schliessen

Filtern

 

Bibliotheken

Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis

Mycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we... Full description

Journal Title: Nature medicine 2016-12, Vol.22 (12), p.1470-1474
Main Author: Lieberman, Tami D
Other Authors: Wilson, Douglas , Misra, Reshma , Xiong, Lealia L , Moodley, Prashini , Cohen, Ted , Kishony, Roy
Format: Electronic Article Electronic Article
Language: English
Subjects:
HIV
Publisher: United States: Nature Publishing Group
ID: ISSN: 1078-8956
Link: https://www.ncbi.nlm.nih.gov/pubmed/27798613
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: cdi_proquest_miscellaneous_1855078724
title: Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis
format: Article
creator:
  • Lieberman, Tami D
  • Wilson, Douglas
  • Misra, Reshma
  • Xiong, Lealia L
  • Moodley, Prashini
  • Cohen, Ted
  • Kishony, Roy
subjects:
  • Adult
  • Aged
  • Autopsies
  • Autopsy
  • Bacteria
  • Bacteriological Techniques
  • Biological diversity
  • Coinfection - microbiology
  • DNA, Bacterial - genetics
  • Female
  • Genetic aspects
  • Genetic diversity
  • Genetic Variation
  • HIV
  • HIV (Viruses)
  • HIV Infections - complications
  • Human immunodeficiency virus
  • Humans
  • Lentivirus
  • Liver - microbiology
  • Lung - microbiology
  • Lymph Nodes - microbiology
  • Male
  • Middle Aged
  • Mycobacterium tuberculosis
  • Mycobacterium tuberculosis - genetics
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Retroviridae
  • South Africa
  • Spleen - microbiology
  • Tuberculosis
  • Tuberculosis - complications
  • Tuberculosis - microbiology
  • Tuberculosis, Hepatic - complications
  • Tuberculosis, Hepatic - microbiology
  • Tuberculosis, Lymph Node - complications
  • Tuberculosis, Lymph Node - microbiology
  • Tuberculosis, Pulmonary - complications
  • Tuberculosis, Pulmonary - microbiology
  • Tuberculosis, Splenic - complications
  • Tuberculosis, Splenic - microbiology
ispartof: Nature medicine, 2016-12, Vol.22 (12), p.1470-1474
description: Mycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we report genomic analysis of 2,693 samples collected post mortem from lung and extrapulmonary biopsies of 44 subjects in KwaZulu-Natal, South Africa, who received minimal antitubercular treatment and most of whom were HIV seropositive. We found that purifying selection occurred within individual patients, without the need for patient-to-patient transmission. Despite negative selection, mycobacteria diversified within individuals to form sublineages that co-existed for years. These sublineages, as well as distinct strains from mixed infections, were differentially distributed throughout the lung, suggesting temporary barriers to pathogen migration. As a consequence, samples taken from the upper airway often captured only a fraction of the population diversity, challenging current methods of outbreak tracing and resistance diagnostics. Phylogenetic analysis indicated that dissemination from the lungs to extrapulmonary sites was as frequent as between lung sites, supporting the idea of similar migration routes within and between organs, at least in subjects with HIV. Genomic diversity therefore provides a record of pathogen diversification and repeated dissemination across the body.
