Genus-wide genomic characterization of Macrococcus: insights into evolution, population structure, and functional potential

Laura M Carroll; Rian Pierneef; Thendo Mafuna; Kudakwashe Magwedere; Itumeleng Matle

doi:10.3389/fmicb.2023.1181376

Genus-wide genomic characterization of Macrococcus: insights into evolution, population structure, and functional potential

Front Microbiol. 2023 Jul 20:14:1181376. doi: 10.3389/fmicb.2023.1181376. eCollection 2023.

Authors

Laura M Carroll^{1

2

3

4}, Rian Pierneef⁵, Thendo Mafuna⁶, Kudakwashe Magwedere⁷, Itumeleng Matle⁸

Affiliations

¹ Department of Clinical Microbiology, SciLifeLab, Umeå University, Umeå, Sweden.
² Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
³ Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
⁴ Integrated Science Lab, Umeå University, Umeå, Sweden.
⁵ Biotechnology Platform, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa.
⁶ Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa.
⁷ Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa.
⁸ Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa.

Abstract

Introduction: Macrococcus species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, Macrococcus spp. can be opportunistic pathogens in both veterinary and human clinical settings. This study aimed to provide insight into the evolution, population structure, and functional potential of the Macrococcus genus, with an emphasis on antimicrobial resistance (AMR) and virulence potential.

Methods: All high-quality, publicly available Macrococcus genomes (n = 104, accessed 27 August 2022), plus six South African genomes sequenced here (two strains from bovine clinical mastitis cases and four strains from beef products), underwent taxonomic assignment (using four different approaches), AMR determinant detection (via AMRFinderPlus), and virulence factor detection (using DIAMOND and the core Virulence Factor Database).

Results: Overall, the 110 Macrococcus genomes were of animal commensal, veterinary clinical, food-associated (including food spoilage), and environmental origins; five genomes (4.5%) originated from human clinical cases. Notably, none of the taxonomic assignment methods produced identical results, highlighting the potential for Macrococcus species misidentifications. The most common predicted antimicrobial classes associated with AMR determinants identified across Macrococcus included macrolides, beta-lactams, and aminoglycosides (n = 81, 61, and 44 of 110 genomes; 73.6, 55.5, and 40.0%, respectively). Genes showing homology to Staphylococcus aureus exoenzyme aureolysin were detected across multiple species (using 90% coverage, n = 40 and 77 genomes harboring aureolysin-like genes at 60 and 40% amino acid [AA] identity, respectively). S. aureus Panton-Valentine leucocidin toxin-associated lukF-PV and lukS-PV homologs were identified in eight M. canis genomes (≥40% AA identity, >85% coverage). Using a method that delineates populations using recent gene flow (PopCOGenT), two species (M. caseolyticus and M. armenti) were composed of multiple within-species populations. Notably, M. armenti was partitioned into two populations, which differed in functional potential (e.g., one harbored beta-lactamase family, type II toxin-antitoxin system, and stress response proteins, while the other possessed a Type VII secretion system; PopCOGenT p < 0.05).

Discussion: Overall, this study leverages all publicly available Macrococcus genomes in addition to newly sequenced genomes from South Africa to identify genomic elements associated with AMR or virulence potential, which can be queried in future experiments.

Keywords: Macrococcus; Macrococcus armenti; Macrococcus caseolyticus; antimicrobial resistance; cattle; taxonomy; virulence; whole-genome sequencing.