1, and fosA3), and virulence genes (eaeA, st, bfpA, lt, stx1, stx2, aggR, iss, ompT, hlyF, iutA, iroN, fyuA, cvaC, and hylA). Statistical analysis was performed via the likelihood-ratio test. In total, 168 strains were obtained, with 73% originating from chicken, 22% from pork, and 17% from beef samples. Notably, strains exhibited greater resistance to tetracycline (51%), ciprofloxacin (46%), and fosfomycin (38%), apart from β-lactams. The detection of antimicrobial resistance in food-isolated strains is noteworthy, underscoring the significance of antimicrobial resistance as a global concern. More than 90% of the strains were biofilm producers, and strains carrying many ExPEC genes were more likely to be biofilm formers (OR 2.42), which increases the problem since the microorganisms have a greater chance of environment persistence and genetic exchange. Regarding molecular characterization, bovine samples showed a higher prevalence of blaCTX-M-1 (OR 6.52), while chicken strains were more likely to carry the fosA3 gene (OR 2.43, CI 1.17-5.05) and presented between 6 to 8 ExPEC genes (OR 2.5, CI 1.33-5.01) compared to other meat samples. Concerning diarrheagenic E. coli genes, two strains harbored eae. It is important to highlight these strains, as they exhibited both biofilm-forming capacities and multidrug resistance (MDR), potentially enabling colonization in diverse environments and causing infections. In conclusion, this study underscores the presence of β-lactamase-producing E. coli strains, mainly in poultry samples, compared to beef and pork samples. Furthermore, all meat sample strains exhibited many virulence-associated extraintestinal genes, with some strains harboring diarrheagenic E. coli (DEC) genes.

Prevalence, antibiotic susceptibility and genomic analysis of Salmonella from retail meats in Shaanxi, China

Salmonella is a major foodborne pathogen that poses a substantial risk to food safety and public health. This study aimed to assess the prevalence, antibiotic susceptibility, and genomic features of Salmonella isolates recovered from 600 retail meat samples (300 pork, 150 chicken and 150 beef) from August 2018 to October 2019 in Shaanxi, China. Overall, 40 (6.67 %) of 600 samples were positive to Salmonella, with the highest prevalence in chicken (21.33 %, 32/150), followed in pork (2.67 %, 8/300), while no Salmonella was detected in beef. A total of 10 serotypes and 11 sequence types (STs) were detected in 40 Salmonella isolates, with the most common being ST198 S. Kentucky (n = 15), ST13 S. Agona (n = 6), and ST17 S. Indiana (n = 5). Resistance was most commonly found to tetracycline (82.50 %), followed by to ampicillin (77.50 %), nalidixic acid (70.00 %), kanamycin (57.50 %), ceftriaxone (55.00 %), cefotaxime (52.50 %), cefoperazone (52.50 %), chloramphenicol (50.00 %), levofloxacin (57.50 %), cefotaxime (52.50 %), kanamycin (52.50 %), chloramphenicol (50.00 %), ciprofloxacin (50.00 %), and levofloxacin (50.00 %). All ST198 S. Kentucky isolates showed multi-drug resistance (MDR; ≥3 antimicrobial categories) pattern. Genomic analysis showed 56 distinct antibiotic resistance genes (ARGs) and 6 target gene mutations of quinolone resistance determining regions (QRDRs) in 40 Salmonella isolates, among which, the most prevalent ARG types were related to aminoglycosides and β-lactams resistance, and the most frequent mutation in QRDRs was GyrA (S83F) (47.5 %). The number of ARGs in Salmonella isolates showed a significant positive correlation with the numbers of insert sequences (ISs) and plasmid replicons. Taken together, our findings indicated retail chickens were seriously contaminated, while pork and beef are rarely contaminated by Salmonella. Antibiotic resistance determinants and genetic relationships of the isolates provide crucial data for food safety and public health safeguarding.

Isolation and characterization of vB_SenS_Ib_psk2 bacteriophage against drug-resistant Salmonella enterica serovar Kentucky

Salmonella enterica serovar Kentucky is one of the food-borne zoonotic pathogens which is isolated in high frequency from poultry meat in the recent decades and is known for its multidrug resistance. The current study was aimed to isolate and characterize a bacteriophage against S. enterica serovar Kentucky isolate, 5925, which showed resistance to at least seven antibiotics and to study its efficiency to decontaminate S. Kentucky from chicken skin. The bacteriophage against S. enterica serovar Kentucky was isolated and was named vB_SenS_Ib_psk2 representing the place, source, and host. Electron microscopy revealed that the phage possesses isometric head and contractile tail, indicative of Siphoviridae family. Molecular detection of major capsid protein E gene yielded 511 bp, and NCBI blast analysis revealed that the phage belonged to the genus chivirus. The optimum temperature and pH for phage survival and multiplication were found to be - 20 to 42 °C and 6-10, respectively. One-step growth curve experiment of vB_SenS_Ib_psk2 revealed a latent period of 20 min and burst size of 253 phages/bacterial cell. The host susceptibility studies revealed that 83% of MDR isolates of S. enterica were susceptible to vB_SenS_Ib_psk2. Artificial spiking studies on chicken skin revealed that high multiplicity of infection (MOI) of phages of 106 pfu/mL is required for significant reduction (p ≤ 0.01) of bacterial concentration (0.14 ± 0.04) after 24-h incubation at 8 °C compared to group 1 (2.55 ± 0.89 cfu/mL).

