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González-Buenfil R, Vieyra-Sánchez S, Quinto-Cortés CD, Oppenheimer SJ, Pomat W, Laman M, Cervantes-Hernández MC, Barberena-Jonas C, Auckland K, Allen A, Allen S, Phipps ME, Huerta-Sanchez E, Ioannidis AG, Mentzer AJ, Moreno-Estrada A. Genetic Signatures of Positive Selection in Human Populations Adapted to High Altitude in Papua New Guinea. Genome Biol Evol 2024; 16:evae161. [PMID: 39173139 PMCID: PMC11339866 DOI: 10.1093/gbe/evae161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2024] [Indexed: 08/24/2024] Open
Abstract
Papua New Guinea (PNG) hosts distinct environments mainly represented by the ecoregions of the Highlands and Lowlands that display increased altitude and a predominance of pathogens, respectively. Since its initial peopling approximately 50,000 years ago, inhabitants of these ecoregions might have differentially adapted to the environmental pressures exerted by each of them. However, the genetic basis of adaptation in populations from these areas remains understudied. Here, we investigated signals of positive selection in 62 highlanders and 43 lowlanders across 14 locations in the main island of PNG using whole-genome genotype data from the Oceanian Genome Variation Project (OGVP) and searched for signals of positive selection through population differentiation and haplotype-based selection scans. Additionally, we performed archaic ancestry estimation to detect selection signals in highlanders within introgressed regions of the genome. Among highland populations we identified candidate genes representing known biomarkers for mountain sickness (SAA4, SAA1, PRDX1, LDHA) as well as candidate genes of the Notch signaling pathway (PSEN1, NUMB, RBPJ, MAML3), a novel proposed pathway for high altitude adaptation in multiple organisms. We also identified candidate genes involved in oxidative stress, inflammation, and angiogenesis, processes inducible by hypoxia, as well as in components of the eye lens and the immune response. In contrast, candidate genes in the lowlands are mainly related to the immune response (HLA-DQB1, HLA-DQA2, TAAR6, TAAR9, TAAR8, RNASE4, RNASE6, ANG). Moreover, we find two candidate regions to be also enriched with archaic introgressed segments, suggesting that archaic admixture has played a role in the local adaptation of PNG populations.
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Affiliation(s)
- Ram González-Buenfil
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Sofía Vieyra-Sánchez
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Consuelo D Quinto-Cortés
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | | | - William Pomat
- Vector-Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Moses Laman
- Vector-Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Mayté C Cervantes-Hernández
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Carmina Barberena-Jonas
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
| | | | - Angela Allen
- Department of Molecular Haematology, MRC Weatherall Institute of Molecular Medicine, Headley Way, Headington, Oxford, OX3 9DS, UK
| | - Stephen Allen
- Department of Clinical Sciences,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya 47500, Selangor, Malaysia
| | - Emilia Huerta-Sanchez
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Alexander G Ioannidis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomedical Data Science, Stanford Medical School, Stanford, CA, USA
| | | | - Andrés Moreno-Estrada
- Advanced Genomics Unit (UGA), Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Irapuato, Guanajuato, Mexico
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2
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Pham BN, Jorry R, Silas VD, Okely AD, Maraga S, Pomat W. Leading causes of deaths in the mortality transition in Papua New Guinea: evidence from the Comprehensive Health and Epidemiological Surveillance System. Int J Epidemiol 2022:6955640. [DOI: 10.1093/ije/dyac232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/10/2022] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
Changing causes of deaths in the mortality transition in Papua New Guinea (PNG) are poorly understood. This study analysed community-level data to identify leading causes of death in the population and variations across age groups and sexes, urban-rural sectors and provinces.
Method
Mortality surveillance data were collected from 2018–20 as part of the Comprehensive Health and Epidemiological Surveillance System (CHESS), using the World Health Organization 2016 verbal autopsy (VA) instrument. Data from 926 VA interviews were analysed, using the InterVA-5 cause of death analytical tool to assign specific causes of death among children (0–14 years), those of working age (15–64 years) and the elderly (65+ years).
Result
Nearly 50% of the total deaths were attributed to non-communicable diseases (NCDs), followed by infectious and parasitic diseases (35%), injuries and external causes (11%) and maternal and neonatal deaths (4%). Leading causes of death among children were acute respiratory tract infections (ARTIs) and diarrhoeal diseases, each contributing to 13% of total deaths. Among the working population, tuberculosis (TB) contributed to 12% of total deaths, followed by HIV/AIDS (11%). TB- and HIV/AIDS-attributed deaths were highest in the age group 25–34 years, at 20% and 18%, respectively. These diseases killed more females of working age (n = 79, 15%) than males (n = 52, 8%). Among the elderly, the leading causes of death were ARTIs (13%) followed by digestive neoplasms (10%) and acute cardiac diseases (9%).
Conclusion
The variations in leading causes of death across the populations in PNG suggest diversity in mortality transition. This requires different strategies to address specific causes of death in particular populations.
