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138800.9959Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy. Animals, humans and food are all interconnected sources of antimicrobial resistance (AMR), allowing extensive and rapid exchange of AMR bacteria and genes. Whole genome sequencing (WGS) was used to characterize 279 Escherichia coli isolates obtained from animals (livestock, companion animals, wildlife), food and humans in Italy. E. coli predominantly belonged to commensal phylogroups B1 (46.6%) and A (29%) using the original Clermont criteria. One hundred and thirty-six sequence types (STs) were observed, including different pandemic (ST69, ST95, ST131) and emerging (ST10, ST23, ST58, ST117, ST405, ST648) extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Eight antimicrobial resistance genes (ARGs) and five chromosomal mutations conferring resistance to highest priority critically important antimicrobials (HP-CIAs) were identified (qnrS1, qnrB19, mcr-1, bla(CTX-M1,15,55), bla(CMY-2), gyrA/parC/parE, ampC and pmrB). Twenty-two class 1 integron arrangements in 34 strains were characterized and 11 ARGs were designated as intI1 related gene cassettes (aadA1, aadA2, aadA5, aad23, ant2_Ia, dfrA1, dfrA7, dfrA14, dfrA12, dfrA17, cmlA1). Notably, most intI1 positive strains belonged to rabbit (38%) and poultry (24%) sources. Three rabbit samples carried the mcr-1 colistin resistance gene in association with IS6 family insertion elements. Poultry meat harbored some of the most prominent ExPEC STs, including ST131, ST69, ST10, ST23, and ST117. Wildlife showed a high average number of virulence-associated genes (VAGs) (mean = 10), mostly associated with an ExPEC pathotype and some predominant ExPEC lineages (ST23, ST117, ST648) were identified.202033172096
120910.9959Molecular Detection of Shiga Toxin-Producing Escherichia coli O177 Isolates, Their Antibiotic Resistance, and Virulence Profiles From Broiler Chickens. The World Health Organization (WHO) describes Shiga toxin-producing Escherichia coli (STEC) as a bacterium that can cause severe food-borne diseases. Common sources of infection include undercooked meat products and faecal contamination in vegetables. This study aimed to isolate, identify and assess the virulence and antibiotic resistance profiles of STEC isolates from broiler chicken faeces. Faecal samples were cultured, and polymerase chain reaction (PCR) was utilized to identify the isolates. Subsequently, the confirmed isolates were screened for seven virulence markers using PCR. The antibiotic susceptibility of the isolates to 13 different antibiotics was determined using the disk diffusion method. PCR was also employed to screen for antibiotic resistance genes. The uidA gene, which encodes the beta-glucuronidase enzyme, was detected in 62 (64.6%) of the 91 presumptively identified E. coli isolates. Of these, 23 isolates (37.1%) were confirmed to be E. coli O177 serogroup through amplification of wzy gene. All E. coli O177 isolates possessed the virulence stx2 gene, while 65% carried the stx1 gene. Among the E. coli O177 isolates, three harboured a combination of vir + stx2 + stx1 + hlyA genes, while one isolate contained a combination of eaeA + stx2 + stx1 + hlyA genes. All E. coli O177 isolates carried one or more antimicrobial resistance (AMR) genes, with 17 isolates (73.7%) identified as multidrug resistance (MDR). This is the first study to report the presence of E. coli O177 serotype from broiler chickens in South Africa. The findings reveal that broiler chicken faeces are a significant reservoir for MDR E. coli O177 and a potential source of AMR genes. These results underscore the importance of continuous surveillance and monitoring of the spread of AMR infectious bacteria in food-producing animals and their environments. The study also emphasizes that monitoring and control of poultry meat should be considered a major public health concern.202439665069
130320.9958Isolation and Characterization of Antimicrobial-Resistant Escherichia coli from Retail Meats from Roadside Butcheries in Uganda. Retail meats are one of the main routes for spreading antimicrobial-resistant bacteria (ARB) from livestock to humans through the food chain. In African countries, retail meats are often sold at roadside butcheries without chilling or refrigeration. Retail meats in those butcheries are suspected to be contaminated by ARB, but it was not clear. In this study, we tested for the presence of antimicrobial-resistant Escherichia coli from retail meats (n = 64) from roadside butcheries in Kampala, Uganda. The meat surfaces were swabbed and inoculated on PetriFilm SEC agar to isolate E. coli. We successfully isolated E. coli from 90.6% of these retail meat samples. We identified the phylogenetic type, antimicrobial susceptibility, and antimicrobial resistance genes prevalence between retail meat isolates (n = 89). Phylogenetic type B1 was identified from 70.8% of the retail meat isolates, suggesting that the isolates originated primarily from fecal contamination during meat processing. Tetracycline (TET)-resistant isolates with tetA and/or tetB gene(s) were the most frequently detected (28.1%), followed by ampicillin (AMP) resistance genes with bla(TEM) (15.7%,) and sulfamethoxazole-trimethoprim (SXT) resistance genes with sul2 (15.7%). No extended-spectrum beta-lactamase-producing isolates were detected. A conjugation assay showed that resistance to AMP, TET, and SXT could be simultaneously transferred to recipients. These findings suggest that antimicrobial-resistant E. coli can easily be transferred from farms to tables from retail meats obtained from roadside butcheries.202032551973
