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The present study aimed to evaluate the prevalence of antimicrobial resistance and clonal relationships in Proteus mirabilis isolated from chicken meat, beef, pork, and community-acquired urinary tract infections (UTI-CA). Chicken meat isolates showed the highest multidrug resistance (MDR), followed by those from pork and UTI-CA, whereas beef had relatively few MDR strains. All sources had strains that carried blaCTX-M-65, whereas blaCTX-M-2 and blaCMY-2 were only detected in chicken meat and UTI-CA isolates. This indicates that chicken meat should be considered an important risk factor for the spread of P. mirabilis carrying ESBL and AmpC. Furthermore, ESBL/AmpC producing strains were resistant to a greater number of antimicrobials and possessed more resistance genes than non-producing strains. In addition, the antimicrobial resistance genes qnrD, aac(6')-Ib-cr, sul1, sul2, fosA3, cmlA, and floR were also found. Molecular typing showed a genetic similarity between chicken meat and UTI-CA isolates, including some strains with 100% similarity, indicating that chicken can be a source of P. mirabilis causing UTI-CA. It was concluded that meat, especially chicken meat, can be an important source of dissemination of multidrug-resistant P. mirabilis in the community.

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Resistant Enterobacterales of avian intestinal origin can contaminate carcasses during broiler processing and thereby spread through the human food chain. This study aimed at assessing the prevalence, diversity and genomic characteristics of ESBL/AmpC Enterobacterales in poultry flocks from different farms and cities in the state of Paraná, Brazil. Enterobacterales isolated from cloacal samples were subjected to antimicrobial susceptibility testing (AST). ESBL/AmpC isolates were whole-genome sequenced and subjected to S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) followed by Southern blotting to determine the location of resistant genes on plasmids. A surprisingly high proportion of E. coli (40.6 %) collected on non-selective plates presented an ESBL/AmpC phenotype. Multidrug resistance was statistically not higher in ESBL/AmpC E. coli having the potential to be Avian Pathogenic (APEC-like) compared to non-APEC-like ESBL/AmpC E. coli isolates. Resistance to antibiotics not authorized for use in poultry in the State of Paraná was observed, suggesting that antimicrobial resistance (AMR) is co-selected by the use of veterinary-licensed antibiotics. Phylogenetic analyzes revealed the presence of identical or highly similar ESBL/AmpC E. coli clones on farms distant up to 100 km of each other; this strongly suggests that the centralization and verticalization of the poultry industry can facilitate the spread of resistant bacteria among different farms, companies, and cities. The molecular characterization of clones and plasmids proved the dominance of the ST224 E. coli lineage and the IncF/blaCTX-M-55 plasmid, possibly indicating the emergence of successful clones and plasmids adapted to the chicken host. Our data contribute to the epidemiological tracking of resistance mechanisms in Enterobacterales from poultry and to knowledge for further One Health studies to control the spread of resistant bacteria from food animals to humans.

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The aim of this work was to detect Escherichia coli isolates displaying resistance to oxyimino-cephalosporins, quinolones, and colistin in feces from livestock in Uruguay. During 2016-2019, fecal samples from 132 broiler and layer chicken flocks, 100 calves, and 50 pigs, were studied in Uruguay. Samples were cultured on MacConkey Agar plates supplemented with ciprofloxacin, ceftriaxone, or colistin. E. coli isolates were identified by mass spectrometry and antibiotic susceptibility testing was performed by disk diffusion agar method and colistin agar test. Antibiotic resistance genes were detected by polymerase chain reaction and sequencing. The most frequently detected resistance gene was qnrB19, recovered from 87 animals. Regarding plasmid-mediated quinolone resistance genes, qnrS1 was the second in prevalence (23 animals) followed by qnrE1, found in 6 chickens and two calves. Regarding resistance to oxyimino-cephalosporins, 8 different ß-lactamase genes were detected: bla CTX-M-8 and bla CMY-2 were found in 23 and 19 animals, respectively; next, bla CTX-M-2 and bla SHV-12 in 7 animals each, followed by bla CTX-M-14 in 5, bla CTX-M-15 and bla SHV2a in 2, and bla CTX-M-55 in a single animal. Finally, the mcr-1 gene was detected only in 8 pigs from a single farm, and in a chicken. Isolates carrying bla CMY-2 and bla SHV-12 were also found in these animals, including two isolates featuring the bla CMY-2/mcr-1 genotype. To the best of our knowledge, this is the first work in which the search for transferable resistance to highest priority critically important antibiotics for human health is carried out in chickens and pigs chains of production animals in Uruguay.