Detection of Salmonella DNA and drug-resistance mutation by PCR-based CRISPR-lbCas12a system

Salmonella is an important foodborne pathogen, which can cause serious public health problems. Rapid and accurate detection of Salmonella infection and drug resistance mutations in patients will provide timely guidance for clinical treatment and avoid disease progression and other related clinical problems. Here, we established a highly sensitive and quick method for Salmonella and drug resistance mutation detection based on polymerase chain reaction (PCR) and CRISPR-lbCas12a system and evaluated its practicability with clinical samples.Specific CRISPR RNAs (crRNAs) and primers are designed for Salmonella DNA and parC gene S80I mutation diagnosis. CrRNAs with and without phosphorylated modification and different crRNA preparation methods are used to assess the effect on the detection system. After optimization, we detected as low as one copy of Salmonella DNA and drug resistance mutation parC S80I with the Salmonella DNA standard. For 94 clinical samples, this method also showed high sensitivity (100%, 95% CI: 84.98-100%) and specificity (98.48%, 95% CI: 90.73-99.92%) with less time (3 h) than plate culture (16 h) and conventional antimicrobial susceptibility testing (over 16 h). Besides, one parC S80I mutant strain was detected, which is consistent with the result of DNA sequencing. Taken together, we established a highly sensitive and specific method for Salmonella infection and parC S80I drug resistance mutation detection with fewer reagents and ordinary instruments. This assay has wide application prospects for fast detection of pathogen (bacterium and virus) infection, drug resistance determination, and proper treatment guidance.

The occurrence and molecular detection of mcr-1 and mcr-5 genes in Enterobacteriaceae isolated from poultry and poultry meats in Malaysia

The advent of antimicrobials-resistant (AMR), including colistin-resistant bacteria, poses a significant challenge to animal and human health, food safety, socio-economic growth, and the global environment. This study aimed to ascertain the colistin resistance prevalence and molecular mechanisms of colistin resistance in Enterobacteriaceae. The colistin resistance was determined using broth microdilution assay, PCR; and Sanger sequencing of mcr genes responsible for colistin resistance in Enterobacteriaceae (n = 627), including Escherichia coli (436), Salmonella spp. (n = 140), and Klebsiella pneumoniae (n = 51), obtained from chicken and chicken meats. Out of 627 Enterobacteriaceae, 8.6% of isolates exhibited colistin resistance phenotypically. Among these colistin resistant isolates, 9.3% (n = 37) were isolated from chicken meat, 7.2% (n = 11) from the cloacal swab of chicken and 7.9% (n = 6) from the litter samples. Overall, 12.96% of colistin-resistant isolates were positive with mcr genes, in which mcr-1 and mcr-5 genes were determined in 11.11% and 1.85% of colistin-resistant isolates, respectively. The E. coli isolates obtained from chicken meats, cloacal swabs and litter samples were found positive for mcr-1, and Salmonella spp. originated from the chicken meat sample was observed with mcr-5, whereas no mcr genes were observed in K. pneumoniae strains isolated from any of the collected samples. The other colistin resistance genes, including mcr-2, mcr-3, mcr-4, mcr-6, mcr-7, mcr-8, mcr-9, and mcr-10 were not detected in the studied samples. The mcr-1 and mcr-5 genes were sequenced and found to be 100% identical to the mcr-1 and mcr-5 gene sequences available in the NCBI database. This is the first report of colistin resistance mcr-5 gene in Malaysia which could portend the emergence of mcr-5 harboring bacterial strains for infection. Further studies are needed to characterize the mr-5 harbouring bacteria for the determination of plasmid associated with mcr-5 gene.

Antimicrobial Resistance Profiles and Co-Existence of Multiple Antimicrobial Resistance Genes in mcr-Harbouring Colistin-Resistant Enterobacteriaceae Isolates Recovered from Poultry and Poultry Meats in Malaysia

The co-existence of the colistin resistance (mcr) gene with multiple drug-resistance genes has raised concerns about the possibility of the development of pan-drug-resistant bacteria that will complicate treatment. This study aimed to investigate the antibiotic resistance profiles and co-existence of antibiotic resistance genes among the colistin-resistant Enterobacteriaceae isolates recovered from poultry and poultry meats. The antibiotic susceptibility to various classes of antibiotics was performed using the Kirby-Bauer disk diffusion method and selected antimicrobial resistance genes were detected using PCR in a total of 54 colistin-resistant Enterobacteriaceae isolates including Escherichia coli (E. coli) (n = 32), Salmonella spp. (n = 16) and Klebsiella pneumoniae (K. pneumoniae) (n = 6) isolates. Most of the isolates had multi-drug resistance (MDR), with antibiotic resistance against up to seven classes of antibiotics. All mcr-harbouring, colistin-resistant Enterobacteriaceae isolates showed this MDR (100%) phenotype. The mcr-1 harbouring E. coli isolates were co-harbouring multiple antibiotic resistance genes. The seven most commonly identified resistance genes (^blaTEM, tetA, floR, aac-3-IV, aadA1, fosA, aac(6_)-lb) were detected in an mcr-1-harbouring E. coli isolate recovered from a cloacal swab. The mcr-5 harbouring Salmonella spp. isolate recovered from poultry meats was positive for ^blaTEM, tetA, floR, aac-3-IV, fosA and aac(6_)-lb genes. In conclusion, the colistin-resistant Enterobacteriaceae with mcr genes co-existing multiple clinically important antimicrobial resistance genes in poultry and poultry meats may cause potential future threats to infection treatment choices in humans and animals.

