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

Luu, Laurence Don Wai; Kasimov, Vasilli; Phillips, Samuel; Myers, Garry; Jelocnik, Martina

doi:10.3389/fcimb.2023.1178736

“…Previously, a study by Moran et al [62] demonstrated that obligate association with host tissues promotes genome reduction in bacteria. Studies on Ct suggested that genome streamlining results from its co-evolution within the eukaryotic host [48,[63][64][65][66], and is facilitated by its ability to acquire essential metabolites from its host [62,[67][68][69]. Our observations contradict prior speculations by Bohlin.…”

Section: Discussioncontrasting

confidence: 79%

Evolutionary Dynamics in the Genome of Ocular Chlamydia trachomatis Strains from Northern Tanzania, pre- and post- Mass Drug Administration

Ghasemian,

Ramadhani,

Harte

et al. 2024

Preprint

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Trachoma, caused by Chlamydia trachomatis (Ct), remains a leading cause of preventable infection induced blindness worldwide. We conducted a four-year longitudinal study in three trachoma-endemic villages in Northern Tanzania, tracking infection dynamics and factors influencing trachomatous scarring progression and persistence pre- and post-Mass Drug Administration (MDA) interventions. We analysed 118 whole genomes of Ct originating from ocular swabs of children. Sample collection was conducted at three-month intervals over four years, encompassing 15 timepoints. We studied Ct phylogeny, patterns of single nucleotide polymorphism (SNP) accumulation in individual isolates and single nucleotide variation (SNV) in the population, with association of clinical signs of trachoma and scarring progression. Seventy-one (60.2%) samples were classified as serovar A (SvA) and 47 (39.8%) as serovar B (SvB) genomes. Initially, SvB dominated among pre-MDA samples (36/40, 90%), but SvA gradually became dominant after the first round of MDA (67/78, 85.9%) (P<0.0001). Two distinct subsets of SvA were found: subset_1 (29 sequences) pre-MDA, aligning with Tanzanian reference strain A/2497; subset_2 (42 sequences) post-MDA, showing a mutation rate roughly twice as high as subset_1, a 6 kbp genome reduction in the PZ, and forming a distinct cluster. Similarly, 13 SvB sequences exhibited diverse PZ genome reduction (~4 and ~10 kbp), yet all grouped with Tanzanian reference strain B/TZ1A828/OT. Importantly, we observed a shift in the types of Ct serovars after the first round of MDA, with the emergence of a unique SvA subset with distinct genetic characteristics compared to those circulating before MDA. The observed decrease in the size of the Ct genome suggests a process where the Tanzanian ocular Ct strains may be streamlining, highlighting ongoing evolution. Further research is needed to understand the factors driving these changes and their impact on Ct biology and response to azithromycin.

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“…psittaci Agilent probes and WGS costs in this study were estimated at AUD$17 000 for 16 samples). Comparatively MLST (combined with omp A genotyping) is a cost-effective and less technical tool for chlamydial molecular epidemiology studies [4, 6, 10]. This study additionally obtained 26 C .…”

Section: Discussionmentioning

confidence: 99%

“…This genomic data limitation is particularly evident for avian strains from Australia ( n =8) and New Zealand (known as Aotearoa in the Māori language) ( n =0). Without WGS, many global studies commonly utilise omp A genotyping and/or multilocus sequence typing (MLST) to provide the initial identity of infecting strains [4]. Recent studies in Australia have also detected C.…”

Section: Introductionmentioning

confidence: 99%

“…Over the past two decades, chlamydial genomic studies have provided essential knowledge about the phylogeny, genetic diversity, epidemiology, virulence factors, and transmission patterns of these intracellular pathogens [1–4]. However, the need for culturing these intracellular organisms has posed a significant challenge in obtaining high-quality genomes from clinical samples.…”

Section: Introductionmentioning

confidence: 99%

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Whole-genome sequencing of Chlamydia psittaci from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers

