Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of chlamydial virulence, evolution, and phylogeny

Abstract

The genus Chlamydia contains important obligate intracellular bacterial pathogens to humans and animals, including C. trachomatis and C. pneumoniae. Since 1998, when the first Chlamydia genome was published, our understanding of how these microbes interact, evolved and adapted to different intracellular host environments has been transformed due to the expansion of chlamydial genomes. This review explores the current state of knowledge in Chlamydia genomics and how whole genome sequencing has revolutionised our understanding of Chlamydia virulence, evolution, and phylogeny over the past two and a half decades. This review will also highlight developments in multi-omics and other approaches that have complemented whole genome sequencing to advance knowledge of Chlamydia pathogenesis and future directions for chlamydial genomics.

Keywords: Chlamydia trachomatis; Chlamydiaceae; genome content; genomics; host tropism; next generation sequencing; tissue tropism; whole genome sequence.

Figure 1

Features of the Chlamydiaceae family including primary host range, clinical manifestations and genome characteristics.

Figure 2

Chromosome comparison of selected genomes from (A) major human and animal Chlamydia pathogens (C. trachomatis, C suis, C pneumoniae, C pecorum, C psittaci and C abortus) and (B) C trachomatis strains from the three main lineages: ocular (A_HAR, B_Jali20), urogenital (D_UW3, E_12-94, G_11074) and LGV (L2_434BU, L2C). The C trachomatis strain D_UW3 was used as the reference. Important genome elements are annotated in red including the plasticity zone (PZ), ompA, pmps, Incs, T3SS, tarP and trp operon. The figure was generated using BRIG (v 0.95).

Figure 3

Comparison of the plasticity zone (PZ) from selected major human and animal Chlamydia species (C. suis, C. trachomatis, C. pecorum, C. psittaci, C. pneumoniae and C. abortus). The PZ elements are depicted in different colours, where biotin modification genes (accB, accC) are in purple, hypothetical protein (hyp) genes are in grey, MAC/perforin (MAC/P) in teal, Phospholipase D (PLD) in blue, purine interconversion genes (guaAB, add) in orange, Tryptophan operon genes (trp) in pink, and chlamydial cytotoxin (tox) gene(s) in yellow.

Figure 4

Phylogenomic relationships of C trachomatis and C psittaci reference strains. Midpoint-rooted maximum-likelihood (ML) core-genome phylogenetic trees constructed using Parsnp version 1.2 of (A) 13 aligned publicly available complete C trachomatis genomes; and (B) 18 aligned publicly available complete C psittaci genomes. For C trachomatis, genome sequences are coloured according to tissue tropism/known genotypes (as depicted in the figure legend). For C psittaci, genome sequences are coloured according to their respective host (as depicted in the figure legend). Corresponding host silhouettes are shown adjacent to sequence names. Bootstrap values greater than 0.8 are shown. Branch lengths represent the nucleotide substitutions per site, as indicated by the scale bar.

Figure 5

Chlamydia intraspecies genetic diversity. Midpoint-rooted maximum-likelihood (ML) phylogenetic analysis of 3,098 bp concatenated MLST sequences alignment representing (A) 20 avian and livestock STs from closely related C buteonis, C psittaci, traditional livestock and novel avian C abortus; and (B) 62 C. pecorum STs from a range of hosts. Phylogenetic trees were constructed using FastTree version 2.1.11, as implemented in Geneious Prime (available at: https://www.geneious.com/). Corresponding host silhouettes are shown adjacent to sequence names. Bootstrap values greater than 0.8 are shown. Branch lengths represent the nucleotide substitutions per site, as indicated by the scale bar.

Figure 6

Chlamydial omics. Representation of the workflows from sample processing to multiple omics analysis methods used in the chlamydial field. Figure created using BioRender (available from https://www.biorender.com/).