Unveiling the Genomic Landscape of Understudied Salmonella enterica Serovars from Poultry and Human: Implications for Food Safety. - Related Documents




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573801.0000Unveiling the Genomic Landscape of Understudied Salmonella enterica Serovars from Poultry and Human: Implications for Food Safety. Despite the bacteria of the genus Salmonella are pathogens of zoonotic importance, the factors associated with some serovars genetic diversity remain unclear. We investigated genotypic profiles of antimicrobial resistance, plasmid replicons, and virulence factors in 301 S. enterica genomes from human and animal sources, supplemented by ten sequenced genomes from fecal samples of laying hens in Brazil. Many antimicrobial resistance genes have been detected across various Salmonella serovars; with a limited number of unique resistance genes predicted in poultry isolates compared to human isolates. Specifically, among the 52 antimicrobial resistance genes identified, 48% were shared between poultry and human isolates, while 21.1% were exclusive to poultry isolates and 30.7% were exclusive to human isolates. Chromosomal mutations in the gyrA and parC genes were also predicted. To the best of our knowledge, this is the first work to report S. Braenderup carrying the SPI-10. SGI-1 was detected in a few isolates of S. Schwarzengrund from poultry and the CS54 island was solely noticed in genomes referring to the serovars S. Saintpaul and S. Braenderup. Among the serovars analyzed, S. Saintpaul showed the lowest plasmid diversity. A total of 161 (161/271) virulence genes were common to all serovars, the remaining genes were exclusively identified within specific serovars, revealing a distinct distribution pattern within the S. enterica population. Overall, our study brings to light the genetic potential of Salmonella serovars frequently neglected in poultry production, which threatens public health, particularly due to multidrug-resistant profiles against active principles used to treat human infections.202540327155
572110.9999One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock. Livestock have been proposed as a reservoir for drug-resistant Escherichia coli that infect humans. We isolated and sequenced 431 E. coli isolates (including 155 extended-spectrum β-lactamase [ESBL]-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1,517 E. coli bacteria associated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, suggesting that E. coli causing serious human infection had not directly originated from livestock. In contrast, we observed highly related isolates from the same animal species on different farms. Screening all 1,948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions in human and livestock isolates. Overall, we identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that within the confines of our sampling framework, there was limited evidence that antimicrobial-resistant pathogens associated with serious human infection had originated from livestock in our region.IMPORTANCE The increasing prevalence of E. coli bloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources of E. coli associated with serious human disease. E. coli from 1,517 patients with bloodstream infections were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was limited overlap in the mobile elements carrying these genes. Within the limitations of sampling, our findings do not support the idea that E. coli causing invasive disease or their resistance genes are commonly acquired from livestock in our region.201930670621
571620.9999Genomic analysis of Salmonella isolated from canal water in Bangkok, Thailand. Antimicrobial resistance (AMR) poses an escalating global public health threat. Canals are essential in Thailand, including the capital city, Bangkok, as agricultural and daily water sources. However, the characteristic and antimicrobial-resistance properties of the bacteria in the urban canals have never been elucidated. This study employed whole genome sequencing to characterize 30 genomes of a causal pathogenic bacteria, Salmonella enterica, isolated from Bangkok canal water between 2016 and 2020. The dominant serotype was Salmonella Agona. In total, 35 AMR genes and 30 chromosomal-mediated gene mutations were identified, in which 21 strains carried both acquired genes and mutations associated with fluoroquinolone resistance. Virulence factors associated with invasion, adhesion, and survival during infection were detected in all study strains. 