120630.9958A National Antimicrobial Resistance Monitoring System Survey of Antimicrobial-Resistant Foodborne Bacteria Isolated from Retail Veal in the United States. ABSTRACT: Little is known about the prevalence of antimicrobial-resistant (AMR) bacteria in veal meat in the United States. We estimated the prevalence of bacterial contamination and AMR in various veal meats collected during the 2018 U.S. National Antimicrobial Resistance Monitoring System (NARMS) survey of retail outlets in nine states and compared the prevalence with the frequency of AMR bacteria from other cattle sources sampled for NARMS. In addition, we identified genes associated with resistance to medically important antimicrobials and gleaned other genetic details about the resistant organisms. The prevalence of Campylobacter, Salmonella, Escherichia coli, and Enterococcus in veal meats collected from grocery stores in nine states was 0% (0 of 358), 0.6% (2 of 358), 21.1% (49 of 232), and 53.5% (121 of 226), respectively, with ground veal posing the highest risk for contamination. Both Salmonella isolates were resistant to at least one antimicrobial agent as were 65.3% (32 of 49) of E. coli and 73.6% (89 of 121) of Enterococcus isolates. Individual drug and multiple drug resistance levels were significantly higher (P < 0.05) in E. coli and Enterococcus from retail veal than in dairy cattle ceca and retail ground beef samples from 2018 NARMS data. Whole genome sequencing was conducted on select E. coli and Salmonella from veal. Cephalosporin resistance (blaCMY and blaCTX-M), macrolide resistance (mph), and plasmid-mediated quinolone resistance (qnr) genes and gyrA mutations were found. We also identified heavy metal resistance genes ter, ars, mer, fieF, and gol and disinfectant resistance genes qac and emrE. An stx1a-containing E. coli was also found. Sequence types were highly varied among the nine E. coli isolates that were sequenced. Several plasmid types were identified in E. coli and Salmonella, with the majority (9 of 11) of isolates containing IncF. This study illustrates that veal meat is a carrier of AMR bacteria.202134015113
199240.9957Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals. The ability of antimicrobial resistance (AR) to transfer, on mobile genetic elements (MGEs) between bacteria, can cause the rapid establishment of multidrug resistance (MDR) in bacteria from animals, thus creating a foodborne risk to human health. To investigate MDR and its association with plasmids in Salmonella enterica, whole genome sequence (WGS) analysis was performed on 193 S. enterica isolated from sources associated with United States food animals between 1998 and 2011; 119 were resistant to at least one antibiotic tested. Isolates represented 86 serotypes and variants, as well as diverse phenotypic resistance profiles. A total of 923 AR genes and 212 plasmids were identified among the 193 strains. Every isolate contained at least one AR gene. At least one plasmid was detected in 157 isolates. Genes were identified for resistance to aminoglycosides (n = 472), β-lactams (n = 84), tetracyclines (n = 171), sulfonamides (n = 91), phenicols (n = 42), trimethoprim (n = 8), macrolides (n = 5), fosfomycin (n = 48), and rifampicin (n = 2). Plasmid replicon types detected in the isolates were A/C (n = 32), ColE (n = 76), F (n = 43), HI1 (n = 4), HI2 (n = 20), I1 (n = 62), N (n = 4), Q (n = 7), and X (n = 35). Phenotypic resistance correlated with the AR genes identified in 95.4% of cases. Most AR genes were located on plasmids, with many plasmids harboring multiple AR genes. Six antibiotic resistance cassette structures (ARCs) and one pseudo-cassette were identified. ARCs contained between one and five resistance genes (ARC1: sul2, strAB, tetAR; ARC2: aac3-iid; ARC3: aph, sph; ARC4: cmy-2; ARC5: floR; ARC6: tetB; pseudo-ARC: aadA, aac3-VIa, sul1). These ARCs were present in multiple isolates and on plasmids of multiple replicon types. To determine the current distribution and frequency of these ARCs, the public NCBI database was analyzed, including WGS data on isolates collected by the USDA Food Safety and Inspection Service (FSIS) from 2014 to 2018. ARC1, ARC4, and ARC5 were significantly associated with cattle isolates, while ARC6 was significantly associated with chicken isolates. This study revealed that a diverse group of plasmids, carrying AR genes, are responsible for the phenotypic resistance seen in Salmonella isolated from United States food animals. It was also determined that many plasmids carry similar ARCs.201931057528
