Genome sequencing, assembly and antibiograms of bacteria isolated from calves in an epidemiological study of bovine respiratory disease complex

Commingling and transportation of cattle is common within the North American beef production system as is the use of macrolide antibiotics to treat or control bovine respiratory disease complex (BRDC). Therefore, the purpose of this project was to evaluate the effects of commingling, transportation, and antibiotic treatment for the control of bovine respiratory disease complex on the diversity and dynamics of nasopharyngeal and rectoanal mucosal bacterial populations in beef calves. Three groups of 60 commercial 5-7-month-old male beef calves were used in this study, each originating either from Missouri, Kentucky or Tennessee and were transported to a backgrounding facility in Kansas in late September 2013. On arrival at the facility, calves from within each source were randomly assigned to receive either a macrolide antibiotic or saline injection and assigned to separate pens according to treatment within source for a total of 6 pens; for the duration of the trial, each pen was prevented from nose-to-nose contact with any other pen. Nasopharyngeal samples from these calves were collected at four time points: at the sale barn before transport (day 0), at the backgrounding facility upon arrival (day 1), and 9 and 28 days later. Additionally, calves were monitored daily for signs of BRDC using a clinical illness scoring (CIS) system and rectal temperature cutoff as described in (DeDonder et al., 2015). If a calf met the case definition for BRDC, they were treated with a macrolide antibiotic, and additional nasopharyngeal samples were obtained at the time of classification of onset of BRDC morbidity. These samples were processed using classical microbiological techniques for bacterial isolation, and some isolates were selected for species identification, antimicrobial resistance testing, and whole genome sequencing. The selection criteria for the nasopharyngeal isolates were either that the bacterial species was not represented by a closed genome in GenBank or that the species was known to be associated with respiratory disease in other mammals.