Local phylogenetic analysis identifies distinct trends in transmitted HIV drug resistance: implications for public health interventions
Identifieur interne : 000166 ( Main/Exploration ); précédent : 000165; suivant : 000167Local phylogenetic analysis identifies distinct trends in transmitted HIV drug resistance: implications for public health interventions
Auteurs : James I. Brooks [Canada] ; Harrison Niznick [Canada] ; Marianna Ofner [Canada] ; Harriet Merks [Canada] ; Jonathan B. Angel [Canada]Source :
- BMC Infectious Diseases [ 1471-2334 ] ; 2013.
Abstract
HIV transmitted drug resistance (TDR) surveillance is usually conducted by sampling from a large population. However, overall TDR prevalence results may be inaccurate for many individual clinical setting. We analyzed HIV genotypes at a tertiary care setting in Ottawa, Ontario in order to evaluate local TDR patterns among sub-populations.
Genotyping reports were digitized from ART naïve patients followed at the Immunodeficiency Clinic at the Ottawa Hospital, between 2008 and 2010. Quality controlled, digitized sequence data were assessed for TDR using the Stanford HIV Database. Patient characteristics were analyzed according to TDR patterns. Finally, a phylogenetic tree was constructed to elucidate the observed pattern of HIV TDR.
Among the 155 clinic patients there was no statistically significantly difference in demographics as compared to the Ontario provincial HIV population. The clinic prevalence of TDR was 12.3%; however, in contrast to the data from Ontario, TDR patterns were inverted with a 21% prevalence among MSM and 5.5% among IDU. Furthermore, nearly 80% of the observed TDR was a D67N/K219Q pattern with 87% of these infections arising from a distinct phylogenetic cluster.
Local patterns of TDR were distinct to what had been observed provincially. Phylogenetic analysis uncovered a cluster of related infections among MSM that appeared more likely to be recent infections. Results support a paradigm of routine local TDR surveillance to identify the sub-populations under care. Furthermore, the routine application of phylogenetic analysis in the TDR surveillance context provides insights into how best to target prevention strategies; and how to correctly measure outcomes.
Url:
DOI: 10.1186/1471-2334-13-509
PubMed: 24171696
PubMed Central: 3816547
Affiliations:
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Brooks</name><affiliation wicri:level="1"><nlm:aff id="I1">National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Division of Infectious Disease, University of Ottawa, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Division of Infectious Disease, University of Ottawa, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author><author><name sortKey="Niznick, Harrison" sort="Niznick, Harrison" uniqKey="Niznick H" first="Harrison" last="Niznick">Harrison Niznick</name><affiliation wicri:level="1"><nlm:aff id="I2">Division of Infectious Disease, University of Ottawa, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Division of Infectious Disease, University of Ottawa, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author><author><name sortKey="Ofner, Marianna" sort="Ofner, Marianna" uniqKey="Ofner M" first="Marianna" last="Ofner">Marianna Ofner</name><affiliation wicri:level="1"><nlm:aff id="I3">Health Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Health Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author><author><name sortKey="Merks, Harriet" sort="Merks, Harriet" uniqKey="Merks H" first="Harriet" last="Merks">Harriet Merks</name><affiliation wicri:level="1"><nlm:aff id="I1">National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author><author><name sortKey="Angel, Jonathan B" sort="Angel, Jonathan B" uniqKey="Angel J" first="Jonathan B" last="Angel">Jonathan B. 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Brooks</name><affiliation wicri:level="1"><nlm:aff id="I1">National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Division of Infectious Disease, University of Ottawa, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Division of Infectious Disease, University of Ottawa, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author><author><name sortKey="Niznick, Harrison" sort="Niznick, Harrison" uniqKey="Niznick H" first="Harrison" last="Niznick">Harrison Niznick</name><affiliation wicri:level="1"><nlm:aff id="I2">Division of Infectious Disease, University of Ottawa, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Division of Infectious Disease, University of Ottawa, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author><author><name sortKey="Ofner, Marianna" sort="Ofner, Marianna" uniqKey="Ofner M" first="Marianna" last="Ofner">Marianna Ofner</name><affiliation wicri:level="1"><nlm:aff id="I3">Health Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Health Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author><author><name sortKey="Merks, Harriet" sort="Merks, Harriet" uniqKey="Merks