Identification of bacteria and potential sources in neonates at risk of infection delivered by Caesarean and vaginal birth

Neonatal gastric aspirates (NGA) are routinely screened in UK hospitals to investigate fetal/neonatal infections associated with cases of adverse pregnancy outcome (APO). The aim of this study was to describe and compare the microbiology of NGA from Caesarean and vaginal deliveries using molecular methods, and to evaluate other possible clinical and non-clinical variables that may have determined the presence of the bacteria in the samples. The value of using NGA and molecular methods to investigate potential pathogens associated with the risk of early infection was also evaluated. Bacteria were identified by a combined molecular approach on the basis of the 16S rRNA gene using both clone analysis and denaturing gradient gel electrophoresis. A total of 43 and 34 different species were identified in the vaginal (n = 121) and Caesarean (n = 119) deliveries, respectively; 26 of the species observed (51 %) were common to both modalities, although usually less prevalent in the Caesarean cases. Multivariate analysis confirmed an association between infection and prolonged rupture of membranes in vaginal deliveries (odds ratio = 5.7, 95 % confidence interval = 1.1–29.0). Various associations between infection and given variables were also shown, including labour, intrapartum antibiotic prophylaxis, and time and place of sample collection. The molecular methods allowed identification of a range of bacteria and potential sources not previously observed in NGA, including possible genito-urinary, gastrointestinal and oral pathogens. NGA represents a valuable sample for investigating potential pathogens associated with APO and the risk of early infection in neonates using molecular methods.