First Comparative Genomics Analysis of Corynebacterium Auriscanis

Overview

Journal Mem Inst Oswaldo Cruz

Specialties Parasitology
Tropical Medicine

Date 2024 Oct 30

PMID 39476150

Authors

Ana Lua de Oliveira Vinhal

Max Roberto Batista de Araujo

Evandro Bento Rodrigues

Diogo Luiz de Carvalho Castro

Carine Rodrigues Pereira

Dirceia Aparecida Costa Custodio

Elaine Maria Seles Dorneles

Flavia Figueira Aburjaile

Bertram Brenig

Vasco Azevedo

Marcus Vinicius Canario Viana

Affiliations

Soon will be listed here.

Abstract

Background: Corynebacterium auriscanis is a bacterial species frequently isolated from dogs with external otitis or dermatitis and a zoonotic pathogen transmitted by dog bite. It is considered an opportunistic pathogen, but its pathogenicity mechanisms are poorly studied. Comparative genomics can identify virulence and niche factors that could contribute to understanding its lifestyle.

Objectives: The objectives of this project was to compare genomes of C. auriscanis to identify genes related to its virulence and lifestyle.

Methods: The genome of strain 32 was sequenced using Illumina HiSeq 2500 (Illumina, CA, USA) and assembled using Unicycler. The two other non-redundant genomes from the same species available in GenBank were included in the analysis. All genomes were annotated and checked for taxonomy, assembly quality, mobile elements, CRISPR-Cas systems, and virulence and antimicrobial resistance genes. The virulence genes in the three genomes were compared to the ones from other pathogens commonly isolated with C. auriscanis.

Findings: The species has 42 virulence factors that can be classified as niche factors, due to the absence of true virulence factors found in primary pathogens. The gene rbpA could confer basal levels of resistance to rifampin.

Main Conclusions: The absence of true virulence factors in the three genomes suggests C. auriscanis has an opportunistic pathogen lifestyle.

References

Ishikawa J, Chiba K, Kurita H, Satoh H . Contribution of rpoB2 RNA polymerase beta subunit gene to rifampin resistance in Nocardia species. Antimicrob Agents Chemother. 2006; 50(4):1342-6. PMC: 1426977. DOI: 10.1128/AAC.50.4.1342-1346.2006. View

Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M . PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. PLoS Comput Biol. 2020; 16(3):e1007732. PMC: 7108747. DOI: 10.1371/journal.pcbi.1007732. View

Ramos J, Baio P, Veras J, Vieira E, Mattos-Guaraldi A, Vieira V . Novel configurations of type I-E CRISPR-Cas system in Corynebacterium striatum clinical isolates. Braz J Microbiol. 2022; 54(1):69-80. PMC: 9944170. DOI: 10.1007/s42770-022-00881-4. View

Wick R, Judd L, Gorrie C, Holt K . Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017; 13(6):e1005595. PMC: 5481147. DOI: 10.1371/journal.pcbi.1005595. View

Toft C, Andersson S . Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet. 2010; 11(7):465-75. DOI: 10.1038/nrg2798. View

Bertelli C, Tilley K, Brinkman F . Microbial genomic island discovery, visualization and analysis. Brief Bioinform. 2018; 20(5):1685-1698. PMC: 6917214. DOI: 10.1093/bib/bby042. View

Liu B, Zheng D, Zhou S, Chen L, Yang J . VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2021; 50(D1):D912-D917. PMC: 8728188. DOI: 10.1093/nar/gkab1107. View

Giovanelli Tacconi Gimenez E, Viana M, de Jesus Sousa T, Aburjaile F, Brenig B, Silva A . Resequencing and characterization of the first genome isolated from camel. PeerJ. 2024; 12:e16513. PMC: 10836205. DOI: 10.7717/peerj.16513. View

Atxaerandio-Landa A, Arrieta-Gisasola A, Laorden L, Bikandi J, Garaizar J, Martinez-Malaxetxebarria I . A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data. Microorganisms. 2022; 10(12). PMC: 9781918. DOI: 10.3390/microorganisms10122364. View

10.

Li W, ONeill K, Haft D, DiCuccio M, Chetvernin V, Badretdin A . RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res. 2020; 49(D1):D1020-D1028. PMC: 7779008. DOI: 10.1093/nar/gkaa1105. View

11.

Tauch A, Burkovski A . Molecular armory or niche factors: virulence determinants of Corynebacterium species. FEMS Microbiol Lett. 2015; 362(23):fnv185. DOI: 10.1093/femsle/fnv185. View

12.

Chaumeil P, Mussig A, Hugenholtz P, Parks D . GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics. 2022; 38(23):5315-5316. PMC: 9710552. DOI: 10.1093/bioinformatics/btac672. View

13.

Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki E, Zaslavsky L . NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016; 44(14):6614-24. PMC: 5001611. DOI: 10.1093/nar/gkw569. View

14.

Alcock B, Raphenya A, Lau T, Tsang K, Bouchard M, Edalatmand A . CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2019; 48(D1):D517-D525. PMC: 7145624. DOI: 10.1093/nar/gkz935. View

15.

Rodrigues D, Ariute J, Rodrigues da Costa F, Benko-Iseppon A, Barh D, Azevedo V . PanViTa: Pan Virulence and resisTance analysis. Front Bioinform. 2023; 3:1070406. PMC: 9942593. DOI: 10.3389/fbinf.2023.1070406. View

16.

Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Neron B . CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018; 46(W1):W246-W251. PMC: 6030898. DOI: 10.1093/nar/gky425. View

17.

Aalbaek B, Bemis D, Schjaerff M, Kania S, Frank L, Guardabassi L . Coryneform bacteria associated with canine otitis externa. Vet Microbiol. 2010; 145(3-4):292-8. DOI: 10.1016/j.vetmic.2010.03.032. View

18.

Chklovski A, Parks D, Woodcroft B, Tyson G . CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods. 2023; 20(8):1203-1212. DOI: 10.1038/s41592-023-01940-w. View

19.

Collins M, Hoyles L, Lawson P, Falsen E, Robson R, Foster G . Phenotypic and phylogenetic characterization of a new Corynebacterium species from dogs: description of Corynebacterium auriscanis sp. nov. J Clin Microbiol. 1999; 37(11):3443-7. PMC: 85662. DOI: 10.1128/JCM.37.11.3443-3447.1999. View

20.

Meier-Kolthoff J, Sarda Carbasse J, Peinado-Olarte R, Goker M . TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 2021; 50(D1):D801-D807. PMC: 8728197. DOI: 10.1093/nar/gkab902. View