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.

Comprehensive profiling of serotypes, antimicrobial resistance and virulence of Salmonella isolates from food animals in China, 2015-2021

Introduction

Salmonella is a ubiquitous foodborne pathogen and mainly transmitted to human farm-to-fork chain through contaminated foods of animal origin.

Methods

In this study, we investigated the serotypes, antimicrobial resistance and virulence of Salmonella from China.

Results

A total of 617 Salmonella isolates were collected from 4 major food animal species across 23 provi nces in China from 2015-2021. Highest Salmonella prevalence were observed in Guangdong (44.4%) and Sandong (23.7%). Chickens (43.0%) was shown to be the major source of Salmonella contamination, followed by pigs (34.5%) and ducks (18.5%). The number of Salmonella increased significantly from 5.51% to 27.23% during 2015-2020. S. Derby (17.3%), S. Enteritidis (13.1%) and S. Typhimurium (11.4%) were the most common serotypes among 41 serotypes identifiedin this study. Antibiotic susceptibility testing showing that the majority of the Salmonella isolates were resistant to neomycin (99.7%), tetracycline (98.1%), ampicillin (97.4%), sulfadiazine/trimethoprim (97.1%), nalidixic acid (89.1%), doxycycline (83.1%), ceftria xone (70.3%), spectinomycin (67.7%), florfenicol (60.0%), cefotaxime (52.0%) and lomefloxacin (59.8%). The rates of resistance to multiple antibiotics in S. Derby and S.Typhimurium were higher than that in S. Enteritidis. However, the rate of resistance to fosfomycin were observed from higher to lower by S. Derby, S. Enteritidis, and S. Typhimurium. Biofilm formation ability analysis found that 88.49%of the Salmonella were able to produce biofilms, of which 236 Salmonella isolates were strong biofilm producer. Among the 26 types of antibiotics resistance genes (ARGs) were identified in this study, 4 ARGs (tetB,sul2,aadA2, and aph(3')-IIa) were highly prevalent. In addition, 5 β-lactam resistance genes (bla _TEM, bla _SHV, bla _CMY-2, bla _CTX-M, and bla _OXA) and 7 quinolone resistance genes (oqxA, oqxB, qnrB, qnrC, qnrD, qnrS, and qeqA) were detected among these isolates. 12 out of 17 virulence genes selected in this study were commonly presented in the chromosomes of tested isolate, with a detection rate of over 80%, including misL, spiA, stn, pagC, iroN, fim, msgA, sopB, prgH, sitC, ttrC, spaN.

Discussion

This study provided a systematical updating on surveillance on prevalence of Salmonella from food animals in China, shedding the light on continued vigilance for Salmonella in food animals.

Antimicrobial resistance in bacteria isolated from the poultry production system in Nepal

SETTING

Twenty poultry farms in five provinces of Nepal were selected for studying bacterial pathogens and their antimicrobial resistance (AMR) patterns.

OBJECTIVE

To document the proportion of cloacal swabs collected from 3,230 broiler and 3,230 layer chickens from September to December 2021 that grew isolates of Escherichia coli, Enterococcus spp. and Salmonella spp. along with their AMR patterns.

DESIGN

This was a cross-sectional descriptive study.

RESULTS

In broiler birds, Enterococcus spp., Salmonella spp. and E. coli were identified in respectively 36%, 39% and 63% of swabs. In layer birds, Enterococcus spp., Salmonella spp. and E. coli were identified in respectively 31%, 48% and 60% of swabs. For both bird types, there was variation in bacterial prevalence between the regions. For all three bacterial isolates, the lowest antimicrobial resistance was found with amikacin. For the other nine antibiotics tested, >50% of bacterial isolates showed resistance; between 60% and 90% of isolates showed resistance to ciprofloxacin and trimethoprim-sulfamethoxazole. Multidrug resistance ranged from 45% to 46% for Salmonella spp., 37-44% for E. coli and 13-17% for Enterococcus spp.

CONCLUSION

This study shows that a large proportion of poultry in Nepal are infected with potentially pathogenic bacteria, and these are frequently resistant to commonly used antibiotics. Nepal urgently needs to implement corrective measures.

Detection and Molecular Identification of Salmonella Pathogenic Islands and Virulence Plasmid Genes of Salmonella in Xuzhou Raw Meat Products

