Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala (Phascolarctos cinereus) Pathogen

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.

One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia

“…psittaci type strain 6BC as a closely related reference for scaffolding. Notably, the previously sequenced strains 8882_placenta and 9945_foetus [7] could now be resolved into the single chromosome and plasmid sequence, which underwent genome circularisation and annotation as described previously [21]. Assembly metrics were assessed using QUAST v5.0.2 [24].…”

“…Using methods previously described [ 21 ], C. psittaci sequences for this study were obtained by using the Burrows–Wheeler Aligner (BWA) v0.7.17 [ 22 ] to map paired-end reads to the plasmid pCps6BC (GenBank: CP002587) and then subsequently to the chromosomes of 6BC (GenBank: CP002586); Horse_pl (GenBank: CP025423), Mat116 (GenBank: CP002744); 01DC11 (GenBank: CP002805); 02DC15 (GenBank: CP002806); 08DC60 (GenBank: CP002807); 84/55 (GenBank: CP003790); GR9 (GenBank: CP003791); MN (GenBank: CP003792); VS225 (GenBank: CP003793); WS/RT/E30 (GenBank: CP003794); M56 (GenBank: CP003795); WC (GenBank: CP003796); CP3 (GenBank: CP003797); NJ1 (GenBank: CP003798); and Rostinovo-70 (GenBank: CP041038). For each strain, C. psittaci sequence data was compiled into a single FASTQ file for each of the forward and reverse reads.…”

“…Following the workflow described by White and colleagues [ 21 ], Trimmomatic v0.36 [ 23 ] was used in paired-end mode to filter the raw reads by removing low-quality bases and read-pairs together with Illumina adaptor sequences. The filtered paired-end reads were then de novo assembled using MGAP ( https://github.com/dsarov/MGAP---Microbial-Genome-Assembler-Pipeline , accessed on 21 January 2022), using the chromosome of the C. psittaci type strain 6BC as a closely related reference for scaffolding.…”

“…The filtered paired-end reads were then de novo assembled using MGAP ( https://github.com/dsarov/MGAP---Microbial-Genome-Assembler-Pipeline , accessed on 21 January 2022), using the chromosome of the C. psittaci type strain 6BC as a closely related reference for scaffolding. Notably, the previously sequenced strains 8882_placenta and 9945_foetus [ 7 ] could now be resolved into the single chromosome and plasmid sequence, which underwent genome circularisation and annotation as described previously [ 21 ]. Assembly metrics were assessed using QUAST v5.0.2 [ 24 ].…”

Animal Chlamydiae: A Concern for Human and Veterinary Medicine

“…They re-evaluated their genomic make-up and discovered new loci of interest that could distinguish between northern and southern koala strains. They also provided new information on putative secreted effectors, which may act as novel virulence factors [ 31 ]. These findings establish the foundation for further work toward identifying and understanding host specificity and adaptation of koala chlamydial infections.…”