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Affiliation(s)
- Bang Nguyen Pham
- Population Health and Demography Unit, Papua New Guinea Institute of Medical Research , Goroka, Papua New Guinea
| | - Ronny Jorry
- Population Health and Demography Unit, Papua New Guinea Institute of Medical Research , Goroka, Papua New Guinea
| | - Vinson D Silas
- Population Health and Demography Unit, Papua New Guinea Institute of Medical Research , Goroka, Papua New Guinea
| | - Anthony D Okely
- School of Health and Society and Early Start, University of Wollongong , Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute , Wollongong, NSW, Australia
| | - Seri Maraga
- Population Health and Demography Unit, Papua New Guinea Institute of Medical Research , Goroka, Papua New Guinea
| | - William Pomat
- Population Health and Demography Unit, Papua New Guinea Institute of Medical Research , Goroka, Papua New Guinea
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3
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Pham BN, Abori N, Silas VD, Jorry R, Rao C, Okely T, Pomat W. Tuberculosis and HIV/AIDS-attributed mortalities and associated sociodemographic factors in Papua New Guinea: evidence from the comprehensive health and epidemiological surveillance system. BMJ Open 2022; 12:e058962. [PMID: 35772818 PMCID: PMC9247692 DOI: 10.1136/bmjopen-2021-058962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE Tuberculosis (TB) and HIV/AIDS are public health concerns in Papua New Guinea (PNG). This study examines TB and HIV/AIDS mortalities and associated sociodemographic factors in PNG. METHOD As part of a longitudinal study, verbal autopsy (VA) interviews were conducted using the WHO 2016 VA Instrument to collect data of 926 deaths occurred in the communities within the catchment areas of the Comprehensive Health and Epidemiological Surveillance System from 2018 to 2020.InterVA-5 cause of deaths analytical tool was used to assign specific causes of death (COD). Multinomial logistic regression analyses were conducted to identify associated sociodemographic factors, estimate adjusted ORs (AOR), 95% CIs and p values. RESULT TB and HIV/AIDS were the leading CODs from infectious diseases, attributed to 9% and 8% of the total deaths, respectively.Young adults (25-34 years) had the highest proportion of deaths from TB (20%) and the risk of dying from TB among this age group was five times more likely than those aged 75+ years (AOR: 5.5 (95% CI 1.4 to 21.7)). Urban populations were 46% less likely to die from this disease compared rural ones although the difference was not significant (AOR: 0.54 (95% CI 0.3 to 1.0)). People from middle household wealth quintile were three times more likely to die from TB than those in the richest quintile (AOR: 3.0 (95% CI 1.3 to 7.4)).Young adults also had the highest proportion of deaths to HIV/AIDS (18%) and were nearly seven times more likely to die from this disease compared with those aged 75+years (AOR: 6.7 (95% CI 1.7 to 25.4)). Males were 48% less likely to die from HIV/AIDS than females (AOR: 0.52 (95% CI 0.3 to 0.9)). The risk of dying from HIV/AIDS in urban population was 54% less likely than their rural counterparts (AOR: 0.46 (95% CI 0.2 to 0.9)). CONCLUSION TB and HIV/AIDS interventions are needed to target vulnerable populations to reduce premature mortality from these diseases in PNG.
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Affiliation(s)
- Bang Nguyen Pham
- Population Health and Demography, Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Norah Abori
- Population Health and Demography, Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Vinson D Silas
- Population Health and Demography, Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ronny Jorry
- Population Health and Demography, Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Chalapati Rao
- School of Population Health Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Tony Okely
- School of Health and Society, the University of Wollongong, Illawarra Health and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Willie Pomat
- Population Health and Demography, Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
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Pele M, Herawati T, Yona S. Factors influencing transmission of tuberculosis in Ngeu Nata culture among Ngada community in Kupang, East Nusa Tenggara, Indonesia: Cross sectional study. J Public Health Res 2021; 10. [PMID: 34060740 PMCID: PMC9309630 DOI: 10.4081/jphr.2021.2335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/04/2022] Open
Abstract
Background Eating “sirih/Betel” (Ngeu Nata) as a culture in Ngada society can become one
of the primary source of Tuberculosis (TB) transmission due to share leaves
and betel liquid reservoirs together with other people. If one of the people
who share leaves is a TB patient, it can transmit TB to other person. The
purpose of this study was to identify the factors that influence TB
transmission in Ngeu Nata culture using the health belief model
approach. Design and Methods This study used cross-sectional, involving 110 respondents, selected by
consecutive sampling. The respondents were Bajawa ethnicity, age 36-67, at
least consume Betel one a day together with other person in Ngada district,
East Nusa Tenggara. Results The results showed that most respondents had high transmission behavior in
betel eating culture (51.8%). Factors related to TB transmission behavior:
medical history of TB (p=0.028), knowledge about TB (p=0.038), the perceived
of severity of TB (p=0.037); the perceived of benefits (p=0.039) and the
perceived of barrier (p=0.038). The dominant factor was knowledge, (OR 2,365
(95% CI) 1,015-5,510). Conclusions Implication: nurses should include aspect of Ngeu Nata cultural in designing
TB education for Bajawa ethnicity in order to prevent TB transmission in
Ngada district, East Nusa Tenggara.