136950.9957Antimicrobial resistance genes in Escherichia coli isolates recovered from a commercial beef processing plantt. The goal of this study was to assess the distribution of antimicrobial resistance (AMR) genes in Escherichia coli isolates recovered from a commercial beef processing plant. A total of 123 antimicrobial-resistant E. coli isolates were used: 34 from animal hides, 10 from washed carcasses, 27 from conveyers for moving carcasses and meat, 26 from beef trimmings, and 26 from ground meat. The AMR genes for beta-lactamase (bla(CMY), bla(SHV), and bla(TEM), tetracycline (tet(A), tet(B), and tet(C)), sulfonamides (sul1, sul2, and sul3), and aminoglycoside (strA and strB) were detected by PCR assay. The distribution of tet(B), tet(C), sul1, bla(TEM), strA, and strB genes was significantly different among sample sources. E. coli isolates positive for the tet(B) gene and for both strA and strB genes together were significantly associated with hide, washed carcass, and ground meat samples, whereas sull gene was associated with washed carcass and beef trimming samples. The bla(TEM) gene was significantly associated with ground meat samples. About 50% of tetracycline-resistant E. coli isolates were positive for tet(A) (14%), tet(B) (15%), or tet(C) (21%) genes or both tet(B) and tet(C) genes together (3%). The sul2 gene or both sul1 and sul2 genes were found in 23% of sulfisoxazole-resistant E. coli isolates, whereas the sul3 gene was not found in any of the E. coli isolates tested. The majority of streptomycin-resistant E. coli isolates (76%) were positive for the strA and strB genes together. The bla(CMY), bla(TEM), and bla(SHV) genes were found in 12, 56, and 4%, respectively, of ampicillin-resistant E. coli isolates. These data suggest that E. coli isolates harboring AMR genes are widely distributed in meat processing environments and can create a pool of transferable resistance genes for pathogens. The results of this study underscore the need for effective hygienic and sanitation procedures in meat plants to reduce the risks of contamination with antimicrobial-resistant bacteria.200919517739
134660.9957High prevalence of multidrug resistant Escherichia coli isolated from fresh vegetables sold by selected formal and informal traders in the most densely populated Province of South Africa. Contaminated fresh produce has increasingly been implicated in foodborne disease outbreaks. As microbiological safety surveillance in South Africa is limited, a total of 545 vegetable samples (spinach, tomato, lettuce, cucumber, and green beans) were purchased from retailers, street traders, trolley vendors and farmers' markets. Escherichia coli, coliforms and Enterobacteriaceae were enumerated and the prevalence of Escherichia coli, Salmonella spp. and Listeria monocytogenes determined. E. coli isolates were characterized phenotypically (antibiotic resistance) and genotypically (diarrheagenic virulence genes). Coliforms, E. coli and Enterobacteriaceae counts were mostly not significantly different between formal and informal markets, with exceptions noted on occasion. When compared to international standards, 90% to 98% tomatoes, 70% to 94% spinach, 82% cucumbers, 93% lettuce, and 80% green bean samples, had satisfactory (≤ 100 CFU/g) E. coli counts. Of the 545 vegetable samples analyzed, 14.86% (n = 81) harbored E. coli, predominantly from leafy green vegetables. Virulence genes (lt, st, bfpA, eagg, eaeA, stx1, stx2, and ipaH) were not detected in the E. coli isolates (n = 67) characterized, however 40.30% were multidrug-resistant. Resistance to aminoglycosides (neomycin, 73.13%; gentamycin, < 10%), penicillins (ampicillin, 38.81%; amoxicillin, 41.79%; augmentin, < 10%), sulfonamides (cotrimoxazole, 22.39%), tetracycline (19.4%), chloramphenicol (11.94%), cephalosporins (cefepime, 34.33%), and carbapenemases (imipenem, < 10%) were observed. This study highlights the need for continued surveillance of multidrug resistant foodborne pathogens in fresh produce retailed formally and informally for potential consumer health risks. PRACTICAL APPLICATION: The results indicate that the microbiological quality of different vegetables were similar per product type, regardless of being purchased from formal retailers or informal street traders, trolley vendors or farmers' markets. Although no pathogenic bacteria (diarrheagenic E. coli, Salmonella spp. or L. monocytogenes) were isolated, high levels of multidrug-resistance was observed in the generic E. coli isolates. These findings highlight the importance of microbiological quality surveillance of fresh produce in formal and informal markets, as these products can be a reservoir of multidrug resistant bacteria harboring antibiotic resistance and virulence genes, potentially impacting human health.202133294974