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Integrative conjugative elements (ICEs) are widespread in many bacterial species, often carrying antibiotic resistance determinants. In the present work, we screened a collection of Proteus mirabilis clinical isolates for the presence of type 1 SXT/R391 ICEs. Among the 76 isolates analyzed, 5 of them carry such elements. The complete sequences of these elements were obtained. One of the isolates carried the CMY-2 beta-lactamase gene in a transposon and is nearly identical to the element ICEPmiJpn1 previously described in Japan, and later shown to be present in other parts of the world, indicating global spread of this element. Nevertheless, the Brazilian isolate carrying ICEPmiJpn1 is not clonally related to the other lineages carrying the same element around the world. The other ICEs identified in this work do not carry known antibiotic resistance markers and are diverse in variable gene content and size, suggesting that these elements may be responsible for the acquisition of other advantageous traits by bacteria. Some sequences carried by these elements in Brazilian strains were not previously found in other SXT/R391 variants.

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Objective: This study aimed to determine the prevalence of fecal carriage of antibiotic-resistant Escherichia coli of healthy household dogs with an emphasis on extended-spectrum ß-lactamases (ESBL), AmpC-type ß-lactamases and resistance to quinolones. Materials and Methods: Rectal swabs were collected from 74 dogs without any clinical evidence of gastrointestinal disease. Samples were cultured on MacConkey agar plates and MacConkey supplemented with 2 µg/mL cefotaxime or 5 µg/mL ciprofloxacin. Isolates were identified with Vitek 2 Compact and susceptibility testing performed by Kirby Bauer disk diffusion method. Minimal inhibitory concentration (MIC) was done on isolates resistant to cefotaxime, ciprofloxacin, and nalidixic acid. PCR amplification was performed to detect CTX-M and CMY-2. Isolates positive for CTX-M and/or CMY-2 were selected for whole-genome sequencing. Results: Multiresistance was detected in 56% of the isolates. A high percentage of resistance was detected for cefazolin (63%), ampicillin (54%), streptomycin (49%), nalidixic acid (42%) and tetracycline (38%). The MIC50 and MIC90 for isolates resistant to cefotaxime (24%) was determined as 16 and >250 µg/mL, respectively; for ciprofloxacin (18%), 125 and 250 µg/mL, respectively. ESBL (CTX-M type) and AmpC (CMY-2 type) were detected in 6 (7.1%) and 14 (19%) of the isolates, respectively. Whole-genome sequence analysis showed high genetic diversity in most of the isolates and a large variety of resistance mechanisms, including mobile genetic elements. Conclusion: The frequency of multidrug-resistant E. coli is worrying, mainly because of the presence of many isolates producing ESBL and AmpC ß-lactamases. Based on the "One Health" concept, considering the relationships between animals, humans, and the environment, these data support the notion that companion animals are important reservoirs of multidrug-resistant bacteria.

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Salmonella enterica serovar Paratyphi B variant Java sequence type 28 is prevalent in poultry and poultry meat. We investigated the evolutionary relatedness between sequence type 28 strains from Europe and Latin America using time-resolved phylogeny and principal component analysis. We sequenced isolates from Colombia, Guatemala, Costa Rica, and the Netherlands and complemented them with publicly available genomes from Europe, Africa, and the Middle East. Phylogenetic time trees and effective population sizes (Ne) showed separate clustering of strains from Latin America and Europe. The separation is estimated to have occurred during the 1980s. Ne of strains increased sharply in Europe around 1995 and in Latin America around 2005. Principal component analysis on noncore genes showed a clear distinction between strains from Europe and Latin America, whereas the plasmid gene content was similar. Regardless of the evolutionary separation, similar features of resistance to ß-lactams and quinolones/fluoroquinolones indicated parallel evolution of antimicrobial resistance in both regions.

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In this study we characterized the genetic environment of blaCTX-M and blaCMY-2 genes carried by 46 Escherichia coli isolates obtained from 20 chicken carcasses produced by five different brands in Brazil, including exporters and antibiotic-free-certified producers, purchased between 2010 and 2014. Similar plasmids characterized according to size and incompatibility group (Inc) were identified in E. coli belonging to different MLST-ST collected, regardless of carcass brand or production system. Hybridization assays with transconjugant strains revealed that blaCMY-2 gene (n = 19) was located on 85 kb plasmids of IncB/O, IncI1, IncFIB, or nontypeable groups. blaCTX-M-8 (n = 9) was located on 90 kb IncI1 plasmids. blaCTX-M-2 (n = 14) was inserted in class 1 integrons and conjugated only by one isolate in a 125 kb IncP plasmid. blaCTX-M-15 (n = 1), rarely described in isolates from food-producing animals in South America, was characterized by whole genome sequencing of transconjugant; the gene was carried in a 49.3 kb IncX1 plasmid. Sequencing of bla gene-flanking regions indicated the association of these genes with previously described insertion sequences. These results suggest that conserved genetic environments are related to ESBL and pAmpC genes in the Brazilian chicken production chain.