ABSTRACT

Virulence genes expressed in Salmonella are a primary contributing factor leading to the high morbidity and mortality of salmonellosis in humans. The pathogenicity of Salmonella is mainly determined by the specific virulence factors that it carries. These factors also confer greater virulence and play a role in infection of a host and transmission of disease, and most Salmonella enterica can cause cross-infections between humans and animals. In this study, 265 samples in total were collected from a farmer's market and two supermarkets in Xuzhou, Jiangsu province, China, including 205 pork samples and 60 chicken samples. The suspected Salmonella isolates were isolated and identified using microbiological and molecular methods, and the confirmed isolates were used for serovar analysis and antimicrobial susceptibility testing. The virulence genes of Salmonella pathogenic islands (SPIs) and Salmonella virulence plasmids (Spv) in Salmonella-positive isolates were subsequently detected. Salmonella was isolated from 29.0% of samples, and all isolates were confirmed by PCR targeting the stn gene. Among the Salmonella isolates, resistance was most frequently observed against ciprofloxacin (84.4%), followed by tetracycline (71.4%) and streptomycin (68.8%). Resistance to amoxicillin-clavulanic acid (6.3%) and aztreonam (5%) was less commonly detected. The presence of the following virulence genes was determined by specific PCRs: hilA (SPI-1), sifA (SPI-2), misL (SPI-3), siiE (SPI-4), sopB (SPI-5), and spvC. The detection rate for SPI-1 to SPI-5 was 93.5, 87.0, 97.4, 97.4, and 97.4%, respectively. In addition, the detection rate of the spvC gene was 96.1%. Except for sopB (94.7%), all isolates of the dominant serovar S. enterica subsp.. enterica serovar Enteritidis contained all virulence genes from SPI-1 to SPI-5. This study demonstrated the epidemiological status of Salmonella in raw meat products in Xuzhou, and the complex antibiotic resistance and high isolation rate of virulence genes observed reveal many potential risks of which the findings presented herein will provide orientation to improve public health safeguards.

HIGHLIGHTS

Physiological Characteristics of Putative Enterobacteria Associated with Meat and Fish Available in Southern Brazilian Retail Markets: Antimicrobial Susceptibility, Toxic Metal Tolerance and Expression of Efflux Pumps

Multidrug-resistant (MDR) mesophilic facultatively anaerobic Gram-negative rods are a public health issue and their spread from animal-source foods to humans is of concern worldwide. Hence, the aim of this study was to examine the antibiotic susceptibility patterns and physiological aspects of such rods, including their tolerance to toxic metals and the screening of efflux pumps expressing isolates among enterobacteria isolated from meat (chicken, beef and pork) and fish samples acquired from retail establishments in a Brazilian urban Centre of over 2,300,000 inhabitants. The study revealed that 62.9% of isolated bacteria were resistant to at least one antimicrobial, of which 32.3% and 8.1% were resistant to one and two of the tested drugs, respectively. A resistance of up to six antimicrobials was also observed (0.9%). Out of the total amount, 22.7% were classified as MDR. Chicken was the meat that harbored most MDR isolates, and fish harbored the least. It was not possible to distinguish the different types of meat or fish considering the resistance patterns. The MDR isolates showed a higher tolerance to mercury and cadmium salts and the increased activity of the efflux mechanisms compared to other susceptible or resistant strains. In One Health. the perspective occurrence of putative MDR bacteria in fresh meat and fish draws attention to the antimicrobial resistance phenomenon in an open environment.

First report of multidrug-resistant Salmonella Infantis in broiler litter in Tolima, Colombia

Background and Aim:

Salmonella has been identified as one of the most widely distributed zoonotic pathogens in broiler litter. Multidrug-resistant strains have been isolated from salmonellosis outbreaks, compromising the success of their treatment. This study aimed to isolate and identify Salmonella spp. serovars in healthy broiler litter in Tolima (Colombia), determine their resistance to different antimicrobials, and detect genes associated with b-lactam resistance that could be useful to control Salmonella spp. in poultry.

Materials and Methods:

In total, 45 broiler litter samples were collected. Salmonella spp. was isolated and identified using selective and differential culture media and biochemical tests. Molecular confirmation of the pathogen was performed with the invA gene and serotyping by Kauffman–White scheme. Antimicrobial susceptibility to 15 antibiotics was determined by Kirby–Bauer method. In cefotaxime-resistant strains, blaCTX-M-F, blaCTX-M-1, blaCMY, and blaTEM genes were evaluated by polymerase chain reaction (PCR).

Results:

In total, 817 presumptive strains were obtained from xylose lysine deoxycholate and SalmonellaShigella agars and subcultured on xylose-lysine-tergitol 4 and MacConkey agars, from which 150 strains were isolated; 29 of these strains were presumptive for Salmonella spp. after performing biochemical tests and 16 were confirmed by PCR as Salmonella Infantis (15) and Gallinarum (1). All strains were found to be multiresistant to antibiotics, showing three different profiles and isolates resistant to cefotaxime, and the blaCTX-M gene was detected.

Conclusion:

This is the first study to isolate S. Infantis from broiler litter in Colombia. All isolates exhibited resistance to the evaluated antimicrobials, suggesting the misuse of antimicrobials in small- and medium-sized poultry farms. The presence of Salmonella enterica serovar Infantis is a public health problem. Thus, regular monitoring of poultry litter is recommended, as these bacteria can be transmitted to humans through animal products or contaminated environments.

Non-typhoidal Salmonella infections across India: emergence of a neglected group of enteric pathogens

Objective

Non-typhoidal Salmonellae (NTS) are a neglected group of enteric pathogens whose prevalence is increasing at alarming rates across India. The disease burden is being underestimated because of a lack of effective surveillance of NTS infections in the Indian population. This study depicts the acquisition of NTS infection, and its persistence and spread through a diverse range of hosts, including humans and animals, and food and environmental sources.

Methods

During the study period from 2016 to 2018, a total of 999 suspected NTS isolates were received from across India and were phenotypically and serologically characterized for the presence of NTS.

