Kettner, J. E. | bioRxiv Science

bioRxiv2024

Prevalence of antimicrobial resistance phenotypes and genes in stable fly- and manure-derived bacterial isolates from clinically relevant taxa in dairy settings

AimsThis study aimed to characterize and compare the antimicrobial resistance (AMR) profiles of clinically relevant bacterial taxa isolated from biting stable flies (Stomoxys spp.) and bovine manure samples collected at a dairy research facility over the course of an entire fly breeding season. The presence of extended-spectrum beta-lactamase (ESBL) and other antimicrobial resistance genes (ARGs) was also examined. Methods and resultsA total of 606 fly- and 180 manure-derived strains were tested via disk diffusion for susceptibility to commonly administered antibiotics used in veterinary and human medicine. A small percentage of Enterobacterales exhibited resistance to the tested antimicrobials, including ceftiofur and other beta-lactam antibiotics. Extended spectrum beta-lactamase genes (TEM, CTX, OXA, CMY) were detected by PCR amplification in ceftiofur-resistant Escherichia coli, Klebsiella and Enterobacter spp. isolates. We additionally identified pirlimycin-resistant Staphylococcus and Mammaliicoccus spp. isolates encoding lnuA, a lincosamide resistance gene found primarily on small mobilizable plasmids. ConclusionsThese findings highlight the significance of stable flies in the carriage of antimicrobial-resistant bacterial strains and plasmid-associated ARGs on dairy farms.

microbiology↗

bioRxiv2024

Stable flies harbor a low complexity microbiota dominated by mastitis-associated bacteria

Hematophagous Stomoxys (stable) fly populations in dairy barns are sustained by a constant availability of cattle hosts and manure, which serve as major reservoirs of both zoonotic and opportunistic bacterial pathogens. However, the overall composition and diversity of bacterial communities associated with Stomoxys flies and the ability of biting flies to acquire and transmit potentially pathogenic bacteria present in their surrounding environment remain to be investigated. Here, we present the first culture-independent examination of Stomoxys-associated bacterial communities through longitudinal sampling of fly and manure samples collected from two connected dairy facilities in South Central Wisconsin. High throughput 16S rRNA gene amplicon sequencing was used to characterize and compare bacterial communities present on or within flies and in manure collected from the same facility. Bacterial alpha diversity was overall higher in manure samples as compared to fly samples, with manure-associated bacterial communities being dominated by members of the Bacteroidales, Eubacteriales, and Oscillospirales. In contrast, flies harbored relatively low-complexity communities dominated by members of the Enterobacterales, Staphylococcales, and Lactobacillales. Clinically relevant bacterial strains, including Escherichia spp. and other taxa associated with mastitic cows housed in the same facilities, were detected in paired fly and manure samples but exhibited dramatically elevated abundances in fly samples as compared to manure samples. Viable colonies of Escherichia, Klebsiella, and Staphylococcus spp. were also readily isolated from fly samples, confirming that flies harbor culturable mastitis associated bacteria. This study provides definitive support for a potential role for biting flies in mediating bacterial pathogen transmission in dairy barns and other agricultural settings. IMPORTANCEDisease prevention on dairy farms has significant implications for cattle health, food security, and zoonosis. Of particular importance is the control of bovine mastitis, which can be caused by a diverse array of environmental bacterial pathogens, including Klebsiella, E. coli, Streptococcus, and Staphylococcus spp. Despite being one of the most significant and costly cattle diseases worldwide, the epidemiology of bovine mastitis is not well understood. This study provides the first culture-dependent and culture-independent evidence to support the potential for biting flies to transmit opportunistic bovine and human pathogens in agricultural settings. It also links carriage of specific bacterial taxa in flies to clinical mastitis cases in cows housed in the same facility at the time of sampling. Altogether, these results indicate that biting flies represent an important, yet understudied biosecurity threat to animal husbandry facilities.

microbiology↗