Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

Genome Medicine
A R LastM J Holland

Abstract

Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa. All Ct sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified 21 Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (odds ratio, OR = 4.07, p* = 0.001) and tarP (OR = 0.34, p* = 0.009). Eight synonymous SNPs associated with disease severity were found in yjfH (rlmB) (OR = 0.13, p* = 0.037), CTA0273 (OR = 0.12, p* = 0.027), trmD (OR = 0.12, p* =...Continue Reading

References

Oct 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·M Nei, W H Li
Nov 1, 1994·The British Journal of Ophthalmology·R L BaileyD C Mabey
Aug 19, 2000·Nature·J C SamuelsonR E Dalbey
Feb 24, 2001·Cellular Microbiology·T HackstadtE R Fischer
Jul 27, 2001·Ophthalmic Epidemiology·S K WestM C Lynch
Jun 5, 2003·The Journal of Clinical Investigation·Harlan D CaldwellGrant McClarty
Jun 20, 2003·Proceedings of the National Academy of Sciences of the United States of America·Robert J BellandHarlan D Caldwell
Jul 30, 2003·Lancet·Anthony W SolomonDavid C W Mabey
Apr 21, 2004·Protein Science : a Publication of the Protein Society·Chin-Sheng YuJenn-Kang Hwang
Jun 10, 2004·Genome Biology·Brian W BrunelleRichard S Stephens
Jun 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·D R CliftonT Hackstadt
Nov 24, 2004·Infection and Immunity·John H CarlsonRobert J Belland
Apr 20, 2005·Proteomics·Paul SkippIan N Clarke
Sep 24, 2005·Infection and Immunity·John H CarlsonHarlan D Caldwell
Jan 20, 2006·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Matthew J BurtonRobin L Bailey
Mar 24, 2006·Molecular Microbiology·John H CarlsonGrant McClarty
Jul 11, 2006·Molecular Microbiology·Shahram MisaghiMichael N Starnbach
Jul 11, 2006·The Journal of Infectious Diseases·Isao MiyairiGerald I Byrne
Oct 24, 2006·Journal of Bacteriology·P Scott Hefty, Richard S Stephens
Sep 30, 2008·PLoS Neglected Tropical Diseases·Aura A AndreasenRobin L Bailey
Oct 15, 2008·Systematic Biology·Alexandros StamatakisJacques Rougemont
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Feb 16, 2010·Clinica Chimica Acta; International Journal of Clinical Chemistry·Jun Lu, David G Grenache
Apr 9, 2010·Tropical Medicine & International Health : TM & IH·Victor H HuDavid C W Mabey

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Citations

Feb 28, 2018·Scientific Reports·Somayeh B ShafieiKhurshid A Guru
Mar 13, 2019·American Journal of Botany·Brian Park, Michael J Donoghue
May 21, 2020·Scientific Data·Luke J Eberhart-PhillipsClemens Küpper
Nov 7, 2019·Parasites & Vectors·Abdulazeem Abdulsalam Ibrahim AlkhidirHarry Pickering
Jan 9, 2019·Frontiers in Cellular and Infection Microbiology·Colette Elizabeth O'NeillIan Nicholas Clarke
Oct 10, 2020·The Journal of Infectious Diseases·Harry PickeringScott D Nash

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Methods Mentioned

BETA
PCA
phase contrast microscopy
PCR
genotyping

Software Mentioned

CELLO
SureDesign
Genome Analysis Tool Kit ( GATK )
RAxML
RADAR
Pfam
SA
SAMtools
PSORTb
PhiPack

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