Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms

Control measures are being introduced globally to reduce the prevalence of antibiotic resistance (ABR) in bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in bacterial species with the potential to be key opportunistic human pathogens, such as Escherichia coli, on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin-resistant (3GC-R) E. coli, which were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from fecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal and vertical transmission of 3GC-R mechanisms. CTX-M-15 and CTX-M-2 were more often produced by isolates from dairy farms, while CTX-M-8 and CMY-2 and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more common in isolates from pig farms. This suggests different selective pressures for antibiotic use in these two animal types. We identified the β-lactamase gene blaROB, which has previously only been reported in the family Pasteurellaceae, in 3GC-R E. coli. blaROB was found alongside a novel florfenicol resistance gene, ydhC, also mobilized from a pig pathogen as part of a new composite transposon. As the first comprehensive genomic survey of 3GC-R E. coli in Argentina, these data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate the zoonotic transmission of resistant bacteria in this region.

IMPORTANCE

Little is known about the ecology of critically important antibiotic resistance among bacteria with the potential to be opportunistic human pathogens (e.g., Escherichia coli) on South American farms. By studying 70 pig and dairy cattle farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli and 3GC-R plasmids were diverse, suggestive of long-term circulation in this region. We identified the de novo mobilization of the resistance gene blaROB from pig pathogens into E. coli on a novel mobile genetic element, which shows the importance of surveying poorly studied regions for antibiotic resistance that might impact human health.

Multidrug-resistant Escherichia coli harbouring mcr-1 and blaCTX-M genes isolated from swine in Argentina

OBJECTIVES

Multidrug-resistant Escherichia coli isolates recovered from food-producing animals are a global public-health concern, especially those with transferable mechanisms of antimicrobial resistance such as extended-spectrum β-lactamase (ESBL) and mcr-1 genes. Here we report for the first time E. coli recovered from diarrhoeic and healthy pigs harbouring bla_CTX-M and/or mcr-1 from Argentinean farms.

METHODS

During 2017, a total of 34 E. coli were recovered from 31 faecal samples from diarrhoeic piglets and healthy fattening pigs from five pig farms in three Argentinean provinces. Antimicrobial susceptibility was evaluated by agar diffusion and resistance genes were identified by PCR. Multiplex PCR was applied to screen for ST69, ST73, ST95 and ST131 clones. Genetic relationships were evaluated by XbaI-PFGE.

RESULTS

A high diversity of resistance profiles was observed (20 profiles among 34 isolates), and 71% of isolates were multidrug-resistant. Resistance to third-generation cephalosporins (3GCs) was observed in 28 isolates and was associated with bla_CTX-M (24), bla_CMY (3) and bla_PER-2 (1) genes. bla_CTX-M alleles were grouped by specific PCR as follow: 17 bla_CTX-M-8/25; 4 bla_CTX-M-1/15; 2 bla_CTX-M-2; and 1 bla_CTX-M-9/14. Twelve isolates were positive for mcr-1, of which six were also resistant to 3GCs and were positive for bla_CTX-M-8/25 (4), bla_CTX-M-1/15 (1) or bla_CMY (1). High genetic diversity was observed, discriminating 29 profiles. One ST131 and two ST95 human-associated clones were detected.

CONCLUSION

Here we describe E. coli isolates recovered from diarrhoeic piglets and healthy fattening pigs harbouring ESBL and/or mcr-1 genes. 3GC resistance was mainly associated with CTX-M, in particular with bla_CTX-M-8/25 alleles.

