A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone.

Introduction: There are concerns that antimicrobial usage (AMU) is driving an increase in multi-drug resistant (MDR) bacteria so treatment of microbial infections is becoming harder in humans and animals. The aim of this study was to evaluate factors, including usage, that affect antimicrobial resistance (AMR) on farm over time. Methods: A population of 14 cattle, sheep and pig farms within a defined area of England were sampled three times over a year to collect data on AMR in faecal Enterobacterales flora; AMU; and husbandry or management practices. Ten pooled samples were collected at each visit, with each comprising of 10 pinches of fresh faeces. Up to 14 isolates per visit were whole genome sequenced to determine presence of AMR genes. Results: Sheep farms had very low AMU in comparison to the other species and very few sheep isolates were genotypically resistant at any time point. AMR genes were detected persistently across pig farms at all visits, even on farms with low AMU, whereas AMR bacteria was consistently lower on cattle farms than pigs, even for those with comparably high AMU. MDR bacteria was also more commonly detected on pig farms than any other livestock species. Discussion: The results may be explained by a complex combination of factors on pig farms including historic AMU; co-selection of AMR bacteria; variation in amounts of antimicrobials used between visits; potential persistence in environmental reservoirs of AMR bacteria; or importation of pigs with AMR microbiota from supplying farms. Pig farms may also be at increased risk of AMR due to the greater use of oral routes of group antimicrobial treatment, which were less targeted than cattle treatments; the latter mostly administered to individual animals. Also, farms which exhibited either increasing or decreasing trends of AMR across the study did not have corresponding trends in their AMU. Therefore, our results suggest that factors other than AMU on individual farms are important for persistence of AMR bacteria on farms, which may be operating at the farm and livestock species level.

The effectiveness of short-duration in-feed organic acid use in finisher pigs for Salmonella control at slaughter.

Reducing the risk of Salmonella contaminated pork products entering the food chain is important for improving food safety. This study aimed to evaluate the effectiveness of the short-duration use of three acidified feed interventions in finisher pigs for reducing the faecal shedding, caecal carriage and carcase contamination of Salmonella at slaughter. We also investigated the presence of Salmonella in transportation vehicles and abattoir lairages used prior to slaughter. In a series of seven farm trials, two groups of pigs received either their normal ration (control), or a ration containing one of three organic acid products (intervention) for a four-week period before slaughter. Product A was trialled on five farms, and Products B and C were trialled on one farm each, included in the ration of intervention pigs at the manufacturers recommended rate. Faecal samples were collected and examined before and after the four-week intervention; caecal content samples and carcase swab samples were collected at slaughter. The lorry used to transport pigs to slaughter and abattoir lairage pens used to hold pigs were also sampled. During one trial (farm ID: AT03), no Salmonella was detected during either farm visit, and therefore this farm was excluded from further analysis of the effectiveness of organic acid interventions. Overall regression analysis indicated there was no significant difference in faecal shedding between the control groups at the baseline visit and the follow-up visit in pigs which received Product A (P = 0.262) or Product B (P = 0.094) in comparison to the control groups. On the other hand, there was evidence to suggest that the use of Product C was associated with an increase in faecal shedding compared to the control groups (P < 0.001). Similarly, Product A was not significantly associated (P > 0.05) with the caecal carriage of Salmonella. However, Product B (P = 0.029) and Product C (P = 0.050) were associated with an increase in caecal carriage in comparison to the control groups. These latter products were only trialled on one farm each, and these results may be attributable to natural random variation.

Genomic network analysis of environmental and livestock F-type plasmid populations.

F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum ß-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.

Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.

Review of pig health and welfare surveillance data sources in England and Wales.

The capability to set baselines and monitor trends of health and welfare conditions is an important requirement for livestock industries in order to maintain economic competitiveness and sustainability. Monitoring schemes evaluate the relative importance of conditions so that: appropriate actions can be determined, prioritised and implemented; new and (re)emerging conditions can be promptly detected and the effectiveness of any actions can be measured. In 2011, the national pig levy board published a strategy document highlighting health and welfare conditions of importance to the pig industry that were to be targeted for control. In this study, existing schemes that could be used to monitor or set baselines for these conditions in pigs were reviewed, in order to evaluate their suitability for this purpose, using a standardised surveillance evaluation framework (SERVAL). The schemes included: government-funded surveillance of endemic and exotic disease and pig welfare; industry surveillance of endemic diseases; regional schemes for improving pig health; national accreditation schemes and information collected by retailers, private veterinary practices and private laboratories. The evaluation of each scheme highlights its capability to monitor any of the targeted conditions. This study identifies the biases, strengths and gaps in each scheme and provides discussion of opportunities for future development.