Results

Of the 999 isolates, 539 (53.95%) were confirmed as NTS, consisting of 17 different NTS serovars. The majority were isolated from human samples (n = 319, 59.18%), followed by food products (n = 99, 18.37%), animals (n = 83, 15.4%) and the environment (n = 38, 7.05%). Some predominant serovars obtained included S. Typhimurium (n = 167, 30.98%), S. Lindenberg (n = 135, 25.05%), S. Enteritidis (n = 56, 10.39%), S. Weltevreden (n = 44, 8.16%), S. Choleraesuis (n = 41, 7.61%) and S. Mathura (n = 33, 6.12%).

Conclusion

This study depicts the NTS disease burden across India, on the basis of the isolation of NTS serovars across diverse geographic locations. The emergence of newer or less common NTS serovars implicated in human infection poses a potential challenge to the healthcare system in India. Therefore, national and regional level surveillance is needed to implement effective control strategies and safeguard community health in India.

Virulence and antimicrobial resistance profile of non-typhoidal Salmonella enterica serovars recovered from poultry processing environments at wet markets in Dhaka, Bangladesh

The rapid emergence of virulent and multidrug-resistant (MDR) non-typhoidal Salmonella (NTS) enterica serovars is a growing public health concern globally. The present study focused on the assessment of the pathogenicity and antimicrobial resistance (AMR) profiling of NTS enterica serovars isolated from the chicken processing environments at wet markets in Dhaka, Bangladesh. A total of 870 samples consisting of carcass dressing water (CDW), chopping board swabs (CBS), and knife swabs (KS) were collected from 29 wet markets. The prevalence of Salmonella was found to be 20% in CDW, 19.31% in CBS, and 17.58% in KS, respectively. Meanwhile, the MDR Salmonella was found to be 72.41%, 73.21%, and 68.62% in CDW, CBS, and KS, respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namely invA, agfA, IpfA, hilA, sivH, sefA, sopE, and spvC. The S. Enteritidis and untyped Salmonella isolates harbored all virulence genes while S. Typhimurium isolates carried six virulence genes, except sefA and spvC. Phenotypic resistance revealed decreased susceptibility to ciprofloxacin, streptomycin, ampicillin, tetracycline, gentamicin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanic acid, and azithromycin. Genotypic resistance showed a higher prevalence of plasmid-mediated blaTEM followed by tetA, sul1, sul2, sul3, and strA/B genes. The phenotypic and genotypic resistance profiles of the isolates showed a harmonic and symmetrical trend. According to the findings, MDR and virulent NTS enterica serovars predominate in wet market conditions and can easily enter the human food chain. The chi-square analysis showed significantly higher associations among the phenotypic resistance, genotypic resistance and virulence genes in CDW, CBS, and KS respectively (p < 0.05).

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.

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.

Antimicrobial resistance in Indian isolates of non typhoidal Salmonella of livestock, poultry and environmental origin from 1990 to 2017

A retrospective antimicrobial resistance study of nontyphoidal Salmonella enterica isolates from India during 1990-2017 was conducted to study the microbial susceptibility to antibiotics. A total of 271 Salmonella enterica isolates from poultry (n = 146), farm animals (n = 55) and environmental sources (n = 70) were tested for susceptibility using 15 antimicrobial drugs. The drug classes include aminoglycosides, phenicols, cephalosporins, penicillins, carbapenems, fluoroquinolones, and sulphonamide-trimethoprim. Study revealed that overall, 133 (49.08%) of 271 isolates were resistant to ≥ 1 antimicrobial drugs and 81 (29.89%) out of 271 isolates were multidrug resistant (resistance to ≥ 3 drugs). Majority (68.96%) of Typhimurium serovars (n = 87) were susceptible to all antibiotics tested, whereas only 5% Kentucky serovars (n = 40) were pan susceptible. All the drugs revealed decreasing trend of susceptibility from 1990 towards 2017 except cephalosporins and carbapenems. Statistical analysis of association between time period and antimicrobial resistance revealed a significance of < 0.05. Molecular detection of genetic determinants associated with antimicrobial resistance revealed the presence of genes like class I integrons, sul1, sul2, catIII, cmlA, dfrA, bla_TEM, bla_AmpC in the resistant isolates. Furthermore, plasmid mediated quinolone resistant determinants like qnrD and qnrS were also reported in the current study.

Detection of virulence and extended spectrum β-lactamase genes in Salmonella by multiplex high-resolution melt curve real-time PCR assay

AIMS

Develop and standardize multiplex high-resolution melt curve (HRM) real-time PCR assays for simultaneous detection of Salmonella virulence and extended spectrum β-lactamase (ESBL) genes in food.

METHODS AND RESULTS

Two sets of multiplex real-time PCR assays targeting six virulence and three ESBL genes with internal amplification control were standardized. The first assay detected hilA, fimH, sipA, bla_TEM and bla_SHV, and the second detected invA, fimA, stn and bla_CMY . The PCR assays were validated with DNA samples from 77 different Salmonella strains. The assay specificity was tested with DNA from 47 non-Salmonella strains. Melt curve analyses showed distinct, well-separated melting peaks of each target gene detected by their respective melting temperatures (T_m ). Different food samples were spiked with 10, 10² and 10³  CFU/ml of Salmonella. The optimized assays were able to detect all target genes in concentrations of as low as 10 CFU/ml in 25 g foods within 10 h of enrichment.