Kasimov

¹

,

White

²

,

Foxwell

³

et al. 2023

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Chlamydia psittaci is a globally distributed veterinary pathogen with zoonotic potential. Although C. psittaci infections have been reported in various hosts, isolation and culture of Chlamydia is challenging, hampering efforts to produce contemporary global C. psittaci genomes. This is particularly evident in the lack of avian C. psittaci genomes from Australia and New Zealand. In this study, we used culture-independent probe-based whole-genome sequencing to expand the global C. psittaci genome catalogue. Here, we provide new C. psittaci genomes from two pigeons, six psittacines, and novel hosts such as the Australian bustard (Ardeotis australis) and sooty shearwater (Ardenna grisea) from Australia and New Zealand. We also evaluated C. psittaci genetic diversity using multilocus sequence typing (MLST) and major outer membrane protein (ompA) genotyping on additional C. psittaci -positive samples from various captive avian hosts and field isolates from Australasia. We showed that the first C. psittaci genomes sequenced from New Zealand parrots and pigeons belong to the clonal sequence type (ST)24 and diverse ‘pigeon-type’ ST27 clade, respectively. Australian parrot-derived strains also clustered in the ST24 group, whereas the novel ST332 strain from the Australian bustard clustered in a genetically diverse clade of strains from a fulmar, parrot, and livestock. MLST and ompA genotyping revealed ST24/ompA genotype A in wild and captive parrots and a sooty shearwater, whilst ‘pigeon-types’ (ST27/35 and ompA genotypes B/E) were found in pigeons and other atypical hosts, such as captive parrots, a little blue penguin/Kororā (Eudyptula minor) and a zebra finch (Taeniopygia guttata castanotis) from Australia and New Zealand. This study provides new insights into the global phylogenomic diversity of C. psittaci and further demonstrates the multi-host generalist capacity of this pathogen.

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“…Although the exact function of these genes within these avian C. abortus strains is still to be elucidated, there is increasing evidence that the chlamydial plasmid plays a vital role in the virulence, persistent infection and pathogenicity in other infecting strains [29]. Therefore, the presence of a chlamydial plasmid within these avian C.…”

Section: Discussionmentioning

confidence: 99%

Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways

Kasimov,

White,

Jelocnik

2023

Microbial Genomics

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Chlamydia abortus, an obligate intracellular bacterium, is a major causative agent of reproductive loss in ruminants, with zoonotic potential. Though this pathogen is primarily known to infect livestock, recent studies have detected and isolated genetically distinct avian strains of C. abortus from wild birds globally. Before this study, only five avian C. abortus genomes were publicly available. Therefore, we performed culture-independent probe-based whole-genome sequencing on clinical swabs positive for avian C. abortus obtained from Australian Torresian crows (Corvus orru) in 2019 and 2020. We successfully obtained draft genomes for three avian C. abortus strains (C1, C2 and C3), each comprising draft chromosomes with lengths of 1 115 667, 1 120 231 and 1 082 115 bp, and associated 7 553 bp plasmids, with a genome completeness exceeding 92 %. Molecular characterization revealed that these three strains comprise a novel sequence type (ST333), whilst phylogenetic analyses placed all three strains in a cluster with other avian C. abortus genomes. Interestingly, these three strains share a distant genomic relation (2693 single nucleotide variants) with the reference strain 15-58d/44 (ST152), isolated from a Eurasian magpie (Pica pica) in Poland, highlighting the need for more publicly available genomes. Broad comparative analyses with other avian C. abortus genomes revealed that the three draft genomes contain conserved Chlamydia genomic features, including genes coding for type III secretion system and polymorphic membrane proteins, and potential virulence factors such as the large chlamydial cytotoxin, warranting further studies. This research provides the first avian C. abortus draft genomes from Australian birds, highlighting Torresian crows as novel reservoir hosts for these potential pathogens, and demonstrates a practical methodology for sequencing novel Chlamydia genomes without relying on traditional cell culture.

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

Cited by 13 publications

References 162 publications

Evolutionary Dynamics in the Genome of Ocular Chlamydia trachomatis Strains from Northern Tanzania, pre- and post- Mass Drug Administration

Evolutionary Dynamics in the Genome of Ocular Chlamydia trachomatis Strains from Northern Tanzania, pre- and post- Mass Drug Administration

Whole-genome sequencing of Chlamydia psittaci from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers

Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways

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