Carbapenemase-Encoding Genes and Colistin Resistance in Gram-Negative Bacteria During the COVID-19 Pandemic in Mexico: Results from the Invifar Network
Ulises Garza–Ramos, Jesús Silva-Sánchez, Luis Esaú López-Jácome, Melissa Hernández-Durán, Claudia Adriana Colín‐Castro, Alejandro Sánchez-Pérez, Jonathan Rodríguez-Santiago, Rayo Morfín‐Otero, Eduardo Rodríguez-Noriega, María-del-Consuelo Velázquez-Acosta, María del Rosario Vázquez-Larios, José Manuel Feliciano-Guzmán, Fabián Rojas‐Larios, Alfredo Ponce‐de‐León, Margarita Lozano-Garcia, Elena Victoria Choy-Chang, Eduardo López-Gutiérrez, Aarón Molina-Jaimes, Mariana Gil-Veloz, Reyna Edith Corte-Rojas, Ismelda López-Ovilla, Jose Luis Ramirez-Mis, Dora Elia Rodríguez-Balderas, Alejandro Molina-Chavarría, Cecilia Padilla-Ibarra, María Angelina Quevedo-Ramos, Christian Daniel Mireles-Dávalos, Nadia Rodríguez-Medina, Daira Rubio-Mendoza, Carlos Córdova‐Fletes, Flora Cruz-López, Dilva Angelina Becerra-Montejano, Roberto Mercado-Longoría, Rebeca Thelma Martínez-Villarreal, Nicolás Rogelio Eric Barlandas-Rendón, Juan Pablo Mena-Ramírez, Carlos Antonio Couoh-May, Margarita Alcaraz-Espejel, César Adame-Álvarez, Lourdes Hernández-Vicente, Elvira Garza‐González
Abstract
In this study, we report the carbapenemase-encoding genes and colistin resistance in Escherichia coli , Klebsiella pneumoniae , Acinetobacter baumannii , and Pseudomonas aeruginosa in the second year of the COVID-19 pandemic. Clinical isolates included carbapenem-resistant K. pneumoniae , carbapenem-resistant E. coli , carbapenem-resistant A. baumannii , and carbapenem-resistant P. aeruginosa . Carbapenemase-encoding genes were detected by PCR. Carbapenem-resistant K. pneumoniae and carbapenem-resistant E. coli isolates were analyzed using the Rapid Polymyxin NP assay. mcr genes were screened by PCR. Pulsed-field gel electrophoresis and whole-genome sequencing were performed on representative isolates. A total of 80 carbapenem-resistant E. coli , 103 carbapenem-resistant K. pneumoniae , 284 carbapenem-resistant A. baumannii , and 129 carbapenem-resistant P. aeruginosa isolates were recovered. All carbapenem-resistant E. coli and carbapenem-resistant K. pneumoniae isolates were included for further analysis. A selection of carbapenem-resistant A. baumannii and carbapenem-resistant P. aeruginosa strains was further analyzed (86 carbapenem-resistant A. baumannii and 82 carbapenem-resistant P. aeruginosa ). Among carbapenem-resistant K. pneumoniae and carbapenem-resistant E. coli isolates, the most frequent gene was bla NDM (86/103 [83.5%] and 72/80 [90%], respectively). For carbapenem-resistant A. baumannii , the most frequently detected gene was bla OXA-40 (52/86, 60.5%), and for carbapenem-resistant P. aeruginosa , was bla VIM (19/82, 23.2%). For carbapenem-resistant A. baumannii , five indistinguishable pulsotypes were detected. Circulation of K. pneumoniae New Delhi metallo-β-lactamase (NDM) and E. coli NDM was detected in Mexico. High virulence sequence types (STs), such as K. pneumoniae ST307, E. coli ST167, P. aeruginosa ST111, and A. baumannii ST2, were detected. Among K. pneumoniae isolates, 18/101 (17.8%) were positive for the Polymyxin NP test (two, 11.0% positive for the mcr-1 gene, and one, 5.6% with disruption of the mgrB gene). All E. coli isolates were negative for the Polymyxin NP test. In conclusion, K. pneumoniae NDM and E. coli NDM were detected in Mexico, with the circulation of highly virulent STs. These results are relevant in clinical practice to guide antibiotic therapies considering the molecular mechanisms of resistance to carbapenems.