Antimicrobial resistance in the microbiome of feedlot watering bowls and bovine respiratory disease associated pathogens.
Date
2023-08-17
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
ORCID
0009-0000-5549-849X
Type
Thesis
Degree Level
Masters
Abstract
Bovine respiratory disease (BRD) is the primary disease of concern to beef production and
is driven by stress, bacteria, viruses, and environmental and management practices. Antimicrobial
use (AMU) to control BRD selects for antimicrobial resistance (AMR) genes (ARGs). Treatment
failure due to AMR necessitates a rapid switch to an effective antimicrobial before a devastating
amount of death loss occurs. Monitoring AMR in a herd through individual animals is impractical.
There is a need for a fast, pragmatic, and scalable methodology to monitor AMR within cattle to
guide effective AMU. Cattle watering bowls (WB) have been previously shown to harbour BRD
pathogens and ARGs but have yet to be explored in the same context as wastewater AMR
monitoring is for public health. This thesis outlines a pilot project of WB sampling as a proxy
method to monitor the presence of ARGs of relevance to BRD associated pathogens.
The microbiomes within watering bowls of two feedlots were genotypically and
phenotypically assessed through water, swab, and sediment sampling. A new feedlot was sampled
(68 water, 63 swab) as pens filled (up to 9 WB) over a series of 8 weeks. The other, older, feedlot
was only sampled in the 8th week (sediment, swab, water) from 20 WB. For phenotypic AMR
detection, samples were inoculated into antimicrobial sensitivity test (AST) panels containing
microdilutions of four antimicrobials (enrofloxacin, florfenicol (FFN), tulathromycin,
oxytetracycline). Bacteria that grew on these plates were isolated (n = 78). A subset (n = 28 new
feedlot, n = 3 old feedlot + H. somni from a deep nasopharyngeal swab) of these underwent further
characterisation on an AST panel containing 10 different antimicrobials. The whole genome of
isolates (n = 10, 6 new, 4 old) was sequenced and analysed for ARGs. These detected ARGs were
compared to a custom dataset of 172 BRD genomes from NCBI. The genetic neighbourhood of
floR, an ARG encoding for the efflux of FFN, within the WB isolates (n = 4) was also compared
to pathogen genomes. For the culture-independent methodology, samples from one feedlot
underwent amplified 16S rRNA sequencing (n = 122), while samples from the other underwent
shotgun metagenomic sequencing (n = 11). The ARGs detected in WB isolates were compared to
the ARGs detected within metagenomic sequencing, and previous datasets of feedlot water.
Multi-drug resistant bacteria were routinely isolated from WBs. When environmental
samples from the last week of sampling were inoculated into media with FFN (>32 µg/mL), 93/96
samples had bacterial growth. By constructing a genotypic AMR profile from two feedlots and by
consulting previous metagenomic datasets from feedlot water, the understudied resistome of the
watering bowl microbiome was shown to provide outstanding coverage of the ARGs (15/16)
detected within 172 BRD genomes. The overlap in genetic neighbourhoods between copies of floR
in WB and BRD genomes confirms the possibility of horizontal gene transfer via a myriad of
transposable elements between both populations. Though further studies are needed to reaffirm
our findings, in this thesis the understudied environmental microbiome within feedlot watering
bowls was found to serve as a potential source of ARGs for BRD pathogens and thus may serve
as a proxy for relevant ARGs within feedlot environments.
Description
Keywords
Microbiology, Beef, Feedlot, Antimicrobial, Antibiotic, Resistance, Cattle, Bovine respiratory disease
Citation
Degree
Master of Science (M.Sc.)
Department
Large Animal Clinical Sciences
Program
Large Animal Clinical Sciences