The Burden of Drug-Resistant Tuberculosis in Papua New Guinea: Results of a Large Population-Based Survey

Evaluation of a population-wide, systematic screening initiative for tuberculosis on Daru island, Western Province, Papua New Guinea

BACKGROUND

A population-wide, systematic screening initiative for tuberculosis (TB) was implemented on Daru island in the Western Province of Papua New Guinea, where TB is known to be highly prevalent. The initiative used a mobile van equipped with a digital X-ray device, computer-aided detection (CAD) software to identify TB-related abnormalities on chest radiographs, and GeneXpert machines for follow-on diagnostic testing. We describe the results of the TB screening initiative, evaluate its population-level impact and examine risk factors associated with TB detection.

METHODS

Through a retrospective review of screening data, we assessed the effectiveness of the screening by examining the enrolment coverage and the proportion of people with TB among screened subjects. A cascade analysis was performed to illustrate the flow of participants in the screening algorithm. We conducted univariate and multivariate analyses to identify factors associated with TB. Furthermore, we estimated the number of additional cases detected by the project by examining the trend of routine TB case notifications during the intervention period, compared to the historical baseline cases and trend-adjusted expected cases.

RESULTS

Of the island's 18,854 residents, 8,085 (42.9%) were enrolled and 7,970 (98.6%) had chest X-ray interpreted by the CAD4TB software. A total of 1,116 (14.0%) participants were considered to have abnormal CXR. A total of 69 Xpert-positive cases were diagnosed, resulting in a detection rate of 853 per 100 000 population screened. 19.4% of people with TB had resistance to rifampicin. People who were in older age groups (aOR 6.6, 95%CI: 1.5-29.1 for the 45-59 age group), were severely underweight (aOR 2.5, 95%CI:1.0-6.1) or underweight (aOR 2.1, 95%CI: 1.1-3.8), lived in households < 5 people (aOR 3.4, 95%CI:1.8-6.6) and had a past history of TB (aOR 2.1, 95%CI: 1.2-3.6) were more likely to have TB. The number of bacteriologically confirmed TB notified during the intervention period was 79.3% and 90.8% higher than baseline notifications and forecasted notifications, respectively.

CONCLUSION

The screening project demonstrated its effectiveness with the high Xpert-positive TB prevalence among the participants and by successfully yielding additional cases of bacteriologically confirmed TB including rifampicin-resistant TB. The results and lessons learnt from the project should inform future TB screening initiatives in Papua New Guinea.

Antimicrobial Resistance in Papua New Guinea: A Narrative Scoping Review

Antimicrobial-resistant bacterial infections are a known threat to the public health of low-income countries and are undercharacterized in Papua New Guinea. A scoping literature review of scientific peer-reviewed publications on antimicrobial resistance in Papua New Guinea was conducted, and their results were summarized. Many of the available data on resistant bacteria in Papua New Guinea have come from Port Moresby and Goroka and have been focused on Staphylococcus aureus, as well as important pediatric pathogens such as Streptococcus pneumoniae and Haemophilus influenzae. Progressive resistance to the commonly used antibiotics penicillin and chloramphenicol among most clinically important bacterial pathogens has prompted healthcare workers to adopt expensive broad-spectrum antibiotics. There is already evidence of resistance to newly adopted antibiotics among several Gram-negative organisms. Drivers of antimicrobial resistance in Papua New Guinea include a high burden of infectious diseases, inappropriate antibiotic prescription practices, poor regulation of antibiotics, incomplete adherence, substandard drug quality, and overcrowding of healthcare facilities. There is a lack of information on antimicrobial resistance among priority pathogens and from several important regions of Papua New Guinea.

Global status of phenotypic pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates: an updated systematic review and meta-analysis

Pyrazinamide (PZA) is an essential first-line tuberculosis drug for its unique mechanism of action active against multidrug-resistant-TB (MDR-TB). Thus, the aim of updated meta-analysis was to estimate the PZA weighted pooled resistance (WPR) rate in M. tuberculosis isolates based on publication date and WHO regions. We systematically searched the related reports in PubMed, Scopus, and Embase (from January 2015 to July 2022). Statistical analyses were performed using STATA software. The 115 final reports in the analysis investigated phenotypic PZA resistance data. The WPR of PZA was 57% (95% CI 48-65%) in MDR-TB cases. According to the WHO regions, the higher WPRs of PZA were reported in the Western Pacific (32%; 95% CI 18-46%), South East Asian region (37%; 95% CI 31-43%), and the Eastern Mediterranean (78%; 95% CI 54-95%) among any-TB patients, high risk of MDR-TB patients, and MDR-TB patients, respectively. A negligible increase in the rate of PZA resistance were showed in MDR-TB cases (55% to 58%). The rate of PZA resistance has been rising in recent years among MDR-TB cases, underlines the essential for both standard and novel drug regimens development.

Global prevalence of drug-resistant tuberculosis: a systematic review and meta-analysis

BACKGROUND

Tuberculosis is a bacterial infectious disease, which affects different parts of a human body, mainly lungs and can lead to the patient's death. The aim of this study is to investigate the global prevalence of drug-resistant tuberculosis using a systematic review and meta-analysis.

METHODS

In this study, the PubMed, Scopus, Web of Science, Embase, ScienceDirect and Google Scholar repositories were systematically searched to find studies reporting the global prevalence of drug-resistant tuberculosis. The search did not entail a lower time limit, and articles published up until August 2022 were considered. Random effects model was used to perform the analysis. The heterogeneity of the studies was examined with the I² test. Data analysis was conducted within the Comprehensive Meta-Analysis software.

RESULTS

In the review of 148 studies with a sample size of 318,430 people, the I² index showed high heterogeneity (I² = 99.6), and accordingly random effects method was used to analyze the results. Publication bias was also examined using the Begg and Mazumdar correlation test which indicated the existence of publication bias in the studies (P = 0.008). According to our meta-analysis, the global pooled prevalence of multi-drug resistant TB is 11.6% (95% CI: 9.1-14.5%).