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Affiliation(s)
- Maria Pele
- Faculty of Nursing, Universitas Indonesia, Depok, West Java.
| | - Tuti Herawati
- Department of Medical Surgical Nursing, Faculty of Nursing Universitas Indonesia, Depok, West Java.
| | - Sri Yona
- Department of Medical Surgical Nursing, Faculty of Nursing Universitas Indonesia, Depok, West Java.
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5
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Kelwaip RA, Fose S, Siddiqui MS, Molumi CP, Apaio LM, Conway DI, Johnson NW, Thomas SJ, Lambert DW, Hunter KD. Oral cancer in Papua New Guinea: looking back and looking forward. Oral Surg Oral Med Oral Pathol Oral Radiol 2020; 130:292-297. [PMID: 32665206 DOI: 10.1016/j.oooo.2020.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/05/2020] [Accepted: 06/01/2020] [Indexed: 12/24/2022]
Abstract
Oral diseases, including cancers, affect 3.5 billion people globally and remain largely untreated in low- to middle-income countries because of lack of resources. In Papua New Guinea (PNG), oral cancer has, for many decades, been identified as the most common cancer in men, but as the GLOBOCAN 2018 data are estimates extrapolated from surrounding countries, the real prevalence of this disease is not known. The PNG National Health Plan (2011-2020) highlights the need to improve health care, but oral health is not identified as a priority. Alcohol, tobacco, and areca nut/betel quid, which are the social and commercial determinants of oral cancer, are common risk factors, and there are robust data linking these risk factors to oral cancer in PNG. Our recent Global Challenges Research Fund Workshop on Oral Cancer, held in Port Moresby, PNG, brought together a number of researchers in oral cancer epidemiology and translational science with clinicians from PNG to assess the current situation and plan ways to move forward. In this article, we will review the literature on oral cancer in PNG, and make suggestions as to how, collaboratively, we can address the issues identified, ultimately, for the benefit of the people of PNG.
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Affiliation(s)
| | - Seth Fose
- National Department of Health, Port Moresby, Papua New Guinea; Port Moresby General Hospital, Port Moresby, Papua New Guinea
| | | | | | | | - David I Conway
- Glasgow Dental School, University of Glasgow, Glasgow, UK
| | - Newell W Johnson
- Menzies Health Institute Queensland & School of Dentistry and Oral Health, Griffith University, Australia and Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Steve J Thomas
- Bristol Dental School, University of Bristol, Bristol, UK
| | - Daniel W Lambert
- School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Keith D Hunter
- School of Clinical Dentistry, University of Sheffield, Sheffield, UK.
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6
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Gouda HN, Hazard RH, Maraga S, Flaxman AD, Stewart A, Joseph JC, Rarau P, Wangnapi R, Poka H, Serina P, Phuanukoonnon S, Pham BN, Vano M, Lupiwa S, Sie A, Kave H, Lehmann D, Siba P, Lopez AD, Riley ID. The epidemiological transition in Papua New Guinea: new evidence from verbal autopsy studies. Int J Epidemiol 2020; 48:966-977. [PMID: 30915430 DOI: 10.1093/ije/dyz018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Recent economic growth in Papua New Guinea (PNG) would suggest that the country may be experiencing an epidemiological transition, characterized by a reduction in infectious diseases and a growing burden from non-communicable diseases (NCDs). However, data on cause-specific mortality in PNG are very sparse, and the extent of the transition within the country is poorly understood. METHODS Mortality surveillance was established in four small populations across PNG: West Hiri in Central Province, Asaro Valley in Eastern Highlands Province, Hides in Hela Province and Karkar Island in Madang Province. Verbal autopsies (VAs) were conducted on all deaths identified, and causes of death were assigned by SmartVA and classified into five broad disease categories: endemic NCDs; emerging NCDs; endemic infections; emerging infections; and injuries. Results from previous PNG VA studies, using different VA methods and spanning the years 1970 to 2001, are also presented here. RESULTS A total of 868 deaths among adolescents and adults were identified and assigned a cause of death. NCDs made up the majority of all deaths (40.4%), with the endemic NCD of chronic respiratory disease responsible for the largest proportion of deaths (10.5%), followed by the emerging NCD of diabetes (6.2%). Emerging infectious diseases outnumbered endemic infectious diseases (11.9% versus 9.5%). The distribution of causes of death differed across the four sites, with emerging NCDs and emerging infections highest at the site that is most socioeconomically developed, West Hiri. Comparing the 1970-2001 VA series with the present study suggests a large decrease in endemic infections. CONCLUSIONS Our results indicate immediate priorities for health service planning and for strengthening of vital registration systems, to more usefully serve the needs of health priority setting.