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The clinical importance of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has increased steadily over the years. The presence of the blaTEM, blaSHV, and blaCTX-M genes in the environment has been recently recognized as an important issue in the dissemination of resistance to cephalosporins. Food animals are considered important vectors for transfer of ESBL genes from the environment to humans. The objective of this study was to characterize the ESBL genes (blaTEM, blaSHV, and blaCTX-M types) that were most prevalent among 343 ceftazidime-resistant E. coli isolates (17 batches from 12 different farms) obtained from cloacal swabs of broiler chicken in southern Brazil. The blaSHV, blaCTX-M, blaTEM, blaIMP-type, blaVIM-type, blaNDM-1, blaKPC-type, blaGES-type, blaOXA-48, and mcr-1 genes were evaluated by polymerase chain reaction. A total of 27 (7.9%) E. coli isolates were positive for ESBL genes as follows: 24 for blaCTX-M (23 blaCTX-M-2 Group and 1 blaCTX-M-8) and 3 for blaSHV (2 blaSHV-2a and 1 blaSHV-18). A random sample of 32 ceftazidime/cefotaxime-resistant isolates that were negative for ESBL genes were evaluated for the presence of blaCMY-2 and 24 (75%) tested positive. We detected the blaCMY-2 gene in isolates from all farms. All isolates positive for ESBL or blaCMY-2 are considered multidrug resistant (resistant to at least three antibiotic classes). Our results suggest that broiler chickens are an important reservoir of blaCMY-2 and ESBL genes, including blaSHV-2a, described for the first time in animals originating from Brazil in this study, and blaSHV-18, which has never been described in Brazil before. This fact highlights the importance of controlling the use of antibiotics in animal production to reduce environmental sources of resistance genes.

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Extended-spectrum ß-lactamase (ESBL), plasmid-mediated AmpC (pAmpC) and MCR-1 phosphoethanolamine transferase enzymes have been pointed out as the main plasmid-mediated mechanisms of resistance to third generation cephalosporins (TGC) and colistin, respectively, and are currently considered a major concern both in human and veterinary medicine. Little data on these resistance determinants prevalence in companion animal infections is available. The aim of this study was to determine the resistance profile of Escherichia coli isolated from pet infections, in Argentina, and to characterize the resistance mechanisms to TGC, as well as the presence of the plasmid-borne colistin resistance gene, mcr-1. A total of 54 E. coli isolates were collected from clinical samples in dogs and cats; from them, 20/54 (37%, CI95: [24%; 51%]) displayed resistance to TGC. In this regard, thirteen pAmpC-producing isolates were positive for blaCMY-2 genes, whereas seven ESBL- producers harboured blaCTX-M-2 (n = 4), blaCTX-M-15 (n = 2) and blaCTX-M-14 (n = 1) genes. One E. coli strain (V80), isolated from a canine urinary tract infection, showed resistance to colistin (MIC = 8 µg/ml) and whole-genome sequencing analysis revealed co-occurrence of mcr-1.1, blaCTX-M-2, aadA1, ant(2'')-Ia, catA1 and sul1 genes; the former being carried by a 60,587-bp IncI2 plasmid, previously reported in human colistin-resistant E. coli. E. coli V80 belonged to ST770 and the highly virulent phylogenetic group B2. In general, most of these multidrug-resistant isolates belonged to the phylogenetic group F (11/20) and to a lesser extent B2 (5/20), B1 (2/20), D (1/20) and E (1/20). In summary, CMY- and CTX-M-type ß-lactamases may constitute the main TGC resistance mechanism in E. coli isolated from pet infections in Argentina, whereas dissemination of colistin resistance mechanism MCR-1 in the human-animal interface has been mediated by IncI2 plasmids.

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In this study we report the characterization of plasmid-mediated CMY-2-producing Salmonella Heidelberg recovered from food, poultry, and poultry environment in Brazil, between 2014 and 2016. The blaCMY-2 resistance gene was allocated in large (90-148 kb) IncI1 type transferable plasmids. Salmonella Heidelberg isolates were genetically related, indicating the dissemination of closely related isolates among food, poultry, and its environment. This is the first report of IncI1 replicon-types of plasmids encoding the blaCMY-2 resistance gene in Salmonella Heidelberg isolates in Brazil, the world's biggest exporter of chickens.

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