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The transmission of antimicrobial resistance bacteria from animals to humans has become an important concern. The extended-spectrum beta-lactamase (ESBL) -AmpC- producing Escherichia coli (ESBL-AmpC EC) and quinolones resistant E. coli are of particular interest. The present study aimed to evaluate the load and prevalence of antibiotic-resistant commensal E. coli along the goose production cycle on 2 free-range farms in central Italy. On A farm, oxytetracycline was administered, while the B farm did not use antibiotics during the geese productive cycle. One hundred geese of 1-day-old from the same batch were divided into the two farms. At hatching, the animals showed an average of E. coli loads was 6.83 ± 0.48 log CFU/g, and 0.28 ± 0.28, 0, 5.12 ± 0.54 log CFU/g for E. coli resistant to nalidixic acid (E. colinal), to cefotaxime (E. colicef) and to tetracyclines (E. colitet), respectively. The loads of E. coli, E. colinal, E. colicef and E. colitet on 224 environmental faecal pools were determined at 8 time points. Antimicrobial susceptibility and molecular characterization of E. colicef isolates were performed. The ANOVA was used to assess the difference in bacterial loads between the two farms. We described more than 50% of resistances for tetracyclines in both farms, and sulphonamides and cephazolin in the A farm. The loads of E. coli and E. colinal in faeces were estimated at approximately 6–7 log (CFU/g) and 5–6 log (CFU/g) in the two farms, respectively. The average load of extended-spectrum beta-lactamase Escherichia coli (ESBL EC) in goose faeces varied broadly along the production cycle: in the first weeks, a sharp increase was observed in both farms, while later on A farm, the burden of ESBL EC remained steady until the end of the production cycle and on B farm the load dramatically decreased from 6 wk of age onward. An increase in the proportion of E. colinal was observed on A farm shortly after the antibiotic administration. Our study shows that the dynamics of antibiotic-resistant E. coli in farmed geese are similar to the ones observed in broilers. However, the risk of the emergence of antibiotic-resistant commensal E. coli, might be mitigated by the adoption of good management practices, including prudent use of antibiotics.

Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of Escherichia coli, the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of blaCTX–M–15 was also investigated. Our results indicated that 57.5% of the E. coli strains were resistant to at least two antibiotic classes and 20% strains were multidrug resistant, i.e., resistant to three or more antibiotic classes. The multiple antibiotic resistance index of about one-third of the E. coli strains was quite high (>0.2), reflecting high contamination of river Yamuna with antibiotics. With regard to plasmid-mediated AMR genes, blaTEM–1 was present in 95% of the strains, followed by qnrS1 and armA (17% each), blaCTX–M–15 (15%), strA-strB (12%), and tetA (7%). Contrary to the earlier reports where blaCTX–M–15 was mostly associated with pathogenic phylogroup B2, our study revealed that the CTX-M-15 type extended-spectrum β-lactamases (ESBLs) were present in the commensal phylogroups A and B1, also. The genetic organization of blaCTX–M–15 was similar to that reported for E. coli, isolated from other parts of the world; and ISEcp1 was present upstream of blaCTX–M–15. The integrons of classes 2 and 3 were absent, but class 1 integron gene intI1 was present in 75% of the isolates, denoting its high prevalence in E. coli of river Yamuna. These evidences indicate that due to high prevalence of plasmid-mediated AMR genes and intI1, commensal E. coli can become vehicles for widespread dissemination of AMR in the environment. Thus, regular surveillance and management of urban rivers is necessary to curtail the spread of AMR and associated health risks.

