Bacterial Contamination of the Surgical Site at the Time of Elective Caesarean Section in Belgian Blue Cows—Part 2: Identified by 16Sr DNA Amplicon Sequencing

SIMPLE SUMMARY: To enhance the antibiotic treatment during the realisation of elective caesarean sections (CSs), a better knowledge of the bacterial composition of the surgical site is required. This study involved 13 cows of a previous dataset of 76 animals. Bacteriology was performed on swabs sampled from visceral and parietal peritoneum during the CS. DNA sequencing was performed on six samples chosen randomly among the culture-positive swabs and seven among the culture-negative swabs. No difference was observed between the microbiota composition of the samples positive or negative to bacterial culture. In fact, a high amount of bacterial DNA was identified in all surgical sites of elective CSs, and the most identified species was Mycoplasma wenyonii. Furthermore, the bacteria cultured were not the dominant species, since most of them were not identified by amplicon sequencing in the same sample in which they were cultured. It is assumed that the most identified bacterial DNA is due to the haematogenous contamination of the surgical site. To understand the role (protector vs. harmful) of these bacteria in the occurrence of post-operative complications and the effect of antibiotic treatment (protector vs. harmful) on the microbiota, further studies are required. ABSTRACT: This study aimed to describe the bacterial composition of the surgical site during elective caesarean sections (CSs) using the 16Sr DNA amplicon sequencing performed in parallel to bacterial culture. The study involved 13 Belgian blue cows of a previous dataset of 76 animals. Bacteriology was performed on swabs sampled from visceral and parietal peritoneum during the CS. Amplicon sequencing was performed in six samples chosen randomly among the swabs positive for bacteriology and seven among the culture-negative swabs. A total of 2542 bacterial operational taxonomic units belonging to 567 genera were identified. The most often identified genus and species were Mycoplasma (44%) and Mycoplasma wenyonii (36%), respectively. Results showed no difference in microbiota composition between the culture-positive and -negative samples. However, a difference was observed between the bacteriology and amplicon sequencing results. Indeed, seven out of nine cultured strains were not identified by amplicon sequencing in the samples in which they were cultured. In contrast to bacteriology, amplicon sequencing unveiled the presence of bacterial DNA in all elective CSs. The most identified DNA is most likely derived from the haematogenous spread of bacteria to the surgical site. Furthermore, the cultured bacteria were not the dominant species in the sample from which they were cultured.