Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers.

Ellen Ruth A Morris,Eman Anis,Noah D Cohen,Anna Aspán,John Pringle,Ivan Ivanov,Andrew E Hillhouse,Ashley G Boyle,Miia Riihimäki,Angela I Bordin

doi:10.1371/journal.pone.0252804

Ellen Ruth A Morris, Eman Anis + Show 8 more

Open Access

https://doi.org/10.1371/journal.pone.0252804

Copy DOI

Abstract

Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor infects other host mammals or vectors, and infection results in short-lived immunity. Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood. Thus, our objective was to use next-generation sequencing technologies to characterize the genome, methylome, and transcriptome of isolates of SEE from horses with acute clinical strangles and inapparent carrier horses-including isolates recovered from individual horses sampled repeatedly-to assess pathogen-associated changes that might reflect specific adaptions of SEE to the host that contribute to inapparent carriage. The accessory genome elements and methylome of SEE isolates from Sweden and Pennsylvania revealed no significant or consistent differences between acute clinical and inapparent carrier isolates of SEE. RNA sequencing of SEE isolates from Pennsylvania demonstrated no genes that were differentially expressed between acute clinical and inapparent carrier isolates of SEE. The absence of specific, consistent changes in the accessory genomes, methylomes, and transcriptomes of acute clinical and inapparent carrier isolates of SEE indicates that adaptations of SEE to the host are unlikely to explain the carrier state of SEE. Efforts to understand the carrier state of SEE should instead focus on host factors.

Highlights

Streptococcus equi subsp. equi (SEE) is a host-specific bacterial pathogen that causes the infectious disease of horses known as strangles [1,2,3,4,5]
We defined the core genome for all isolates within a region, which differs from the approach taken in another study where the core genome was delineated by removing prophages, and the integrative and conjugative element (ICE)- from the SEE 4047 genome, and any regions of other SEE genomes > 200 base-pairs that did not match the core genome were considered as part of the accessory genome [10]
Harris et al demonstrated that the prophages φSeq2–4, and ICESe1 and ICESe2 were highly conserved among SEE isolates [10]

Summary

Introduction

Streptococcus equi subsp. equi (SEE) is a host-specific bacterial pathogen that causes the infectious disease of horses known as strangles [1,2,3,4,5]. Equi (SEE) is a host-specific bacterial pathogen that causes the infectious disease of horses known as strangles [1,2,3,4,5]. Other clinical signs of disease can be observed, including dissemination of infection to other organs and immune-mediated sequelae such as vasculitis and myositis [3, 5]. The persistence of the disease appears to be attributable to the ability of SEE to survive in horses that are infected but do not show clinical signs. The most likely source of spread and persistence of SEE is horses that appear healthy but shed SEE undetected (so-called inapparent carrier horses) [3, 9, 10]; these carriers transmit SEE to susceptible horses, thereby perpetuating the disease in nature [11, 12]

Objectives

Methods

Results

Conclusion