Comparative Genomics Suggests a Taxonomic Revision of the Staphylococcus cohnii Species Complex

Abstract

Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

Complete Genome Sequence of Weissella confusa LM1 and Comparative Genomic Analysis

“…With the rapid development of sequencing techniques, the genomes of diverse bacterial strains have been sequenced. This advancement promoted research on comparative genomics, which helped illustrate the relationships between genotypes and phenotypes ( Wang et al, 2018 ), thereby addressing the effects of isolation source on the genetic variations ( Mao et al, 2021 ), revealing horizontal gene transfer ( Singh et al, 2021 ), and performing taxonomic revision ( Lavecchia et al, 2021 ). As the importance of Weissella species has been recognized, attempts have been made to explore their evolutionary relationship and genomic characteristics.…”

Extensive Horizontal Gene Transfer within and between Species of Coagulase-Negative Staphylococcus

“…Staphylococcus pettenkoferi clusters within the Auricularis species group, rather than the Saprophyticus species group as previously reported ( Lamers et al 2012 ). The use of genomic analysis to resolve complex or conflicting taxonomic assignments in Staphylococcus has been previously demonstrated ( Madhaiyan et al 2020 ; Lavecchia et al 2021 ), and our results will further inform future classification efforts in this genus.…”

SxsA, a novel surface protein mediating cell aggregation and adhesive biofilm formation of Staphylococcus xylosus

“…In S. cohnii , however, sxs A is not part of the core genome, as it was only identified in a small group of strains, all isolated from a dairy environment/bovine mastitis infection (either SNUC strains originating from Canada or SC strains, originating from Germany). When considering a recent taxonomic revision published by Lavecchia et al (2021), which revealed three phylogenetically distinct lines within S. cohnii , sxs A‐positive isolates all correspond to group A2, a group proposed by the authors to be reclassified to Staphylococcus cohnii subsp. barensis .…”