CONCLUSIONS

The global prevalence of drug-resistant tuberculosis was found to be very high, thus health authorities should consider ways to control and manage the disease to prevent a wider spread of tuberculosis and potentially subsequent deaths.

Contact screening and management in a high-transmission MDR-TB setting in Papua New Guinea: Progress, challenges and future directions

Daru, South Fly District, Papua New Guinea is a high transmission setting for multidrug-resistant tuberculosis (MDR-TB). An emergency response by the Government in 2014 established a high-quality model for treatment and care. Household contact screening and management commenced in 2016 with TB preventive treatment (TPT) for well young child (&lt;5 years) contacts of people with drug-susceptible TB and later expanded to young child contacts of MDR-TB. The model of care is community-based and led by non-specialist health workers, under supervision. An electronic medical record system supports care, reporting and operational research. Community engagement and education has been central, with a concerted focus on peer-led counselling and patient-centred services to improve TPT uptake and completion. Challenges include the application of households as the unit of intervention for detection of active TB and TPT provision. Our implementation experience in Daru has highlighted significant population mixing dynamics with most transmission likely occurring outside the household. We propose a community-wide screening approach with the provision of TPT based on testing to include older children, adolescents, and young adults. As there is the possibility of MDR-TB infection irrespective of the drug susceptibility of the household index case, a novel option is a combination TPT regimen of 6 months of daily isoniazid and levofloxacin (6HLfx). A sensitive aged-related algorithm to detect and exclude active TB is being developed. Ongoing community engagement, quality data systems with operational research to evaluate approaches are critical in high transmission MDR-TB settings.

Beyond patient delay, navigating structural health system barriers to timely care and treatment in a high burden TB setting in Papua New Guinea

Tuberculosis (TB) is a major public health issue in Papua New Guinea, with incidence rates particularly high in the South Fly District of Western Province. We present three case studies, along with additional vignettes, that were derived from interviews and focus groups carried out between July 2019 and July 2020 of people living in rural areas of the remote South Fly District depicting their challenges accessing timely TB diagnosis and care; most services within the district are only offered offshore on Daru Island. The findings detail that rather than 'patient delay' attributed to poor health seeking behaviours and inadequate knowledge of TB symptoms, many people were actively trying to navigate structural barriers hindering access to and utilisation of limited local TB services. The findings highlight a fragile and fragmented health system, a lack of attention given to primary health services, and undue financial burdens placed on people living in rural and remote areas associated with costly transportation to access functioning health services. We conclude that a person-centred and effective decentralised model of TB care as outlined in health policies is imperative for equitable access to essential health care services in Papua New Guinea.

Characteristics of Drug-sensitive and Drug-resistant Tuberculosis Cases among Adults at Tuberculosis Referral Hospitals in Indonesia

As Indonesia's rifampin resistance testing rates are lower than global testing rates per the 2020 WHO global tuberculosis (TB) report, prevalence of multidrug-resistant TB may be underestimated. Our study aimed to evaluate prevalence and patterns of TB drug resistance (DR) within Indonesia. We conducted a cross-sectional analysis of baseline data collected from 2017-2018 as part of a cohort study of adults with presumed pulmonary TB at 7 DR-TB referral hospitals in Indonesia. Bacteriological examinations (acid-fast bacilli, GeneXpert, sputum culture) and drug-susceptibility testing were performed following the guidelines of the National TB Program. Of 447 participants with complete bacteriological examinations, 312 (69.8%) had positive sputum cultures for Mycobacterium tuberculosis. The proportion of MDR and pre-extensively drug-resistant was higher in previously treated compared with newly diagnosed participants (52.5% [73/139] versus 15% [26/173]). Compared with drug-sensitive case, drug-resistant TB was associated with cavities. Given the difference between rates of DR in TB referral hospitals from our study compared with the WHO survey in 2019 that showed 17.7% and 3.3% DR among previously treated and newly diagnosed participants globally, further characterization of Indonesia's TB epidemiology in the general population is needed. Strategies, including public policies to optimize case finding, strengthen capacity for resistance testing, and prevent loss to follow-up will be critical to reduce the burden of TB in Indonesia.

Evolution and spread of a highly drug resistant strain of Mycobacterium tuberculosis in Papua New Guinea

BACKGROUND

Molecular mechanisms determining the transmission and prevalence of drug resistant tuberculosis (DR-TB) in Papua New Guinea (PNG) are poorly understood. We used genomic and drug susceptibility data to explore the evolutionary history, temporal acquisition of resistance and transmission dynamics of DR-TB across PNG.

METHODS

We performed whole genome sequencing on isolates from Central Public Health Laboratory, PNG, collected 2017-2019. Data analysis was done on a composite dataset that also included 100 genomes previously sequenced from Daru, PNG (2012-2015).

RESULTS

Sampled isolates represented 14 of the 22 PNG provinces, the majority (66/94; 70%) came from the National Capital District (NCD). In the composite dataset, 91% of strains were Beijing 2.2.1.1, identified in 13 provinces. Phylogenetic tree of Beijing strains revealed two clades, Daru dominant clade (A) and NCD dominant clade (B). Multi-drug resistance (MDR) was repeatedly and independently acquired, with the first MDR cases in both clades noted to have emerged in the early 1990s, while fluoroquinolone resistance emerged in 2009 (95% highest posterior density 2000-2016). We identified the presence of a frameshift mutation within Rv0678 (p.Asp47fs) which has been suggested to confer resistance to bedaquiline, despite no known exposure to the drug. Overall genomic clustering was significantly associated with rpoC compensatory and inhA promoter mutations (p < 0.001), with high percentage of most genomic clusters (12/14) identified in NCD, reflecting its role as a potential national amplifier.

CONCLUSIONS

The acquisition and evolution of drug resistance among the major clades of Beijing strain threaten the success of DR-TB treatment in PNG. With continued transmission of this strain in PNG, genotypic drug resistance surveillance using whole genome sequencing is essential for improved public health response to outbreaks. With occurrence of resistance to newer drugs such as bedaquiline, knowledge of full drug resistance profiles will be important for optimal treatment selection.