language: eng
source:
identifier: ISSN: 1078-8956
fulltext: no_fulltext
issn:
  • 1078-8956
  • 1546-170X
url: Link


@attributes
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
RANK2.7130978
LOCALfalse
PrimoNMBib
record
control
sourceidgale_proqu
recordidTN_cdi_proquest_miscellaneous_1855078724
sourceformatXML
sourcesystemPC
galeidA479831827
sourcerecordidA479831827
originalsourceidFETCH-LOGICAL-1579t-9a95a0412c659d9986d1e2200dd96cca59734d936c0c222a6baddf4d11d4dddd0
addsrcrecordideNqNkl1vFCEUhidGYz80_gMziYnVi1mBgZnhsmm03aSmiR-Nd4QFpkszAyMHqvvvZa3aTm2McAEhz3lzzstbFM8wWmBUd2_cuKAEsQfFLma0qXCLvjzMd9R2VcdZs1PsAVwihGrE-ONih7Qt7xpc7xZwbJwfrSq1vTIBbNyU1pUyRT_BpgQ5ToOBMpgrIwcov9m4tq5ae4i5AMCM1slovSt9X54szysJ4JWV0ejy_Ub5lVTRBJvGMqaVCSoNHiw8KR71Wc08_XXuF5_fvf10dFKdnh0vjw5PK8xaHisuOZOIYqIaxjXPDWtsCEFIa94oJRlva6p53SikCCGyWUmte6ox1lTnhfaLV9e6U_Bfk4EoRgvKDIN0xicQuGMsO9QS-h9ozbJ7lDQZfXEHvfQpuDxIpmhTNxTX-Ia6kIMR1vU-Bqm2ouKQZvNr3JE2U4t7qLx1dlZ5Z3qb32cFz-8pELeB1zMgi0TzPV7IBCCWHz_Mxf7Fnp3P2Ze32HVOQ1yDH9L282EOHlyDKniAYHoxBTvKsBEYiW1WhRvFNqs3s0xpNRr9h_sdzgxUd6SUjT_jloe2w1-CPwCNwu8b
sourcetypeAggregation Database
isCDItrue
recordtypearticle
pqid1846364131
display
typearticle
titleGenomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis
creatorLieberman, Tami D ; Wilson, Douglas ; Misra, Reshma ; Xiong, Lealia L ; Moodley, Prashini ; Cohen, Ted ; Kishony, Roy
creatorcontribLieberman, Tami D ; Wilson, Douglas ; Misra, Reshma ; Xiong, Lealia L ; Moodley, Prashini ; Cohen, Ted ; Kishony, Roy
descriptionMycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we report genomic analysis of 2,693 samples collected post mortem from lung and extrapulmonary biopsies of 44 subjects in KwaZulu-Natal, South Africa, who received minimal antitubercular treatment and most of whom were HIV seropositive. We found that purifying selection occurred within individual patients, without the need for patient-to-patient transmission. Despite negative selection, mycobacteria diversified within individuals to form sublineages that co-existed for years. These sublineages, as well as distinct strains from mixed infections, were differentially distributed throughout the lung, suggesting temporary barriers to pathogen migration. As a consequence, samples taken from the upper airway often captured only a fraction of the population diversity, challenging current methods of outbreak tracing and resistance diagnostics. Phylogenetic analysis indicated that dissemination from the lungs to extrapulmonary sites was as frequent as between lung sites, supporting the idea of similar migration routes within and between organs, at least in subjects with HIV. Genomic diversity therefore provides a record of pathogen diversification and repeated dissemination across the body.
identifier
0ISSN: 1078-8956
1EISSN: 1546-170X
2DOI: 10.1038/nm.4205
3PMID: 27798613
languageeng
publisherUnited States: Nature Publishing Group
subjectAdult ; Aged ; Autopsies ; Autopsy ; Bacteria ; Bacteriological Techniques ; Biological diversity ; Coinfection - microbiology ; DNA, Bacterial - genetics ; Female ; Genetic aspects ; Genetic diversity ; Genetic Variation ; HIV ; HIV (Viruses) ; HIV Infections - complications ; Human immunodeficiency virus ; Humans ; Lentivirus ; Liver - microbiology ; Lung - microbiology ; Lymph Nodes - microbiology ; Male ; Middle Aged ; Mycobacterium tuberculosis ; Mycobacterium tuberculosis - genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Retroviridae ; South Africa ; Spleen - microbiology ; Tuberculosis ; Tuberculosis - complications ; Tuberculosis - microbiology ; Tuberculosis, Hepatic - complications ; Tuberculosis, Hepatic - microbiology ; Tuberculosis, Lymph Node - complications ; Tuberculosis, Lymph Node - microbiology ; Tuberculosis, Pulmonary - complications ; Tuberculosis, Pulmonary - microbiology ; Tuberculosis, Splenic - complications ; Tuberculosis, Splenic - microbiology
