Phase variation in Mannheimia haemolytica challenges the static genome paradigm

Authors: Harhay, Gregory; McClure, Kelsey; Brader, Kerry; Kuhn, Kristen; Smith, Timothy; Harhay, Dayna

Submitted to: Microbiology Spectrum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2025
Publication Date: 7/23/2025
Citation: Harhay, G.P., McClure, K.K., Brader, K.D., Kuhn, K.L., Smith, T.P.L., Harhay, D.M. 2025. Phase variation in Mannheimia haemolytica challenges the static genome paradigm. Microbiology Spectrum. Article e00010-25. https://doi.org/10.1128/spectrum.00010-25.
DOI: https://doi.org/10.1128/spectrum.00010-25

Interpretive Summary: Problem Statement: Mannheimia haemolytica is a bacterium that causes bovine respiratory disease (BRD) in cattle, leading to significant antibiotic use in feedyards. Despite its known role in human respiratory infections, there is limited research on how this bacterium behaves under low-oxygen (anaerobic) conditions in cattle lungs. The study aims to understand how the bacterium's genome changes in response to anaerobic conditions and how these changes might contribute to its transformation from a harmless resident in the cattle's upper respiratory tract to a harmful lung pathogen. Accomplishments: The researchers conducted experiments comparing the genome sequences of M. haemolytica grown under aerobic (with oxygen) and anaerobic (without oxygen) conditions. They discovered two mechanisms of phase variation in the bacterium's genome: homologous recombination between rRNA operons (large-scale genome changes) and slipped strand mispairing at simple sequence repeats (small-scale genome changes). The large-scale genome changes were only observed under anaerobic conditions. Contribution to Solving the Problem: The study's findings suggest that the bacterium's genome adapts dynamically to low-oxygen environments, which may help it survive and persist in infected lung tissue. This adaptability could lead to the development of phase variants that are more resistant to antibiotics. The researchers propose that dynamic genome models considering these variations should be developed to better understand the bacterium's behavior and improve strategies for mitigating its impact on cattle health. This approach could lead to more effective treatments and management practices for BRD, ultimately reducing the need for antibiotics in cattle.

Technical Abstract: Mannheimia haemolytica is a key agent in bovine respiratory disease (BRD), driving antibiotic use in feedyard cattle. As a facultative anaerobe commonly found in the upper respiratory tracts of cattle, its role under anaerobic conditions in BRD has not been extensively studied despite the known importance of anaerobiosis in human respiratory infections. Utilizing a combined omics approach, we refuted the null hypothesis that the M. haemolytica genome sequence is independent of the environment. This finding provides the rationale for research exploring how anaerobiosis-driven genome plasticity might contribute to a transition from a commensal to a virulent state. Genome sequencing of colony morphology variants from aerobic and anaerobic cultures revealed phase variation via homologous recombination between ribosomal RNA (rRNA) operons and slipped strand mispairing at simple sequence repeats (SSRs), frameshifting genes “on” and “off.” Homologous recombination was exclusive to anaerobic conditions. SSR length variation in a DNA methyltransferase gene, targeting 5'-GACAT, correlated with methylation status. We observed statistically significant differences in the fraction of methylated motifs in isolates derived from anaerobic and aerobic cultures, as well as in the transcript abundances of genes in a nitrate reduction pathway and in a ribosomal protein class among anaerobic culture-derived colonial variants. We propose that instead of representing a M. haemolytica isolate’s genome as a single static sequence, dynamic genome models should be developed. These models should account for the stochastic changes in genome sequence induced by phase variation, represented as a probability-weighted mixture of homologous recombinants and SSR switches.