Factors associated with loss to follow-up among TB patients in rural Papua New Guinea

BACKGROUND

Papua New Guinea (PNG) is a lower middle-income country that has struggled to contain TB. The loss of patients to follow-up is a major contributing factor towards the high disease burden.

OBJECTIVE

To describe persons with drug-susceptible TB (DS-TB) registered for treatment at the Gaubin Rural Hospital (GRH) on Karkar Island, Madang Province, PNG, and to investigate factors associated with patient loss to follow-up (LTFU).

DESIGN

A retrospective cohort study was conducted using data from GRH DS-TB registers. Factors associated with LTFU were investigated using univariable and multivariable logistic regression.

RESULTS

A total of 722 patients were registered for DS-TB treatment and eligible for inclusion between 1 January 2014 and 30 June 2018, of whom 97 (13.4%) were lost to follow-up. Male sex was associated with an increased odds of LTFU (adjusted OR [aOR] 1.9, 95% CI 1.2-3.0; P = 0.005), as was travel time to GRH >3 h (aOR 3.7, 95%, CI 2.2-6.3; P < 0.001).

CONCLUSION

A high LTFU rate has been identified in patients with TB in PNG. This study found male sex and increased travel time from treatment location to be associated with unsuccessful treatment adherence, highlighting the need for further interventions to improve adherence.

Differential yield of universal versus selective drug susceptibility testing of patients with tuberculosis in high-burden countries: a systematic review and meta-analysis

Introduction

Although universal drug susceptibility testing (DST) is a component of the End-TB Strategy, over 70% of drug-resistant tuberculosis (DR-TB) cases globally remain undetected. This detection gap reflects difficulties in DST scale-up and substantial heterogeneity in policies and implemented practices. We conducted a systematic review and meta-analysis to assess whether implementation of universal DST yields increased DR-TB detection compared with only selectively testing high-risk groups.

Methods

PubMed, Embase, Global Health, Cochrane Library and Web of Science Core Collection were searched for publications reporting on the differential yield of universal versus selective DST implementation on the proportion of DR-TB, from January 2007 to June 2019. Random-effects meta-analyses were used to calculate respective pooled proportions of DR-TB cases detected; Higgins test and prediction intervals were used to assess between-study heterogeneity. We adapted an existing risk-of-bias assessment tool for prevalence studies.

Results

Of 18 736 unique citations, 101 studies were included in the qualitative synthesis. All studies used WHO-endorsed DST methods, and most (87.1%) involved both high-risk groups and the general population. We found only cross-sectional, observational, non-randomised studies that compared universal with selective DST strategies. Only four studies directly compared the testing approaches in the same study population, with the proportion of DR-TB cases detected ranging from 2.2% (95% CI: 1.4% to 3.2%) to 12.8% (95% CI: 11.4% to 14.3%) with selective testing, versus 4.4% (95% CI: 3.3% to 5.8%) to 9.8% (95% CI: 8.9% to 10.7%) with universal testing. Broad population studies were very heterogeneous. The vast majority (88/101; 87.1%) reported on the results of universal testing. However, while 37 (36.6%)/101 included all presumptive TB cases, an equal number of studies applied sputum-smear as a preselection criterion. A meaningful meta-analysis was not possible.

Conclusion

Given the absence of randomised studies and the paucity of studies comparing strategies head to head, and selection bias in many studies that applied universal testing, our findings have limited generalisability. The lack of evidence reinforces the need for better data to inform policies.

Xpert MTB/RIF and Xpert Ultra assays for screening for pulmonary tuberculosis and rifampicin resistance in adults, irrespective of signs or symptoms

BACKGROUND

Tuberculosis is a leading cause of infectious disease-related death and is one of the top 10 causes of death worldwide. The World Health Organization (WHO) recommends the use of specific rapid molecular tests, including Xpert MTB/RIF or Xpert Ultra, as initial diagnostic tests for the detection of tuberculosis and rifampicin resistance in people with signs and symptoms of tuberculosis. However, the WHO estimates that nearly one-third of all active tuberculosis cases go undiagnosed and unreported. We were interested in whether a single test, Xpert MTB/RIF or Xpert Ultra, could be useful as a screening test to close this diagnostic gap and improve tuberculosis case detection.

OBJECTIVES

To estimate the accuracy of Xpert MTB/RIF and Xpert Ultra for screening for pulmonary tuberculosis in adults, irrespective of signs or symptoms of pulmonary tuberculosis in high-risk groups and in the general population. Screening "irrespective of signs or symptoms" refers to screening of people who have not been assessed for the presence of tuberculosis symptoms (e.g. cough). To estimate the accuracy of Xpert MTB/RIF and Xpert Ultra for detecting rifampicin resistance in adults screened for tuberculosis, irrespective of signs and symptoms of pulmonary tuberculosis in high-risk groups and in the general population.

SEARCH METHODS

We searched 12 databases including the Cochrane Infectious Diseases Group Specialized Register, MEDLINE and Embase, on 19 March 2020 without language restrictions. We also reviewed reference lists of included articles and related Cochrane Reviews, and contacted researchers in the field to identify additional studies.

SELECTION CRITERIA

Cross-sectional and cohort studies in which adults (15 years and older) in high-risk groups (e.g. people living with HIV, household contacts of people with tuberculosis) or in the general population were screened for pulmonary tuberculosis using Xpert MTB/RIF or Xpert Ultra. For tuberculosis detection, the reference standard was culture. For rifampicin resistance detection, the reference standards were culture-based drug susceptibility testing and line probe assays.

DATA COLLECTION AND ANALYSIS

Two review authors independently extracted data using a standardized form and assessed risk of bias and applicability using QUADAS-2. We used a bivariate random-effects model to estimate pooled sensitivity and specificity with 95% credible intervals (CrIs) separately for tuberculosis detection and rifampicin resistance detection. We estimated all models using a Bayesian approach. For tuberculosis detection, we first estimated screening accuracy in distinct high-risk groups, including people living with HIV, household contacts, people residing in prisons, and miners, and then in several high-risk groups combined.

