Research Summary - 3
Improved Molecular Detection and Characterization of Mannheimia haemolytica from Cattle and Their Environment
| Date/Time: |
9/13/2025
10:30
|
| Author: |
Paul S Morley |
| Clinic: |
VERO Program, Texas A&M University |
| City, State, ZIP: |
Canyon, TX 79015 |
S.C. Tamm, MS, MS
1
;
E. Doster, DVM, PhD
1
;
C.A. Wolfe, BS, BS
1
;
L.J. Pinnell, PhD
1
;
W.B. Crosby, DVM, PhD
2
;
A.R. Woolums, DVM, MSc, PhD, DACVIM, DACVM
2
;
P.S. Morley, DVM, PhD, DACVIM
1
;
1VERO Program, Texas A&M University, Canyon, TX, 79015
2Mississippi State University, Starkville, MS
Introduction:
Bovine respiratory disease (BRD) is a major cause of morbidity and mortality in cattle, with Mannheimia haemolytica (Mh) being a key pathogen. Traditional detection methods require animal restraint and challenging sampling, and laboratory methods lack sensitivity and the ability to readily characterize organism diversity within larger microbial communities. This study explores culture-independent methods, including target-enriched (TE) sequencing, which offers tremendous improvements in sensitivity for detecting and characterizing Mh at the strain level. Our team successfully designed and validated a targeted sequencing workflow for Mh, demonstrating that TE sequencing enables deep genomic characterization even when Mh is present at extremely low relative abundances within complex nasal microbial communities.
Materials and methods:
Samples were collected from five cattle populations, including nasal swabs, water bowl swabs, and rope samples. DNA was extracted and analyzed using qPCR, 16S rRNA gene sequencing, and TE shotgun sequencing. Bioinformatics pipelines characterized microbial communities, Mh classification at the genus and species level, antimicrobial resistance genes (ARGs), and Mh genetic sequence variants (GSVs). The targeted method significantly enriched Mh-classified reads, illustrating the utility of targeted shotgun sequencing for enriching rare taxa from high-background microbial populations.
Results:
Mh was detected in 84.5% of samples using qPCR, with TE sequencing identifying Mh in 100% of samples. TE sequencing provided strain-level resolution, revealing multiple genetic variants within all samples, highlighting previously unrecognized diversity in Mh communities. Examining different types of samples collected from different groups of beef cattle, we demonstrated the ability to detect multiple strains of Mh in individual samples and how these profiles vary by sample type and animal cohort. Environmental samples showed unique microbial compositions compared to nasal samples. Notably, 16S rRNA sequencing detected Mannheimia genus organisms in a lower percentage of samples compared to qPCR and TE sequencing, highlighting the superior sensitivity of TE sequencing in identifying Mh.
Significance:
The discovery of multiple genetic variants of Mh offers new insights into its ecology, potentially impacting our understanding of disease pathogenesis, virulence, and vaccine development. TE sequencing enhances strain-level characterization, revealing the complexity and diversity of Mh communities in cattle environments, which may influence disease dynamics. This dramatic gain in efficiency underscores the potential of targeted sequencing in enriching rare taxa, providing a powerful tool for studying pathogens like Mh in complex microbial environments. This study demonstrates the utility of TE sequencing in detecting and characterizing Mh in cattle and their environments, highlighting its potential for improving BRD management strategies and informing future research on disease mechanisms and prevention. The ability to detect and characterize multiple strains of Mh across different sample types and cattle cohorts provides a deeper understanding of the pathogen's ecology and its role in BRD.
