Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors

Chen, Yuhao; Brook, Thomas C.; Soe, Cho Zin; O’Neill, Ian; Alcon-Giner, Cristina; Leelastwattanagul, Onnicha; Phillips, Sarah; Caim, Shabhonam; Clarke, Paul; Hall, Lindsay J.; Hoyles, Lesley

doi:10.1099/mgen.0.000377

Cited by 51 publications

(81 citation statements)

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“…While annotations for genomes are improving, we have previously noted and continue to notice issues with identities attributed to K. oxytoca genomes in public repositories (3). Consequently, the identity of all genomes included in this work was first confirmed by ANI analysis (Supplementary Table 1), with bla OXY gene and phylogenetic analyses supporting our findings (Supplementary Material).…”

Section: Assigning Mlst Sequence Types To Speciessupporting

confidence: 72%

“…Of the 354 known MLST sequence types, 342 (96.6 %) were associated with specific members of the K. oxytoca complex (Supplementary (3). An MSA of the preterm-associated genomes' BGC against the reference sequence (11)…”

Section: Assigning Mlst Sequence Types To Speciesmentioning

confidence: 99%

“…sequences can be used to differentiate species of the complex (2), as can genome-based average nucleotide identity (ANI) and phylogenomic analyses (1,3). All members of the K. oxytoca complex can be differentiated by MALDI-TOF (1), but reference databases currently in routine clinical use lack reference spectra of the different species to allow identification beyond K. oxytoca.…”

Section: Introductionmentioning

confidence: 99%

“…Recent work has demonstrated genomic characterization of K. oxytoca strains is inadequate, with large numbers of genomes deposited in public databases erroneously assigned to K. oxytoca instead of K. michiganensis or K. grimontii (3)(4)(5)(6). Consequently, K. michiganensis and K. grimontii are clinically relevant but under-reported in the literature (3,7). Given that the bla OXY gene has diversified in parallel to housekeeping genes in the K. oxytoca complex, it is likely that the K. oxytoca multi-locus sequence typing (MLST) scheme (8) can be used to speciate all members of this genetically diverse group of bacteria.…”

Section: Introductionmentioning

confidence: 99%

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Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

Shibu¹,

McCuaig²,

McCartney³

et al. 2020

Preprint

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As part of ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive strains originally identified as Klebsiella oxytoca. Average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis. In addition to encoding GES-5, the strains encoded SHV-66, a β-lactamase not previously identified in K. michiganensis. The strains further encoded a range of virulence factors and the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii. This BGC, associated with antibiotic-associated haemorrhagic colitis, has not previously been reported in K. michiganensis, and this finding led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7,170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four (K. oxytoca, K. pasteurii, K. grimontii, K. michiganensis) of the six species of the complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.Data statementSupplementary data associated with this article are available from figshare.Data summaryDraft genome sequences for PS_Koxy1, PS_Koxy2 and PS_Koxy4 have been deposited with links to BioProject accession number PRJNA562720 in the NCBI BioProject database.IMPACT STATEMENTExtended analyses of the genomes of Klebsiella spp. have revealed the kleboxymycin biosynthetic gene cluster (BGC) is restricted to species of the Klebsiella oxytoca complex (K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii). Species- and/or gene-specific differences in the cluster’s sequences may be relevant to virulence of K. oxytoca and related species. The finding of the kleboxymycin BGC in the preterm infant gut microbiota may have implications for disease presentation in a subset of neonates.

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Section: Assigning Mlst Sequence Types To Speciessupporting

confidence: 72%

Section: Assigning Mlst Sequence Types To Speciesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

Shibu¹,

McCuaig²,

McCartney³

et al. 2020

Preprint

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“…There is increasing interest in detection and typing of K. pneumoniae direct from gut metagenome data 58 , due to the role of K. pneumoniae gut colonization as a source of acute infections and as a contributor to chronic diseases 7,8 . We tested Kleborate’s performance by application to n=40 metagenomes from which at least one KpSC isolate was cultured and sequenced, as part of the Baby Biome Study 59 .…”

Section: Resultsmentioning

confidence: 99%

Genomic surveillance framework and global population structure forKlebsiella pneumoniae

Mmc

et al. 2020

Preprint

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K. pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.

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In vitro fermentation of Bangia fusco-purpurea polysaccharide by human gut microbiota and the protective effects of the resultant products on Caco-2 cells from lipopolysaccharide-induced injury

Zheng

Zhang

et al. 2022

International Journal of Biological Macromolecules

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Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors

Abstract: Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis (NEC), nos… Show more

Cited by 51 publications

References 100 publications

Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

Genomic surveillance framework and global population structure forKlebsiella pneumoniae

In vitro fermentation of Bangia fusco-purpurea polysaccharide by human gut microbiota and the protective effects of the resultant products on Caco-2 cells from lipopolysaccharide-induced injury

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