CONCLUSIONS

Multiplex HRM real-time PCR assays can be used as rapid detection methods for detecting Salmonella in foods.

SIGNIFICANCE AND IMPACT OF STUDY

The assays developed in this study will allow for accurate detection of virulence and ESBL genes in Salmonella that are present in low concentrations in food samples.

Salmonella from Farm to Table: Isolation, Characterization, and Antimicrobial Resistance of Salmonella from Commercial Broiler Supply Chain and Its Environment

Antimicrobial resistance (AMR) in poultry production chain is one of the major food safety concerns due to indiscriminate usage of antibiotics and the presence of pathogens such as Salmonella which causes infections in various stages of production. In the present study, 182 samples were collected from commercial broiler supply chain, viz., three hatcheries (n = 29), three commercial broiler farms (CBF; n = 99), and three retail meat shops (RMS; n = 54), and used for isolation and identification of Salmonella using three different selective agar media and a selective enrichment medium followed by PCR confirmation targeting the hilA gene. The overall prevalence of Salmonella was 47/182 (25.82%), and a significantly higher (P < 0.05) prevalence was observed in retail meat shops (46.29%), CBF (19.19%), and hatcheries (10.34%). Comparison of three agar media for isolation of Salmonella revealed that all the media were equally selective. However, PCR amplification of hilA gene fragment was significantly higher (P < 0.01) in selective enrichment culture tetrathionate brilliant green bile broth (TTB) as compared to all solid (agar-based) media. Susceptibility pattern against most frequently used antibiotics revealed that 100% of the isolates were resistant to at least one antibiotic. High resistance was observed for doxycycline (94.34%), followed by cefpodoxime (84.91%), ciprofloxacin (72.64%), gentamicin (65.09%), enrofloxacin (61.32%), colistin sulphate (40.42%), amikacin (34.91%), ampicillin (33.96%), neomycin (33.02), cefotaxime (30.19%), ceftazidime (29.25%), trimethoprim-sulfamethoxazole (23.58%), amoxicillin+clavulanic acid (21.70%), and chloramphenicol (12.26%); 16.98% of the isolates were ex-tended spectrum β-lactamase (ESBL) producers, and 76.41% were multidrug resistant (MDR). MDR Salmonella were significantly higher (P < 0.01) in RMS (91.66%) followed by CBF (82.75%), whereas no MDR isolates were present in the isolates from hatcheries. The results indicated a higher prevalence of Salmonella and AMR for commonly used antibiotics in the complete broiler supply chain, especially RMS and CBF. Also, this study idicated that TTB enrichment followed by PCR and colony PCR was found to be rapid, specific and time-saving method.

Occurrence and antimicrobial resistance of Salmonella isolated from retail meats in Anhui, China

Salmonella is considered one of the major foodborne pathogens associated with severe infections. Little attempt has been focused on the distribution of Salmonella in retail meats and the analysis of its phenotypic characteristics in Anhui Province. The aim of this study was to characterize the prevalence of Salmonella serovars, antimicrobial susceptibility, antimicrobial resistance genes, and virulence genes in Salmonella recovered from retail meats in Anhui, China. Out of the 120 samples collected from supermarket chains and open-air markets, 16 samples (13.3%) were positive for Salmonella, of which Salmonella enterica serovars Enteritidis and Typhimurium were the common serotypes. Significant differences in incidence were found between supermarket chains and open-air markets (p < 0.05). Overall, all 16 isolates were resistant to at least two tested antimicrobials, while 12 isolates showed multiple antimicrobial resistant phenotypes. High resistance was observed for ampicillin (87.5%), doxycycline (75.0%), and tetracycline (62.5%). The sul2 was detected in all isolates, and the aac(6')-Ib-cr (93.8%) and the tetA (81.3%) were predominant in 10 resistance genes conferring five classes of antimicrobials. In addition, the correlation between resistance phenotypes and genes of tetracyclines and aminoglycosides was more than 80%. Interestingly, all the Salmonella isolates contained the genes mogA, mgtC, sopB, and spvB, whereas the siiE was variably represented. The findings in this study showed high prevalence, antimicrobial resistance, and the existence of virulence genes, suggesting that effective measures are required to ensure microbial safety from retail meats.

In silico molecular docking and in vitro antimicrobial efficacy of phytochemicals against multi-drug-resistant enteroaggregative Escherichia coli and non-typhoidal Salmonella spp

BACKGROUND

In the wake of emergence of antimicrobial resistance, bioactive phytochemical compounds are proving to be important therapeutic agents. The present study envisaged in silico molecular docking as well as in vitro antimicrobial efficacy screening of identified phytochemical ligands to the dispersin (aap) and outer membrane osmoporin (OmpC) domains of enteroaggregative Escherichia coli (EAEC) and non-typhoidal Salmonella spp. (NTS), respectively.

MATERIALS AND METHODS

The evaluation of drug-likeness, molecular properties, and bioactivity of the identified phytocompounds (thymol, carvacrol, and cinnamaldehyde) was carried out using Swiss ADME, while Protox-II and StopTox servers were used to identify its toxicity. The in silico molecular docking of the phytochemical ligands with the protein motifs of dispersin (PDB ID: 2jvu) and outer membrane osmoporin (PDB ID: 3uu2) were carried out using AutoDock v.4.20. Further, the antimicrobial efficacy of these compounds against multi-drug resistant EAEC and NTS strains was determined by estimating the minimum inhibitory concentrations and minimum bactericidal concentrations. Subsequently, these phytochemicals were subjected to their safety (sheep and human erythrocytic haemolysis) as well as stability (cationic salts, and pH) assays.

