Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin

Romanò, Alicia; Ivanovic, Ivana; Segessemann, Tina; Vazquez Rojo, Laura; Widmer, Jérôme; Egger, Lotti; Dreier, Matthias; Sesso, Lorenzo; Vaccani, Michael; Schuler, Martin; Frei, Daniel; Frey, Juerg; Ahrens, Christian H.; Steiner, Adrian; Graber, Hans Ulrich (2023). Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin. Frontiers in Microbiology, 14 10.3389/fmicb.2023.1183018

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Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were
analyzed three times within one year to identify the most abundant species of
the intramammary bacteriome. Aseptically collected milk samples were cultured
and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were
bacteriologically positive and 80% of the 1,024 quarters were positive for at least
one bacterial species. 84.5% of the quarters were healthy with somatic cell counts
(SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical
mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different
bacterial species including 23 predominant species. Non-aureus staphylococci
and mammaliicocci (NASM) were most prevalent (14 different species; 73.5%
quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for
74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates
of the predominant species were selected and subjected to short-read whole
genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While
complete genomes of eight type strains were available, the remaining 15 were
de novo assembled with long reads as a resource for the community. The 23
complete genomes served for reference-based assembly of the Illumina WGS
data. Both chromosomes and mobile genetic elements were examined for
antibiotic resistance genes (ARGs) using in-house and online software tools.
ARGs were then correlated with phenotypic antibiotic resistance data from
minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial
resistance was isolate-specific. Resistance to clindamycin and oxacillin was
most frequently observed (65 and 30%) in Staphylococcus xylosus but could not
be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the
observed antimicrobial resistance could be explained by the presence of mobile
genetic elements like tetK carried on small plasmids. This represents a possible
mechanism of transfer between non-pathogenic bacteria and pathogens of
the mammary gland within and between herds.

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