Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens

Abstract

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

Environmental Biofilms as Reservoirs for Antimicrobial Resistance

“…With regard to agriculture and aquaculture practices, 51 antibiotics have been reported as being in use according to the World Health Organization ( WHO, 2017 ), including the six most-common classes of antibiotics: tetracyclines, quinolones, aminoglycosides, polymyxins, macrolides, penicillins, and sulfonamides ( Chekabab et al, 2021 ). It is important to note that antibiotic usage for humans and animals often occurs within similar drug classes (e.g., gentamicin/aminoglycoside, ampicillin/ β-lactams, ciprofloxacin/fluoroquinolones, trimethoprim/antifolate, and tetracycline) ( Finley et al, 2013 ; EUCAST, 2019 ); thus, the potential for cross-resistance to those drugs used in either setting exists.…”

“…Tetracyclines and macrolides have historically seen extensive use in agriculture (Ebmeyer et al, 2021) and ARGs conferring resistance to these antibiotics are among the most prevalent (Chekabab et al, 2020(Chekabab et al, , 2021. In China, most of the veterinary antibiotics consist of tetracyclines and sulfonamides (Zhou et al, 2020).…”

Impact of Raised without Antibiotics Measures on Antimicrobial Resistance and Prevalence of Pathogens in Sow Barns

“…The impact of antibiotic treatments on the prevalence of pathogens and ARGs in the gut microbiome of piglets and grower-finisher pigs has previously been examined [ 14 , 15 , 16 , 17 ]; however, limited information is available on the potential differential effects of these treatments on the abundance of pathogens and ARGs in the gut and nasal microbiome of sows. The monitoring of antimicrobial usage in the Canadian swine industry through the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) is mainly focused on grower-finisher pigs, with no data on sows available [ 13 ].…”

“…A subset of the taxonomic profiles belonging to bacterial pathogens was used to identify the total complement of pathogens (the pathome). As described in a study by Chekabab et al [ 14 ], microbes were classified and identified on the species-, subspecies-, and strain-levels. The relative abundance and frequency of the identified organisms were quantified using GenBook comparators and the GENIUS software implemented within the CosmosID algorithm.…”

“…Furthermore, the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS), which monitors antimicrobial usage in the Canadian swine industry, is mostly focused on grower-finisher pigs, with no data on sows available [ 13 ]. The impact of antibiotic treatments on the prevalence of pathogens and antimicrobial-resistant genes (ARGs) in the gut microbiome of piglets and grower-finisher pigs has previously been examined [ 14 , 15 , 16 , 17 ]; however, little is known about the potential differential effects of these treatments on the abundance of pathogens and ARGs in the gut and nasal microbiome of sows [ 12 ]. Additionally, while the gut microbiome of pigs has been extensively studied, the impact of antimicrobial treatment on the nasal microbiome has yet to be investigated [ 18 , 19 ].…”