Enterotoxigenic Escherichia coli Subclinical Infection in Pigs: Bacteriological and Genotypic Characterization and Antimicrobial Resistance Profiles

Enterotoxigenic Escherichia coli (ETEC) is the major pathogen responsible for neonatal diarrhea, postweaning diarrhea, and edema disease in pigs. Although it can be harmless, ETEC is also present in the intestines of other animal species and humans, causing occasional diarrhea outbreaks. The evaluation of this pathogen's presence in food sources is becoming an increasingly important issue in human health. In order to determine the prevalence of ETEC in nondiarrheic pigs, 990 animals from 11 pig farms were sampled. Using end-time polymerase chain reaction (PCR), eltA, estI genes, or both, were detected in 150 (15.2%) animals. From the positive samples, 40 (26.6%) ETEC strains were isolated, showing 19 antibiotic-resistance patterns; 52.5% of these strains had multiple antibiotic resistances, and 17.5% carried the intI2 gene. The most prevalent genotypes were rfb(O157)/estII/aidA (32.5%) and estI/estII (25.0%). The estII gene was identified most frequently (97.5%), followed by estI (37.5%), astA (20.0%), and eltA (12.5%). The genes coding the fimbriae F5, F6, and F18 were detected in three single isolates. The aidA gene was detected in 20 ETEC strains associated with the estII gene. Among the isolated ETEC strains, stx(2e)/estI, stx(2e)/estI/estII, and stx(2e)/estI/estII/intI2 genotypes were identified. The ETEC belonged to 12 different serogroups; 37.5% of them belonged to serotype O157:H19. Isolates were grouped by enterobacterial repetitive intergenic consensus-PCR into 5 clusters with 100.0% similarity. In this study, we demonstrated that numerous ETEC genotypes cohabit and circulate in swine populations without clinical manifestation of neonatal diarrhea, postweaning diarrhea, or edema disease in different production stages. The information generated is important not only for diagnostic and epidemiological purposes, but also for understanding the dynamics and ecology of ETEC in pigs in different production stages that can be potentially transmitted to humans from food animals.

Wild-type minimal inhibitory concentration distributions in bacteria of animal origin in Argentina

The aim of this study was to determine the antimicrobial resistance profiles of indicator bacteria isolated from domestic animal feces. Minimal inhibitory concentration (MIC) was determined by agar dilution. Interpretative criteria on the basis of wild-type MIC distributions and epidemiological cutoff values (ECOFF or ECV) were used according to the 'European Committee on Antimicrobial Susceptibility Testing' (EUCAST) data. Results from 237 isolates of Escherichia coli showed reduced susceptibility for ampicillin, streptomycin and tetracycline, the antimicrobials commonly used in intensive breeding of pigs and hens. Regarding all the species of the genus Enterococcus spp., there are only ECOFF or ECV for vancomycin. Of the 173 Enterococcus spp. isolated, only one showed reduced susceptibility to vancomycin and was classified as 'non-wild-type' (NWT) population. This is the first report in Argentina showing data of epidemiological cutoff values in animal bacteria.

[Genotypic characterization of toxigenic Escherichia coli isolated from pigs with postweaning diarrhea (PWD) and edema disease (ED)]

The purpose of this work was to characterize 47 Escherichia coli strains isolated from 32 pigs diagnosed with postweaning diarrhea and three pigs with edema disease by PCR. Forty two (95.5 %) of the strains isolated from diarrheic pigs were characterized as enterotoxigenic E. coli (ETEC) and 2 (4.5 %) as Shiga toxin-producing E. coli (STEC). Fourteen (33.3 %) ETEC strains were positive for est/estII/fedA genes. The most complex genotype was eltA/estI/faeG/aidA. Strains isolated from pigs with ED were classified as porcine STEC and were stx2e/aidA carriers. Eleven (25 %) strains carried the gene encoding adhesin protein AIDA-I. However, genes coding for F5, F6, F41, intimin and Paa were not detected. The development of vaccines generating antibodies against prevalent E. coli adhesins in Argentina could be useful for the prevention of PWD and ED.