MAIN RESULTS

We included a total of 21 studies: 18 studies (13,114 participants) evaluated Xpert MTB/RIF as a screening test for pulmonary tuberculosis and one study (571 participants) evaluated both Xpert MTB/RIF and Xpert Ultra. Three studies (159 participants) evaluated Xpert MTB/RIF for rifampicin resistance. Fifteen studies (75%) were conducted in high tuberculosis burden and 16 (80%) in high TB/HIV-burden countries. We judged most studies to have low risk of bias in all four QUADAS-2 domains and low concern for applicability. Xpert MTB/RIF and Xpert Ultra as screening tests for pulmonary tuberculosis In people living with HIV (12 studies), Xpert MTB/RIF pooled sensitivity and specificity (95% CrI) were 61.8% (53.6 to 69.9) (602 participants; moderate-certainty evidence) and 98.8% (98.0 to 99.4) (4173 participants; high-certainty evidence). Of 1000 people where 50 have tuberculosis on culture, 40 would be Xpert MTB/RIF-positive; of these, 9 (22%) would not have tuberculosis (false-positives); and 960 would be Xpert MTB/RIF-negative; of these, 19 (2%) would have tuberculosis (false-negatives). In people living with HIV (1 study), Xpert Ultra sensitivity and specificity (95% CI) were 69% (57 to 80) (68 participants; very low-certainty evidence) and 98% (97 to 99) (503 participants; moderate-certainty evidence). Of 1000 people where 50 have tuberculosis on culture, 53 would be Xpert Ultra-positive; of these, 19 (36%) would not have tuberculosis (false-positives); and 947 would be Xpert Ultra-negative; of these, 16 (2%) would have tuberculosis (false-negatives). In non-hospitalized people in high-risk groups (5 studies), Xpert MTB/RIF pooled sensitivity and specificity were 69.4% (47.7 to 86.2) (337 participants, low-certainty evidence) and 98.8% (97.2 to 99.5) (8619 participants, moderate-certainty evidence). Of 1000 people where 10 have tuberculosis on culture, 19 would be Xpert MTB/RIF-positive; of these, 12 (63%) would not have tuberculosis (false-positives); and 981 would be Xpert MTB/RIF-negative; of these, 3 (0%) would have tuberculosis (false-negatives). We did not identify any studies using Xpert MTB/RIF or Xpert Ultra for screening in the general population. Xpert MTB/RIF as a screening test for rifampicin resistance Xpert MTB/RIF sensitivity was 81% and 100% (2 studies, 20 participants; very low-certainty evidence), and specificity was 94% to 100%, (3 studies, 139 participants; moderate-certainty evidence).

AUTHORS' CONCLUSIONS

Of the high-risks groups evaluated, Xpert MTB/RIF applied as a screening test was accurate for tuberculosis in high tuberculosis burden settings. Sensitivity and specificity were similar in people living with HIV and non-hospitalized people in high-risk groups. In people living with HIV, Xpert Ultra sensitivity was slightly higher than that of Xpert MTB/RIF and specificity similar. As there was only one study of Xpert Ultra in this analysis, results should be interpreted with caution. There were no studies that evaluated the tests in people with diabetes mellitus and other groups considered at high-risk for tuberculosis, or in the general population.

Retrospective analysis of multidrug-resistant tuberculosis case notifications in Australia (1999-2018)

This study describes the epidemiology and treatment outcomes of multidrug-resistant tuberculosis (MDR-TB) cases notified in Australia between 1999 and 2018, and investigates whether current data fields in the national tuberculosis (TB) dataset allow description and measurement of surveillance information pertaining to the diagnosis and clinical management of MDR-TB. In May 2019, de-identified demographic, clinical, laboratory, drug susceptibility, treatment, risk factor and outcome data for all MDR-TB case notifications were extracted from the Australian National Notifiable Disease Surveillance System. The dataset included ten treatment outcome categories, which were aggregated to four categorical outcomes for descriptive and inferential analyses. The majority of cases were overseas-born (91%). Absolute case numbers increased over time; however, the MDR-TB notification rate remained fairly stable during the study period. Treatment success was achieved in nearly two-thirds of cases (62.1%). Whilst timeframes between initial presentation, specimen collection, case notification and treatment commencement were calculated, current data fields in the national dataset precluded measurement and description of other parameters deemed important for MDR-TB surveillance. This study demonstrates that while Australia's MDR-TB burden is low, cases will continue to occur until TB control improves in countries with which Australia shares cultural and migration links. Australia should continue to support national and regional TB control programmes to sustain progress towards national elimination of TB. This study's findings support a review of data fields in the national TB dataset with potential expansion or adjustment to improve national data reporting, including the monitoring of evidence-based recommendations for the prevention and management of MDR-TB.

Drug-resistant tuberculosis diagnosis since Xpert® MTB/RIF introduction in Papua New Guinea, 2012-2017

SETTING

Xpert® MTB/RIF was introduced in Papua New Guinea in 2012 for the diagnosis of tuberculosis (TB) and of rifampicin-resistant TB (RR-TB), a marker of multi-drug-resistant TB (MDR-TB).

OBJECTIVE

To assess the concordance of Xpert with phenotypic drug susceptibility testing (DST) performed at the supranational reference laboratory and to describe the patterns of drug-resistant TB observed.

DESIGN

This was a retrospective descriptive study of laboratory data collected from April 2012 to December 2017.

RESULTS

In 69 months, 1408 specimens with Xpert results were sent for mycobacterial culture and DST; Mycobacterium tuberculosis was cultured from 63% (884/1408) and DST was completed in 99.4%. The concordance between Xpert and culture for M. tuberculosis detection was 98.6%. Of 760 RR-TB cases, 98.7% were detected using Xpert; 98.5% of 620 MDR-TB cases were identified using phenotypic DST. Phenotypic resistance to second-line drugs was detected in 59.4% (522/879) of specimens tested, including 29 with fluoroquinolone resistance; the majority were from the National Capital District and Daru Island.

CONCLUSION

The high concordance between phenotypic DST and Xpert in identifying RR-TB cases supports the scale-up of initial Xpert testing in settings with high rates of drug resistance. However, rapid DST in addition to the detection of RR-TB is required.

