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 ß-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.

Detection of Mycoplasma hyopneumoniae in nasal and laryngeal swab specimens in endemically infected pig herds.

BACKGROUND: Apparently, laryngeal swabs (LS) are more sensitive than nasal swabs (NS) and allow earlier detection of Mycoplasma hyopneumoniae by PCR. However, antecedents about the compared detection of M hyopneumoniae with NS and LS in growing pigs, from naturally infected herds, are lacking in the literature. Thus, this study compared the PCR detection of M hyopneumoniae from NS and LS in pigs of various ages. METHODS: A longitudinal study was performed at two farms where NS and LS were collected from three consecutive groups of 20 pigs at 3, 6, 10, 16 and 22 weeks of age. All samples were analysed by nested PCR for M hyopneumoniae detection. RESULTS: The probability of PCR detection of M hyopneumoniae was higher in LS for pigs of all ages (odds ratio (OR)=1.87; 95 per cent confidence interval (CI) 1.31-2.67) and in 22-week-old pigs (OR=4.87; 95 per cent CI 2.86-8.30). The agreement between both sample types was low to moderate (kappa 0.087-0.508), highlighting that M hyopneumoniae does not appear to colonise the respiratory tract in a generalised and consistent fashion. CONCLUSIONS: The results suggest that LS could be employed at different ages to achieve greater bacterial detection. Considering that LS is a minimally invasive, highly sensitive sample compared with the traditional NS, it could be suggested to employ this sample type for M hyopneumoniae detection in naturally infected pigs.