Abstract
Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from “normal skin microbiome” and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.
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Data availability
The genome sequences generated in this study are deposited in NCBI’s GenBank and can be accessed through the following IDs: GCA_002865925.1; GCA_002775055.1; GCA_002775105.1.
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Acknowledgements
HNRJ was the recipient of a Ph.D scholarship from FAPESB. LGCP was the recipient of a research fellowship from CNPq.
Funding
This study was partially supported by grants from FAPESB, CNPq, CAPES, and FINEP in Brazil, through the following funding schemes: Fundação de Amparo à Pesquisa do Estado da Bahia—BOL0505/2018 and JCB17/2013; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES-PROCAD 071/2013; Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq Nº 09/2018; and Financiadora de Estudos e Projetos, MCT/FINEP/CT-INFRA01/2013.
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H.N.R.J., J.N.R., D.J.P.G.R., D.A.A., C.S.S., and J.V.O.C.: investigation, formal analysis, methodology, software, data curation, visualization, writing—original draft; H.N.R.J., C.S., and L.S.S: investigation, formal analysis, methodology, visualization, writing—review and editing; V.V.V., J.N., R.T.J.R, V.A., E.R.G.R.A., A.L.M-G., and L.G.C.P: conceptualization, funding, resources, project administration, supervision, writing—review and editing.
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Jesus, H.N.R., Ramos, J.N., Rocha, D.J.P.G. et al. The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum. Funct Integr Genomics 23, 5 (2023). https://doi.org/10.1007/s10142-022-00932-x
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DOI: https://doi.org/10.1007/s10142-022-00932-x