131770.9957Antibiotic resistance and virulence genes profile of Non typhodial Salmonella species isolated from poultry enteritis in India. Salmonella species (spp) is the most important gastrointestinal pathogen present ubiquitously. Non typhoidal Salmonella (NTS) is commonly associated with gastroenteritis in humans. Layer birds once get infection with NTS, can become persistently infected with Salmonella Typhimurium and intermittently shed the bacteria. It results in a high risk of potential exposure of eggs to the bacteria. The current study was conducted to determine the serotype diversity, presence of virulence genes, antibiotic resistance pattern, and genes of NTS from poultry enteritis. Out of 151 intestinal swabs from poultry total 118 NTS were isolated, which were characterized serologically as S. Typhimurium (51 strains), S. Weltevreden (57 strains) and untypable (10 strains). Most effective antibiotics were amikacin, gentamycin and ceftriaxone (33.05%) followed by ampicillin, azithromycin and ciprofloxacin (16.69%), co-trimoxazole (13.55%), and tetracycline (6.78%). Multidrug resistance recorded in 17.70% (N = 21/118) strains. Antimicrobial-resistant genes i.e. blaTEM, blaSHV, blaCTX-M, tet(A), tet(B), tet(C), sul1, sul2, sul3. blaTEM and tet(A) were present in 95% (20/21). Eleven virulence genes i.e. invA, hilA, sivH, tolC, agfA, lpfA, spaN, pagC, spiA, iroN and fliC 2 were present in all the 30 isolates. While, sopE was present in only 2 isolates, NTS strains with characteristics of pathogenicity and multidrug resistance from poultry enteritis were detected. Multidrug resistance showed the necessity of prudent use of antibiotics in the poultry industry.202438430331
260780.9956A walk on the wild side: Wild ungulates as potential reservoirs of multi-drug resistant bacteria and genes, including Escherichia coli harbouring CTX-M beta-lactamases. Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales have been classified as critical priority pathogens by the World Health Organization (WHO). ESBL are universally distributed and, in 2006, were firstly reported on a wild animal. Understanding the relative contributions of wild animals to ESBL circulation in the environment is urgently needed. In this work, we have conducted a nationwide study in Portugal to investigate the occurrence of bacteria carrying clinically significant antimicrobial resistance genes (ARG), using widely distributed wild ungulates as model species. A total of 151 antimicrobial resistant-Enterobacterales isolates were detected from 181 wild ungulates: 50% (44/88) of isolates from wild boar (Sus scrofa), 40.3% (25/62) from red deer (Cervus elaphus), 41.4% (12/29) from fallow deer (Dama dama) and 100% (2/2) from mouflon (Ovis aries subsp. musimon). Selected isolates showed a diversified resistance profile, with particularly high values corresponding to ampicillin (71.5%) and tetracycline (63.6%). Enterobacterales strains carried bla(TEM), tetA, tetB, sul2, sul1 or dfrA1 ARG genes. They also carried bla(CTX-M)-type genes, which are prevalent in human infections, namely CTX-M-14, CTX-M-15 and CTX-M-98. Strikingly, this is the first report of CTX-M-98 in wildlife. Almost 40% (n = 59) of Enterobacterales were multi-drug resistant. The diversity of plasmids carried by ESBL isolates was remarkable, including IncF, K and P. This study highlights the potential role of wild ungulates as environmental reservoirs of CTX-M ESBL-producing E. coli and in the spill-over of AMR bacteria and their determinants. Our findings suggest that wild ungulates are useful as strategic sentinel species of AMR in terrestrial environments, especially in response to potential sources of anthropogenic pollution, providing early warning of potential risks to human, animal and environmental health.202235489528
135090.9956High occurrence of Enterococcus faecalis, Enterococcus faecium, and Vagococcus lutrae harbouring oxazolidinone resistance genes in raw meat-based diets for companion animals - a public health issue, Switzerland, September 2018 to May 2020. IntroductionEnterococci harbouring genes encoding resistance to florfenicol and the oxazolidinone antimicrobial linezolid have emerged among food-producing animals and meat thereof, but few studies have analysed their occurrence in raw meat-based diets (RMBDs) for pets.AimWe aimed to examine how far RMBDs may represent a source of bacteria with oxazolidinone resistance genes.MethodsFifty-nine samples of different types of RMBDs from 10 suppliers (three based in Germany, seven in Switzerland) were screened for florfenicol-resistant Gram-positive bacteria using a selective culture medium. Isolates were phenotypically and genotypically characterised.ResultsA total of 27 Enterococcus faecalis, Enterococcus faecium, and Vagococcus lutrae isolates were obtained from 24 of the 59 samples. The optrA, poxtA, and cfr genes were identified in 24/27, 6/27 and 5/27 isolates, respectively. Chloramphenicol and linezolid minimum inhibitory concentrations (MICs) ranged from 24.0 mg/L-256.0 mg/L, and 1.5 mg/L-8.0 mg/L, respectively. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoints, 26 of 27 isolates were resistant to chloramphenicol (MICs ≥ 32 mg/L), and two were resistant to linezolid (MICs ≥ 8 mg/L). Multilocus sequence typing analysis of the 17 E. faecalis isolates identified 10 different sequence types (ST)s, with ST593 (n = 4 isolates) and ST207 (n = 2 isolates) occurring more than once, and two novel STs (n = 2 isolates). E. faecium isolates belonged to four different STs (168, 264, 822, and 1846).ConclusionThe high occurrence in our sample of Gram-positive bacteria harbouring genes encoding resistance to the critical antimicrobial linezolid is of concern since such bacteria may spread from companion animals to humans upon close contact between pets and their owners.202336757316
