A snapshot of Chlamydia trachomatis genetic diversity using multilocus sequence type analysis in an Australian metropolitan setting

Abstract

High-resolution screening methodologies which enable the differentiation of Chlamydia trachomatis at the strain level, directly from clinical samples, can provide the detailed information required for epidemiological questions such as the dynamics of treatment failure. In addition, they give a detailed snapshot of circulating C. trachomatis genetic variation, data which are currently lacking for the Australian population. In the context of two Australian clinical trials, we assessed the genetic diversity of C. trachomatis and compared these to strains circulating globally. We used high-resolution multilocus sequence typing (MLST) of five highly variable genetic regions of C. trachomatis to examine variation in Australia. Samples with established genovars were drawn from a pool of 880 C. trachomatis-positive samples from two clinical studies, whereby 76 sample pairs which remained C. trachomatis-positive for the same genovar after treatment underwent MLST analysis to distinguish between treatment failure and reinfection. MLST analysis revealed a total of 25 sequence types (STs), six new allele variants and seven new STs not described anywhere else in the world, when compared to those in the international C. trachomatis MLST database. Of the eight most common global STs, seven were found in Australia (four derived from men who have sex with men (MSM) and three from heterosexuals). Newly identified STs were predominantly found in samples from the MSM population. In conclusion, MLST provided a diverse C. trachomatis strain profile, with novel circulating STs, and could be used to identify local sexual networks to focus on interventions such as testing and partner notification to prevent reinfection.

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

“…Core genome and/or traditional MLST-derived phylogeny is highly congruent with WGS and/or SNP-derived phylogenies, and avoids the need to reconstruct computationally heavy phylogenies ( Jolley et al., 2018 ; Patiño et al., 2018 ; Versteeg et al., 2018a ; Jelocnik et al., 2019 ; Floridia-Yapur et al., 2021 ). Chlamydial MLST was effectively used in uncovering the global epidemiology of C. trachomatis strains ( Herrmann et al., 2015 ; Danielewski et al., 2017 ), identifying clonal psittacine, horse and human strains of C. psittaci during an outbreak ( Anstey et al., 2021 ) as well closely related but genetically diverse avian chlamydial strains ( Figure 5A ), distinguishing diverse koala C. pecorum strains to aid in translocation of animals ( Figure 5B ) ( Fernandez et al., 2019 ) and other examples ( Batteiger et al., 2014 ).…”

Chlamydiae from Down Under: The Curious Cases of Chlamydial Infections in Australia

“…In the same study, seven new STs not described anywhere else in the world were also characterised, five identified within MSM and two within heterosexuals, indicating that the epidemiology might be more complex than previously thought [23]. Molecular Ct studies can certainly be improved in Australia as they can be utilized as a valuable epidemiological tool to track new and/or persistent infections or determine treatment failure, particularly as there is growing concern about the latter [23,41,46].…”

“…These symptoms can lead to severe disease sequalae and complications, such as ulcerative proctitis in men and pelvic inflammatory disease (PID) and infertility in women. Furthermore, Ct re-infection is also common as is the risk of increased susceptibility to other infections [21][22][23][24]. As Ct can ascend to the upper genital tract, serious sequalae including PID, which can lead to ectopic pregnancy (EP) and chronic pelvic pain or infertility, are commonly observed in the Australian hospital settings.…”

“…Molecular assays targeting the ompA gene revealed that Ct genovars E and F are commonly found in Australian heterosexual men and women, while genovars G and D are the most common in MSM with genovar L2 also occurring [46]. Recent multilocus sequence typing (MLST) of chlamydia-positive rectal samples from MSM and self-collected UGT swabs from heterosexual women and men from a cosmopolitan setting revealed that most infections reflect the global diversity-sequence types (STs) associated with MSM (ST52, ST58, ST108, ST109) and heterosexuals (ST3, ST12, ST55, ST56) were delineated [23]. In the same study, seven new STs not described anywhere else in the world were also characterised, five identified within MSM and two within heterosexuals, indicating that the epidemiology might be more complex than previously thought [23].…”

“…Recent multilocus sequence typing (MLST) of chlamydia-positive rectal samples from MSM and self-collected UGT swabs from heterosexual women and men from a cosmopolitan setting revealed that most infections reflect the global diversity-sequence types (STs) associated with MSM (ST52, ST58, ST108, ST109) and heterosexuals (ST3, ST12, ST55, ST56) were delineated [23]. In the same study, seven new STs not described anywhere else in the world were also characterised, five identified within MSM and two within heterosexuals, indicating that the epidemiology might be more complex than previously thought [23]. Molecular Ct studies can certainly be improved in Australia as they can be utilized as a valuable epidemiological tool to track new and/or persistent infections or determine treatment failure, particularly as there is growing concern about the latter [23,41,46].…”