75.9% of the study stains were multidrug-resistant and all the strains harbored the necessary virulence factors associated with salmonellosis. One strain carried 20 resistance genes, including mcr-3.1, mutations in GyrA, ParC, and ParE, and typhoid toxin-associated genes. Fifteen plasmid replicon types were detected, with Col(pHAD28) being the most common type. Comparative analysis of nine S. Agona from Bangkok and 167 from public databases revealed that specific clonal lineages of S. Agona might have been circulating between canal water and food sources in Thailand and globally. These findings provide insight into potential pathogens in the aquatic ecosystem and support the inclusion of environmental samples into comprehensive AMR surveillance initiatives as part of a One Health approach. This approach aids in comprehending the rise and dissemination of AMR and devising sustainable intervention strategies.IMPORTANCEBangkok is the capital city of Thailand and home to a large canal network that serves the city in various ways. The presence of pathogenic and antimicrobial-resistant Salmonella is alarming and poses a significant public health risk. The present study is the first characterization of the genomic of Salmonella strains from Bangkok canal water. Twenty-two of 29 strains (75.9%) were multidrug-resistant Salmonella and all the strains carried essential virulence factors for pathogenesis. Various plasmid types were identified in these strains, potentially facilitating the horizontal transfer of AMR genes. Additional investigations indicated a potential circulation of S. Agona between canal water and food sources in Thailand. The current study underscores the role of environmental water in an urban city as a reservoir of pathogens and these data obtained can serve as a basis for public health risk assessment and help shape intervention strategies to combat AMR challenges in Thailand.202438563788
573930.9998Emergence and Comparative Genome Analysis of Salmonella Ohio Strains from Brown Rats, Poultry, and Swine in Hungary. Rats are particularly important from an epidemiological point of view, because they are regarded as reservoirs for diverse zoonotic pathogens including enteric bacteria. This study is the first to report the emergence of Salmonella serovar Ohio in brown rats (Rattus norvegicus) and food-producing animals in Hungary. We first reveal the genomic diversity of the strains and their phylogenomic relationships in the context of the international collection of S. Ohio genomes. This pathogen was detected in 4.3% (4/92) of rats, captured from multiple sites in Hungary. A whole-genome-based genotype comparison of S. Ohio, Infantis, Enteritidis, and Typhimurium strains showed that 76.4% (117/153) of the virulence and antimicrobial resistance genes were conserved among these serovars, and none of the genes were specific to S. Ohio. All S. Ohio strains lacked virulence and resistance plasmids. The cgMLST phylogenomic comparison highlighted a close genetic relationship between rat and poultry strains of S. Ohio from Hungary. These strains clustered together with the international S. Ohio genomes from aquatic environments. Overall, this study contributes to our understanding of the epidemiology of Salmonella spp. in brown rats and highlights the importance of monitoring to minimize the public health risk of rodent populations. However, further research is needed to understand the route of infection and evolution of this serovar.202439201506
572940.9998Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. Food animals are known reservoirs of multidrug-resistant (MDR) Escherichia coli, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR E. coli isolates from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, β-lactams, sulfonamides, and tetracyclines were the most frequent antimicrobial resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (blaCMY-2, blaCTX-M, mph(A), erm(B), aac(6')Ib-cr, and qnrS1). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR E. coli isolated from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates (50%) were identified as sequence types that are the causative agents of extra-intestinal infections (ExPECs), such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as stx, tir, and eae, were more likely to be harbored by antimicrobial-susceptible strains, while factors associated with extraintestinal infections such as the sit system, aerobactin, and pap fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR E. coli that harbor various resistance genes and virulence factors associated with human infections. Evidence of co-occurrence of ARGs with MRGs, BRGs, and iron-scavenging genes (sit and aerobactin) may lead to management strategies for reducing colonization of resistant bacteria in the calf gut.202235298535
556050.9998Linezolid- and Multidrug-Resistant Enterococci in Raw Commercial Dog Food, Europe, 2019-2020. We describe enterococci in raw-frozen dog food commercialized in Europe as a source of genes encoding resistance to the antibiotic drug linezolid and of strains and plasmids enriched in antibiotic-resistance and virulence genes in hospitalized patients. Whole-genome sequencing was fundamental to linking isolates from dog food to human cases across Europe.202134287135
