High-resolution Microbiome Analysis Reveals Exclusionary Klebsiella Species Competition in Preterm Infants at Risk for Necrotizing Enterocolitis

Abstract

Intestinal colonization with Klebsiella has been linked to necrotizing enterocolitis (NEC), but methods of analysis usually failed to discriminate Klebsiella species or strains. A novel ~2,500-base amplicon (StrainID) that spans the 16S and 23S rRNA genes was used to generate amplicon sequence variant (ASV) fingerprints for Klebsiella oxytoca and Klebsiella pneumoniae species complexes (KoSC and KpSC, respectively) and co-occurring fecal bacterial strains from 10 preterm infants with NEC and 20 matched controls. Complementary approaches were used to identify cytotoxin-producing isolates of KoSC. Klebsiellaspecies colonized most preterm infants, were more prevalent in NEC subjects versus controls, and replaced Escherichiain NEC subjects. Single KoSC or KpSC ASV fingerprinted strains dominated the gut microbiota, suggesting exclusionary Klebsiella competition for luminal resources. Enterococcus faecaliswas co-dominant with KoSC but present infrequently with KpSC. Cytotoxin-producing KoSC members were identified in most NEC subjects and were less frequent in controls. Few Klebsiellastrains were shared between subjects. We conclude that inter-species Klebsiella competition, within an environment of KoSC and E. faecalis cooperation, appears to be an important factor for the development of NEC. Preterm infants seem to acquire Klebsiella primarily through routes other than patient-to-patient transmission.

Antimicrobial susceptibility profile of Klebsiella pneumoniae isolated from some dairy products in Libya as a foodborne pathogen

“…The present study demonstrated that the presence of K. pneumoniae in PIF is considered to be a major cause of infections among infants resulting from the improper preparation and conservation of these products, especially at hospitals and homes, which could cause a health risk for infants. Klebsiella species have been associated with necrotizing enterocolitis in infants, as documented by Coleman et al [37]. These species have been classified as category B organisms and are intended to cause infections in infants.…”