COMPARATIVE GENOMICS OF THE FIRST LATIN AMERICAN ISOLATE OF CORYNEBACTERIUM GLUCURONOLYTICUM ISOLATED FROM THE GENITOURINARY TRACT

Eduarda Guimarães Sousa; Marcus Vinicius Canário Viana; Ana Lua de Oliveira Vinhal; Diogo Luiz de Carvalho Castro; Vasco A de C Azevedo; Max R. Batista de Araújo

Paper Title

Authors

Eduarda Guimarães Sousa
Marcus Vinicius Canário Viana
Ana Lua de Oliveira Vinhal
Diogo Luiz de Carvalho Castro
Vasco A de C Azevedo
Max R. Batista de Araújo

Modality

Poster

Subject area

DNA and Genomics

Publishing Date

21/11/2024

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting-2024/836366-comparative-genomics-of-the-first-latin-american-isolate-of-corynebacterium-glucuronolyticum-isolated-from-the-ge

ISBN

978-65-272-0843-3

Keywords

Comparative genomics, Corynebacterium glucuronolyticum, Virulence

Summary

Many other species, in addition to Corynebacterium diphtheriae, are clinically important and have their pathogenicity recognized for humans. Being widely distributed in the environment, non-diphtheria species of Corynebacterium have emerged as opportunistic pathogens, with increasing reports of their isolation in patients with serious diseases not preventable by vaccines. Among the non-diphtheria species is Corynebacterium glucuronolyticum. We provide clinical data and genomic analyzes relevant to understanding its pathogenesis. A 38-year-old man presenting with mild lower abdomen pain and urinary symptoms, including malaise, fever, and dysuria, was seen by his general practitioner. Without any known immune deficit presented, screening tests for sexually transmitted infections were conducted. Serological examinations gave negative results HIV and hepatitis B/C. Polymerase Chain Reaction (PCR) gave negative results for Chlamydia trachomatis, Mycoplasma spp., Trichomonas vaginalis, and Neisseria gonorrhoeae but positive results for Ureaplasma urealyticum. After an oriented period of treatment with doxycycline, PCR remained positive. The treatment was then established with norfloxacin. Although the new PCR result was negative, the symptoms remained. Semen and urine samples, were collected for microbiological evaluation. Using MALDI-TOF MS it was possible to identify C. glucuronolyticum with 99.9% confidence and named C. glucoronolyticum IHP2022. Additionally, Bacterial genomic DNA was extracted and whole genome sequencing was performed by the Illumina® HiSeq platform. The genome was assembled de novo and submitted the taxonomic classification of the bacterial isolate was performed using Ribosomal Multilocus Sequence Typing (rMLST) database for species identification, GTDB-Tk and Type Strain Genome Server (TYGS). The close reference genomes identified by TYGS were used to build an Average Nucleotide Identity (ANI) heatmap using PyANI with BLASTn. DNA-DNA hybridization (DDH) was determined in silico using the BLAST method’s Genome-to-Genome Distance Calculator (GGDC) v.3.0. The results were based on recommended formula 2 (identities/HSP length). Fourteen C. glucuronolyticum strains were available from GenBank, however only 11 were used to perform the comparative analysis. We excluded three alternative genome assemblies of type strain DSM44120. The genomes were downloaded using NCBI’s Datasets v. 15.2.0. Those genomes were subjected to analysis of quality, taxonomy, genome annotation, and prediction of virulence and antimicrobial resistance genes and CRISPR-Cas systems. An ANI heatmap was generated using PyANI with ANIb algorithm . A pangenome analysis was performed using PPanGGOLiN followed by functional annotation using eggNOG-mapper and COG Classifier. For phylogenetic inference, we used type strain C. diphtheriae NCTC11397T as an outgroup. The tree was inferred using OrthoFinder with the parameter “-M msa”. The tree was visualized using iTOL. C. glucuronolyticum IHP2022 has a genome size of 2,88 Mbp with a G+C content of 59,04%. No plasmid was found. The isolate was classified as C. glucuronolyticum due to its rMLST profile, and dDDH of 86,8% (TYGS) and ANI of 98,63 % in comparison to C. glucuronolyticum DSM44120T (GTDB-Tk). Through comparative analyses, 2,280 genes belonging to the persistent pangenome, 110 to Shell and 1637 to cloud were detected. Some virulence factors such as groEL2, mprA, ndk and leuD were identified in all genomes. Regarding virulence genes, rpoB2, RbpA and tetW were also predicted in all.

Title of the Event: 20º Congresso Brasileiro de Bioinformática: X-Meeting 2024
City of the Event: Salvador
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

SOUSA, Eduarda Guimarães et al.. COMPARATIVE GENOMICS OF THE FIRST LATIN AMERICAN ISOLATE OF CORYNEBACTERIUM GLUCURONOLYTICUM ISOLATED FROM THE GENITOURINARY TRACT.. In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/836366-COMPARATIVE-GENOMICS-OF-THE-FIRST-LATIN-AMERICAN-ISOLATE-OF-CORYNEBACTERIUM-GLUCURONOLYTICUM-ISOLATED-FROM-THE-GE. Access in: 15/12/2025