Implementation of screening and management of household contacts of tuberculosis cases in Daru, Papua New Guinea

SETTING

Daru Island, Western Province, Papua New Guinea (PNG).

OBJECTIVE

To describe the implementation of a screening programme for household contacts of tuberculosis (TB) cases residing on Daru Island.

DESIGN

This was a retrospective descriptive study evaluating two periods of implementation: introduction and expansion of a screening programme for household contacts of drug-resistant TB (DR-TB) cases (March 2016 to September 2017), and inclusion of drug-susceptible TB (DS-TB) cases with provision of preventive therapy for eligible contacts between October 2017 and March 2018.

RESULTS

In the first period, the contact screening programme was established and strengthened by increasing coverage over time. There was a large number of contacts (median 8) in each household, and a high uptake of screening. In the second period of evaluation, respectively 412 and 223 contacts of 42 DS-TB and 25 DR-TB index cases were screened. Overall, 156 (24.6%) contacts reported TB-related symptoms and 9 (1.4%) were diagnosed with active TB. All 9 commenced TB treatment: 5 had DS-TB and 4 had DR-TB. Of 82 child contacts of DS-TB cases eligible for preventive therapy, 57 (69.5%) commenced treatment and 45 completed treatment.

CONCLUSION

Community-based household contact screening and management was successfully implemented under programme conditions in this high burden TB and DR-TB setting in PNG.

A mortality review of adult inpatients with tuberculosis in Mendi, Papua New Guinea

SETTING

Mendi Provincial Hospital, Southern Highlands Province, Papua New Guinea (PNG).

BACKGROUND

PNG is a high burden country for tuberculosis (TB) and TB-human immunodeficiency virus (HIV). TB is the second most common cause of death in PNG.

OBJECTIVE

To identify the number of adult inpatients with TB who died between 1 January 2015 and 30 August 2017; describe these patients' characteristics and identify contributing factors that could be modified.

DESIGN

This was a retrospective case series review.

RESULTS

Among 905 inpatients with TB during the study period, there were 90 deaths. The patients who died were older than those who survived (median age 40 years vs. 32 years, P = 0.011). The majority of patients who died lived less than 3 hours from the hospital (71%), were diagnosed after admission (79%) and were clinically diagnosed (77%). HIV status was not known in 50% of the deaths. Of patients with a known status, 27% (12/45) were HIV-positive. The median symptom duration prior to presentation was 28 days, with females presenting later than males (84 vs. 28 days, P = 0.008).

CONCLUSION

This study highlights areas where community and hospital-based management of TB could be improved to potentially reduce TB mortality, including earlier detection and treatment, improved bacteriological diagnosis and increased HIV testing.

The emergency response to multidrug-resistant tuberculosis in Daru, Western Province, Papua New Guinea, 2014-2017

SETTING

A response to an outbreak of multidrug-resistant tuberculosis (MDR-TB) on Daru Island, South Fly District (SFD), Western Province, Papua New Guinea (PNG) was implemented by a national emergency response taskforce.

OBJECTIVE

To describe programmatic interventions for TB in SFD and evaluate characteristics of TB case notifications, drug resistance and treatment outcomes.

DESIGN

This was a retrospective cohort study based on routine programmatic data for all patients enrolled on TB treatment at Daru General Hospital from 2014 to 2017.

RESULTS

The response involved high-level political commitment, joint planning, resource mobilisation, community engagement and strengthening TB case detection and treatment. Of 1548 people enrolled on TB treatment, 1208 (78%) had drug-susceptible TB (DS-TB) and 333 (21.5%) had MDR-TB. There was an increase in MDR-TB as a proportion of all TB. Treatment success rates increased over the study period from 55% to 86% for DS-TB, and from 70% to 81% for MDR-TB from 2014 to 2015. The 2014 case notification rate for TB in SFD was 1031/100 000, decreasing to 736/100 000 in 2017.

CONCLUSION

The outbreak was stabilised through the response from the national and provincial governments and international partners. Additional interventions are needed to decrease the TB burden in Daru.

Impact of GxAlert on the management of rifampicin-resistant tuberculosis patients, Port Moresby, Papua New Guinea

Setting

GxAlert is an automatic electronic notification service that provides immediate Xpert^® MTB/RIF testing results. It was implemented for the notification of patients with rifampicin resistant-tuberculosis (RR-TB) at Port Moresby General Hospital, Port Moresby, Papua New Guinea, in May 2015.

Objective

To determine if there were differences in pre-treatment attrition, the time to treatment initiation and patient outcomes in the 12 months pre- and post-introduction of GxAlert for RR-TB patients.

Design

This was a retrospective cohort study.

Results

The median time from Xpert testing to treatment initiation decreased from 35 days [IQR 13-131] prior to GxAlert to 10 days [IQR 3-29] after GxAlert (P = 0.001), with the cumulative proportion of patients initiating treatment within 30 days increasing from 25% (95%CI 17-37) to 54% (95%CI 44-64; P < 0.001) over these periods. However, our analysis of the time to treatment prior to the introduction of GxAlert suggests that a decrease had already occurred prior to implementation. There was no difference in interim clinical outcomes between the periods.

Conclusion

Although a decrease in time to treatment initiation cannot be attributed to GxAlert, there was a significant improvement over the 2-year period, suggesting that considerable improvements have been made in timely RR-TB patient management in Port Moresby.

Outcomes in children treated for tuberculosis with the new dispersible fixed-dose combinations in Port Moresby

Setting

The new child-friendly fixed dose combinations (FDCs) were introduced at Port Moresby General Hospital, Papua New Guinea, in 2016 for the first-line treatment of children (aged <15 years) with tuberculosis (TB) who weighed <25 kg.

Objective

To describe the characteristics and outcomes for children treated with the new FDCs, and to identify risk factors for unfavourable treatment outcomes.

Design

This was a retrospective cohort study of all children treated for TB with the FDCs from August 2016 to August 2017.