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Affiliation(s)
- Hebe N Gouda
- School of Public Health, University of Queensland, Brisbane, QLD, Australia
| | - Riley H Hazard
- University of Melbourne, School of Population and Global Health, Melbourne, VIC, Australia
| | - Seri Maraga
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Abraham D Flaxman
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Andrea Stewart
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Jonathan C Joseph
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Patricia Rarau
- University of Melbourne, School of Population and Global Health, Melbourne, VIC, Australia.,Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Regina Wangnapi
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Harry Poka
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Peter Serina
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA
| | - Suparat Phuanukoonnon
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea.,Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Bang N Pham
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Miriam Vano
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Sebeya Lupiwa
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Albert Sie
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Helen Kave
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Deborah Lehmann
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands, Papua New Guinea
| | - Alan D Lopez
- University of Melbourne, School of Population and Global Health, Melbourne, VIC, Australia
| | - Ian D Riley
- University of Melbourne, School of Population and Global Health, Melbourne, VIC, Australia
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7
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Guernier-Cambert V, Diefenbach-Elstob T, Klotoe BJ, Burgess G, Pelowa D, Dowi R, Gula B, McBryde ES, Refrégier G, Rush C, Sola C, Warner J. Diversity of Mycobacterium tuberculosis in the Middle Fly District of Western Province, Papua New Guinea: microbead-based spoligotyping using DNA from Ziehl-Neelsen-stained microscopy preparations. Sci Rep 2019; 9:15549. [PMID: 31664101 PMCID: PMC6820861 DOI: 10.1038/s41598-019-51892-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/25/2019] [Indexed: 11/29/2022] Open
Abstract
Tuberculosis remains the world's leading cause of death from an infectious agent, and is a serious health problem in Papua New Guinea (PNG) with an estimated 36,000 new cases each year. This study describes the genetic diversity of Mycobacterium tuberculosis among tuberculosis patients in the Balimo/Bamu region in the Middle Fly District of Western Province in PNG, and investigates rifampicin resistance-associated mutations. Archived Ziehl-Neelsen-stained sputum smears were used to conduct microbead-based spoligotyping and assess genotypic resistance. Among the 162 samples included, 80 (49.4%) generated spoligotyping patterns (n = 23), belonging predominantly to the L2 Lineage (44%) and the L4 Lineage (30%). This is consistent with what has been found in other PNG regions geographically distant from Middle Fly District of Western Province, but is different from neighbouring South-East Asian countries. Rifampicin resistance was identified in 7.8% of the successfully sequenced samples, with all resistant samples belonging to the L2/Beijing Lineage. A high prevalence of mixed L2/L4 profiles was suggestive of polyclonal infection in the region, although this would need to be confirmed. The method described here could be a game-changer in resource-limited countries where large numbers of archived smear slides could be used for retrospective (and prospective) studies of M. tuberculosis genetic epidemiology.
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Affiliation(s)
- Vanina Guernier-Cambert
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia.
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, 50010, IA, USA.
| | - Tanya Diefenbach-Elstob
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Bernice J Klotoe
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Graham Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Daniel Pelowa
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Robert Dowi
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Bisato Gula
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Emma S McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Guislaine Refrégier
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Catherine Rush
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
| | - Christophe Sola
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Orsay, France
| | - Jeffrey Warner
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
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8
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Kitur U, Adair T, Riley I, Lopez AD. Estimating the pattern of causes of death in Papua New Guinea. BMC Public Health 2019; 19:1322. [PMID: 31640631 PMCID: PMC6805633 DOI: 10.1186/s12889-019-7620-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 09/13/2019] [Indexed: 01/21/2023] Open
Abstract
Background Papua New Guinea (PNG) is a diverse country with high mortality and evidence of increased prevalence of non-communicable diseases (NCDs), but there is no reliable cause of death (COD) data because civil registration is insufficient and routine health data comprise only a small proportion of deaths. This study aims to estimate cause-specific mortality fractions (CSMFs) for five broad groups of causes (endemic infections, emerging infections, endemic NCDs, emerging NCDs and injuries), by sex for each of PNG’s provinces. Methods CSMFs are calculated as the average of estimates obtained from: (1) Empirical cause method: Utilising available Verbal Autopsy (VA) data and Discharge Health Information System (DHIS) data, and applying statistical models of community versus facility CODs; and (2) Expected cause patterns method: Utilising existing estimates of mortality levels in each province and statistical models of the relationship between all-cause and cause-specific mortality using Global Burden of Disease (GBD) data. Results An estimated 41% of male and 49% of female deaths in PNG are due to infectious, maternal (female only), neonatal and nutritional causes. Furthermore, 45% of male and 42% of female deaths arise from NCDs. Infectious diseases, maternal, neonatal and nutritional conditions account for more than half the deaths in a number of provinces, including lower socioeconomic status provinces of Gulf and Sandaun, while provinces with higher CSMFs from emerging NCDs (e.g. ischemic heart disease, stroke) tend to be those where socioeconomic status is comparatively high (e.g. National Capital District, Western Highlands Province, Manus Province, New Ireland Province and East New Britain Province). Provinces with the highest estimated proportion of deaths from emerging infectious diseases are readily accessible by road and have the highest rates of sexually transmitted infections (STIs), while provinces with the highest CSMFs from endemic infectious, maternal, neonatal and nutritional causes are geographically isolated, have high malaria and high all-cause mortality. Conclusions Infectious, maternal, neonatal and nutritional causes continue to be an important COD in PNG, and are likely to be higher than what is estimated by the GBD. Nonetheless, there is evidence of the emergence of NCDs in provinces with higher socioeconomic status. The introduction of routine VA for non-facility deaths should improve COD data quality to support health policy and planning to control both infectious and NCDs.