ispartofNature medicine, 2016-12, Vol.22 (12), p.1470-1474
rights
0COPYRIGHT 2016 Nature Publishing Group
1Copyright Nature Publishing Group Dec 2016
lds50peer_reviewed
oafree_for_read
citedbyFETCH-LOGICAL-1579t-9a95a0412c659d9986d1e2200dd96cca59734d936c0c222a6baddf4d11d4dddd0
citesFETCH-LOGICAL-1579t-9a95a0412c659d9986d1e2200dd96cca59734d936c0c222a6baddf4d11d4dddd0
orcidid0000-0002-5512-9456 ; 0000-0001-7636-5936
links
openurl$$Topenurl_article
thumbnail$$Usyndetics_thumb_exl
backlink$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27798613$$D View this record in MEDLINE/PubMed
search
creatorcontrib
0Lieberman, Tami D
1Wilson, Douglas
2Misra, Reshma
3Xiong, Lealia L
4Moodley, Prashini
5Cohen, Ted
6Kishony, Roy
title
0Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis
1Nature medicine
addtitleNat Med
descriptionMycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we report genomic analysis of 2,693 samples collected post mortem from lung and extrapulmonary biopsies of 44 subjects in KwaZulu-Natal, South Africa, who received minimal antitubercular treatment and most of whom were HIV seropositive. We found that purifying selection occurred within individual patients, without the need for patient-to-patient transmission. Despite negative selection, mycobacteria diversified within individuals to form sublineages that co-existed for years. These sublineages, as well as distinct strains from mixed infections, were differentially distributed throughout the lung, suggesting temporary barriers to pathogen migration. As a consequence, samples taken from the upper airway often captured only a fraction of the population diversity, challenging current methods of outbreak tracing and resistance diagnostics. Phylogenetic analysis indicated that dissemination from the lungs to extrapulmonary sites was as frequent as between lung sites, supporting the idea of similar migration routes within and between organs, at least in subjects with HIV. Genomic diversity therefore provides a record of pathogen diversification and repeated dissemination across the body.
subject
0Adult
1Aged
2Autopsies
3Autopsy
4Bacteria
5Bacteriological Techniques
6Biological diversity
7Coinfection - microbiology
8DNA, Bacterial - genetics
9Female
10Genetic aspects
11Genetic diversity
12Genetic Variation
13HIV
14HIV (Viruses)
15HIV Infections - complications
16Human immunodeficiency virus
17Humans
18Lentivirus
19Liver - microbiology
20Lung - microbiology
21Lymph Nodes - microbiology
22Male
23Middle Aged
24Mycobacterium tuberculosis
25Mycobacterium tuberculosis - genetics
26Phylogeny
27Polymorphism, Single Nucleotide
28Retroviridae
29South Africa
30Spleen - microbiology
31Tuberculosis
32Tuberculosis - complications
33Tuberculosis - microbiology
34Tuberculosis, Hepatic - complications
35Tuberculosis, Hepatic - microbiology
36Tuberculosis, Lymph Node - complications
37Tuberculosis, Lymph Node - microbiology
38Tuberculosis, Pulmonary - complications