Results

Of 713 children included, 488 (68%) were diagnosed with pulmonary TB. Only 6 (0.8%) TB cases were bacteriologically confirmed and human immunodeficiency virus (HIV) status was known in 50%. Treatment outcomes were favourable in 425 (60%) children. Of 288 children with unfavourable outcomes, there were 242 (84%) with loss to follow-up (LTFU) and 25 (8.4%) were known to have died. Children who were severely underweight (weight-for-age Z score <-3) on presentation were at greater risk of LTFU compared to children of normal weight on multivariable analysis (aRR 1.3, 95%CI 1.0-1.6, P < 0.05).

Conclusion

Alternative models of care to decrease LTFU during treatment are needed, including integration with nutritional support. Improving diagnosis through microbiological confirmation of TB and HIV are major challenges to be addressed.

Mycobacterium tuberculosis Drug Resistance and Transmission among Human Immunodeficiency Virus-Infected Patients in Ho Chi Minh City, Vietnam

Vietnam has a high burden of tuberculosis (TB) and multidrug-resistant (MDR) TB, but drug resistance patterns and TB transmission dynamics among TB/human immunodeficiency virus (HIV) coinfected patients are not well described. We characterized 200 Mycobacterium tuberculosis isolates from TB/HIV coinfected patients diagnosed at the main TB referral hospital in Ho Chi Minh City, Vietnam. Phenotypic drug susceptibility testing (DST) for first-line drugs, spoligotyping, and 24-locus mycobacterial interspersed repetitive unit (MIRU-24) analysis was performed on all isolates. The 24-locus mycobacterial interspersed repetitive unit clusters and MDR isolates were subjected to whole genome sequencing (WGS). Most of the TB/HIV coinfected patients were young (162/174; 93.1% aged < 45 years) males (173; 86.5% male). Beijing (98; 49.0%) and Indo-Oceanic (70; 35.0%) lineage strains were most common. Phenotypic drug resistance was detected in 84 (42.0%) isolates, of which 17 (8.5%) were MDR; three additional MDR strains were identified on WGS. Strain clustering was reduced from 84.0% with spoligotyping to 20.0% with MIRU-24 typing and to 13.5% with WGS. Whole genome sequencing identified five additional clusters, or members of clusters, not recognized by MIRU-24. In total, 13 small (two to three member) WGS clusters were identified, with less clustering among drug susceptible (2/27; 7.4%) than among drug-resistant strains (25/27; 92.6%). On phylogenetic analysis, strains from TB/HIV coinfected patients were interspersed among strains from the general community; no major clusters indicating transmission among people living with HIV were detected. Tuberculosis/HIV coinfection in Vietnam was associated with high rates of drug resistance and limited genomic evidence of ongoing M. tuberculosis transmission among HIV-infected patients.

Human Genetic Variation and HIV/AIDS in Papua New Guinea: Time to Connect the Dots

PURPOSE OF REVIEW

Human genetic polymorphisms known to influence HIV acquisition and disease progression occur in Papua New Guinea (PNG). However, no genetic association study has been reported so far. In this article, we review research findings, with a view to stimulate genotype-to-phenotype research.

RECENT FINDINGS

PNG, a country in Oceania, has a high prevalence of HIV and many sexually transmitted infections. While limited data is available from this country regarding the distribution of human genetic polymorphisms known to influence clinical outcomes of HIV/AIDS, genetic association studies are lacking. Our studies, in the past decade, have revealed that polymorphisms in chemokine receptor-ligand (CCR2-CCR5, CXCL12), innate immune (Toll-like receptor, β-defensin), and antiretroviral drug-metabolism enzyme (CYP2B6, UGT2B7) genes are prevalent in PNG. Although our results need to be validated in further studies, it is urgent to pursue large-scale, comprehensive genetic association studies that include these as well as additional genetic polymorphisms.

Pharmacogenomics in Papua New Guineans: unique profiles and implications for enhancing drug efficacy while improving drug safety

Papua New Guinea (PNG) can be roughly divided into highland, coastal and island peoples with significant mitochondrial DNA differentiation reflecting early and recent distinct migrations from Africa and East Asia, respectively. Infectious diseases such as tuberculosis, malaria and HIV severely impact on the health of its peoples for which drug therapy is the major treatment and pharmacogenetics has clinical relevance for many of these drugs. Although there is generally little information about known single nucleotide polymorphisms in the population, in some instances, their frequencies have been shown to be higher than anywhere worldwide. For example, CYP2B6*6 is over 50%, and CYP2C19*2 and *3 are over 40 and 25%, respectively. Conversely, CYP2A6*9, 2B6*2, *3, *4 and *18, and 2C8*3 appear to be much lower than in Whites. CYP2D6 known variants are unclear, and for phase II enzymes, only UGT2B7 and UGT1A9 data are available, with variant frequencies either slightly lower than or similar to Whites. Although almost all PNG people tested are rapid acetylators, but which variant(s) define this phenotype is not known. For HLA-B*13:01, HLA-B*35:05 and HLA-C*04:01, the frequencies show some regioselectivity, but the clinical implications with respect to adverse drug reactions are not known. There are minimal phenotype data for the CYPs and nothing is known about drug transporter or receptor genetics. Determination of genetic variants that are rare in Whites or Asians but common in PNG people is a topic of both scientific and clinical importance, and further research needs to be carried out. Optimizing the safety and efficacy of infectious disease drug therapy through pharmacogenetic studies that have translation potential is a priority.

Molecular Evidence of Drug-Resistant Tuberculosis in the Balimo Region of Papua New Guinea

Papua New Guinea (PNG) has a high burden of tuberculosis (TB), including drug-resistant TB (DR-TB). DR-TB has been identified in patients in Western Province, although there has been limited study outside the provincial capital of Daru. This study focuses on the Balimo region of Western Province, aiming to identify the proportion of DR-TB, and characterise Mycobacterium tuberculosis (MTB) drug resistance-associated gene mutations. Sputum samples were investigated for MTB infection using published molecular methods. DNA from MTB-positive samples was amplified and sequenced, targeting the rpoB and katG genes to identify mutations associated with rifampicin and isoniazid resistance respectively. A total of 240 sputum samples were collected at Balimo District Hospital (BDH). Of these, 86 were classified as positive based on the results of the molecular assays. For samples where rpoB sequencing was successful, 10.0% (5/50, 95% CI 4.4–21.4%) were considered rifampicin-resistant through detection of drug resistance-associated mutations. We have identified high rates of presumptive DR-TB in the Balimo region of Western Province, PNG. These results emphasise the importance of further surveillance, and strengthening of diagnostic and treatment services at BDH and throughout Western Province, to facilitate detection and treatment of DR-TB, and limit transmission in this setting.