551460.9998Resistance and virulence gene analysis and molecular typing of Escherichia coli from duck farms in Zhanjiang, China. INTRODUCTION: The widespread use of antibiotics in animal agriculture has increased the resistance of Escherichia coli, and pathogenic E. coli often harbor complex virulence factors. Antimicrobial resistance in pathogenic bacteria can cause public health problems. Correlation analyses of the resistance, virulence, and serotype data from the pathogenic bacteria found on farms and in the surrounding environment can thus provide extremely valuable data to help improve public health management. METHODS: In this investigation, we have assessed the drug resistance and virulence genes as well as the molecular typing characteristics of 30 E. coli strains isolated from duck farms in the Zhanjiang area of China. Polymerase chain reaction was used to detect the drug resistance and virulence genes as well as serotypes, and whole-genome sequencing was used to analyze the multilocus sequence typing. RESULTS: The detection rates for the oqxA resistance gene and fimC virulence gene were highest (93.3%, respectively). There were no correlations between the drug resistance and virulence gene numbers in the same strain. The epidemic serotype was O81 (5/24), ST3856 was an epidemic sequence type, and strains I-9 and III-6 carried 11 virulence genes. The E. coli strains from the duck farms in the Zhanjiang area were thus found to have a broad drug resistance spectrum, various virulence genes, complex serotypes, and certain pathogenicity and genetic relationship. DISCUSSION: Monitoring the spread of pathogenic bacteria and the provision of guidance regarding the use of antibiotics in the livestock and poultry industries will be required in the future in the Zhanjiang area.202337396302
203870.9998Salmonella enterica Serotype 4,[5],12:i:- in Swine in the United States Midwest: An Emerging Multidrug-Resistant Clade. BACKGROUND: Salmonella 4,[5],12:i:-, a worldwide emerging pathogen that causes many food-borne outbreaks mostly attributed to pig and pig products, is expanding in the United States. METHODS: Whole-genome sequencing was applied to conduct multiple comparisons of 659 S. 4,[5],12:i:- and 325 Salmonella Typhimurium from different sources and locations (ie, the United States and Europe) to assess their genetic heterogeneity, with a focus on strains recovered from swine in the US Midwest. In addition, the presence of resistance genes and other virulence factors was detected and the antimicrobial resistance phenotypes of 50 and 22 isolates of livestock and human origin, respectively, was determined. RESULTS: The S. 4,5,12:i:- strains formed two main clades regardless of their source and geographic origin. Most (84%) of the US isolates recovered in 2014-2016, including those (48 of 51) recovered from swine in the US Midwest, were part of an emerging clade. In this clade, multiple genotypic resistance determinants were predominant, including resistance against ampicillin, streptomycin, sulfonamides, and tetracyclines. Phenotypic resistance to enrofloxacin (11 of 50) and ceftiofur (9 of 50) was found in conjunction with the presence of plasmid-mediated resistance genes (qnrB19/qnrB2/qnrS1 and blaCMY-2/blaSHV-12, respectively). Higher similarity was also found between S. 4,[5],12:i:- from the emerging clade and S. Typhimurium from Europe than with S. Typhimurium from the United States. CONCLUSIONS: Salmonella 4,[5],12:i:- currently circulating in swine in the US Midwest are likely to be part of an emerging multidrug-resistant clade first reported in Europe, and can carry plasmid-mediated resistance genes that may be transmitted horizontally to other bacteria, and thus may represent a public health concern.201829069323
550080.9998Whole genome sequence analyses-based assessment of virulence potential and antimicrobial susceptibilities and resistance of Enterococcus faecium strains isolated from commercial swine and cattle probiotic products. Enterococcus faecium is one of the more commonly used bacterial species as a probiotic in animals. The organism, a common inhabitant of the gut of animals and humans, is a major nosocomial pathogen responsible for a variety infections in humans and sporadic infections in animals. In swine and cattle, E. faecium-based probiotic products are used for growth promotion and gut functional and health benefits. The objective of this study was to utilize whole genome sequence-based analysis to assess virulence potential, detect antimicrobial resistance genes, and analyze phylogenetic relationships of E. faecium strains from commercial swine and cattle probiotics. Genomic DNA extracted from E. faecium strains, isolated from commercial probiotic products of swine (n = 9) and cattle (n = 13), were sequenced in an Illumina MiSeq platform and analyzed. Seven of the nine swine strains and seven of the 13 cattle strains were identified as Enterococcus lactis, and not as E. faecium. None of the 22 probiotic strains carried major virulence genes required to initiate infections, but many carried genes involved in adhesion to host