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Affiliation(s)
- Urarang Kitur
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Carlton, Victoria, Australia. .,National Department of Health, P.O. Box 807, Waigani, National Capital District, Papua New Guinea.
| | - Tim Adair
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Carlton, Victoria, Australia
| | - Ian Riley
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Carlton, Victoria, Australia
| | - Alan D Lopez
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Carlton, Victoria, Australia
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9
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Watch V, Aipit J, Kote-Yarong T, Rero A, Bolnga JW, Lufele E, Laman M. The burden of presumed tuberculosis in hospitalized children in a resource-limited setting in Papua New Guinea: a prospective observational study. Int Health 2018; 9:374-378. [PMID: 29228220 PMCID: PMC6957116 DOI: 10.1093/inthealth/ihx043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/04/2017] [Indexed: 11/13/2022] Open
Abstract
Background In Papua New Guinea, TB is considered to be a major public health problem, but little is known about the prevalence and prognosis of presumed TB in children. Methods As part of a prospective hospital-based surveillance on the northern coast of mainland Papua New Guinea, the authors investigated the admission prevalence and case fatality rate associated with presumed TB over a 6-year period (2011-2016). All children admitted who were diagnosed with TB were followed-up until discharge or death. Results Of 8992 paediatric admissions, 734 patients (8.2%) were diagnosed with presumed TB and there were 825 deaths, with TB accounting for 102 (12.4%). Extrapulmonary TB was the final diagnosis in 384 admissions {prevalence 4.3% [384/8992 (95% CI 3.9-4.7)]} with a case fatality rate of 21.4% [82/384 (95% CI 17.4-25.9)]. TB meningitis, disseminated TB and pericardial TB had high case fatality rates of 29.0% (53/183), 28.9% (11/38) and 25% (4/16), respectively. Severe malnutrition was more common in patients with pulmonary compared with extrapulmonary TB (25.4% vs 15.6%; p<0.01). Conclusions Improved community-based case detection strategies, routine BCG vaccinations and other effective forms of TB control need revitalization and sustainability to reduce the high case fatality rates associated with childhood TB in Papua New Guinea.
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Affiliation(s)
- Villa Watch
- Modilon General Hospital, Department of Paediatrics, Madang Province
| | - Jimmy Aipit
- Modilon General Hospital, Department of Paediatrics, Madang Province
| | - Tina Kote-Yarong
- Modilon General Hospital, Department of Paediatrics, Madang Province
| | - Allanie Rero
- Modilon General Hospital, Department of Paediatrics, Madang Province
| | - John W Bolnga
- Modilon General Hospital, Department of Obstetrics and Gynaecology, Madang Province
| | - Elvin Lufele
- Papua New Guinea Institute of Medical Research, Madang Province, Papua New Guinea
| | - Moses Laman
- Modilon General Hospital, Department of Paediatrics, Madang Province.,Papua New Guinea Institute of Medical Research, Madang Province, Papua New Guinea
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10
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Kasa Tom S, Welch H, Kilalang C, Tefuarani N, Vince J, Lavu E, Johnson K, Magaye R, Duke T. Evaluation of Xpert MTB/RIF assay in children with presumed pulmonary tuberculosis in Papua New Guinea. Paediatr Int Child Health 2018; 38:97-105. [PMID: 28490246 DOI: 10.1080/20469047.2017.1319898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND The Gene Xpert MTB/ RIF assay (Xpert) is used for rapid, simultaneous detection of Mycobacterium tuberculosis (MTB) and rifampicin resistance. This study examined the accuracy of Xpert in children with suspected pulmonary tuberculosis (PTB). METHODS Children admitted to Port Moresby General Hospital with suspected PTB were prospectively enrolled between September 2014 and March 2015. They were classified into probable, possible and TB-unlikely groups. Sputum or gastric aspirates were tested by Xpert and smear microscopy; mycobacterial culture was undertaken on a subset. Children were diagnosed with TB on the basis of standard criteria which were used as the primary reference standard. Xpert, smear for acid-fast bacilli (AFB) and the Edwards TB score were compared with the primary reference standard. RESULTS A total of 93 children ≤14 years with suspected PTB were enrolled; 67 (72%) were classified as probable, 21 (22%) possible and 5 (5.4%) TB-unlikely. Eighty were treated for TB based on the primary reference standard. Xpert was positive in 26/93 (28%) MTB cases overall, including 22/67 (33%) with probable TB and 4/21 (19%) with possible TB. Three (13%) samples identified rifampicin resistance. Xpert confirmed more cases of TB than AFB smear (26 vs 13, p = 0.019). The sensitivity of Xpert, AFB smear and an Edwards TB score of ≥7 was 31% (25/80), 16% (13/80) and 90% (72/80), respectively, and the specificity was 92% (12/13), 100% (13/13) and 31% (4/13), respectively, when compared with the primary reference standard. CONCLUSION Xpert sensitivity is sub-optimal and cannot be relied upon for diagnosing TB, although a positive result is confirmatory. A detailed history and examination, standardised clinical criteria, radiographs and available tests remain the most appropriate way of diagnosing TB in children in resource-limited countries. Xpert helps confirm PTB better than AFB smear, and identifies rifampicin resistance. Practical guidelines should be used to identify children who will benefit from an Xpert assay.
