Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis (NEC), nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella, as previous studies have focused on the recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. The aim of this study was to better characterize preterm-associated Klebsiella populations using phenotypic and genotypic approaches. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for Klebsiella spp., and virulence and antimicrobial resistance genes identified. Antibiotic susceptibility profiling and in vitro macrophage and iron assays were undertaken for the Klebsiella strains. Metapangenome analyses with a manually curated genome dataset were undertaken to examine the diversity of Klebsiella oxytoca and related bacteria in a publicly available shotgun metagenome dataset. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. ‘healthy’) encoded multiple β-lactamases. No difference was observed between isolates recovered from healthy and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut. There is little difference in the phenotypic and genomic characteristics of Klebsiella isolates recovered from healthy and sick infants. Identification of β-lactamases in all isolates may prove problematic when defining treatment regimens for NEC or sepsis, and suggests that healthy preterm infants contribute to the resistome. Refined analyses with curated sequence databases are required when studying closely related species present in metagenomic data.
Date Issued
2020-05-21
Date Acceptance
2020-04-26
Citation
Microbial Genomics, 2020, 6 (6), pp.1-20
ISSN
2057-5858
Publisher
Microbiology Society
Start Page
1
End Page
20
Journal / Book Title
Microbial Genomics
Volume
6
Issue
6
Copyright Statement
© 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between
the Microbiology Society and the corresponding author’s institution (https://creativecommons.org/licenses/by/4.0/deed.ast).
the Microbiology Society and the corresponding author’s institution (https://creativecommons.org/licenses/by/4.0/deed.ast).
Sponsor
Medical Research Council (MRC)
Medical Research Council (MRC)
Identifier
https://www.microbiologyresearch.org/docserver/fulltext/mgen/10.1099/mgen.0.000377/mgen000377.pdf?expires=1591022085&id=id&accname=guest&checksum=3574753A32F3FB77B7FD4E34E1D90A2C
Grant Number
MR/L01632X/1
MR/L01632X/1
Subjects
Klebsiella oxytoca
microbiome
shotgun metagenomics
taxonomy
0604 Genetics
0605 Microbiology
Publication Status
Published
Date Publish Online
2020-05-21