Double-carbapenemase-producing Enterobacteriaceae: complete genome sequencing of isolates from hospitals in Paraguay, 2021.

Background: Motivation for the study. To generate knowledge about the current situation of antimicrobial resistance in Enterobacteriaceae using whole genome sequencing. Main findings. This study presents the first genome sequencing of double-carbapenemase-producing Enterobacteriaceae from patients with extended hospital stays in Paraguay. Of the seven double-carbapenemase-producing Enterobacteriaceae isolates, six were Klebsiella subsp pneumoniae. Implications. Our findings highlight the urgent need to strengthen measures to prevent and control healthcareassociated infections in order to prevent the spread of these highly resistant bacteria.

Objectives.: To describe the whole genome sequencing of double-carbapenemase-producing Enterobacteriaceae isolates circulating in Paraguay.

Materials and methods.: We conducted genomic studies on seven Enterobacteriaceae isolates, previously confirmed as double-carbapenemase producers by PCR, from patients with extended hospital stays and broad-spectrum antimicrobial treatment in seven hospitals in Paraguay. Genome sequencing included Unicycler assembly and multilocus sequence typing (MLST).

Results.: Of the seven Enterobacterales isolates producing dual carbapenemases, six were Klebsiella pneumoniae subsp. pneumoniae and one was Enterobacter cloacae subsp. cloacae. The co-production of bla KPC-2/bla NDM-1 and bla KPC-2/bla NDM-5 was confirmed in K. pneumoniae. We found co-production of bla NDM-1/bla OXA-163 in E. cloacae, along with other antimicrobial resistance genes of chromosomal and plasmid origin. The MLST sequence types of the K. pneumoniae isolates were ST11, ST15, ST133, ST273, and ST1303, and that of E. cloacae was ST976. Two of the six K. pneumoniae ST11 isolates, from two different hospitals in the capital, were genetically related and both carried bla KPC-2 and bla NDM-5.

Conclusions.: We report the first genome sequencing of double-carbapenemase-producing Enterobacterales from patients with extended hospital stays in Paraguay. The analysis revealed diverse resistance profiles and clones, carriage of multiple carbapenemases, and other resistance genes of chromosomal and plasmid origin. These findings emphasize the need to strengthen hospital infection control and implement effective therapeutic interventions.

Background: Motivation for the study. To generate knowledge about the current situation of antimicrobial resistance in Enterobacteriaceae using whole genome sequencing. Main findings. This study presents the first genome sequencing of double-carbapenemase-producing Enterobacteriaceae from patients with extended hospital stays in Paraguay. Of the seven double-carbapenemase-producing Enterobacteriaceae isolates, six were Klebsiella subsp pneumoniae. Implications. Our findings highlight the urgent need to strengthen measures to prevent and control healthcareassociated infections in order to prevent the spread of these highly resistant bacteria.