RESULTS

All the three identified phytochemicals ligands were found to be zero violators of Lipinski's rule of five and exhibited drug-likeness. The compounds tested were categorized as toxicity class-4 by Protox-II and were found to be non- cardiotoxic by StopTox. The docking studies employing 3D model of dispersin and ompC motifs with the identified phytochemical ligands exhibited good binding affinity. The identified phytochemical compounds were observed to be comparatively stable at different conditions (cationic salts, and pH); however, a concentration-dependent increase in the haemolytic assay was observed against sheep as well as human erythrocytes.

CONCLUSIONS

In silico molecular docking studies provided useful insights to understand the interaction of phytochemical ligands with protein motifs of pathogen and should be used routinely before the wet screening of any phytochemicals for their antibacterial, stability, and safety aspects.

A review of chemical and microbial contamination in food: What are the threats to a circular food system?

A circular food system is one in which food waste is processed to recover plant nutrients and returned to the soil to enable the production of more food, rather than being diverted to landfill or incineration. The approach may be used to reduce energy and water use in food production and contribute to the sustainability of the system. Anaerobic digestion and composting are common food waste treatment technologies used to stabilize waste and produce residual materials that can replenish the soil, thus contributing to a circular food system. This approach can only be deemed safe and feasible, however, if food waste is uncontaminated or any contaminants are destroyed during treatment. This review brings together information on several contaminant classes at different stages of the food supply chain, their possible sources, and their fates during composting and digestion. The main aim is to identify factors that could impede the transition towards a safe, reliable and efficient circular food system. We investigated heavy metals, halogenated organic compounds, foodborne pathogens and antibiotic resistance genes (ARGs) in the food system and their fates during digestion and composting. Production and processing stages were identified as major entry points for these classes of contaminants. Heavy metals and foodborne pathogens pose less risk in a circular system than halogenated organics or antibiotic resistance. Given the diversity of properties among halogenated organic compounds, there is conflicting evidence about their fate during treatment. There are relatively few studies on the fate of ARGs during treatment, and these have produced variable results, indicating a need for more research to clarify their fate in the final products. Repeated land application of contaminated food waste residuals can increase the risk of accumulation and jeopardize the safety of a circular food system. Thus, careful management of the system and research into the fate of the contaminants during treatment is needed.

Highly prevalent multidrug resistance and QRDR mutations in Salmonella isolated from chicken, pork and duck meat in Southern China, 2018-2019

This study was undertaken to investigate the prevalence, serotype distribution and antimicrobial resistance in Salmonella isolated from retail meat in Southern China, and to characterize the major mechanisms that mediate the ciprofloxacin resistance of isolates. High levels of Salmonella contamination were detected in pork (67.0%), duck (50.5%) and chicken (46.2%). Thirty different serotypes were identified among 500 detected Salmonella isolates, as well as significant differences in serotypes between different retail meat samples. Notably, 405 (80.1%) isolates exhibited multidrug resistance (MDR). Meanwhile, we also found that 74 (14.8%) Salmonella isolates were resistant to ciprofloxacin and the major mechanisms underlying this resistance were investigated. The commonest mutations in gyrA S83F (40.5%) and D87N (35.1%), and in parC was T57S (71.6%) and S80I (35.1%). Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) analysis revealed that the S. Kentucky isolates that were resistant to ciprofloxacin mostly belonged to ST198 (21/23, 91.3%) and PFGE revealed the presence of various genotypes. This study identified a diversity of Salmonella serotypes and a high prevalence of multidrug resistance (MDR) among Salmonella isolated from retail meat in Southern China, which indicates that foodborne Salmonella potentially constitutes a potential food safety risk.

Direct Detection of Viable but Non-culturable (VBNC) Salmonella in Real Food System by a Rapid and Accurate PMA-CPA Technique

Salmonella enterica is a typical foodborne pathogen with multiple toxic effects, including invasiveness, endotoxins, and enterotoxins. Viable but nonculturable (VBNC) is a type of dormant form preserving the vitality of microorganisms, but it cannot be cultured by traditional laboratory techniques. The aim of this study is to develop a propidium monoazide-crossing priming amplification (PMA-CPA) method that can successfully detect S. enterica rapidly with high sensitivity and can identify VBNC cells in food samples. Five primers (4s, 5a, 2a/1s, 2a, and 3a) were specially designed for recognizing the specific invA gene. The specificity of the CPA assay was tested by 20 different bacterial strains, including 2 standard S. enterica and 18 non-S. enterica bacteria strains covering Gram-negative and Gram-positive isolates. Except for the two standard S. enterica ATCC14028 and ATCC29629, all strains showed negative results. Moreover, PMA-CPA can detect the VBNC cells both in pure culture and three types of food samples with significant color change. In conclusion, the PMA-CPA assay was successfully applied on detecting S. enterica in VBNC state from food samples.

