Publicación:

Genomic Characterization of Emerging Carbapenem-Resistant Klebsiella pneumoniae Infections at a Public Hospital in Lima, Peru

Resumen

Introduction:In contrast to other countries in Latin America, Peru had been notoriously spared by the global dissemination of carbapenem-resistant Klebsiella pneumoniae (CR-Kp) until recently. Isolated cases of KPC-producing K. pneumoniae have been reported since 2013 in Lima. However, by 2017, rapid emergence of CR-Kp took place at a tertiary care hospital in Lima. Here, we provide a description of the molecular characteristics of the CR-Kp isolates recovered during this emergence. Methods:We conducted a retrospective study of the emerging cases of CR-Kp infections diagnosed at a tertiary hospital in Lima, from July 2015 to December 2017. Kp was isolated from various clinical samples and profiled using the VITEK system and standard biochemical tests. Whole genome sequencing was performed in an Illumina MiSeq instrument at 50-100x coverage, and bioinformatic analysis was conducted using CLC Genomics Workbench v12 (Qiagen Bioinformatics). De novo assemblies were generated to identify virulence and antibiotic resistance genes. Reference-based mappings were used to infer maximum-likelihood phylogenies from SNP alignments. Results:Fifty-nine unique CR-Kp clinical cases were identified during the study period. A significant increase in the number of cases was observed in 2017 compared to previous years. Carbapenemase genes of were detected in 40 isolates (95%): 24 (60%) were blaNDM-1; 13 (32%) were blaKPC-2, and 3 (8%) were blaIMP-16. Isolates carrying blaKPC were more prevalent during years 2015-2016 and blaNDM-isolates were more prevalent during 2017 (p<0.0001). Multiple sequence types were identified, suggesting that the increase in cases was due to infection from multiple carbapenem-resistant clones. Conclusion:Multiclonal expansion of CR-Kp strains has occurred at our institution and blaKPC has been replaced by blaNDM as the most prevalent carbapenem resistance mechanism since 2017.