1993100.9956Co-occurrence of antibiotic and disinfectant resistance genes in extensively drug-resistant Escherichia coli isolated from broilers in Ilorin, North Central Nigeria. OBJECTIVES: The occurrence of multidrug-resistant (MDR) bacteria in poultry poses the public health threat of zoonotic transmission to humans. Hence, this study assessed the occurrence of drug-resistant Escherichia coli in broilers in the largest live bird market in Kwara State, Nigeria in December 2020. METHODS: Presumptive E. coli isolates were isolated using the European Union Reference Laboratory guideline of 2017 and confirmed via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Broth microdilution was performed on confirmed E. coli isolates to determine the minimum inhibitory concentration. Five extensively drug-resistant (XDR) isolates were selected for Illumina whole genome sequencing to predict the resistome, phylotype, sequence type, serotype, and diversity of mobile genetic elements in these isolates. RESULTS: Of the 181 broiler caecal samples, 73 E. coli isolates were obtained, of which 67 (82.0%) and 37 (50.6%) were determined as MDR (resistant to at least three classes of antibiotics) and XDR (resistant to at least five classes of antibiotics), respectively. Whole genome sequencing revealed diverse sequence types, phylogroups, and serotypes (ST165/B1 - O80:H19, ST115/A - Unknown: H7, ST901/B1 - O109:H4, ST4087/F - O117:H42, and ST8324/A - O127:H42). The XDR E. coli isolates encoded resistance to fluoroquinolones, fosfomycin, sulfamethoxazole, ampicillin and cephalosporins, trimethoprim, aminoglycosides, chloramphenicol, tetracycline, and macrolides. Mutations in the gyrA gene conferring resistance to fluoroquinolones were also detected. There was a positive correlation between phenotypic resistance patterns and the antibiotic resistance genes that were detected in the sequenced isolates. The XDR isolates also harbored two disinfectant resistance genes (qacE and sitABCD) that conferred resistance to hydrogen peroxide and quaternary ammonium compounds, respectively. The genome of the XDR isolates harbored several mobile genetic elements and virulence-associated genes, which were conserved in all sequenced XDR isolates. CONCLUSIONS: This is the first report of co-carriage of antibiotic resistance genes and disinfectant resistance genes in E. coli isolated from broilers in Ilorin, Nigeria. Our findings suggest that poultry are potential carriers of clonally diverse, pathogenic, MDR/XDR E. coli, which may have detrimental zoonotic potentials on human health.202236375754
1730110.9956Molecular Epidemiology of mcr-Encoded Colistin Resistance in Enterobacteriaceae From Food-Producing Animals in Italy Revealed Through the EU Harmonized Antimicrobial Resistance Monitoring. Colistin resistance by mobilisable mcr genes has been described in bacteria of food-animal origin worldwide, which has raised public health concerns about its potential foodborne transmission to human pathogenic bacteria. Here we provide baseline information on the molecular epidemiology of colistin-resistant, mcr-positive Escherichia coli and Salmonella isolates in food-producing animals in Italy in 2014-2015. A total 678, 861 and 236 indicator E. coli, Extended Spectrum Beta-Lactamase (ESBL)/AmpC-producing E. coli, and Salmonella isolates, respectively, were tested for colistin susceptibility. These isolates were collected according to the EU harmonized antimicrobial resistance monitoring program and are representative of at least 90 and 80% of the Italian poultry (broiler chickens and turkeys) and livestock (pigs and bovines < 12 months) production, respectively. Whole genome sequencing by Illumina technology and bioinformatics (Center for Genomic Epidemiology pipeline) were used to type 42 mcr-positive isolates by PCR. Colistin resistance was mainly observed in the ESBL/AmpC E. coli population, and was present in 25.9, 5.3, 6.5, and 3.9% of such isolates in turkeys, broilers, pigs, and bovines, respectively. Most colistin-resistant isolates (141/161, 87.5%) harbored genes of the mcr-1 group. mcr-1 was also detected in a small proportion of Salmonella isolates (3/146, 2.0%) in turkeys. Additional mcr types were mcr-3 in four ESBL-producing E. coli from bovines, and two mcr-4 in ESBL (n = 1) and indicator E. coli (n = 1) from pigs and bovines. We describe notable diversity of mcr variants with predominance of mcr-1.1 and mcr-1.2 on conjugative IncX4 plasmids in E. coli and in Salmonella serovars Typhimurium, Newport, Blockley from turkey. A new variant, mcr-1.13 was detected in the chromosome in E. coli in turkey and pig isolates. Additionally, we describe mcr-3.2 and mcr-4.3 in E. coli from bovines, and mcr-4.2 in E. coli from pigs. These findings elucidate the epidemiology of colistin resistance in food-producing animals in Italy along with its genetic background, and highlight the likelihood of mcr horizontal transfer between commensal bacteria and major food-borne pathogens (Salmonella) within the same type of productions. Thorough action and strategies are needed in order to mitigate the risk of mcr transfer to humans, in a "One Health" perspective.201829951045