Asymmetrical Development across Transboundary Regions: The Case of the Torres Strait Treaty Region (Australia and Papua New Guinea)

While there is much theoretical study of the evolution of border disparities, there is little empirical analysis of development asymmetries across border regions, and their causes or solutions. Often disparities among countries hinder the ability of transboundary agreements and other development initiatives to generate sustainable development. This study quantifies development progress amongst communities in Australia and Papua New Guinea (PNG) covered by the Torres Strait Treaty, 26 years after its inception. Using regional census data from 2011 we found contrasting patterns of human development, with markedly poorer education levels in PNG. This asymmetry was confirmed by a Human Development Index of 0.735 for the Torres Strait and 0.270 for the neighbouring province in PNG. From a survey of 1089 PNG households in 2012–2013 we calculated that 63% of people in the villages were multidimensional poor, and 28% were ‘vulnerable to poverty’. Poverty was positively correlated with poor health, which has implications for the control of tuberculosis in the region. While Treaty provisions may have reduced poverty amongst some PNG villages closest to Australian communities, development initiatives by Ok Tedi mine in compensation for its environmental impacts have not. Our study highlights the causes of the sustainable development gap between PNG and Australian communities, and the necessity for transboundary agreements and institutions to have the capacity to adapt to their unintended consequences and rapid global change.

The burden of presumed tuberculosis in hospitalized children in a resource-limited setting in Papua New Guinea: a prospective observational study

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.

A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions

A better understanding of the genomic changes that facilitate the emergence and spread of drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report the use of the MinION nanopore sequencer (Oxford Nanopore Technologies) to sequence and assemble an extensively drug-resistant (XDR) isolate, which is part of a modern Beijing sub-lineage strain, prevalent in Western Province, Papua New Guinea. Using 238-fold coverage obtained from a single flow-cell, de novo assembly of nanopore reads resulted into one contiguous assembly with 99.92 % assembly accuracy. Incorporation of complementary short read sequences (Illumina) as part of consensus error correction resulted in a 4 404 064 bp genome with 99.98 % assembly accuracy. This assembly had an average nucleotide identity of 99.7 % relative to the reference genome, H37Rv. We assembled nearly all GC-rich repetitive PE/PPE family genes (166/168) and identified variants within these genes. With an estimated genotypic error rate of 5.3 % from MinION data, we demonstrated identification of variants to include the conventional drug resistance mutations, and those that contribute to the resistance phenotype (efflux pumps/transporter) and virulence. Reference-based alignment of the assembly allowed detection of deletions and insertions. MinION sequencing provided a fully annotated assembly of a transmissible XDR strain from an endemic setting and showed its utility to provide further understanding of genomic processes within Mycobacterium tuberculosis.

Planetary Overload, Limits to Growth and Health

Since the use of atomic weapons in 1945 visionaries have warned that without major changes the survival of global civilization is in question. These concerns deepened in following decades, during the Cold War, with The Limits to Growth, the best-selling environmental book of the 1970s. Yet, since then, most concern has faded, fuelled by technological developments and a shift in dominant global ideology. Public health, with a few exceptions (one of which is the book Planetary Overload), has been slow to recognize this debate, even as evidence emerges that civilization may indeed be at risk, driven by an increasingly ominous complex of events. This article outlines the key relevant literature and concepts, attempting to bring emerging and future health consequences to the attention of health workers, including the idea of a "social vaccine," conveying sufficient anxiety to provoke action for environmental protection, but insufficient to induce paralysis.

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

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.

Performance of syndromic management for the detection and treatment of genital Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis among women attending antenatal, well woman and sexual health clinics in Papua New Guinea: a cross-sectional study

OBJECTIVE

Papua New Guinea (PNG) has among the highest estimated prevalences of genital Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Trichomonas vaginalis (TV) of any country in the Asia-Pacific region. Diagnosis and treatment of these infections have relied on the WHO-endorsed syndromic management strategy that uses clinical presentation without laboratory confirmation to make treatment decisions. We evaluated the performance of this strategy in clinical settings in PNG.

DESIGN

Women attending antenatal (ANC), well woman (WWC) and sexual health (SHC) clinics in four provinces were invited to participate, completed a face-to-face interview and clinical examination, and provided genital specimens for laboratory testing. We estimated the performance characteristics of syndromic diagnoses against combined laboratory diagnoses.

RESULTS

1764 women were enrolled (ANC=765; WWC=614; SHC=385). The prevalences of CT, NG and TV were highest among women attending ANC and SHC. Among antenatal women, syndromic diagnosis of sexually transmitted infection had low sensitivity (9%-21%) and positive predictive value (PPV) (7%-37%), but high specificity (76%-89%) and moderate negative predictive value (NPV) (55%-86%) for the combined endpoint of laboratory-confirmed CT, NG or TV. Among women attending WWC and SHC, 'vaginal discharge syndrome' had moderate to high sensitivity (72%-78%) and NPV (62%-94%), but low specificity (26%-33%) and PPV (8%-38%). 'Lower abdominal pain syndrome' had low sensitivity (26%-41%) and PPV (8%-23%) but moderate specificity (66%-68%) and high NPV (74%-93%) among women attending WWC, and moderate-high sensitivity (67%-79%) and NPV (62%-86%) but low specificity (26%-28%) and PPV (14%-33%) among SHC attendees.

CONCLUSION

The performance of syndromic management for the detection and treatment of genital chlamydia, gonorrhoea and trichomonas was poor among women in different clinical settings in PNG. New diagnostic strategies are needed to control these infections and to prevent their adverse health outcomes in PNG and other high-burden countries.