39Tuberculosis, Pulmonary - microbiology
40Tuberculosis, Splenic - complications
41Tuberculosis, Splenic - microbiology
issn
01078-8956
11546-170X
fulltextfalse
rsrctypearticle
creationdate2016
recordtypearticle
recordideNqNkl1vFCEUhidGYz80_gMziYnVi1mBgZnhsmm03aSmiR-Nd4QFpkszAyMHqvvvZa3aTm2McAEhz3lzzstbFM8wWmBUd2_cuKAEsQfFLma0qXCLvjzMd9R2VcdZs1PsAVwihGrE-ONih7Qt7xpc7xZwbJwfrSq1vTIBbNyU1pUyRT_BpgQ5ToOBMpgrIwcov9m4tq5ae4i5AMCM1slovSt9X54szysJ4JWV0ejy_Ub5lVTRBJvGMqaVCSoNHiw8KR71Wc08_XXuF5_fvf10dFKdnh0vjw5PK8xaHisuOZOIYqIaxjXPDWtsCEFIa94oJRlva6p53SikCCGyWUmte6ox1lTnhfaLV9e6U_Bfk4EoRgvKDIN0xicQuGMsO9QS-h9ozbJ7lDQZfXEHvfQpuDxIpmhTNxTX-Ia6kIMR1vU-Bqm2ouKQZvNr3JE2U4t7qLx1dlZ5Z3qb32cFz-8pELeB1zMgi0TzPV7IBCCWHz_Mxf7Fnp3P2Ze32HVOQ1yDH9L282EOHlyDKniAYHoxBTvKsBEYiW1WhRvFNqs3s0xpNRr9h_sdzgxUd6SUjT_jloe2w1-CPwCNwu8b
startdate201612
enddate201612
creator
0Lieberman, Tami D
1Wilson, Douglas
2Misra, Reshma
3Xiong, Lealia L
4Moodley, Prashini
5Cohen, Ted
6Kishony, Roy
generalNature Publishing Group
scope
0CGR
1CUY
2CVF
3ECM
4EIF
5NPM
6AAYXX
7CITATION
8IOF
93V.
107QG
117QL
127QP
137QR
147T5
157TK
167TM
177TO
187U7
197U9
207X7
217XB
2288A
2388E
2488I
258AO
268FD
278FE
288FH
298FI
308FJ
318FK
328G5
33ABUWG
34AZQEC
35BBNVY
36BENPR
37BHPHI
38C1K
39DWQXO
40FR3
41FYUFA
42GHDGH
43GNUQQ
44GUQSH
45H94
46HCIFZ
47K9.
48LK8
49M0S
50M1P
51M2O
52M2P
53M7N
54M7P
55MBDVC
56P64
57PADUT
58PQEST
59PQQKQ
60PQUKI
61PRINS
62Q9U
63RC3
647X8
orcidid
0https://orcid.org/0000-0002-5512-9456
1https://orcid.org/0000-0001-7636-5936
sort
creationdate201612
titleGenomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis
authorLieberman, Tami D ; Wilson, Douglas ; Misra, Reshma ; Xiong, Lealia L ; Moodley, Prashini ; Cohen, Ted ; Kishony, Roy
facets
frbrtype5
frbrgroupidcdi_FETCH-LOGICAL-1579t-9a95a0412c659d9986d1e2200dd96cca59734d936c0c222a6baddf4d11d4dddd0
rsrctypearticles
prefilterarticles
languageeng
creationdate2016
topic
0Adult
1Aged
2Autopsies
3Autopsy
4Bacteria
5Bacteriological Techniques
6Biological diversity
7Coinfection - microbiology
8DNA, Bacterial - genetics
9Female
10Genetic aspects
11Genetic diversity
12Genetic Variation
13HIV
14HIV (Viruses)
15HIV Infections - complications
16Human immunodeficiency virus
17Humans
18Lentivirus
19Liver - microbiology
20Lung - microbiology
21Lymph Nodes - microbiology
22Male
23Middle Aged
24Mycobacterium tuberculosis
25Mycobacterium tuberculosis - genetics
26Phylogeny
27Polymorphism, Single Nucleotide
28Retroviridae
29South Africa
30Spleen - microbiology
31Tuberculosis
32Tuberculosis - complications
33Tuberculosis - microbiology
34Tuberculosis, Hepatic - complications
35Tuberculosis, Hepatic - microbiology
36Tuberculosis, Lymph Node - complications
37Tuberculosis, Lymph Node - microbiology
38Tuberculosis, Pulmonary - complications
39Tuberculosis, Pulmonary - microbiology
40Tuberculosis, Splenic - complications
41Tuberculosis, Splenic - microbiology
toplevelpeer_reviewed
creatorcontrib
0Lieberman, Tami D
1Wilson, Douglas
2Misra, Reshma
3Xiong, Lealia L
4Moodley, Prashini
5Cohen, Ted
6Kishony, Roy
collection
0Medline
1MEDLINE
2MEDLINE (Ovid)
3MEDLINE
4MEDLINE
5PubMed
6CrossRef
7Gale General OneFile
8ProQuest Central (Corporate)
9Animal Behavior Abstracts
10Bacteriology Abstracts (Microbiology B)
11Calcium & Calcified Tissue Abstracts
12Chemoreception Abstracts
13Immunology Abstracts
14Neurosciences Abstracts
15Nucleic Acids Abstracts
16Oncogenes and Growth Factors Abstracts
17Toxicology Abstracts