1366120.9956Day-old chicks are a source of antimicrobial resistant bacteria for laying hen farms. Antimicrobial resistant bacteria are rarely detected in laying hens and the objective of this longitudinal study was to test day-old chick as a source. Four different commercial batches raised on the same farm were monitored from day-old chick to laying hens using Escherichia coli as a model. Ten colonies from each of the eight samplings per batch were tested for antimicrobial susceptibility using 14 antimicrobials. Overall (313 isolates), higher resistance percentages were detected for tetracycline (26.8%), followed by sulphonamides (16.3%), ampicillin (16.0%) and quinolones (10.9% and 9.3% for ciprofloxacin and nalidixic acid, respectively). Resistance percentages of bacteria from day-old chicks were higher than those of pullets and hens (p < 0.05) for tetracycline, sulphonamides, trimethoprim and chloramphenicol. Forty different phenotypic resistance profiles were detected, led by fully susceptible (182 isolates; 58.1%), and followed by single tetracycline (28 isolates; 8.9%) and ciprofloxacin/ nalidixic acid (11 isolates; 3.5%) profiles. By whole-genome sequencing, 17 genes and mutations of five chromosomal genes related to resistance were detected, the most frequent being tetA, bla(TEM-1B) and sul1. Using multilocus sequencing analysis, 58 different MLST types were detected, most of them only in a particular sample. The ST155 (27/142) was the most frequently detected, followed by ST10 (19/142) and ST48 (9/142). The fate on the farm of the detected E. coli populations in old-day chicks was not clear, but our data suggest that they did not remain in the predominant faecal population of pullets and laying hens.201930827391
2962130.9955Prevalence of antimicrobial resistance in fecal Escherichia coli and Salmonella enterica in Canadian commercial meat, companion, laboratory, and shelter rabbits (Oryctolagus cuniculus) and its association with routine antimicrobial use in commercial meat rabbits. Antimicrobial resistance (AMR) in zoonotic (e.g. Salmonella spp.), pathogenic, and opportunistic (e.g. E. coli) bacteria in animals represents a potential reservoir of antimicrobial resistant bacteria and resistance genes to bacteria infecting humans and other animals. This study evaluated the prevalence of E. coli and Salmonella enterica, and the presence of associated AMR in commercial meat, companion, research, and shelter rabbits in Canada. Associations between antimicrobial usage and prevalence of AMR in bacterial isolates were also examined in commercial meat rabbits. Culture and susceptibility testing was conducted on pooled fecal samples from weanling and adult commercial meat rabbits taken during both summer and winter months (n=100, 27 farms), and from pooled laboratory (n=14, 8 laboratory facilities), companion (n=53), and shelter (n=15, 4 shelters) rabbit fecal samples. At the facility level, E. coli was identified in samples from each commercial rabbit farm, laboratory facility, and 3 of 4 shelters, and in 6 of 53 companion rabbit fecal samples. Seventy-nine of 314 (25.2%; CI: 20.7-30.2%) E. coli isolates demonstrated resistance to >1 antimicrobial agent. At least one E. coli isolate resistant to at least one antimicrobial agent was present in samples from 55.6% of commercial farms, and from 25% of each laboratory and shelter facilities, with resistance to tetracycline being most common; no resistance was identified in companion animal samples. Salmonella enterica subsp. was identified exclusively in pooled fecal samples from commercial rabbit farms; Salmonella enterica serovar London from one farm and Salmonella enterica serovar Kentucky from another. The S. Kentucky isolate was resistant to amoxicillin/clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, streptomycin, and tetracycline, whereas the S. London isolate was pansusceptible. Routine use of antimicrobials on commercial meat rabbit farms was not significantly associated with the presence of antimicrobial resistant E. coli or S. enterica on farms; trends towards resistance were present when resistance to specific antimicrobial classes was examined. E. coli was widely prevalent in many Canadian domestic rabbit populations, while S. enterica was rare. The prevalence of AMR in isolated bacteria was variable and most common in isolates from commercial meat rabbits (96% of the AMR isolates were from commercial meat rabbit fecal samples). Our results highlight that domestic rabbits, and particularly meat rabbits, may be carriers of phenotypically antimicrobial-resistant bacteria and AMR genes, possibly contributing to transmission of these bacteria and their genes to bacteria in humans through food or direct contact, as well as to other co-housed animal species.201729254727