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Key Words
- CPHL, Central Public Health Laboratory, PNG
- FLD, first-line drugs
- FNAB, fine-needle aspiration biopsy
- GA, gastric aspirate
- MDR TB, multidrug resistant tuberculosis
- MTB, Mycobacterium tuberculosis
- PMGH, Port Moresby General Hospital
- PNG, Papua New Guinea
- PTB, pulmonary tuberculosis
- Papua New Guinea
- QMRL, Queensland Mycobacterial Reference Laboratory, Australia
- SLD, second-line drugs
- TST, tuberculin skin test
- Tuberculosis
- Xpert
- children
- diagnostic
- resource-limited
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Affiliation(s)
- Sharon Kasa Tom
- a School of Medicine and Health Science , University of Papua New Guinea , Port Moresby , Papua New Guinea.,b Port Moresby General Hospital , Port Moresby , Papua New Guinea
| | - Henry Welch
- a School of Medicine and Health Science , University of Papua New Guinea , Port Moresby , Papua New Guinea.,b Port Moresby General Hospital , Port Moresby , Papua New Guinea.,c Baylor College of Medicine and Texas Children's Hospital , Houston , TX , USA
| | | | - Nakapi Tefuarani
- a School of Medicine and Health Science , University of Papua New Guinea , Port Moresby , Papua New Guinea.,b Port Moresby General Hospital , Port Moresby , Papua New Guinea
| | - John Vince
- a School of Medicine and Health Science , University of Papua New Guinea , Port Moresby , Papua New Guinea.,b Port Moresby General Hospital , Port Moresby , Papua New Guinea
| | - Evelyn Lavu
- d Central Public Health Laboratory , National Department of Health , Port Moresby , Papua New Guinea
| | - Karen Johnson
- d Central Public Health Laboratory , National Department of Health , Port Moresby , Papua New Guinea
| | - Ruth Magaye
- d Central Public Health Laboratory , National Department of Health , Port Moresby , Papua New Guinea
| | - Trevor Duke
- a School of Medicine and Health Science , University of Papua New Guinea , Port Moresby , Papua New Guinea.,e Department of Paediatrics , MCRI, Royal Children's Hospital, University of Melbourne , Victoria , Australia
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11
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Bainomugisa A, Lavu E, Hiashiri S, Majumdar S, Honjepari A, Moke R, Dakulala P, Hill-Cawthorne GA, Pandey S, Marais BJ, Coulter C, Coin L. Multi-clonal evolution of multi-drug-resistant/extensively drug-resistant Mycobacterium tuberculosis in a high-prevalence setting of Papua New Guinea for over three decades. Microb Genom 2018; 4. [PMID: 29310751 PMCID: PMC5857374 DOI: 10.1099/mgen.0.000147] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An outbreak of multi-drug resistant (MDR) tuberculosis (TB) has been reported on Daru Island, Papua New Guinea. Mycobacterium tuberculosis strains driving this outbreak and the temporal accrual of drug resistance mutations have not been described. Whole genome sequencing of 100 of 165 clinical isolates referred from Daru General Hospital to the Supranational reference laboratory, Brisbane, during 2012–2015 revealed that 95 belonged to a single modern Beijing sub-lineage strain. Molecular dating suggested acquisition of streptomycin and isoniazid resistance in the 1960s, with potentially enhanced virulence mediated by an mycP1 mutation. The Beijing sub-lineage strain demonstrated a high degree of co-resistance between isoniazid and ethionamide (80/95; 84.2 %) attributed to an inhA promoter mutation combined with inhA and ndh coding mutations. Multi-drug resistance, observed in 78/95 samples, emerged with the acquisition of a typical rpoB mutation together with a compensatory rpoC mutation in the 1980s. There was independent acquisition of fluoroquinolone and aminoglycoside resistance, and evidence of local transmission of extensively drug resistant (XDR) strains from 2009. These findings underline the importance of whole genome sequencing in informing an effective public health response to MDR/XDR TB.