cells, which may benefit the probiotic strains to colonize and persist in the gut. Strains also carried genes encoding resistance to a few medically important antibiotics, which included aminoglycosides [aac(6')-Ii, aph(3')-III, ant(6)-Ia], macrolide, lincosamide and streptogramin B (msrC), tetracyclines [tet(L) and tet(M)], and phenicols [cat-(pc194)]. The comparison of the genotypic to phentypic AMR data showed presence of both related and unrelated genes in the probiotic strains. Swine and cattle probiotic E. faecium strains belonged to diverse sequence types. Phylogenetic analysis of the probiotic strains, and strains of human (n = 29), swine (n = 4), and cattle (n = 4) origin, downloaded from GenBank, indicated close clustering of strains belonging to the same species and source, but a few swine and cattle probiotic strains clustered closely with other cattle and human fecal strains. In conclusion, the absence of major virulence genes characteristic of the clinical E. faecium strains suggests that these probiotic strains are unlikely to initiate opportunistic infection. However, the carriage of AMR genes to medically important antibiotics and close clustering of the probiotic strains with other human and cattle fecal strains suggests that probiotic strains may pose risk to serve as a source of transmitting AMR genes to other gut bacteria.202235150575
573690.9998Comparative Genomic Analysis and Antimicrobial Resistance Profile of Enterococcus Strains Isolated from Raw Sheep Milk. The role of Enterococcus spp. in food is debated since this group of lactic acid bacteria contains opportunistic pathogenic strains, some of which exhibit a multidrug-resistant profile. In livestock farms, the use of antibiotics is the most common practice to deal with mastitis-causing bacteria. However, the heavy usage and/or misuse of antibiotics has led to the emergence of antibiotic resistance. This study aimed to genetically and phenotypically characterize Enterococcus strains isolated from raw sheep milk. Samples were collected over one year from the bulk tank of a dairy sheep farm and cultured on selective media. Isolates were purified and analyzed by whole-genome sequencing and antimicrobial susceptibility testing. The isolates were divided into clusters and the corresponding species were identified along with their genes related to virulence and antibiotic resistance. The pan-, core- and accessory-genomes of the strains were determined. Finally, the antibiotic-resistant profile of selected strains was examined and associated with their genomic characterization. These findings contribute to a better understanding of Enterococci epidemiology, providing comprehensive profiles of their virulence and resistance genes. The presence of antibiotic-resistant bacteria in raw sheep milk destined for the production of cheese should raise awareness.202540872636
5735100.9998A Comprehensive Virulence and Resistance Characteristics of Listeria monocytogenes Isolated from Fish and the Fish Industry Environment. Listeria monocytogenes is an important pathogen, often associated with fish, that can adapt and survive in products and food processing plants, where it can persist for many years. It is a species characterized by diverse genotypic and phenotypic characteristics. Therefore, in this study, a total of 17 L. monocytogenes strains from fish and fish-processing environments in Poland were characterized for their relatedness, virulence profiles, and resistance genes. The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IIa and IIb; sequence types (ST) were ST6 and ST121; and clonal complexes (CC) were CC6 and CC121. Core genome multilocus sequence typing (cgMLST) analysis was applied to compare the present isolates with the publicly available genomes of L. monocytogenes strains recovered in Europe from humans with listeriosis. Despite differential genotypic subtypes, most strains had similar antimicrobial resistance profiles; however, some of genes were located on mobile genetic elements that could be transferred to commensal or pathogenic bacteria. The results of this study showed that molecular clones of tested strains were characteristic for L. monocytogenes isolated from similar sources. Nevertheless, it is worth emphasizing that they could present a major public health risk due to their close relation with strains isolated from human listeriosis.202336834997
