Molecular epidemiology of Clostridium neonatale and its relationship with the occurrence of necrotizing enterocolitis in preterm neonates

M Hosny; E Baptiste; A Levasseur; B La Scola

doi:10.1016/j.nmni.2019.100612

Molecular epidemiology of Clostridium neonatale and its relationship with the occurrence of necrotizing enterocolitis in preterm neonates

New Microbes New Infect. 2019 Oct 15:32:100612. doi: 10.1016/j.nmni.2019.100612. eCollection 2019 Nov.

Authors

M Hosny¹, E Baptiste¹, A Levasseur¹, B La Scola¹

Affiliation

¹ Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique, Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, France.

Abstract

Clostridia-especially Clostridium butyricum-are among the taxa most frequently identified from stool samples of preterm neonates with necrotizing enterocolitis (NEC). Recently, Clostridium neonatale has also been detected from epidemic cases, but using a culture-based approach we were unable to confirm this discovery in a local cohort. In order to investigate this link by a molecular approach, a specific rpoB-based quantitative real-time PCR was developed to detect C. neonatale directly from patients' stool specimens. Design of this rpoB-based quantitative real-time PCR was based on the genomic analysis of seven clinical isolates of C. neonatale. It was tested on stool samples from 88 preterm neonates with necrotizing enterocolitis and 71 matched controls. C. neonatale was significantly more prevalent in stools from preterm neonates with necrotizing enterocolitis than in controls (respectively 30/88 (34%) versus 9/71 (13%); p 0.003). Whole-genome analysis also allowed the identification of three genomic clusters of C. neonatale. This clustering was associated with a geographical location regardless of isolation from the NEC or control, suggesting asymptomatic carriage. Although less prevalent than C. butyricum in our cohort, C. neonatale is significantly associated with the occurrence of necrotizing enterocolitis.

Keywords: Clonal lineage; Clostridium neonatale; Core-genome phylogeny; Necrotizing enterocolitis; rpoB-based specific quantitative real-time polymerase chain reaction.