H" first="Harriet" last="Merks">Harriet Merks</name><affiliation wicri:level="1"><nlm:aff id="I1">National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author><author><name sortKey="Angel, Jonathan B" sort="Angel, Jonathan B" uniqKey="Angel J" first="Jonathan B" last="Angel">Jonathan B. Angel</name><affiliation wicri:level="1"><nlm:aff id="I2">Division of Infectious Disease, University of Ottawa, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Division of Infectious Disease, University of Ottawa, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I4">Ottawa Hospital Research Institute, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Ottawa Hospital Research Institute, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Infectious Diseases</title><idno type="eISSN">1471-2334</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>HIV transmitted drug resistance (TDR) surveillance is usually conducted by sampling from a large population. However, overall TDR prevalence results may be inaccurate for many individual clinical setting. We analyzed HIV genotypes at a tertiary care setting in Ottawa, Ontario in order to evaluate local TDR patterns among sub-populations.</p></sec><sec><title>Method</title><p>Genotyping reports were digitized from ART naïve patients followed at the Immunodeficiency Clinic at the Ottawa Hospital, between 2008 and 2010. Quality controlled, digitized sequence data were assessed for TDR using the Stanford HIV Database. Patient characteristics were analyzed according to TDR patterns. Finally, a phylogenetic tree was constructed to elucidate the observed pattern of HIV TDR.</p></sec><sec><title>Results</title><p>Among the 155 clinic patients there was no statistically significantly difference in demographics as compared to the Ontario provincial HIV population. The clinic prevalence of TDR was 12.3%; however, in contrast to the data from Ontario, TDR patterns were inverted with a 21% prevalence among MSM and 5.5% among IDU. Furthermore, nearly 80% of the observed TDR was a D67N/K219Q pattern with 87% of these infections arising from a distinct phylogenetic cluster.</p></sec><sec><title>Conclusions</title><p>Local patterns of TDR were distinct to what had been observed provincially. Phylogenetic analysis uncovered a cluster of related infections among MSM that appeared more likely to be recent infections. Results support a paradigm of routine local TDR surveillance to identify the sub-populations under care. 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sortKey="Hue, S" uniqKey="Hue S">S Hué</name></author><author><name sortKey="Xu, L" uniqKey="Xu L">L Xu</name></author><author><name sortKey="Wrin, T" uniqKey="Wrin T">T Wrin</name></author><author><name sortKey="Lie, Y" uniqKey="Lie Y">Y Lie</name></author><author><name sortKey="Hellmann, N" uniqKey="Hellmann N">N Hellmann</name></author><author><name sortKey="Petropoulos, C" uniqKey="Petropoulos C">C Petropoulos</name></author><author><name sortKey="Workman, J" uniqKey="Workman J">J Workman</name></author><author><name sortKey="Ratcliffe, D" uniqKey="Ratcliffe D">D Ratcliffe</name></author><author><name sortKey="Choudhury, B" uniqKey="Choudhury B">B Choudhury</name></author><author><name sortKey="Pillay, D" uniqKey="Pillay D">D Pillay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Degruttola, V" uniqKey="Degruttola V">V DeGruttola</name></author><author><name sortKey="Smith, Dm" uniqKey="Smith D">DM Smith</name></author><author><name sortKey="Little, Sj" uniqKey="Little S">SJ Little</name></author><author><name sortKey="Miller, V" uniqKey="Miller V">V Miller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wald, E" uniqKey="Wald E">E Wald</name></author><author><name sortKey="Mason, E" uniqKey="Mason E">E Mason</name></author><author><name sortKey="Bradley, J" uniqKey="Bradley J">J Bradley</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Canada</li></country></list><tree><country name="Canada"><noRegion><name sortKey="Brooks, James I" sort="Brooks, James I" uniqKey="Brooks J" first="James I" last="Brooks">James I. Brooks</name></noRegion><name sortKey="Angel, Jonathan B" sort="Angel, Jonathan B" uniqKey="Angel J" first="Jonathan B" last="Angel">Jonathan B. Angel</name><name sortKey="Angel, Jonathan B" sort="Angel, Jonathan B" uniqKey="Angel J" first="Jonathan B" last="Angel">Jonathan B. Angel</name><name sortKey="Brooks, James I" sort="Brooks, James I" uniqKey="Brooks J" first="James I" last="Brooks">James I. Brooks</name><name sortKey="Merks, Harriet" sort="Merks, Harriet" uniqKey="Merks H" first="Harriet" last="Merks">Harriet Merks</name><name sortKey="Niznick, Harrison" sort="Niznick, Harrison" uniqKey="Niznick H" first="Harrison" last="Niznick">Harrison Niznick</name><name sortKey="Ofner, Marianna" sort="Ofner, Marianna" uniqKey="Ofner M" first="Marianna" last="Ofner">Marianna Ofner</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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