5515110.9998Wildlife Waterfowl as a Source of Pathogenic Campylobacter Strains. BACKGROUND: The aim of the study was to determine whether free-living birds belonging to game species whose meat is used for human consumption can constitute a reservoir of pathogenic Campylobacter strains, spreading these bacteria to other hosts or directly contributing to human infection. METHODS: A total of 91 cloacal swabs were taken from different species of wildlife waterfowl to estimate the Campylobacter prevalence, the genetic diversity of the isolates, and the presence of virulence genes and to evaluate the antimicrobial resistance. RESULTS: The presence of Campylobacter spp. was confirmed in 32.9% of samples. Based on flaA-SVR sequencing, a total of 19 different alleles among the tested Campylobacter isolates were revealed. The virulence genes involved in adhesion were detected at high frequencies among Campylobacter isolates regardless of the host species. The highest resistance was observed for ciprofloxacin. The resistance rates to erythromycin and tetracycline were observed at the same level. CONCLUSIONS: These results suggest that wildlife waterfowl belonging to game species may constitute a reservoir of Campylobacter, spreading these bacteria to other hosts or directly contributing to human disease. The high distribution of virulence-associated genes among wildlife waterfowl Campylobacter isolates make them potentially able to induce infection in humans.202235215056
5619120.9998Whole Genome Sequencing of Escherichia coli and Enterococcus spp. in wildlife-livestock interface: a pilot study. OBJECTIVES: This pilot study provides a multidisciplinary investigation to monitor livestock-wildlife interface. Ecological data, microbiological investigations, and whole genome sequencing were used to characterize eight bacterial isolates obtained from sympatric domestic and wild ruminants in Maiella National Park (Italy) in terms of genetic patterns of antimicrobial resistance. METHODS: Using selective culturing of fresh fecal samples of monitored and georeferenced populations of Apennine chamois, goats, red deer, and sheep, Escherichia coli, Enterococcus faecium, and Enterococcus faecalis isolates were isolated and subjected to minimum inhibitory concentration determination and whole genome sequencing. RESULTS: The analyzed isolates showed phenotypic and genotypic resistance to tetracycline and critically important antibiotics such as linezolid and carbapenems. Virulence genes related to biofilm regulation and Shiga toxins were also detected. Furthermore, serotypes related to nosocomial infections, harbouring plasmids recognized as important mobile resistance gene transmitters, were identified. CONCLUSIONS: This multidisciplinary pilot study represents a promising initial step to identify the environmental drivers and the transmission routes of antimicrobial resistance and virulence factors, providing new data on bacteria from rare and endangered species such as Apennine chamois.202336764655
5516130.9998Listeria monocytogenes isolates from food and food environment harbouring tetM and ermB resistance genes. Listeria monocytogenes is a foodborne pathogen that has become an important cause of human and animal diseases worldwide. The purpose of this study was to evaluate the serotypes, virulence potential, antimicrobial resistance profile, and genetic relationships of 50 L. monocytogenes isolates from food and food environment in southern Brazil. In this study, the majority of L. monocytogenes isolates belonged to the serotypes 1/2b (42%) and 4b (26%), which are the main serotypes associated with human listeriosis. In addition, all isolates harboured internalin genes (inlA, inlC, inlJ), indicating a virulence potential. The isolates were sensitive to most of the antimicrobial compounds analysed, and five isolates (10%) were multi-resistant. Two isolates harboured antimicrobial resistance genes (tetM and ermB) and in one of them, the gene was present in the plasmid. Moreover, according to the pulsed field gel electrophoresis assay, two multi-resistant isolates were a single clone isolated from food and the processing plant. The isolates were susceptible to the most frequently used antibiotics for listeriosis treatment. However, the presence of multidrug-resistant isolates and antimicrobial resistance genes including in the plasmid could even be transferred between bacterial species, suggesting a potential health risk to consumers and a potential risk of spreading multi-resistance genes to other bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: Listeria monocytogenes is an important agent of foodborne diseases. The results of this study suggest a potential capacity of L. monocytogenes isolates from food and food environment to cause human infections. Antimicrobial multi-resistance profiles were detected in 10%, and two isolates harboured tetM and ermB resistance genes. Moreover, the present research can help to build up a better knowledge about antimicrobial resistance of L. monocytogenes. Additionally, we found one isolate carrying tetM resistance gene in a plasmid, that suggests a possible transmission between commensal and/or other pathogenic bacteria of food environment, thereby raising up concerns regarding bacterial resistance.201626518475