Prevalence and Multidrug Resistance Pattern of Salmonella Carrying Extended-Spectrum β-Lactamase in Frozen Chicken Meat in Bangladesh

ABSTRACT

Salmonella is an important foodborne pathogen that causes public health problems globally, and the increase of antimicrobial resistance in Salmonella has intensified the problem. Chicken meat is an important reservoir and disseminator of Salmonella to humans. This study aimed at estimating the burden of Salmonella carrying extended-spectrum β-lactamase (ESBL) and their antimicrobial resistance pattern in 113 domestic frozen chicken meat samples purchased from supershops available in five divisional megacities of Bangladesh. The study also focused on the determination of β-lactamase-, and plasmid-mediated quinolone resistance-encoding genes. All samples were analyzed for the presence of Salmonella using selective media and PCR assay. Antimicrobial susceptibility test was done by disk diffusion test, and ESBL screening was performed by double-disk synergy tests. Resistance genes were detected using multiplex PCR. Of samples, 65.5% were positive for Salmonella spp., and, of these, 58.1% isolates were ESBL producers. All the isolates were multidrug resistant (MDR): 40.5% were resistant to both three to five and six to eight antimicrobial classes; 17.6% were resistant to 9 to 11 classes, and 1.4% isolates to 12 to 15 classes. The highest rates of resistance were observed against oxytetracycline (100%), followed by trimethoprim-sulfamethoxazole (89.2%), tetracycline (86.5%), nalidixic acid (83.8%), amoxicillin (74.3%), and pefloxacin (70.3%). Notably, 48.6% of isolates demonstrated resistance to imipenem. One (1.4%) isolate was possibly extensively drug resistant. All the isolates were positive for the blaTEM gene, 2.7% were positive for blaCTX-M-1, and 20.3% for blaNDM-1. The prevalence of qnrA and qnrS genes was 4.1 and 6.8%, respectively. This study shows that ESBL-producing Salmonella are widespread in frozen chicken meat in Bangladesh, which puts greater responsibility on food processors and policy makers to ensure food safety.

HIGHLIGHTS

Bacteriophages as antibiotic resistance genes carriers in agro-food systems

Antibiotic resistance genes (ARGs) are a global health concern. Antibiotic resistance occurs naturally, but misuse of antibiotics in humans and animals is accelerating the process of antibiotic resistance emergency, which has been aggravated by exposure to molecules of antibiotics present in clinical and agricultural settings and the engagement of many countries in water reuse especially in Middle East and North Africa region. Bacteriophages have the potential to be significant actors in ARGs transmission through the transduction process. These viruses have been detected along with ARGs in non impacted habitats and in anthropogenic impacted environments like wastewater, reclaimed water and manure amended soil as well as minimally processed food and ready to eat vegetables. The ubiquity of bacteriophages and their persistence in the environment raises concern about their involvement in ARGs transmission among different biomes and the generation of pathogenic-resistant bacteria that pose a great threat to human health. The aim of this review is to give an overview of the potential role of bacteriophages in the dissemination and the transfer of ARGs to pathogens in food production and processing and the consequent contribution to antibiotic resistance transmission through faecal oral route carrying ARGs to our dishes.

Isolation of Pure Individual Fatty Acids from Chicken Skin Using Supercritical CO2 Extractor or Cooling Centrifuge

Chicken skin -a poultry meat industries waste- has been used in this work as a source for the production of pure free fatty acids. Chicken skin fat was extracted using dry rendering method. Physical and chemical parameters of that fat were determined. Also, its fatty acids composition has been identified by GC-MS after its esterification as oleic, palmitic, linoleic, stearic, myristic, lauric, linolenic, behenic, arachidonic, arachidic, palmitoleic, and paullinic acids, and others as traces. The extracted fat was then hydrolyzed into mixture of free fatty acids and glycerol, the free fatty acid mixture was separated, then it was cooled in order to separate saturated and unsaturated fatty acids from each other. Oleic, Palmitic, Linoleic and Stearic Acids were extracted individually in pure form using supercritical CO₂ extractor. Moreover, oleic, linoleic, palmitoleic, linolenic, and paullinic acids were extracted individually in pure form using cooling centrifuge sigma 3-18KS. All of the separated individual fatty acids were confirmed according to their melting point, GC-MS after esterification, elemental analysis and mass spectrometry (ms) of the corresponding methyl ester in order to detect the corresponding molecular ion peak. Therefore, these new two methods could afford the very expensive pure fatty acids with a low cast.

A Review of Antimicrobial Resistance in Poultry Farming within Low-Resource Settings

The emergence, spread, and persistence of antimicrobial resistance (AMR) remain a pressing global health issue. Animal husbandry, in particular poultry, makes up a substantial portion of the global antimicrobial use. Despite the growing body of research evaluating the AMR within industrial farming systems, there is a gap in understanding the emergence of bacterial resistance originating from poultry within resource-limited environments. As countries continue to transition from low- to middle income countries (LMICs), there will be an increased demand for quality sources of animal protein. Further promotion of intensive poultry farming could address issues of food security, but it may also increase risks of AMR exposure to poultry, other domestic animals, wildlife, and human populations. Given that intensively raised poultry can function as animal reservoirs for AMR, surveillance is needed to evaluate the impacts on humans, other animals, and the environment. Here, we provide a comprehensive review of poultry production within low-resource settings in order to inform future small-scale poultry farming development. Future research is needed in order to understand the full extent of the epidemiology and ecology of AMR in poultry within low-resource settings.