5246140.9955Food Service Pork Chops from Three U.S. Regions Harbor Similar Levels of Antimicrobial Resistance Regardless of Antibiotic Use Claims. Pork products from animals "raised without antibiotics" (RWA) are assumed to harbor lower levels of antimicrobial resistance (AMR) than conventional (CONV) pork products with no claims regarding use of antimicrobial agents during production. A total of 372 pork chop samples from CONV (n = 190) and RWA (n = 182) production systems were collected over 13 months from three food service suppliers. The following bacteria were cultured: Escherichia coli, tetracycline-resistant (TET(r)) E. coli, third-generation cephalosporin-resistant (3GC(r)) E. coli, Salmonella enterica, TET(r) Salmonella, 3GC(r) Salmonella, nalidixic acid-resistant Salmonella, Enterococcus spp., TET(r) Enterococcus, erythromycin-resistant Enterococcus, Staphylococcus aureus, and methicillin-resistant S. aureus. Production system did not significantly impact the detection of cultured bacteria (P > 0.05). Metagenomic DNA was isolated from each sample, and equal amounts of metagenomic DNA were pooled by supplier, month, and production system for 75 pooled samples (38 CONV, 37 RWA). Quantitative PCR was used to assess the abundances of the following 10 AMR genes: aac(6')-Ie-aph(2″)-Ia, aadA1, bla(CMY-2), bla(CTX-M), bla(KPC-2), erm(B), mecA, tet(A), tet(B), and tet(M). For all 10 AMR genes, abundances did not differ significantly (P > 0.05) between production systems. These results suggest that use of antimicrobial agents during swine production minimally impacts the AMR of bacteria in pork chops.201931532250
1090150.9955Distribution of extended-spectrum cephalosporin resistance determinants in Salmonella enterica and Escherichia coli isolated from broilers in southern Japan. This study was conducted to investigate the distribution and diversity of extended-spectrum cephalosporin (ESC) resistance determinants in Salmonella enterica and Escherichia coli obtained from the same cecal samples and to provide evidence of transmission of the resistance determinants among these bacteria in broiler farms in southern Japan. Salmonella enterica and E. coli were characterized by serotyping and multilocus sequence typing, respectively. An antimicrobial susceptibility test, plasmid analysis, and identification and localization of resistance genes were performed to determine the relatedness of ESC resistance determinants among the isolates. Of 48 flocks examined, 14 had S. enterica. In total, 57 S. enterica isolates were obtained, 45 of which showed ESC resistance. Extended-spectrum cephalosporin-resistant E. coli were also obtained from all of these ESC-resistant Salmonella-positive samples. β-Lactamase genes, blaTEM-52 (38 isolates), blaCTX-M-14 (1 isolate), and blaCMY-2 (6 isolates), were carried by conjugative untypable or IncP plasmids detected in the S. enterica serovars Infantis and Manhattan. The β-lactamase genes blaCTX-M-14 (3 isolates), blaCTX-M-15 (3 isolates), blaSHV-2 (1 isolate), blaSHV-12 (2 isolates), and blaCMY-2 (32 isolates) associated with IncI1-Iγ, IncFIB, IncFIC, IncK, IncB/O, and IncY plasmids were detected in E. coli co-isolates. Restriction mapping revealed similar plasmids in Salmonella Infantis and Salmonella Manhattan and in different sequence types of E. coli. Intraspecies transmission of plasmids was suggested within S. enterica and E. coli populations, whereas interspecies transmission was not observed. This study highlights the importance of plasmids as carriers of ESC resistance determinants.201323687161
2948160.9955Fecal cultivable aerobic microbiota of dairy cows and calves acting as reservoir of clinically relevant antimicrobial resistance genes. Antimicrobial resistance has become a global threat to public health since multidrug-resistant (MDR) bacteria have been reported worldwide carrying different antimicrobial resistance genes (ARGs), and animals have been described as a reservoir of ARGs. The presence of antimicrobial-resistant bacteria and ARGs in the food matrix is a risk to public health. This study aimed to research the presence of clinically relevant ARGs for important antimicrobials and genetic elements in fecal samples from dairy cows and calves on a Brazilian farm. In this study, a total of 21 fecal samples were collected, and then, the DNA of cultivable aerobic bacteria was extracted. Fifty-seven ARGs and twenty-three genetic elements were researched by PCR and confirmed by sequencing. Several ARGs that confer resistance to β-lactams, tetracyclines, fluoroquinolones, sulphonamides, phenicols, aminoglycoside, glycopeptides, and macrolides were detected. A total of 200 amplicons from 23 ARGs (bla(CTX-M-Gp2), bla(CMY), bla(SHV), tetA, tetB, tetC, qepA, qnrB, qnrS, oqxA, oqxB, vanC1, vanC2/3, aadA, sul1, sul2, sul3, ermB, mefAE, floR, cmlA, aadA, aph(3')-Ia, aac(3')-Ia), and 145 amplicons from 12 genetic elements (IncF, IncFIA, IncFIB, IncI1, IncY, IncU, IncK, IncP, IncR, IncHI1, ColE-like, intI1) were detected. The results presented in this study call attention to the monitoring of antimicrobial resistance in dairy farms worldwide. MDR bacteria and ARGs can spread to different sources, including milk products, which are one of the most consumed products worldwide, representing a potential risk to human health.202032246396
