Epsilon Open Archive

Abstract

The early life of calves in southern Vietnam and in Sweden were studied in this thesis, with the focus on colostrum quality, gut microbial communities and antimicrobialresistant Escherichia coli. The first of four studies showed that most cows on smallholder farms in Vietnam produced colostrum of good quality and that only around 10% of calves suffered from failure of passive immune transfer. In a second study, bacterial communities in colostrum and in calf faeces samples collected at birth and at 14 days of age were identified by terminal restriction fragment length polymorphism (T-RFLP). The results showed that the microbial communities in colostrum and faeces differed in composition, with greater similarities in composition between colostrum and faeces from newborn calves than faeces from 14-day-old calves. Microbial composition also differed significantly between faeces from newborn and 14-day-old calves. Sequencing of 16S rRNA gene amplicons from a subset of faeces samples from healthy calves and calves treated for diarrhoea with antimicrobial drugs revealed significant differences between the groups, with higher relative abundances of Faecalibacterium and Butyricicoccus in healthy calves. In a third study, bacterial composition in intestinal contents and in mucosal scrapings collected from various gut segments in two- and seven-day-old calves was characterized by sequencing 16S rRNA gene amplicons using Illumina MiSeq. It was found that microbial community composition was associated with intestinal segment, with major differences in composition between proximal and distal parts of the gastrointestinal tract. However, microbial composition showed high similarity for segments in close proximity within the gut. Lactobacillus was present in quite high levels in the abomasum and duodenum, whereas Escherichia were more associated with the ileum, caecum, colon and faeces. Microbial composition and diversity altered with age and, although the microbiota in mucosa and gut content remained similar in general, certain microbial groups dominated in either mucosa or gut content. The fourth study revealed high levels of multidrug-resistance in Escherichia coli isolated from Vietnamese calves (53% of isolates tested), with blacCTM-M-1 (2 isolates), blacCTM-M-9 (1 isolate) and blacCMY-2 (1 isolate) being the main β-lactamase resistance groups detected. There was a high incidence of plasmid-mediated quinolone resistance (PMQR) genes in the E. coli isolates (21%). Overall, these results suggest that colostrum feeding and health are key factors affecting gut microbial community in the early life of dairy calves, but that antimicrobial resistance is an emerging problem on smallholder dairy farms in Vietnam.