Carbapenemase-Encoding Genes and Colistin Resistance in Gram-Negative Bacteria During the COVID-19 Pandemic in Mexico: Results from the Invifar Network

Abstract

In this study, we report the carbapenemase-encoding genes and colistin resistance in <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, and <i>Pseudomonas aeruginosa</i> in the second year of the COVID-19 pandemic. Clinical isolates included carbapenem-resistant <i>K. pneumoniae</i>, carbapenem-resistant <i>E. coli</i>, carbapenem-resistant <i>A. baumannii</i>, and carbapenem-resistant <i>P. aeruginosa</i>. Carbapenemase-encoding genes were detected by PCR. Carbapenem-resistant <i>K. pneumoniae</i> and carbapenem-resistant <i>E. coli</i> isolates were analyzed using the Rapid Polymyxin NP assay. <i>mcr</i> genes were screened by PCR. Pulsed-field gel electrophoresis and whole-genome sequencing were performed on representative isolates. A total of 80 carbapenem-resistant <i>E. coli</i>, 103 carbapenem-resistant <i>K. pneumoniae</i>, 284 carbapenem-resistant <i>A. baumannii</i>, and 129 carbapenem-resistant <i>P. aeruginosa</i> isolates were recovered. All carbapenem-resistant <i>E. coli</i> and carbapenem-resistant <i>K. pneumoniae</i> isolates were included for further analysis. A selection of carbapenem-resistant <i>A. baumannii</i> and carbapenem-resistant <i>P. aeruginosa</i> strains was further analyzed (86 carbapenem-resistant <i>A. baumannii</i> and 82 carbapenem-resistant <i>P. aeruginosa</i>). Among carbapenem-resistant <i>K. pneumoniae</i> and carbapenem-resistant <i>E. coli</i> isolates, the most frequent gene was <i>bla</i>_NDM (86/103 [83.5%] and 72/80 [90%], respectively). For carbapenem-resistant <i>A. baumannii</i>, the most frequently detected gene was <i>bla</i>_OXA-40 (52/86, 60.5%), and for carbapenem-resistant <i>P. aeruginosa</i>, was <i>bla</i>_VIM (19/82, 23.2%). For carbapenem-resistant <i>A. baumannii</i>, five indistinguishable pulsotypes were detected. Circulation of <i>K. pneumoniae</i> New Delhi metallo-β-lactamase (NDM) and <i>E. coli</i> NDM was detected in Mexico. High virulence sequence types (STs), such as <i>K. pneumoniae</i> ST307, <i>E. coli</i> ST167, <i>P. aeruginosa</i> ST111, and <i>A. baumannii</i> ST2, were detected. Among <i>K. pneumoniae</i> isolates, 18/101 (17.8%) were positive for the Polymyxin NP test (two, 11.0% positive for the <i>mcr-1</i> gene, and one, 5.6% with disruption of the <i>mgrB</i> gene). All <i>E. coli</i> isolates were negative for the Polymyxin NP test. In conclusion, <i>K. pneumoniae</i> NDM and <i>E. coli</i> 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.