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

Abstract

The objectives of this study are to determine the occurrence of antimicrobial resistance (AMR) genes using whole-genome sequence (WGS) of Streptococcus uberis (S. uberis) and Streptococcus dysgalactiae (S. dysgalactiae) 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 (>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 (1). 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), TEM-127, TEM-163, TEM-89, TEM-95, Linb, Lnub, Ermb, Ermc, and TetS] present only in S. uberis genomes and 2 genes unique (EF-TU and TEM-71) to the S. dysgalactiae genomes; 11 AMR genes [APH(3′), TEM-1, TEM-136, TEM-157, TEM-47, TetM, bl2b, gyrA, parE, phoP, and rpoB] were found in both bacterial species. Two-way tabulations showed association between the phenotypic susceptibility to lincosamides and the presence of linB (P = 0.002) and lnuB (P < 0.001) genes and the between the presence of tetM (P = 0.015) and tetS (P = 0.064) genes and phenotypic resistance to tetracyclines only for the S. uberis 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 >11 AMR genes present in the genome, compared with <7 AMR genes (P < 0.001). The odds of resistance was lower for S. dysgalactiae than S. uberis (P = 0.031). When the within-herd somatic cell count was >250,000 cells/mL, a trend toward higher odds of resistance compared with the baseline category of <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 (P = 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.

Diversity of β-lactam resistance genes in gram-negative rods isolated from a municipal wastewater treatment plant

“…The bla TEM-68 variant probably evolved from bla TEM-47 , and both are not very frequent in Poland. Outside this area, there was a report from Canada, where bla TEM-47 was found in Streptococcus dysgalactiae (Vélez et al 2017). To the best of our knowledge, this study reports the first isolate carrying a bla TEM-47/68 variant found outside the clinical setting in Poland.…”

Tackling Multidrug Resistance in Streptococci – From Novel Biotherapeutic Strategies to Nanomedicines

“…In fact, pyogenic streptococci have been recognized as non-β-lactamase-producing bacteria, where resistance to β-lactams is essentially mediated by alterations to the binding site of penicillin-binding proteins (PBPs) ( Vannice et al, 2019 ). Nevertheless, a recent study based on whole-genome sequencing revealed the presence of β-lactamases determinants of S. uberis and SDSD isolates bovine mastitis ( Vélez et al, 2017 ). Still, there is a need for actional studies to assess the potential of these β-lactamases, and the role of these species as a reservoir of determinants of resistance.…”

“…Resistance to tetracyclines (TET) among streptococci strains is often found in high rates ( Nakamur et al, 2011 ; Emaneini et al, 2014 ; Gherardi et al, 2014 ; Vélez et al, 2017 ; Gizachew et al, 2019 ). In streptococci, genes encoding resistance to TET are frequently acquired by MGEs, which also harbor erythromycin resistance determinants ( Brenciani et al, 2004 , 2007 , 2011 ; Emaneini et al, 2014 ; Cattoir, 2016 ).…”

Complete Genome Sequence of a New Zealand Isolate of the Bovine Pathogen Streptococcus uberis

“…Opportunistic infection of the bovine mammary gland by S. uberis can lead to the bacterium acting as a major pathogen, causing the inflammatory disease mastitis ( 3 ). Economic losses associated with bovine mastitis have been estimated at $35 billion per year globally, with S. uberis being the leading cause of bovine mastitis in New Zealand ( 4 ) and the United Kingdom ( 5 ) and a major cause in the Unites States ( 6 ), Canada ( 7 ), and Chile ( 8 ), among other countries.…”