[Antimicrobial resistance in indicator and zoonotic bacteria isolated from domestic animals in Argentina]

Antimicrobial resistance profiles in indicator and zoonotic bacteria isolated from faeces of healthy animals without clinical signs of the following species: bovine, equine, ovine, porcine, layer hens, and canine, were studied. The chosen antimicrobials are frequently used in veterinary and human medicine. The agar diffusion was the method used. The obtained results of 240 Escherichia coli, 189 Enterococcus spp., 11 Campylobacter spp. and 2 Salmonella Gaminara (16:d:1,7) showed a greater percentage of resistance and multiresistance in intensive breeding animals, porcine and layer hens. The observed resistance to ampicillin, streptomycin, tetracycline and nalidixic acid in E. coli coincides with the antimicrobials most commonly used on animal farms, the same as tetracycline and erythromycin in Enterococcus spp. The strains of Salmonella Gaminara (16:d:1,7) were susceptible to the antimicrobials tested. In Campylobacter spp. the scarce number of isolates hindered an adequate interpretation of the results. Owing to the lack of data in our country on antimicrobial resistance in indicator and zoonotic bacteria in domestic animals, we consider that the obtained values could be used as a starting point for a future monitoring program.

[Antimicrobial resistance of Escherichia coli isolated from pigs in Argentina]

Antimicrobial resistance of Escherichia coil isolated from pigs in Argentina. Sixty-nine Escherichia coli isolates from healthy pigs or with clinical signs non-compatible with diarrhea caused by this microorganism, were studied. The purpose was to determine the resistance profile against antimicrobials frequently used in veterinary and human medicine. The agar diffusion method was used. High resistance percentages against antimicrobials used in swine farms such as ampicillin, streptomycin and tetracycline were observed, as well as against trimetoprim-sulfametoxazole and chloramphenicol, compounds that were stopped being used several years ago. Sixty two percent of isolates showed multidrug-resistance. The results obtained in this work corroborate the hypothesis that the phenotypic distribution of resistance and possibly that of its genetic determinants, are directly influenced by the antimicrobial treatments used.

Avian cholera in a southern giant petrel (Macronectes giganteus) from Antarctica

A southern giant petrel (Macronectes giganteus) was found dead at Potter Peninsula, King George Island, South Shetland, Antarctica. The adult male was discovered approximately 48 hr after death. Macroscopic and microscopic lesions were compatible with avian cholera and the bacterium Pasteurella multocida subsp. gallicida, serotype A1 was isolated from lung, heart, liver, pericardial sac, and air sacs. In addition, Escherichia coli was isolated from pericardial sac and air sacs. This is the first known report of avian cholera in a southern giant petrel in Antarctica.

[Serotyping of strains of Serpulina hyosenteriae isolated form swine with porcine dysentery symptoms in the province of Buenos Aires]

Seventeen Serpulina hyodysenteriae strains isolated from faeces, rectal swabs and intestinal contents of pigs with Swine Dysentery, from farms located in Buenos Aires province were serotyped. Samples on selective media (trypticase soy agar added by 5% ovine blood, 400 mg/l spectinomicin, 30 mg/l colistin, 30 mg/l vancomycin) were streaked and incubated under anaerobic atmosphere for 72 h at 42 degrees C. Suspected S. hyodysenteriae growth were identified by strong beta-hemolytic zone, without colonies, and the spirillar morphology, using the Victoria Blue 4-R stain were criteria following by S. hyodysenteriae preliminar identification. The following antigens were made by phenolic extraction from a concentrated inocula washed twice in PBS pH 7: whole-cell (WC), boiled cell (BC) and lipopolysaccharide (LPS). Two serological test were: coagglutination and immunodiffusion, using polyclonal rabbit antisera against the 9 serotypes of S. hyodysenteriae and S. innocens, using WC and BC like antigens for the first test and BC and LPS for the second. The Dot-ELISA Test was performed using BC and LPS antigens and monoclonal antibodies (AbM) against serotypes 1, 2, 3, 8, 9 of S. hyodysenteriae, AbM species-specific and AbM against S. innocens. All isolated S. hyodysenteriae strains belonged to serotype 8. Like in other countries occurred, it would exit a high regional prevalence of S. hyodysenteriae serotype, being the serotype 8 in Argentine.