The pan-genome of Treponema pallidum reveals differences in genome plasticity between subspecies related to venereal and non-venereal syphilis.

Genome, Bacterial / genetics Genomic Islands / genetics Humans Phylogeny Syphilis / microbiology Treponema pallidum / classification
Core genome Pan-genome Singletons Syphilis Treponema pallidum

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
10 Jan 2020
Historique:
received: 10 10 2019
accepted: 24 12 2019
entrez: 12 1 2020
pubmed: 12 1 2020
medline: 9 6 2020
Statut: epublish

Résumé

Spirochetal organisms of the Treponema genus are responsible for causing Treponematoses. Pathogenic treponemes is a Gram-negative, motile, spirochete pathogen that causes syphilis in human. Treponema pallidum subsp. endemicum (TEN) causes endemic syphilis (bejel); T. pallidum subsp. pallidum (TPA) causes venereal syphilis; T. pallidum subsp. pertenue (TPE) causes yaws; and T. pallidum subsp. Ccarateum causes pinta. Out of these four high morbidity diseases, venereal syphilis is mediated by sexual contact; the other three diseases are transmitted by close personal contact. The global distribution of syphilis is alarming and there is an increasing need of proper treatment and preventive measures. Unfortunately, effective measures are limited. Here, the genome sequences of 53 T. pallidum strains isolated from different parts of the world and a diverse range of hosts were comparatively analysed using pan-genomic strategy. Phylogenomic, pan-genomic, core genomic and singleton analysis disclosed the close connection among all strains of the pathogen T. pallidum, its clonal behaviour and showed increases in the sizes of the pan-genome. Based on the genome plasticity analysis of the subsets containing the subspecies T pallidum subsp. pallidum, T. pallidum subsp. endemicum and T. pallidum subsp. pertenue, we found differences in the presence/absence of pathogenicity islands (PAIs) and genomic islands (GIs) on subsp.-based study. In summary, we identified four pathogenicity islands (PAIs), eight genomic islands (GIs) in subsp. pallidum, whereas subsp. endemicum has three PAIs and seven GIs and subsp. pertenue harbours three PAIs and eight GIs. Concerning the presence of genes in PAIs and GIs, we found some genes related to lipid and amino acid biosynthesis that were only present in the subsp. of T. pallidum, compared to T. pallidum subsp. endemicum and T. pallidum subsp. pertenue.

Sections du résumé

BACKGROUND BACKGROUND
Spirochetal organisms of the Treponema genus are responsible for causing Treponematoses. Pathogenic treponemes is a Gram-negative, motile, spirochete pathogen that causes syphilis in human. Treponema pallidum subsp. endemicum (TEN) causes endemic syphilis (bejel); T. pallidum subsp. pallidum (TPA) causes venereal syphilis; T. pallidum subsp. pertenue (TPE) causes yaws; and T. pallidum subsp. Ccarateum causes pinta. Out of these four high morbidity diseases, venereal syphilis is mediated by sexual contact; the other three diseases are transmitted by close personal contact. The global distribution of syphilis is alarming and there is an increasing need of proper treatment and preventive measures. Unfortunately, effective measures are limited.
RESULTS RESULTS
Here, the genome sequences of 53 T. pallidum strains isolated from different parts of the world and a diverse range of hosts were comparatively analysed using pan-genomic strategy. Phylogenomic, pan-genomic, core genomic and singleton analysis disclosed the close connection among all strains of the pathogen T. pallidum, its clonal behaviour and showed increases in the sizes of the pan-genome. Based on the genome plasticity analysis of the subsets containing the subspecies T pallidum subsp. pallidum, T. pallidum subsp. endemicum and T. pallidum subsp. pertenue, we found differences in the presence/absence of pathogenicity islands (PAIs) and genomic islands (GIs) on subsp.-based study.
CONCLUSIONS CONCLUSIONS
In summary, we identified four pathogenicity islands (PAIs), eight genomic islands (GIs) in subsp. pallidum, whereas subsp. endemicum has three PAIs and seven GIs and subsp. pertenue harbours three PAIs and eight GIs. Concerning the presence of genes in PAIs and GIs, we found some genes related to lipid and amino acid biosynthesis that were only present in the subsp. of T. pallidum, compared to T. pallidum subsp. endemicum and T. pallidum subsp. pertenue.

Identifiants

DOI: 10.1186/s12864-019-6430-6 PMID: 31924165 PMC: PMC6953169
pubmed: 31924165
doi: 10.1186/s12864-019-6430-6
pii: 10.1186/s12864-019-6430-6
pmc: PMC6953169
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

33

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Auteurs

Arun Kumar Jaiswal (AK)

PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil.

Sandeep Tiwari (S)

PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. sandip_sbtbi@yahoo.com.
ORCID: 0000-0002-8554-1660

Syed Babar Jamal (SB)

Department of Biological Sciences, National University of Medical Sciences, Abid Majeed Road, Rawalpindi, Punjab, 46000, Pakistan.

Letícia de Castro Oliveira (L)

PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil.

Leandro Gomes Alves (LG)

Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil.

Vasco Azevedo (V)

PG Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.

Preetam Ghosh (P)

Department of Computer Science, Virginia Commonwealth University, Richmond, VA-23284, USA.

Carlo Jose Freira Oliveira (CJF)

Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil.

Siomar C Soares (SC)

Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, MG, Brazil. siomars@gmail.com.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › The pan-genome of Treponema pallidum reveals...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées dispersées › Ilots génomiques › The pan-genome of Treponema pallidum reveals...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › The pan-genome of Treponema pallidum reveals...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › The pan-genome of Treponema pallidum reveals...
questionsmedicales.fr › Maladies urogénitales › Maladies génitales › Syphilis › The pan-genome of Treponema pallidum reveals...
questionsmedicales.fr › Bactéries › Spirochaetales › Spirochaetaceae › Treponema › Treponema pallidum › The pan-genome of Treponema pallidum reveals...