18Virology and AIDS Abstracts
19Health & Medical Collection
20ProQuest Central (purchase pre-March 2016)
21Biology Database (Alumni Edition)
22Medical Database (Alumni Edition)
23Science Database (Alumni Edition)
24ProQuest Pharma Collection
25Technology Research Database
26ProQuest SciTech Collection
27ProQuest Natural Science Collection
28Hospital Premium Collection
29Hospital Premium Collection (Alumni Edition)
30ProQuest Central (Alumni) (purchase pre-March 2016)
31Research Library (Alumni Edition)
32ProQuest Central (Alumni Edition)
33ProQuest Central Essentials
34Biological Science Collection
35ProQuest Central
36Natural Science Collection
37Environmental Sciences and Pollution Management
38ProQuest Central Korea
39Engineering Research Database
40Health Research Premium Collection
41Health Research Premium Collection (Alumni)
42ProQuest Central Student
43Research Library Prep
44AIDS and Cancer Research Abstracts
45SciTech Premium Collection
46ProQuest Health & Medical Complete (Alumni)
47ProQuest Biological Science Collection
48Health & Medical Collection (Alumni Edition)
49Medical Database
50Research Library
51Science Database
52Algology Mycology and Protozoology Abstracts (Microbiology C)
53Biological Science Database
54Research Library (Corporate)
55Biotechnology and BioEngineering Abstracts
56Research Library China
57ProQuest One Academic Eastern Edition
58ProQuest One Academic
59ProQuest One Academic UKI Edition
60ProQuest Central China
61ProQuest Central Basic
62Genetics Abstracts
63MEDLINE - Academic
jtitleNature medicine
delivery
delcategoryRemote Search Resource
fulltextno_fulltext
addata
au
0Lieberman, Tami D
1Wilson, Douglas
2Misra, Reshma
3Xiong, Lealia L
4Moodley, Prashini
5Cohen, Ted
6Kishony, Roy
formatjournal
genrearticle
ristypeJOUR
atitleGenomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis
jtitleNature medicine
addtitleNat Med
date2016-12
risdate2016
volume22
issue12
spage1470
epage1474
pages1470-1474
issn1078-8956
eissn1546-170X
abstractMycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we report genomic analysis of 2,693 samples collected post mortem from lung and extrapulmonary biopsies of 44 subjects in KwaZulu-Natal, South Africa, who received minimal antitubercular treatment and most of whom were HIV seropositive. We found that purifying selection occurred within individual patients, without the need for patient-to-patient transmission. Despite negative selection, mycobacteria diversified within individuals to form sublineages that co-existed for years. These sublineages, as well as distinct strains from mixed infections, were differentially distributed throughout the lung, suggesting temporary barriers to pathogen migration. As a consequence, samples taken from the upper airway often captured only a fraction of the population diversity, challenging current methods of outbreak tracing and resistance diagnostics. Phylogenetic analysis indicated that dissemination from the lungs to extrapulmonary sites was as frequent as between lung sites, supporting the idea of similar migration routes within and between organs, at least in subjects with HIV. Genomic diversity therefore provides a record of pathogen diversification and repeated dissemination across the body.
copUnited States
pubNature Publishing Group
pmid27798613
doi10.1038/nm.4205
tpages5
orcidid
0https://orcid.org/0000-0002-5512-9456
1https://orcid.org/0000-0001-7636-5936
oafree_for_read