2021170.9955Diversity of Plasmids and Antimicrobial Resistance Genes in Multidrug-Resistant Escherichia coli Isolated from Healthy Companion Animals. The presence and transfer of antimicrobial resistance genes from commensal bacteria in companion animals to more pathogenic bacteria may contribute to dissemination of antimicrobial resistance. The purpose of this study was to determine antimicrobial resistance gene content and the presence of genetic elements in antimicrobial resistant Escherichia coli from healthy companion animals. In our previous study, from May to August, 2007, healthy companion animals (155 dogs and 121 cats) from three veterinary clinics in the Athens, GA, USA area were sampled and multidrug-resistant E. coli (n = 36; MDR, resistance to ≥ 2 antimicrobial classes) were obtained. Of the 25 different plasmid replicon types tested by PCR, at least one plasmid replicon type was detected in 94% (34/36) of the MDR E. coli; four isolates contained as many as five different plasmid replicons. Nine replicon types (FIA, FIB, FII, I2, A/C, U, P, I1 and HI2) were identified with FIB, FII, I2 as the most common pattern. The presence of class I integrons (intI) was detected in 61% (22/36) of the isolates with eight isolates containing aminoglycoside- and/or trimethoprim-resistance genes in the variable cassette region of intI. Microarray analysis of a subset of the MDR E. coli (n = 9) identified the presence of genes conferring resistance to aminoglycosides (aac, aad, aph and strA/B), β-lactams (ampC, cmy, tem and vim), chloramphenicol (cat), sulfonamides (sulI and sulII), tetracycline [tet(A), tet(B), tet(C), tet(D) and regulator, tetR] and trimethoprim (dfrA). Antimicrobial resistance to eight antimicrobials (ampicillin, cefoxitin, ceftiofur, amoxicillin/clavulanic acid, streptomycin, gentamicin, sulfisoxazole and trimethoprim-sulfamethoxazole) and five plasmid replicons (FIA, FIB, FII, I1 and I2) were transferred via conjugation. The presence of antimicrobial resistance genes, intI and transferable plasmid replicons indicate that E. coli from companion animals may play an important role in the dissemination of antimicrobial resistance, particularly to human hosts during contact.201525653018
1208180.9955Different Multidrug-Resistant Salmonella spp. Serovars Isolated from Slaughter Calves in Southern Brazil. Bovines are carriers of Salmonella spp., a relevant foodborne pathogen, acting as contamination sources in slaughterhouses. Calves are prone to infection, and antimicrobial resistance may occur in such bacteria. This study aimed to determine the prevalence and virulence determinants of Salmonella spp. recovered from calves in the Rio Grande do Sul state, Brazil. Eighty-five calves' carcasses were evaluated (leather and veal meat). Thirteen Salmonella spp. isolates (8%) from 11 animals (13%) were obtained only from leather, indicating that contamination occurred before slaughter and that the meat was safe regarding this aspect. The serotypes S. Minnesota, S. Abony, S. Cerro, and S. Gafsa were identified, and all isolates were multidrug-resistant. The isolates had at least 19 virulence-related genes, and the bla(OXA-48) resistance gene was detected in three (23%). The data suggest that treating infections caused by these bacteria may be difficult in animals from these farms and can also be an extended human health problem.202236459239
1204190.9955Wild Birds as Drivers of Salmonella Braenderup and Multidrug Resistant Bacteria in Wetlands of Northern Italy. In this study, the antimicrobial resistance profiles of bacterial strains obtained from wild avian species recovered in wetlands of Northern Italy were described. Cloacal swabs collected from 67 aquatic birds, hunted or found dead in two private hunting grounds, were submitted to microbiological investigations and antimicrobial susceptibility testing using the Vitek 2 system, while specific PCR protocols were applied to screen for genes associated with the resistance. One hundred fifty-seven bacterial strains were characterized. The most frequent isolates were Enterococcus faecalis (36/157; 22.9%) and Escherichia coli (23/157; 14.6%). Seventy-seven isolates (77/157; 49%) were resulted resistant to at least one antibiotic, and eight isolates (8/157; 5%) were classified as multidrug resistant bacteria. Resistance for critically important antibiotics (linezolid, vancomycin, carbapenems, third-generation cephalosporins, and fluoroquinolones) was also described. Salmonella spp. was obtained from a Eurasian teal (Anas crecca), and it was subsequently analyzed by whole genome sequencing, revealing the serovar Salmonella Braenderup ST22. The phylogenetic analysis, performed with all ST22 described in 2021 and 2022, placed the strain under study in a large clade associated with human salmonellosis cases. These results suggest that migratory aquatic birds may be considered as relevant carriers of critically important antibiotic resistant bacteria and zoonotic food-borne pathogens potentially able to impact public health.202440303189