AUTHOR=Vélez Julián Reyes , Cameron Marguerite , Rodríguez-Lecompte Juan Carlos , Xia Fangfang , Heider Luke C. , Saab Matthew , McClure J. Trenton , Sánchez Javier 

TITLE=Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds

JOURNAL=Frontiers in Veterinary Science

VOLUME=4

YEAR=2017

URL=https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2017.00063

DOI=10.3389/fvets.2017.00063

ISSN=2297-1769

ABSTRACT=<p>The objectives of this study are to determine the occurrence of antimicrobial resistance (AMR) genes using whole-genome sequence (WGS) of <italic>Streptococcus uberis</italic> (<italic>S. uberis</italic>) and <italic>Streptococcus dysgalactiae</italic> (<italic>S. dysgalactiae</italic>) isolates, recovered from dairy cows in the Canadian Maritime Provinces. A secondary objective included the exploration of the association between phenotypic AMR and the genomic characteristics (genome size, guanine–cytosine content, and occurrence of unique gene sequences). Initially, 91 isolates were sequenced, and of these isolates, 89 were assembled. Furthermore, 16 isolates were excluded due to larger than expected genomic sizes (&gt;2.3 bp × 1,000 bp). In the final analysis, 73 were used with complete WGS and minimum inhibitory concentration records, which were part of the previous phenotypic AMR study, representing 18 dairy herds from the Maritime region of Canada (<xref ref-type="bibr" rid="B1">1</xref>). A total of 23 unique AMR gene sequences were found in the bacterial genomes, with a mean number of 8.1 (minimum: 5; maximum: 13) per genome. Overall, there were 10 AMR genes [ANT(6), <italic>TEM</italic>-127, <italic>TEM</italic>-163, <italic>TEM</italic>-89, <italic>TEM</italic>-95, <italic>Linb, Lnub, Ermb, Ermc</italic>, and <italic>TetS</italic>] present only in <italic>S. uberis</italic> genomes and 2 genes unique (<italic>EF</italic>-<italic>TU</italic> and <italic>TEM</italic>-71) to the <italic>S. dysgalactiae</italic> genomes; 11 AMR genes [<italic>APH</italic>(3′), <italic>TEM</italic>-1, <italic>TEM</italic>-136, <italic>TEM</italic>-157, <italic>TEM</italic>-47, <italic>TetM, bl2b, gyrA, parE, phoP</italic>, and <italic>rpoB</italic>] were found in both bacterial species. Two-way tabulations showed association between the phenotypic susceptibility to lincosamides and the presence of <italic>linB</italic> (<italic>P</italic> = 0.002) and <italic>lnuB</italic> (<italic>P</italic> &lt; 0.001) genes and the between the presence of <italic>tetM</italic> (<italic>P</italic> = 0.015) and <italic>tetS</italic> (<italic>P</italic> = 0.064) genes and phenotypic resistance to tetracyclines only for the <italic>S. uberis</italic> isolates. The logistic model showed that the odds of resistance (to any of the phenotypically tested antimicrobials) was 4.35 times higher when there were &gt;11 AMR genes present in the genome, compared with &lt;7 AMR genes (<italic>P</italic> &lt; 0.001). The odds of resistance was lower for <italic>S. dysgalactiae</italic> than <italic>S. uberis</italic> (<italic>P</italic> = 0.031). When the within-herd somatic cell count was &gt;250,000 cells/mL, a trend toward higher odds of resistance compared with the baseline category of &lt;150,000 cells/mL was observed. When the isolate corresponded to a post-mastitis sample, there were lower odds of resistance when compared with non-clinical isolates (<italic>P</italic> = 0.01). The results of this study showed the strength of associations between phenotypic AMR resistance of both mastitis pathogens and their genotypic resistome and other epidemiological characteristics.</p>