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.

In-feed nutritional additive probiotic Saccharomyces boulardii RC009 can substitute for prophylactic antibiotics and improve the production and health of weaning pigs

Background and Aims

Non-therapeutic antibiotic use is associated with the current decrease in antibiotic therapeutic efficiency and the emergence of a wide range of resistant strains, which constitutes a public health risk. This study aimed to evaluate the use of Saccharomyces cerevisiae var. boulardii RC009 as a nutritional feed additive to substitute the prophylactic use of antibiotics and improve the productive performance and health of post-weaning piglets.

Materials and Methods

Four regular nutritional phases were prepared. Post-weaning pigs (21-70 days old) received one of two dietary treatments: T1-basal diet (BD-control group) with in-feed antibiotics as a prophylactic medication (one pulse of Tiamulin in P3 and one pulse of Amoxicillin in P4); and T2-BD without in-feed antibiotics but with Saccharomyces boulardii RC009 (1 × 1012 colony forming unit/T feed). The feed conversion ratio (FCR), total weight gain (TWG-kg), and daily weight gain (DWG-kg) were determined. A post-weaning growth index (GI) was calculated and animals (160 days old) from each treatment were analyzed at the abattoir after sacrifice for carcass weight and respiratory tract lesions.

Results

Pigs consuming probiotics had higher TWG and DWG than the control group. The group of animals with low body weight obtained the same results. Saccharomyces boulardii administration decreased diarrhea, and FCR reduction was related to a GI improvement. A significant increase in carcass weight and muscle thickness reduction was observed in animals received the probiotic post-weaning.

Conclusion

Saccharomyces boulardii RC009, a probiotic additive, was found to improve the production parameters of pigs post-weaning and enhance their health status, indicating that it may be a promising alternative to prophylactic antibiotics.