Pilot study on nasal microbiota dynamics and MRSA carriage of a pig cohort housed on straw bedding.

Methicillin-resistant Staphylococcus aureus (MRSA) can be transmitted between pigs and humans on farms. Hence, the reduction of MRSA carriage in pigs could decrease the risk of zoonotic transmission. Recently, straw bedding has been found to significantly reduce MRSA carriage in pigs. The mechanisms behind this effect remain unclear but changes in the nasal microbiome may play a role. In this exploratory study, the nasal microbiota of pigs kept on straw was examined using V1/V2 16S rRNA gene sequencing. Nasal swabs were collected from 13 pigs at six different time points during the course of a full fattening cycle resulting in 74 porcine samples. In addition, straw samples were collected at each time point. Eleven out of 13 pigs were MRSA positive at housing-in. We found a strong temporal pattern in the microbial communities. Both microbial diversity and abundance of Staphylococcus species peaked in week 5 after introduction to the straw stable decreased in week 10, when all pigs turned MRSA-negative, and increased again toward the end of the fattening period. These findings show that the introduction of pigs into a new environment has a huge impact on their nasal microbiota, which might lead to unfavorable conditions for MRSA. Moreover, other Staphylococcus species may play a role in eliminating MRSA carriage. We designed a follow-up study including two different husbandry systems to further assess these effects.

Prevalence of LA-MRSA in pigsties: analysis of factors influencing the (De)colonization process.

Professional pig husbandry is often associated with a more or less high load of LA-MRSA. Possible risk factors for LA-MRSA colonization in pig herds have already been identified in studies suggesting that housing conditions may affect LA-MRSA prevalence. In Europe, pigs are kept under variety of conditions. The aim of this study is to identify husbandry and housing condition factors that affect colonization with LA-MRSA. 78 pig farms were selected and assigned to three categories according to housing conditions: conventional, alternative and organic. Animal and surface samples were taken and examined for the presence of LA-MRSA at beginning and end of one fattening period per farm. Altogether, a significant (p < 0.05) decrease in colonization with LA-MRSA from beginning to end of the fattening periods in pigs and surfaces can be observed. Alternative farms showed a higher dynamic in the colonization. In organic farms, almost no colonization was found. Influencing housing condition factors that determine LA-MRSA status at the end of the fattening period are the number of pigs in the building, LA-MRSA status at the beginning of fattening period, material of the floor (straw bedding), strictness of black-white separation and antibiotic treatment during the fattening period. For pig farming in general, knowledge and measures to reduce the colonization with LA-MRSA would be important.

Farming Practice Influences Antimicrobial Resistance Burden of Non-Aureus Staphylococci in Pig Husbandries.

Non-aureus staphylococci (NAS) are ubiquitous bacteria in livestock-associated environments where they may act as reservoirs of antimicrobial resistance (AMR) genes for pathogens such as Staphylococcus aureus. Here, we tested whether housing conditions in pig farms could influence the overall AMR-NAS burden. Two hundred and forty porcine commensal and environmental NAS isolates from three different farm types (conventional, alternative, and organic) were tested for phenotypic antimicrobial susceptibility and subjected to whole genome sequencing. Genomic data were analysed regarding species identity and AMR gene carriage. Seventeen different NAS species were identified across all farm types. In contrast to conventional farms, no AMR genes were detectable towards methicillin, aminoglycosides, and phenicols in organic farms. Additionally, AMR genes to macrolides and tetracycline were rare among NAS in organic farms, while such genes were common in conventional husbandries. No differences in AMR detection existed between farm types regarding fosfomycin, lincosamides, fusidic acid, and heavy metal resistance gene presence. The combined data show that husbandry conditions influence the occurrence of resistant and multidrug-resistant bacteria in livestock, suggesting that changing husbandry practices may be an appropriate means of limiting the spread of AMR bacteria on farms.

Prevalence and zoonotic transmission of colistin-resistant and carbapenemase-producing Enterobacterales on German pig farms.

The treatment of infections due to colistin-resistant (Col-E) and carbapenemase-producing (CPE) Enterobacterales challenges clinicians both in human and veterinary medicine. Preventing zoonotic transmission of these multidrug-resistant bacteria is a Public Health priority. This study investigates the prevalence of Col-E and CPE on 81 pig farms in North-West Germany as well as among 138 directly exposed humans working on these farms. Between March 2018 and September 2020, 318 samples of porcine feces were taken using boot swabs. Farm workers provided a stool sample. Both a selective culture-based approach and a molecular detection of colistin (mcr-1 to mcr-5) and carbapenem resistance determinants (bla OXA-48/bla VIM/bla KPC/bla NDM) was used to screen all samples. Isolates from farm workers and farms were compared using core genome multilocus-sequence typing (cgMLST) and plasmid-typing. CPE were cultured neither from porcine feces nor from human stool samples. In one stool sample, bla OXA-48 was detected, but no respective CPE isolate was found. Col-E were found in 18/318 porcine (5.7%) samples from 10/81 (12.3%) farms and 2/138 (1.4%) farmers, respectively. All Col-E isolates were Escherichia coli harboring mcr-1. Both farm workers colonized with Col-E worked on farms where no Col-E were detected in porcine samples. In conclusion, CPE were absent on German pig farms. This supports findings of culture-based national monitoring systems and provides evidence that even when improving the diagnostic sensitivity by using molecular detection techniques in addition to culture, CPE are not prevalent. Col-E were prevalent in porcine feces despite a recent decrease in colistin usage among German livestock and absence of colistin treatments on the sampled farms. Farmers carried Col-E, but zoonotic transmission was not confirmed.