5737140.9998Survey of Colistin Resistance in Commensal Bacteria from Penaeus vannamei Farms in China. Aquatic environments are important reservoirs for drug resistance. Aquatic foods may act as carriers to lead antibiotic-resistant commensal bacteria into the human gastrointestinal system, then contacting gut microbiota and spreading antibiotic resistance. Here, several shrimp farms were investigated to identify colistin resistance among commensal bacteria of aquaculture. A total of 884 (41.6%) colistin-resistant isolates were identified among 2126 strains. Electroporation demonstrated that colistin-resistant fragments were present in some commensal bacteria that could be transferred to other bacteria. Most of the resistant bacteria were Bacillus spp., with 69.3% of the Bacillus species exhibiting multiple drug resistance. Bacillus licheniformis was prevalent, with 58 strains identified that comprised six sequence types (ST) based on multilocus sequence typing. Whole-genome sequencing and comparisons with previous B. licheniformis genomes revealed a high degree of genomic similarity among isolates from different regions. Thus, this species is widely distributed, and this study provides new insights into global antibiotic-resistant characteristics of B. licheniformis. Sequence analyses further revealed some of these strains are even pathogenic and virulent, suggesting the antibiotic resistance and hazards of commensal bacteria in aquaculture should be considered. Considering the "One Health" perspective, improved monitoring of aquatic food is needed to prevent the spread of drug-resistant commensal bacteria from food-associated bacteria to humans.202337297388
4967150.9998Whole-genome sequencing of toxigenic Clostridioides difficile reveals multidrug resistance and virulence genes in strains of environmental and animal origin. BACKGROUND: Clostridioides difficile has been recognized as an emerging pathogen in both humans and animals. In this context, antimicrobial resistance plays a major role in driving the spread of this disease, often leading to therapeutic failure. Moreover, recent increases in community-acquired C. difficile infections have led to greater numbers of investigations into the animal origin of the disease. The aim of this study was to evaluate the genetic similarities between 23 environmental and animal isolates by using whole-genome sequencing and to determine antimicrobial resistance and virulence factor genes in toxigenic C. difficile strains to provide important data for the development of diagnostic methods or treatment guidelines. RESULTS: The most common sequence type was ST11 (87%), followed by ST2 (9%) and ST19 (4%). In addition, 86.95% of the strains exhibited multidrug resistance, with antimicrobial resistance to mainly aminoglycosides, fluoroquinolones, tetracycline and B-lactams; nevertheless, one strain also carried other resistance genes that conferred resistance to lincosamide, macrolides, streptogramin a, streptogramin b, pleuromutilin, oxazolidinone and amphenicol. In addition, a wide range of virulence factor genes, such as those encoding adherence factors, exoenzymes and toxins, were found. However, we observed variations between toxinotypes, ribotypes and sequence types. CONCLUSIONS: The results of this study demonstrated significant genetic similarity between ST11 strains isolated from environmental sampling and from animal origin; these strains may represent a reservoir for community-acquired C. difficile infection, which is becoming a growing public health threat due to the development of multridug resistant (MDR) bacteria and the number of virulence factors detected.202439434132
5618160.9998An Epidemiological Study on Salmonella in Tibetan Yaks from the Qinghai-Tibet Plateau Area in China. Salmonella is an important foodborne pathogen that can cause a range of illnesses in humans; it has also been a key focus for monitoring in the field of public health, including gastroenteritis, sepsis, and arthritis, and can also cause a decline in egg production in poultry and diarrhea and abortion in livestock, leading to death in severe cases, resulting in huge economic losses. This study aimed to investigate the isolation rate, antimicrobial resistance, serotypes, and genetic diversity of Salmonella isolated from yak feces in various regions on the Qinghai-Tibet Plateau. A total of 1222 samples of yak dung were collected from major cities in the Qinghai-Tibet Plateau area, and the sensitivity of the isolated bacteria to 10 major classes of antibiotics was determined using the K-B paper disk diffusion method for drug susceptibility. Meanwhile, the serotypes of the isolated bacteria were analyzed using the plate agglutination test for serum antigens, and their carriage of drug resistance and virulence genes was determined using PCR and gel electrophoresis experiments. The isolated bacteria were also classified using MLST (Multi-Locus Sequence Typing). The overall isolation rate for Salmonella was 18.25% (223/1222), and the results of the antibiotic susceptibility tests showed that 98.65% (220/223) of the isolated bacteria were resistant to multiple antibiotics. In the 223 isolates of Salmonella, eight classes of 20 different resistance genes, 30 serotypes, and 15 different types of virulence genes were detected. The MLST analysis identified 45 distinct sequence types (STs), including five clonal complexes, of which ST34, ST11, and ST19 were the most common. These findings contribute valuable information about strain resources, genetic profiles, and typing data for Salmonella in the Qinghai-Tibet Plateau area, facilitating improved bacterial surveillance, identification, and control in yak populations. They also provide certain data supplements for animal Salmonella infections globally, filling research gaps.202439765601
