학술논문
Whole genome analysis of Gram-negative bacteria using the EPISEQ CS application and other bioinformatic platforms
Document Type
article
Author
Ulises Garza-Ramos; Nadia Rodríguez-Medina; Carlos Córdova-Fletes; Daira Rubio-Mendoza; Christopher J. Alonso-Hernández; Luis Esaú López-Jácome; Rao Morfín-Otero; Eduardo Rodríguez-Noriega; Fabián Rojas-Larios; María del Rosario Vázquez-Larios; Alfredo Ponce-de-Leon; Elena Victoria Choy-Chang; Rafael Franco-Cendejas; Bernardo Alfonso Martinez-Guerra; Cecilia Teresita Morales-de-La-Peña; Juan Pablo Mena-Ramírez; Eduardo López-Gutiérrez; Ricardo García-Romo; Bertha Ballesteros-Silva; Alejandro Valadez-Quiroz; Laura Karina Avilés-Benítez; José Manuel Feliciano-Guzmán; Talia Pérez-Vicelis; María del Consuelo Velázquez-Acosta; Cecilia Padilla-Ibarra; Laura Isabel López-Moreno; Reyna Edith Corte-Rojas; Carlos Antonio Couoh-May; María Angelina Quevedo-Ramos; Maribel López-García; Gabriela Chio-Ortiz; Mariana Gil-Veloz; Alejandro Molina-Chavarria; Javier Paul Mora-Domínguez; Daniel Romero-Romero; Francisco Javier May-Tec; Elvira Garza-González
Source
Journal of Global Antimicrobial Resistance, Vol 33, Iss , Pp 61-71 (2023)
Subject
Language
English
ISSN
2213-7165
Abstract
ABSTRACT: Objectives: To determine genomic characteristics and molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa from medical centres of Mexico using whole genome sequencing data analysed with the EPISEQⓇ CS application and other bioinformatic platforms. Methods: Clinical isolates collected from 28 centres in Mexico included carbapenem-non-susceptible K. pneumoniae (n = 22), E. coli (n = 24), A. baumannii (n = 16), and P. aeruginosa (n = 13). Isolates were subjected to whole genome sequencing using the Illumina (MiSeq) platform. FASTQ files were uploaded to the EPISEQⓇ CS application for analysis. Additionally, the tools Kleborate v2.0.4 and Pathogenwatch were used as comparators for Klebsiella genomes, and the bacterial whole genome sequence typing database was used for E. coli and A. baumannii. Results: For K. pneumoniae, both bioinformatic approaches detected multiple genes encoding aminoglycoside, quinolone, and phenicol resistance, and the presence of blaNDM-1 explained carbapenem non-susceptibility in 18 strains and blaKPC-3 in four strains. Regarding E. coli, both EPISEQⓇ CS and bacterial whole genome sequence typing database analyses detected multiple virulence and resistance genes: 20 of 24 (83.3%) strains carried blaNDM, 3 of 24 (12.4%) carried blaOXA-232, and 1 carried blaOXA-181. Genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, trimethoprim, and macrolides were also detected by both platforms. Regarding A. baumannii, the most frequent carbapenemase-encoding gene detected by both platforms was blaOXA-72, followed by blaOXA-66. Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, blaVIM, blaIMP, and blaGES were the more frequently detected. Multiple virulence genes were detected in all strains. Conclusion: Compared to the other available platforms, EPISEQⓇ CS enabled a comprehensive resistance and virulence analysis, providing a reliable method for bacterial strain typing and characterization of the virulome and resistome.