Association between Clostridium neonatale and the occurrence of necrotizing enterocolitis in preterm neonates

Abstract Clostridia are among taxa most frequently identified from necrotizing enterocolitis preterm neonates’ stool samples, especially Clostridium butyricum. 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 polymerase chain reaction was developed to detect C. neonatale directly from patients’ stool specimens. Design of this rpoB-based quantitative real-time polymerase 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%]; vs. 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 in 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.