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Affiliation(s)
- Arnold Bainomugisa
- 1Faculty of Medicine, University of Queensland, Brisbane, Australia.,2Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Evelyn Lavu
- 3Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Stenard Hiashiri
- 4Western Province Health Office, Western Province, Papua New Guinea
| | | | - Alice Honjepari
- 4Western Province Health Office, Western Province, Papua New Guinea
| | - Rendi Moke
- 6National Department of Health, Port Moresby, Papua New Guinea
| | - Paison Dakulala
- 6National Department of Health, Port Moresby, Papua New Guinea
| | | | - Sushil Pandey
- 8Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia
| | - Ben J Marais
- 7School of Public Health, University of Sydney, Sydney, Australia
| | - Chris Coulter
- 8Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia
| | - Lachlan Coin
- 2Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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12
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Guernier V, Diefenbach-Elstob T, Pelowa D, Pollard S, Burgess G, McBryde ES, Warner J. Molecular diagnosis of suspected tuberculosis from archived smear slides from the Balimo region, Papua New Guinea. Int J Infect Dis 2017; 67:75-81. [PMID: 29229499 DOI: 10.1016/j.ijid.2017.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a serious health problem in Papua New Guinea (PNG) with an estimated 30000 new cases and 3800 deaths each year. In the Balimo region of the Western Province, diagnosis relies on clinical manifestations and on the microscopic detection of acid-fast bacilli (AFB) in sputum smears, a technique with limited sensitivity. METHODS A molecular diagnosis assay targeting DNA extracted from archived sputum smear slides collected from the Balimo region (2012-2014) was conducted, without the need for a viable culture. The presence of Mycobacterium sp on 1162 slides prepared from 345 sputum samples was assessed using a real-time PCR (qPCR) approach. RESULTS The qPCR technique identified the presence of mycobacteria in 35.4% of the smear slides and 59.7% of the tested sputum samples. Poor agreement was observed between the two diagnosis methods (smear AFB microscopy versus qPCR), with 100 AFB-positive sputum samples compared to 206 qPCR-positive sputum samples overall. Treatment was initiated in 90.2% of the smear-positive cases. Unnecessary treatment of 'false-positive' TB cases (AFB-negative/qPCR-negative) was very low (8.6%) and was even lower when the nine patients diagnosed with extrapulmonary TB were excluded from the analysis. However, the prevalence of false-negatives (AFB-negative/qPCR-positive) was high (28.5%). CONCLUSIONS Undetected smear-negative TB is occurring in the Balimo region of PNG, as well as some unnecessary empirical treatment. Molecular methods of diagnosis could greatly reduce the frequency of inappropriate clinical assessment, as well as providing point-of-care diagnosis. This may provide substantial patient and programmatic benefits, including lowering the economic burden on patients from rural areas seeking medical diagnosis in Balimo.
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Affiliation(s)
- Vanina Guernier
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia.
| | - Tanya Diefenbach-Elstob
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia; College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
| | - Daniel Pelowa
- Balimo District Hospital, Balimo, Western Province, Papua New Guinea
| | - Sandra Pollard
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
| | - Graham Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
| | - Emma S McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia; Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia.
| | - Jeffrey Warner
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia; College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
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13
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Chaidir L, Sengstake S, de Beer J, Oktavian A, Krismawati H, Muhapril E, Kusumadewi I, Annisa J, Anthony R, van Soolingen D, Achmad TH, Marzuki S, Alisjahbana B, van Crevel R. Predominance of modern Mycobacterium tuberculosis strains and active transmission of Beijing sublineage in Jayapura, Indonesia Papua. INFECTION GENETICS AND EVOLUTION 2016; 39:187-193. [PMID: 26825253 DOI: 10.1016/j.meegid.2016.01.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/13/2016] [Accepted: 01/22/2016] [Indexed: 12/27/2022]
Abstract
Mycobacterium tuberculosis genotype distribution is different between West and Central Indonesia, but there are no data on the most Eastern part, Papua. We aimed to identify the predominant genotypes of M. tuberculosis responsible for tuberculosis in coastal Papua, their transmission, and the association with patient characteristics. A total of 199 M. tuberculosis isolates were collected. Spoligotyping was applied to describe the population structure of M. tuberculosis, lineage identification was performed using a combination of lineage-specific markers, and genotypic clusters were identified using a combination of 24-locus-MIRU-VNTR and spoligotyping. A high degree of genetic diversity was observed among isolates based on their spoligopatterns. Strains from modern lineage 4 made up almost half of strains (46.9%), being more abundant than the ancient lineage 1 (33.7%), and modern lineage 2 (19.4%). Thirty-five percent of strains belonged to genotypic clusters, especially strains in the Beijing genotype. Previous TB treatment and mutations associated with drug resistance were more common in patients infected with strains of the Beijing genotype. Papua shows a different distribution of M. tuberculosis genotypes compared to other parts of Indonesia. Clustering and drug resistance of modern strains recently introduced to Papua may contribute to the high tuberculosis burden in this region.
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Affiliation(s)
- Lidya Chaidir
- Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia.
