Microbiological Findings and Associated Histopathological Lesions in Neonatal Diarrhoea Cases between 2020 and 2022 in a French Veterinary Pig Practice

Simple Summary Morbidity, mortality and loss of productivity due to enteric diseases in neonatal piglets are still major issues worldwide. Neonatal diarrhoea also represents a significant concern regarding antibiotic usage in suckling piglets. For pig veterinary practitioners, the diagnosis of neonatal diarrhoea cases is an ongoing challenge and more case reports, retrospective studies and prospective research are needed to improve knowledge. Anamnesis, clinical signs, and gross and microscopic lesions are the basics needed for a presumptive diagnosis of the pathogen(s) involved at the herd level. However, the role of some pathogens is still under discussion, which makes diagnosis all the more challenging. The aim of our retrospective study was to describe the aetiologies of neonatal diarrhoea cases in a French veterinary pig practice and to determine their associations with histological findings in the small and large intestine. Fifty one cases (48.1%) were positive for only one pathogen and 54 (50.9%) were positive for more than one pathogen. Clostridium perfringens type A was the most frequently detected pathogen (61.3%), followed by Enterococcus hirae (43.4%), rotavirus type A (38.7%) and type C (11.3%) and enterotoxigenic Escherichia coli (3.8%). Only Enterococcus hirae and rotaviruses were associated with relevant lesions in the small intestine. Abstract This retrospective study described the aetiologies of neonatal diarrhoea cases and their associations with histological findings. A total of 106 diarrhoeic neonatal piglets were selected. Cultures, MALDI typings, PCRs and evaluation of intestinal lesions were performed. A total of 51 cases (48.1%) were positive for only one pathogen and 54 (50.9%) were positive for more than one pathogen. Clostridium perfringens type A was the most frequently detected pathogen (61.3%), followed by Enterococcus hirae (43.4%), rotavirus type A (38.7%), rotavirus type C (11.3%) and enterotoxigenic Escherichia coli (3.8%). Only lesions in the small intestine were correlated with detected pathogens. The detection of rotavirus was associated with an increased probability of observing villous atrophy (p < 0.001), crypt hyperplasia (p = 0.01) and leucocyte necrosis in the lamina propria (p = 0.05). The detection of Clostridium perfringens type A was associated with an increased probability of observing bacilli in close proximity to the mucosa (p < 0.001) and a decreased probability of observing epithelial necrosis (p = 0.04). Detection of Enterococcus hirae was associated with an increased probability of observing enteroadherent cocci (p < 0.001). Multivariate regression logistic models revealed that epithelial necrosis was more likely to occur in Enterococcus hirae-positive piglets (p < 0.02) and neutrophilic infiltrate was more likely to occur in Clostridium perfringens type A- and Enterococcus hirae-positive piglets (p = 0.04 and p = 0.02, respectively).