Abstract

Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock and the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics and genetic diversity in both koala and livestock hosts. In contrast to a variety of C. pecorum molecular studies, to date, only four complete and 16 draft genomes have been published. Of those, only five draft genomes are from koalas. Here, using whole-genome sequencing and a comparative genomics approach, we describe the first two complete C. pecorum genomes collected from diseased koalas. A de novo assembly of DBDeUG_2018 and MC/MarsBar_2018 resolved the chromosomes and chlamydial plasmids each as single, circular contigs. Robust phylogenomic analyses indicate biogeographical separation between strains from northern and southern koala populations, and between strains infecting koala and livestock hosts. Comparative genomics between koala strains identified new, unique, and shared loci that accumulate single-nucleotide polymorphisms and separate between northern and southern, and within northern koala strains. Furthermore, we predicted novel type III secretion system effectors. This investigation constitutes a comprehensive genome-wide comparison between C. pecorum from koalas and provides improvements to annotations of a C. pecorum reference genome. These findings lay the foundations for identifying and understanding host specificity and adaptation behind chlamydial infections affecting koalas.

Highlights

  • Chlamydia pecorum, a member of the family Chlamydiaceae, is a globally disseminated intracellular pathogen of livestock, free-range ruminants, and the koala (Phascolarctos cinereus) [1]

  • This investigation was motivated by the lack of high quality, closed koala C. pecorum reference genomes, and as such expands on previous descriptions from incomplete draft assemblies and resolves the genomic architecture of two C. pecorum ST69 strains collected from diseased koalas [15,23]

  • As whole-genome sequencing (WGS) may not be available for some studies, we identified several candidate gene markers (such as the loci MarsBar_0283 (ChPn 76 kDa homologue), 0335 (SINC homologue), 0564, 0593, and 0613 (ORF663 homologue), in addition to outer membrane protein A (ompA) and selected pmp genes for future evaluation together with C. pecorum-multilocus sequence typing (MLST) for C. pecorum intraspecies fine-detailed molecular epidemiology

Read more

Summary

Introduction

A member of the family Chlamydiaceae, is a globally disseminated intracellular pathogen of livestock, free-range ruminants, and the koala (Phascolarctos cinereus) [1]. C. pecorum molecular studies utilising genotyping of the outer membrane protein A (ompA) and/or C. pecorum-specific multilocus sequence typing (MLST) have revealed important observations about infection dynamics and strain diversity within and between koala and livestock hosts [5,6,7,8,9,10,11,12]. These molecular analyses showed that the global

Methods
Results
Discussion
Conclusion
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call