Molecular diversity in mechanisms of carbapenem resistance in paediatric Enterobacteriaceae

Abstract

Development of carbapenem resistance in Enterobacteriaceae has impacted Clinical and Laboratory Standards Institute (CLSI) guidelines, infection control approaches and treatment strategies. The clinical, phenotypic and genotypic characteristics of carbapenem-resistant Enterobacteriaceae (CRE) infections at paediatric referral centres are not well described. CRE were identified through the clinical microbiology laboratory at Seattle Children's Hospital (Seattle, WA). Clinical data were retrieved from medical records. Resistance testing, polymerase chain reaction (PCR) for resistance determinants, and Escherichia coli transformation were carried out for each isolate. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used to characterise strain relatedness. PCR amplification and sequencing as well as sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) were used to investigate porin alterations. Six CRE isolates were identified between 2002 and 2010. Significant molecular diversity was documented in their mechanisms of resistance, including plasmid-mediated serine carbapenemase (KPC) and metallo-β-lactamase (IMP), chromosomally encoded β-lactamase (SME) and porin alterations with extended-spectrum β-lactamases. Patients had underlying health conditions and were from geographically diverse regions. In one case, PFGE of serial isolates documented the development of resistance in a previously susceptible strain. Molecular investigation of this strain identified insertion of the genetic mobile element insertion sequence ISEcp1 in the ompK36 gene, conferring a functional porin alteration as demonstrated by SDS-PAGE. This is the first description of porin disruption by ISEcp1 in a CTX-M-15-positive isolate. This is the largest report of paediatric CRE to date. This diverse description of demographic, phenotypic and molecular characteristics highlights the challenge of CRE infections in high-risk paediatric patients and that attention to emerging resistance mechanisms (including membrane alteration) at paediatric referral centres is essential.

Fig. 1

Pulsed-field gel electrophoresis (PFGE) of sequential isolates from Case 5. ESBL, extended-spectrum β-lactamase; CR, carbapenem-resistant; Amp-R, ampicillin-resistant.

Fig. 2

Polymerase chain reaction (PCR) amplification of OmpK36 in Case 5. * Sequencing of a larger amplicon in lane 4 revealed insertion of ISEcp1 after nucleotide position 505 in the OmpK36 locus, suggesting porin defect via gene disruption by the insertion sequence. Amp-R, ampicillin-resistant; ESBL, extended-spectrum β-lactamase; CR, carbapenem-resistant.

Fig. 3

Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis of Case 5 isolates. * Loss of the OmpK36 band in a carbapenem-resistant (CR) isolate, demonstrating functional porin alteration consistent with sequencing results. ESBL, extended-spectrum β-lactamase.