Predicting phenotype and emerging strains among Chlamydia trachomatis infections.
Chlamydia trachomatis is a global cause of blinding trachoma and sexually transmitted infections (STIs). We used comparative genomics of the family Chlamydiaceae to select conserved housekeeping genes for C. trachomatis multilocus sequencing, characterizing 19 reference and 68 clinical isolates from 6 continental/subcontinental regions. There were 44 sequence types (ST). Identical STs for STI isolates were recovered from different regions, whereas STs for trachoma isolates were restricted by continent. Twenty-nine of 52 alleles had nonuniform distributions of frequencies across regions (p<0.001). Phylogenetic analysis showed 3 disease clusters: invasive lymphogranuloma venereum strains, globally prevalent noninvasive STI strains (ompA genotypes D/Da, E, and F), and nonprevalent STI strains with a trachoma subcluster. Recombinant strains were observed among STI clusters. Single nucleotide polymorphisms (SNPs) were predictive of disease specificity. Multilocus and SNP typing can now be used to detect diverse and emerging C. trachomatis strains for epidemiologic and evolutionary studies of trachoma and STI populations worldwide.
Dean
Deborah
D
Children's Global Health Initiativ, Children's Hospital Oakland Research Institute, Oakland, California 94609, USA. ddean@chori.org
Bruno
William J
WJ
Wan
Raymond
R
Gomes
João P
JP
Devignot
Stéphanie
S
Mehari
Tigist
T
de Vries
Henry J C
HJ
Morré
Servaas A
SA
Myers
Garry
G
Read
Timothy D
TD
Spratt
Brian G
BG
D001426:Bacterial Proteins / Q000235:genetics*; D015373:Bacterial Typing Techniques; D002690:Chlamydia Infections / Q000382:microbiology* / Q000473:pathology; D002692:Chlamydia trachomatis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D021821:Communicable Diseases, Emerging / Q000382:microbiology* / Q000473:pathology; D004269:DNA, Bacterial / Q000032:analysis; D023281:Genomics; D006801:Humans; D008219:Lymphogranuloma Venereum / Q000382:microbiology* / Q000473:pathology; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011237:Predictive Value of Tests; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012749:Sexually Transmitted Diseases / Q000382:microbiology / Q000473:pathology; D013045:Species Specificity; D014141:Trachoma / Q000382:microbiology* / Q000473:pathology
D001426:Bacterial Proteins; D004269:DNA, Bacterial