| | - Sarah Sengstake
- KIT Biomedical Research, Royal Tropical Institute, Mauritskade 63, 1092 AD, Amsterdam, The Netherlands
| | - Jessica de Beer
- Tuberculosis Reference Laboratory, Center for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Antonius Oktavian
- Papua Biomedical Research Center, National Institute for Health Research, Indonesian Ministry of Health, Jl Kesehatan 10, Dok II, Jayapura, Papua, Indonesia
| | - Hana Krismawati
- Papua Biomedical Research Center, National Institute for Health Research, Indonesian Ministry of Health, Jl Kesehatan 10, Dok II, Jayapura, Papua, Indonesia
| | - Erfin Muhapril
- Department of Pulmonology, Jayapura General Hospital, Jl Kesehatan 1, Dok II, Jayapura, Papua, Indonesia
| | - Inri Kusumadewi
- Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia
| | - Jessi Annisa
- Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia
| | - Richard Anthony
- KIT Biomedical Research, Royal Tropical Institute, Mauritskade 63, 1092 AD, Amsterdam, The Netherlands
| | - Dick van Soolingen
- Tuberculosis Reference Laboratory, Center for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA, Bilthoven, The Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6500 HB, Nijmegen, The Netherlands
| | | | - Sangkot Marzuki
- Eijkman Institute for Molecular Biology, Jl Diponegoro 69, Jakarta, Indonesia
| | - Bachti Alisjahbana
- Faculty of Medicine, Universitas Padjadjaran, Eijkman 38 Bandung, Indonesia; Department of Internal Medicine, Hasan Sadikin Hospital, Jl Pasteur 38, Bandung, Indonesia
| | - Reinout van Crevel
- Department of Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 8, 6500 HB Nijmegen, The Netherlands
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14
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Non-tuberculous mycobacteria: baseline data from three sites in Papua New Guinea, 2010-2012. Western Pac Surveill Response J 2015; 6:24-9. [PMID: 26798558 DOI: 10.5365/wpsar.2015.6.2.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE To determine the proportion of non-tuberculous mycobacteria (NTM) in samples of pulmonary tuberculosis (TB) cases from Papua New Guinea who were diagnosed using acid-fast microscopy. METHODS As part of a case detection study for TB, conducted in three provincial hospitals in Papua New Guinea, sputum samples of suspected tuberculous cases aged 15 years or older were collected from November 2010 to July 2012. Mycobacterial species isolated from sputum and grown in culture were examined to distinguish between NTM and the Mycobacterium tuberculosis complex (MTBC). RESULTS NTM were detected in 4% (9/225) of sputum samples grown in culture. Five (2.2%) of them were identified as NTM only and four (1.8%) were identified as mixed cultures containing both MTBC and NTM. Four different NTM species were identified; M. fortuitum, M. intracellulare, M. terrae and M. avium. DISCUSSION This is the first report from Papua New Guinea identifying NTM in three different locations. As NTM cannot be distinguished from M. tuberculosis through smear microscopy, the presence of NTM can lead to a false-positive diagnosis of tuberculosis. The prevalence of NTM should be determined and a diagnostic algorithm developed to confirm acid-fast bacilli in a smear as M. tuberculosis.
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15
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Ley SD, Harino P, Vanuga K, Kamus R, Carter R, Coulter C, Pandey S, Feldmann J, Ballif M, Siba PM, Phuanukoonnon S, Gagneux S, Beck HP. Diversity of Mycobacterium tuberculosis and drug resistance in different provinces of Papua New Guinea. BMC Microbiol 2014; 14:307. [PMID: 25476850 PMCID: PMC4264550 DOI: 10.1186/s12866-014-0307-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/24/2014] [Indexed: 01/07/2023] Open
Abstract
Background Papua New Guinea (PNG) is a high tuberculosis (TB) burden country of the WHO Western Pacific Region, but so far research on drug resistance (DR) and genotypes of Mycobacterium tuberculosis (M. tuberculosis) was only conducted in few provinces in the country. The aim of the present study was to obtain baseline data on the level of drug resistance and the genotypic diversity of circulating M. tuberculosis in additional provinces and to investigate the differences between three selected sites across PNG. Results Genotyping of 147 M. tuberculosis clinical isolates collected in Goroka, Eastern Highlands Province, in Alotau, Milne Bay Province and in Madang, Madang Province revealed three main lineages of M. tuberculosis: Lineage 4 (European-American lineage), Lineage 2 (East-Asian lineage) and Lineage 1 (Indo-Oceanic lineage). All three lineages were detected in all three sites, but the individual lineage compositions varied significantly between sites. In Madang Lineage 4 was the most prevalent lineage (76.6%), whereas in Goroka and Alotau Lineage 2 was dominating (60.5% and 84.4%, respectively) (p < 0.001). Overall, phenotypic drug susceptibility testing showed 10.8% resistance to at least one of the first-line drugs tested. Of all resistant strains (23/212) 30.4% were Streptomycin mono-resistant, 17.4% were Isoniazid mono-resistant and 13% were Rifampicin mono-resistant. Multi-drug resistant (MDR) TB was found in 2.8% of all tested cases (6/212). The highest amount of MDR TB was found in Alotau in Milne Bay Province (4.6%). Conclusion A large number of drug resistant TB infections are present in the country and MDR TB has already been detected in all three surveyed regions of PNG, highlighting the importance of monitoring drug resistance and making it a high priority for the National Control Program. Due to the high prevalence of Lineage 2 in Milne Bay Province and given the frequent association of this lineage with drug resistance, monitoring of the latter should especially be scaled up in that province.
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Affiliation(s)
- Serej D Ley
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland. .,Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.
| | - Paul Harino
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.
| | - Kilagi Vanuga
- Goroka Provincial Hospital, Goroka, Papua New Guinea.
| | - Ruben Kamus
- Alotau Provincial Hospital, Alotau, Papua New Guinea.
| | - Robyn Carter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia.
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia.
| | - Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Australia.
| | - Julia Feldmann
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Marie Ballif
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Peter M Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.
| | | | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Hans-Peter Beck
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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