Culture and Next-generation sequencing-based drug susceptibility testing unveil high levels of drug-resistant-TB in Djibouti: results from the first national survey

Djibouti is a small country in the Horn of Africa with a high TB incidence (378/100,000 in 2015). Multidrug-resistant TB (MDR-TB) and resistance to second-line agents have been previously identified in the country but the extent of the problem has yet to be quantified. A national survey was conducted to estimate the proportion of MDR-TB among a representative sample of TB patients. Sputum was tested using XpertMTB/RIF and samples positive for MTB and resistant to rifampicin underwent first line phenotypic susceptibility testing. The TB supranational reference laboratory in Milan, Italy, undertook external quality assurance, genotypic testing based on whole genome and targeted-deep sequencing and phylogenetic studies. 301 new and 66 previously treated TB cases were enrolled. MDR-TB was detected in 34 patients: 4.7% of new and 31% of previously treated cases. Resistance to pyrazinamide, aminoglycosides and capreomycin was detected in 68%, 18% and 29% of MDR-TB strains respectively, while resistance to fluoroquinolones was not detected. Cluster analysis identified transmission of MDR-TB as a critical factor fostering drug resistance in the country. Levels of MDR-TB in Djibouti are among the highest on the African continent. High prevalence of resistance to pyrazinamide and second-line injectable agents have important implications for treatment regimens.

Molecular diagnosis of suspected tuberculosis from archived smear slides from the Balimo region, Papua New Guinea

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.

Increasing isoniazid preventive therapy uptake in an HIV program in rural Papua New Guinea

Setting: Tuberculosis (TB) is the leading cause of death among people living with the human immunodeficiency virus (PLHIV) in Papua New Guinea. Despite a policy for isoniazid preventive therapy (IPT) among PLHIV, implementation has been slow. Objective: We prospectively evaluated a standardized guided screening process, including TB diagnostic support, to increase IPT initiation in adult PLHIV on antiretro-viral treatment. Design: The guided process included a paper-based IPT screening tool that prompted review of patient history and TB symptoms and sputum analysis by smear microscopy and Xpert^® MTB/RIF. Chest X-ray was performed at the provider's discretion. We quantified the yield of this guided process on IPT initiation and detection of TB and rifampicin resistance, and examined the contributions of each diagnostic modality. Results: Among 532 patients, TB was ruled out and IPT initiated in 450 (84%). TB was diagnosed and treatment was started in 82 (15%) patients. Xpert detected rifampicin resistance in one of 21 patients (5%, 95%CI 0.24-21.3) with a positive Xpert result. All TB cases were diagnosed by chest X-ray and/or Xpert. No cases were diagnosed by sputum smear alone. Conclusion: A standardized guided process, including TB diagnostic support, successfully enabled IPT initiation and identified a large burden of undetected TB.

A preliminary assessment of Toll-like receptor and β-defensin gene polymorphisms in Papua New Guinea - what does it mean for HIV/AIDS?

Polymorphisms in Toll-like receptor (TLR) and human β-defensin (hBD, encoded by DEFB) genes have been evaluated for their associations with HIV infection and disease outcomes. Those studies, conducted in various populations under a variety of study designs, generally revealed that specific single nucleotide polymorphisms (SNPs) in TLR1, 2, 3, 4, 6, 7, 8, and 9 genes, and copy number variation (CNV) in DEFB4 (encoding hBD-2), DEFB103A (encoding hBD-3), and DEFB104A (encoding hBD-4) genes are among potential genetic factors that can affect susceptibility to HIV infection and/or disease progression. The information regarding their prevalence in Papua New Guinea (PNG) is very limited for TLR SNPs, and not available for DEFB CNV. The present study provides a preliminary assessment of these genetic polymorphisms in samples collected from the Wosera (East Sepik Province, n = 29) and Liksul (Madang Province, n = 23) areas. Wosera samples were analyzed for a total of 41 SNPs in 8 TLR genes (TLR1, 2, 3, 4, 6, 7, 8, and 9), and both sample sets were analyzed for CNV in DEFB4/103A/104A genes. A number of TLR SNPs were not detected, and many other SNPs were present at low frequencies (minor allele frequencies ≤0.05) in the Wosera samples. The DEFB4/103A/104A copy numbers were significantly different between the two sample sets (p = 0.024). Validation of these results, using larger sample sizes as well as samples from other areas of PNG, is warranted. In addition, genetic association studies are needed to estimate the effects of these polymorphisms on HIV infection and disease progression in PNG.

Epidemiology of Drug-Resistant Tuberculosis

As we move into the era of the Sustainable Development Goals (SDGs), the World Health Organization (WHO) has developed the End TB strategy 2016-2035 with a goal to end the global epidemic of tuberculosis (TB) by 2035. Achieving the targets laid out in the Strategy will require strengthening of the whole TB diagnosis and treatment cascade, including improved case detection, the establishment of universal drug susceptibility testing and rapid treatment initiation. An estimated 3.9% of new TB cases and 21% of previously treated cases had rifampicin-resistant (RR) or multidrug-resistant (MDR) TB in 2015. These levels have remained stable over time, although limited data are available from major high burden settings. In addition to the emergence of drug resistance due to inadequate treatment, there is growing evidence that direct transmission is a large contributor to the RR/MDR-TB epidemic. Only 340,000 of the estimated 580,000 incident cases of RR/MDR-TB were notified to WHO in 2015. Among these, only 125,000 were initiated on second-line treatment. RR/MDR-TB epidemics are likely to be driven by direct transmission. The most important risk factor for MDR-TB is a history of previous treatment. Other risk factors vary according to setting but can include hospitalisation, incarceration and HIV infection. Children have the same risk of MDR-TB as adults and represent a diagnostic and treatment challenge. Rapid molecular technologies have revolutionized the diagnosis of drug-resistant TB. Until capacity can be established to test every TB patient for rifampicin resistance, countries should focus on gradually expanding their coverage of testing. DNA sequencing technologies are being increasingly incorporated into patient management and drug resistance surveillance. They offer additional benefits over conventional culture-based phenotypic testing, including a faster turn-around time for results, assessment of resistance patterns to a range of drugs, and investigation of strain clustering and transmission.