Etiological Characterization of the Cutaneous Ulcer Syndrome in Papua New Guinea Using Shotgun Metagenomics
Por:
Noguera-Julian, M, Gonzalez-Beiras, C, Parera, M, Ubals, M, Kapa, A, Paredes, R and Mitja, O
Publicada:
1 feb 2019
Resumen:
Background. Treponema pallidum subsp pertenue and Haemophilus ducreyi are causative agents of cutaneous ulcer (CU) in yaws-endemic regions in the tropics. However, a significant proportion of CU patients remain polymerase chain reaction (PCR) negative for both bacterial agents. We aimed to identify potential additional etiological agents of CU in a yaws-endemic region.
Methods. This population-based cohort study included children in Lihir Island (Papua New Guinea) examined during a yaws eradication campaign in October 2013-October 2014. All consenting patients with atraumatic exudative ulcers of >1 cm diameter were enrolled. Lesional swabs were collected for real-time PCR testing for T. pallidum subsp pertenue and H. ducreyi. We then performed shotgun whole DNA metagenomics sequencing on extracted DNA and taxonomically assigned shotgun sequences using a human microbiome reference.
Results. Sequence data were available for 122 samples. Shotgun sequencing showed high classification agreement relative to PCR testing (area under the curve for T. pallidum/H. ducreyi was 0.92/0.85, respectively). Clustering analysis of shotgun data revealed compositional clusters where the dominant species (median relative abundance ranged from 32% to 66%) was H. ducreyi (23% of specimens), T. pallidum subsp pertenue (16%), Streptococcus dysgalactiae (12%), Arcanobacterium haemolyticum (8%), and Corynebacterium diphtheriae (8%). Sample clustering derived from ulcer microbial composition did not show geographical patterns.
Conclusions. These data suggest a diverse etiology of skin ulcers in yaws-endemic areas, which may help design more accurate diagnostic tools and more effective antimicrobial treatment approaches to the cutaneous ulcer syndrome.
Filiaciones:
:
irsiCaixa AIDS Res Inst, Badalona, Spain
Univ Autonoma Barcelona, Barcelona, Spain
Univ Cent Catalunya, Univ Vic, Vic, Spain
Gonzalez-Beiras, C:
Lisbon Inst Hyg & Trop Med, Lisbon, Portugal
:
irsiCaixa AIDS Res Inst, Badalona, Spain
Ubals, M:
Univ Barcelona, Hosp Clin, Barcelona Inst Global Hlth, Barcelona, Spain
Kapa, A:
Newcrest Min, Lihir Med Ctr Int SOS, Port Moresby, Papua N Guinea
:
irsiCaixa AIDS Res Inst, Badalona, Spain
Univ Autonoma Barcelona, Barcelona, Spain
Univ Cent Catalunya, Univ Vic, Vic, Spain
Hosp Univ Germans Trias I Pujol, HIV Unit, Badalona, Spain
Mitja, O:
Univ Barcelona, Hosp Clin, Barcelona Inst Global Hlth, Barcelona, Spain
Newcrest Min, Lihir Med Ctr Int SOS, Port Moresby, Papua N Guinea
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