Whole-Genome Sequencing for Molecular Characterization of Carbapenem-Resistant Enterobacteriaceae Causing Lower Urinary Tract Infection among Pediatric Patients

Abstract

Antibiotic resistance is a growing public health problem globally, incurring health and cost burdens. The occurrence of antibiotic-resistant bacterial infections has increased significantly over the years. Gram-negative bacteria display the broadest resistance range, with bacterial species expressing extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases. All carbapenem-resistant Enterobacteriaceae (CRE) isolates from pediatric urinary tract infections (UTIs) between October 2015 and November 2019 (n = 30). All isolates underwent antimicrobial resistance phenotypic testing using the Phoenix NMIC/ID-5 panel, and carbapenemase production was confirmed using the NG-Test CARBA 5 assay. Whole-genome sequencing was performed on the CREs. The sequence type was identified using the Achtman multi-locus sequence typing scheme, and antimicrobial resistance markers were identified using ResFinder and the CARD database. The most common pathogens causing CRE UTIs were E. coli (63.3%) and K. pneumoniae (30%). The most common carbapenemases produced were OXA-48-like enzymes (46.6%) and NDM enzymes (40%). Additionally, one E. coli harbored IMP-26, and two K. pneumoniae possessed mutations in ompK37 and/or ompK36. Lastly, one E. coli had a mutation in the marA porin and efflux pump regulator. The findings highlight the difference in CRE epidemiology in the pediatric population compared to Qatar’s adult population, where NDM carbapenemases are more common.

Complete Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Environmental Isolate from Zanzibar, Tanzania, Harboring Novel Insertion Elements and Two bla CTX-M-15 Genes

“…Both the chromosomal and plasmid copies of bla CTX-M-15 are associated with IS Ecp1 ( 7 ). Point mutations in the efflux pump regulators acrR and ramR ( 8 ) and the porin genes ompK36 and ompK37 ( 9 ) were identified using ResFinder analyses ( 10 ). Thirty IS elements were annotated on the plasmid.…”

Genomic epidemiology revealed the emergence and worldwide dissemination of ST383 carbapenem-resistant hypervirulent Klebsiella pneumoniae and hospital acquired infections of ST196 Klebsiella quasipneumoniae in Qatar

“…K. pneumoniae is the most common species among CRE. Carbapenem resistance in K. pneumoniae is primarily driven by production of carbapenemases, with extended spectrum beta-lactamases (ESBL) playing a supplementary role (4, 6–9). In the aforementioned study, genes encoding metallo-β-lactamases were detected in 45.8% of the isolates, and OXA-48-like enzymes in 40.3%.…”

Early Years of Carbapenem-Resistant Enterobacterales Epidemic in Abu Dhabi

“…Multiple studies of varying scale and details have reported the local emergence of such isolates. With the exception of few [ 2 , 3 ], most of these studies, however, were restricted to the identification of the major groups of carbapenemases produced, and larger studies seldom provided a detailed molecular analysis of the clones present [ 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 ].…”