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.

A simplified scoring system for the diagnosis of diarrhea and respiratory diseases in dairy calves.

Objective: To compare the capacity of a simplified calf health scoring chart (SIM score) with the University of Wisconsin's calf health scoring chart (WIN score) for the diagnosis of calf diarrhea and calf respiratory disease (RD). Animals and procedures: Holstein calves (N = 222) were clinically evaluated for diarrhea and RD diagnosis using the WIN and SIM scores. The WIN score was based on fecal consistency for diagnosis of diarrhea (0 = feces of normal consistency to 3 = watery feces; score ≥ 2 = positive diagnosis); and on nasal discharge, ocular discharge, coughing, ear position, and rectal temperature for diagnosis of RD (each clinical sign receives a score of 0 to 3; aggregate score ≥ 5 = positive diagnosis). The SIM score was based on a hide cleanliness score for diagnosis of diarrhea [0 = negative (calf was clean) and 1 = positive (tail head region, thighs, and/or legs were soiled)]; and on nasal discharge, ocular discharge, coughing, and ear position for diagnosis of RD (rectal temperature measurement was not required and each clinical sign had 2 levels of severity; aggregate score ≥ 5 = positive diagnosis). Results: In the RD diagnosis, the SIM score had a sensitivity of 88.24%, a specificity of 95.01%, a positive predictive value (PPV) of 55.56%, and a negative predictive value (NPV) of 99.13%. In the diarrhea diagnosis, the SIM score had a sensitivity of 94.62%, a specificity of 49.64%, a PPV of 18.22%, and an NPV of 98.73%. Conclusion: Compared with the WIN score, the SIM score is a reliable test for diagnosing RD but not for diagnosing diarrhea.

Un système de notation simplifié pour le diagnostic de la diarrhée et des maladies respiratoires chez les veaux laitiers. Objectif: Comparer la capacité d'un tableau de notation simplifié de la santé du veau (score SIM) avec le tableau de notation de la santé du veau (score WIN) de l'University of Wisconsin pour le diagnostic de la diarrhée du veau et de la maladie respiratoire du veau (RD). Animaux et procédures: Des veaux Holstein (N = 222) ont été évalués cliniquement pour le diagnostic de diarrhée et de RD à l'aide des scores WIN et SIM. Le score WIN était basé sur la consistance fécale pour le diagnostic de diarrhée (0 = fèces de consistance normale à 3 = fèces aqueuses; score ≥ 2 = diagnostic positif ); et sur l'écoulement nasal, l'écoulement oculaire, la toux, la position des oreilles et la température rectale pour le diagnostic de RD (chaque signe clinique reçoit un score de 0 à 3; score global ≥ 5 = diagnostic positif ). Le score SIM était basé sur un score de propreté de la peau pour le diagnostic de diarrhée [0 = négatif (le mollet était propre) et 1 = positif (la région de la tête de la queue, les cuisses et/ou les pattes étaient souillées); et sur l'écoulement nasal, l'écoulement oculaire, la toux et la position des oreilles pour le diagnostic de RD (la mesure de la température rectale n'était pas requise et chaque signe clinique avait 2 niveaux de gravité; score global ≥ 5 = diagnostic positif ). Résultats: Dans le diagnostic de RD, le score SIM avait une sensibilité de 88,24 %, une spécificité de 95,01 %, une valeur prédictive positive (VPP) de 55,56 % et une valeur prédictive négative (VPN) de 99,13 %. Dans le diagnostic de diarrhée, le score SIM avait une sensibilité de 94,62 %, une spécificité de 49,64 %, une VPP de 18,22 % et une VPN de 98,73 %. Conclusion: Comparé au score WIN, le score SIM est un test fiable pour diagnostiquer le RD mais pas pour diagnostiquer la diarrhée.(Traduit par Dr Serge Messier).