Patterns of within-host spread ofChlamydia trachomatisbetween vagina, endocervix and rectum revealed by comparative genomic analysis

Abstract

Chlamydia trachomatis, a gram-negative obligate intracellular bacterium, commonly causes sexually transmitted infections (STIs). Little is known about C. trachomatis transmission within the host, which is important for understanding disease epidemiology and progression. We used RNA-bait enrichment and whole-genome sequencing to compare rectal, vaginal and endocervical samples collected at the same time from 26 study participants who attended Fijian Ministry of Health and Medical Services clinics and tested positive for C. trachomatis at each anatomic site. The 78 C. trachomatis genomes from participants were from two major clades of the C. trachomatis phylogeny (the prevalent urogenital and anorectal clade and non-prevalent urogenital and anorectal clade). For 21 participants, genome sequences were almost identical in each anatomic site. For the other five participants, two distinct C. trachomatis strains were present in different sites; in two cases, the vaginal sample was a mixture of strains. The absence of large numbers of fixed SNPs between C. trachomatis strains within many of the participants could indicate recent acquisition of infection prior to the clinic visit without sufficient time to accumulate significant variation in the different body sites. This model suggests that many C. trachomatis infections may be resolved relatively quickly in the Fijian population, possibly reflecting common prescription or over-the-counter antibiotics usage.

Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages

“…Conversely, the proximity of villages with SvA prevalence may contribute to increased circulation of SvA strains among the villages, enhancing the overall diversity and the exchange of variations within the SvA population. Previously, differences in the rate of mutation accumulation in the chromosome of Ct strains was explained by the influence of various factors, including adaptation dynamics, different mutation accumulation and repair speed, geographical specifications, and the influence of mass community-level treatment [15,24,27,61,[111][112][113][114]. We emphasize that a more extensive investigation in a larger trachoma-endemic involving an extended timeframe, is necessary to investigate our speculation suggesting different mutation accumulation rates in the chromosome of ocular Ct strains.…”

Comparison of genomic diversity between single and pooledStaphylococcus aureuscolonies isolated from human colonisation cultures

“…There has also been little analysis of what the increased sequencing and storage costs from sampling multiple colonies or pools yield over single colonies. However, pool-seq can still provide insights into the natural history of even well-studied pathogens, and inform us about the fate of adaptations that enhance virulence and antibiotic-resistance (1,(18)(19)(20)(21). Therefore, optimising sampling strategies and genomic workflow design is essential to minimise the number of samples processed while maximising the information obtained from each clinical sample.…”

Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures

“…There has also been little analysis of what the increased sequencing and storage costs from sampling multiple colonies or pools yield over single colonies. However, pool-seq can still provide insights into the natural history of even well-studied pathogens, and inform us about the fate of adaptations that enhance virulence and antibiotic resistance [2,[19][20][21][22]. Therefore, optimizing sampling strategies and genomic workflow design is essential to minimize the number of samples processed while maximizing the information obtained from each clinical sample.…”