Intensive pig production systems often rely on the use of antimicrobials and heavy metal feed additives to maintain animal health and welfare. To gain insight into the carriage of antimicrobial resistance genes (ARGs) in the faecal flora of commercially reared healthy swine, we characterised the genome sequences of 117 porcine commensal E. coli that carried the class 1 integrase gene (intI1+). Isolates were sourced from 42 healthy sows and 126 of their offspring from a commercial breeding operation in Australia in 2017. intI1+ E. coli was detected in 28/42 (67%) sows and 90/126 (71%) piglets. Phylogroup A, particularly clonal complex 10, and phylogroup B1 featured prominently in the study collection. ST10, ST20, ST48 and ST361 were the dominant sequence types. Notably, 113/117 isolates (96%) carried three or more ARGs. Genes encoding resistance to -lactams, aminoglycosides, trimethoprim, sulphonamides, tetracyclines and heavy metals were dominant. ARGs encoding resistance to last-line agents, such as carbapenems and third generation cephalosporins, were not detected. IS26, an insertion sequence noted for its ability to capture and mobilise ARGs, was present in 108/117 (92%) intI1+ isolates, and it played a role in determining class 1 integron structure. Our data shows that healthy Australian pig faeces are an important reservoir of multidrug resistant E. coli that carry genes encoding resistance to multiple first-generation antibiotics and virulence-associated genes.

Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a “highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem”. In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.

The spread of resistant bacteria from livestock to the food industry promoted an increase of alternative poultry production systems, such as organic and antibiotic-free ones, based on the lack of antimicrobial use, except in cases in which welfare is compromised. We aimed to investigate the antibiotic susceptibility of commensal Escherichia coli isolated from organic, antibiotic-free, and conventional broiler farms and slaughterhouses toward several antimicrobials critically important for human health. To assess antimicrobial susceptibility, all E. coli isolates and extended spectrum beta-lactamase (ESBL) E. coli were analysed by the microdilution method. The prevalence of tigecycline, azithromycin and gentamicin E. coli-resistant strains was highest in organic samplings. Conversely, the lowest prevalence of resistant E. coli strains was observed for cefotaxime, ceftazidime and ciprofloxacin in organic systems, representing a significant protective factor compared to conventional systems. All E. coli strains were colistin-susceptible. Contamination of the external environment by drug-resistant bacteria could play a role in the presence of resistant strains detected in organic systems. Of interest is the highest prevalence of cephalosporin resistance of E. coli in conventional samplings, since they are not permitted in poultry. Our results suggest that monitoring of antibiotic resistance of the production chain may be helpful to detect “risks” inherent to different rearing systems.

The objective of this study was to establish the prevalence and antimicrobial resistant patterns of commensal Escherichia coli isolated from healthy dogs. In total, 55 rectal swabs from clinically healthy dogs, kept outside (n = 20), and inside a house (n = 20) and from dogs kept at an animal shelter (n = 15), were collected for isolation of Escherichia coli. Resistance patterns to 11 antimicrobial agents were tested using E-test (Epsilometer test) to determine the MIC (Minimum Inhibitory Concentration). Multiplex polymerase chain reaction (M-PCR) amplification was used to detect selected genes conferring resistance to beta-lactams, tetracycline, aminoglycoside, sulphanilamide, quinolone, and phenicol classes of antimicrobial agents. Forty-eight E. coli strains were isolated from 55 (87.3%) dogs. Multi-drug resistance was present in 38% of resistant isolates. E. coli isolates showed the highest resistance rates to streptomycin (85.1%), ampicillin (77.1%), sulfamethoxazole (70.8%) and tetracycline (64.6%). The isolates were most sensitive to enrofloxacin (87.5%) and chloramphenicol (72.9%). Bacterial resistance genes were determined to tetracycline (tet) (9.7%) trimethoprim/sulfamethoxazole (dfrA1) (16.7%,), and chloramphenicol (catA1) (5.5%). In general, the prevalence of antimicrobial resistance in E. coli isolates from shelter dogs population was higher than in those from dogs kept inside and outside (P, Cilj ovoga istraživanja bio je utvrditi prevalenciju i antimikrobno rezistentne oblike komenzalne bakterije Escherichia coli, izolirane iz zdravih pasa. Za izolaciju bakterija Escherichia coli korišteno je ukupno 55 briseva rektuma zdravih pasa od kojih je jedna skupina držana na otvorenom (n = 20), jedna skupina u kući (n = 20), a jedna je skupina držana u skloništu za životinje (n = 15). Analiza oblika rezistencije na 11 antimikrobnih sredstava provedena je E-testom (test Epsilometar) za određivanje minimalne inhibitorne koncentracije (MIK). Multipleks reakcija lančanom polimerazom (M-PCR) upotrijebljena je za pronalaženje odabranih gena odgovornih za otpornost na beta-laktame, tetraciklin, aminoglikozid, sulfanilamid, kinolon i fenikol klase antimikrobnih sredstava. Od 55 pasa izolirano je 48 sojeva (87,3 %) E. coli. Višestruka otpornost na lijekove bila je prisutna u 38 % rezistentnih izolata. Izolati E. coli pokazali su najveću stopu rezistencije na streptomicin (85,1 %), ampicilin (77,1 %), sulfametoksazol (70,8 %) i tetraciklin (64,6 %). Najveća osjetljivost izolata utvrđena je na enrofloksacin (87,5 %) i kloramfenikol (72,9 %). Bakterijski geni za otpornost određeni su za tetraciklin (tet) (9,7 %) trimetoprim/sulfametoksazol (dfrA1) (16,7 %) i kloramfenikol (catA1) (5,5 %). Općenito, prevalencija antimikrobne rezistencije izolata E. coli iz skupine pasa držanih u skloništima bila je veća nego kod pasa držanih u kući ili na otvorenom (P

Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial resistance and virulence-associated genes (VAGs) and the zoonotic potential of commensalEscherichia colifrom swine is largely unknown. Furthermore, little is known about the role of commensalE. colias contributors to the mobilisation of antimicrobial resistance genes between food animals and the environment. Here, we report whole genome sequence analysis of 141E. colifrom the faeces of healthy pigs. Most strains belonged to phylogroups A and B1 and carried i) a class 1 integron; ii) VAGs linked with extraintestinal infection in humans; iii) antimicrobial resistance genesblaTEM, aphAl, cmlA, strAB, tet(A)A,dfrA12, dfrA5, sul1, sul2, sul3; iv)IS26;and v) heavy metal resistance genes (merA, cusA, terA). Carriage of the sulphonamide resistance genesul3was notable in this study. The 141 strains belonged to 42 multilocus sequence types, but clonal complex 10 featured prominently. Structurally diverse class 1 integrons that were frequently associated with IS26 carried unique genetic features that were also identified in extraintestinal pathogenicE. coli(ExPEC) from humans. This study provides the first detailed genomic analysis and point of reference for commensalE. coliof porcine origin, facilitating tracking of specific lineages and the mobile resistance genes they carry.Conflict of Interest StatementNone to declare.

The objective of the study was to examine the characteristics of the resistance profiles of Escherichia coli isolated from healthy pigs from three farms in Western Poland. The sensitivity to 13 antimicrobial agents was tested by a disk diffusion method, and the presence of 13 resistance genes was determined by PCR. The majority of the isolates were multi-resistant. The most common multi-resistance patterns were streptomycin, trimethoprim, sulfisoxazole, ampicillin, tetracycline. Although some resistance genes, such as strA/strB, blaTEM, sul1, sul2, and tetA, were equally represented in isolates from each farm, differences in the distribution of tetB and tetC, hfrV, dhfrXII, and sul1 resistance genes were observed among the isolates from different farms. Approximately one-third (35.9%) of the isolates possessed a class 1 integron. The four major different variable regions of the class 1 integron contained streptomycin (aadA1, aadA2, and aadA5) and/or trimethoprim (dhfrI, dhfrV and dhfrXVII), and/or sulphonamides (sul1) resistance genes. The results of this study emphasise that uncontrolled use of antibiotics causes the development of resistance and provides the evidence of frequent occurrence of more than one gene encoding the resistance to the same antimicrobial agent in the multi-resistant strains.

Diarrhoeagenic Escherichia coli (DEC) are an important cause of diarrhoea in children and are associated with high antibiotic resistance. However, there are few studies on the molecular mechanisms of resistance in this group of bacteria. The aim of this study was to determine the mechanisms associated with antibiotic resistance in the most common phenotypes of DEC. A total of 369 E. coli strains [commensal strains and DEC from children with (‘DEC-diarrhoea’) or without (‘DEC-control’) diarrhoea] isolated from children aged