1935170.9998Antibiotic Susceptibility Profile and Tetracycline Resistance Genes Detection in Salmonella spp. Strains Isolated from Animals and Food. Salmonella spp. is among the leading causes of foodborne infections in humans and a large number of animals. Salmonella spp. is a pathogen involved in the dissemination of antimicrobial resistance because it can accumulate antibiotic resistance genes (ARGs). In this study, the antibiotic resistance profile to 15 antibiotics, belonging to six different classes, of 60 strains of Salmonella spp. collected from pets, farm animals, wildlife, and food in Sicily (Italy) was investigated by the Kirby-Bauer method. Given that almost 33.3% of the Salmonella spp. strains were resistant to tetracycline, Real-Time PCR analysis was applied on all the 60 strains to detect the presence of eight selected tet resistance genes. Besides, the presence of the int1 gene, related to the horizontal gene transfer among bacteria, was also investigated in all the strains by Real-Time PCR analysis. Our data showed that 56% of the isolated strains harbored one or more tet resistance genes and that these strains were most frequently isolated from animals living in close contact with humans. Concerning int1, 17 strains (28.3%) harbored this genetic element and eight of these simultaneously contained tet genes. The results of this study highlight the importance of using a molecular approach to detect resistance genetic determinants, whose spread can increase the diffusion of multidrug-resistant strains. Besides, the study of zoonotic bacteria such as Salmonella spp. which significantly contribute to ARGs dissemination should always follow a One Health approach that considers the health of humans, animals, and the environment to be closely related.202134356729
1977180.9998Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli. INTRODUCTION: Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants. OBJECTIVES: In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources. RESULTS: The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers. CONCLUSION: This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.202133717039
2565190.9998Phenotypic and genotypic characterization of antibiotic-resistant bacteria from Swiss ready-to-eat meat products. Antimicrobial resistance is a global health concern, which is partly driven by rising meat consumption, which has led to the intensive farming of livestock that relies on antibiotics. ready-to-eat animal products can carry antibiotic-resistant bacteria, posing risks to humans since they are often consumed without further cooking. While countries such as Switzerland limit antibiotic use in agriculture, contamination of meat with antibiotic-resistant bacteria can still occur during meat processing, and non-antibiotic agents such as heavy metals may contribute to the co-selection of resistance. This study aimed to characterize antibiotic-resistant bacteria in ready-to-eat meat products from various Swiss butcheries. Presumptive resistant bacteria were isolated using selective plating and analyzed phenotypically and genotypically. A total of 53 bacteria-antibiotic resistance combinations were identified, including Enterobacterales resistant to third-generation cephalosporins, vancomycin-resistant Enterococci, and one strain of methicillin-resistant Staphylococcus aureus. Of the 804 products sampled, 177 antibiotic-resistant bacteria were isolated, 148 of which showed multidrug resistance. Notably, these strains remained susceptible to last-resort antibiotics such as carbapenems and colistin. Whole-genome sequencing of 31 selected isolates revealed 164 antibiotic resistance genes spanning 25 classes, confirming resistance to beta-lactams, cephalosporins, and tetracyclines. We also detected genes conferring resistance to metals, suggesting co-selection pressures. Long-read sequencing revealed that the majority of the antibiotic resistance genes were chromosomal, while others were plasmid-encoded, indicating the potential for horizontal gene transfer. This study demonstrates that ready-to-eat meat products are reservoirs of antibiotic and metal resistance genes, as well as antibiotic-resistant bacteria, even at low levels. From a One Health perspective, our results highlight the importance of extending AMR surveillance across the food chain and underscore the need to include non-traditional bacterial indicators.202541001059