Impact of milk-feeding programs on fecal bacteria population and antimicrobial resistance genes in Escherichia coli isolated from feces in preweaned calves

Abstract Text:

The objectives of this study were to characterize fecal bacteria communities and evaluate the presence of antimicrobial resistance genes isolated from fecal Escherichia coli of dairy calves fed two different milk feeding programs. Fifteen Holstein newborn female calves (38.4 ± 3.21 kg BW) were fed pasteurized waste milk (pWM) with beta-lactam antimicrobials residues, and 10 calves (39.2 ± 4.89 kg BW) were fed milk replacer (MR) with similar nutrient composition (27.5% CP, 32.1% fat) to waste milk (28.6% CP, 30.0% fat) from birth to weaning at 49 d of age. Fecal samples of 8 calves fed MR and 11 calves fed pWM were obtained on d 42 to profile fecal bacteria populations. The DNA was extracted and amplified for Eubacteria sequencing using Illumina Miseq platforms. Samples were filtered and assigned to a reference taxonomy using the SILVA reference database. A first analysis was made to assess differences in alpha and beta diversity between the 2 milk-feeding sources using QIIME. An ANOVA was used to identify differences at order level between feeding practices. Furthermore, 25 E. coli isolates from fecal swabs of all calves at 35 d of age were used to identify resistance genes. A total of 10 resistance genes corresponding to aminoglycosides (aadA, strA/strB and aac(3)IV), beta-lactam (blaCMY-2), tetracyclines (tetA, tetB and tetC) and sulfonamides (sul1, sul2 and sul3) were examined by PCR and analyzed using a binary logistic regression to assess differences between feeding practices. Chao1 and Shannon alpha diversity indexes were similar in calves regardless of the feeding program followed. The prevalence of Clostridiales order was greater (P < 0.05) whereas Bacteroidales tended (P = 0.07) to be lower in pWM calves (0.58 ± 0.029 and 0.33 ± 0.032, respectively) than in those fed MR (0.44 ± 0.034 and 0.46 ± 0.038, respectively). A high prevalence of sul1, sul2, tetA, aadA, strA/strB and aac(3)IV were found in both treatments (0.43 ± 0.142, 0.62 ± 0.137, 0.50 ± 0.141, 043 ± 0.142, 0.63 ± 0.138, 0.43 ± 0.149, respectively) whereas the prevalence of CMY-2 in pWM calves (0.67 ± 0.122) was greater (P < 0.05) than in MR fed calves (0.10 ± 0.095). In conclusion, milk feeding practices can cause shifts in calf gut bacteria populations. High prevalence of extended spectrum beta-lactamase resistance genes has been found in fecal E. coli isolates from pWM fed calf.

Keywords: calf feeding programs, fecal bacteria population, resistance genes.