Emergence of New Delhi Metallo-β-Lactamase (NDM-5) in <i>Klebsiella quasipneumoniae</i> from Neonates in a Nigerian Hospital

Abstract

Outbreaks of infection occur more often than they are reported in most developing countries, largely due to poor diagnostic services. A <i>Klebsiella</i> species bacteremia outbreak in a newborn unit with high mortality was recently encountered at a location being surveilled for childhood bacteremia. These surveillance efforts offered the opportunity to determine the cause of this neonatal outbreak. In this report, we present the whole-genome sequences of New Delhi metallo-β-lactamase (NDM-5)-containing <i>Klebsiella quasipneumoniae</i> subsp. <i>similipneumoniae</i> bloodstream isolates from a neonatal bacteremia outbreak at a tertiary hospital in Nigeria and as part of the largest collection of <i>K. pneumoniae</i> bloodstream isolates from children in Africa. Comparative analysis of the genetic environment surrounding the NDM-5 genes revealed nearly perfect sequence identity to <i>bla</i>_NDM-5-bearing IncX3-type plasmids from other members of the <i>Enterobacteriaceae</i><b>IMPORTANCE</b> Carbapenem-resistant <i>Klebsiella pneumoniae</i> is of global health importance, yet there is a paucity of genome-based studies in Africa. Here we report fatal blood-borne NDM-5-producing <i>K. quasipneumoniae</i> subsp. <i>similipneumoniae</i> infections from Nigeria, Africa. New Delhi metallo-β-lactamase (NDM)-producing <i>Klebsiella</i> spp. are responsible for high mortality and morbidity, with the NDM-5 variant showing elevated carbapenem resistance. The prevalence of NDM-5 in <i>Klebsiella</i> has been limited primarily to <i>K. pneumoniae</i>, with only one isolate being collected from Africa. During an outbreak of sepsis in a teaching hospital in Nigeria, five NDM-5-producing <i>K. quasipneumoniae</i> subsp. <i>similipneumoniae</i> sequence type 476 isolates were identified. Given the increased resistance profile of these strains, this study highlights the emerging threat of <i>bla</i>_NDM-5 dissemination in hospital environments. The observation of these NDM-5-producing isolates in Africa stresses the urgency to improve monitoring and clinical practices to reduce or prevent the further spread of resistance.