High prevalence of pre-treatment HIV drug resistance in Papua New Guinea: findings from the first nationally representative pre-treatment HIV drug resistance study.

BACKGROUND: Determining the prevalence of pre-treatment HIV drug resistance (PDR) is important to assess the effectiveness of first-line therapies. To determine PDR prevalence in Papua New Guinea (PNG), we conducted a nationally representative survey. METHODS: We used a two-stage cluster sampling method to recruit HIV treatment initiators with and without prior exposure to antiretroviral therapies (ART) in selected clinics. Dried blood spots were collected and tested for PDR. RESULTS: A total of 315 sequences were available for analysis. The overall PDR prevalence rate was 18.4% (95% CI 13.8-24.3%). The prevalence of PDR to non-nucleoside analog reverse-transcriptase inhibitors (NNRTIs) was 17.8% (95% CI 13.6-23.0%) and of PDR to nucleoside reverse transcriptase inhibitors (NRTIs) was 6.3% (95% CI 1.6-17.1%). The PDR prevalence rate among people reinitiating ART was 42.4% (95% CI 29.1-56.4%). CONCLUSIONS: PNG has a high PDR prevalence rate, especially to NNRTI-based first-line therapies. Our findings suggest that removing NNRTIs as part of first-line treatment is warranted and will lead to improving viral suppression rates in PNG.

Association of protein intakes and variation of diet-scalp hair nitrogen isotopic discrimination factor in Papua New Guinea highlanders.

OBJECTIVES: We present new nitrogen isotopic discrimination factor between diets and scalp hairs (Δ(15) NHair-Diet : δ(15) NHair - δ(15) NDiet ) for indigenous residents in three communities in the Papua New Guinea Highlands who consumed various amounts and qualities of protein. The Δ(15) N is important for precise evaluation of the dietary habits of human populations; in both contemporary and traditional lifestyles. Several hypotheses have been proposed regarding factors that affect Δ(15) N values, based largely on observations from animal feeding experiments. However, variations and factors controlling Δ(15) N in humans are not well understood, mainly due to the difficulty of controlling the diets of participants. MATERIALS AND METHODS: These residents were studied because they have maintained relatively traditional dietary habits, which allow quantitative recording of diets. Δ(15) N was estimated by comparing hair δ(15) N values to mean dietary δ(15) N values calculated from the recorded intake of each food item and their δ(15) N values. RESULTS: The results showed that: i) there was a significant difference in Δ(15) N among study locations (3.9 ± 0.9‰ for most urbanized, 5.2 ± 1.0‰ for medium and 5.0 ± 0.9‰ for least urbanized communities; range = 1.2-7.3‰ for all participants); and ii) estimated Δ(15) N values were negatively correlated with several indicators of animal protein intake (% nitrogen in diet: range = 0.9-7.6%). DISCUSSION: We hypothesize that a combination of several factors, which presumably included urea recycling and amino acid and protein recycling and/or de novo synthesis during metabolic processes, altered the Δ(15) N values of the participants.

Development, validation, and use of a semi-quantitative food frequency questionnaire for assessing protein intake in Papua New Guinean Highlanders.

OBJECTIVES: The aim of this article was to develop a semi-quantitative food frequency questionnaire (FFQ) and evaluate its validity to estimate habitual protein intake, and investigate current dietary protein intakes of Papua New Guinea (PNG) Highlanders. METHODS: A 32-item FFQ was developed and tested among 135 healthy male and female volunteers. The FFQ-estimated daily total and animal protein intakes were compared with biomarkers and 3-day Weighed Food Records (WFR) by correlation analyses, Bland-Altman plot analyses and joint classification analyses. RESULTS: The FFQ-estimated total protein intake significantly correlated with urinary nitrogen in the first morning void after adjusting urinary creatinine concentration (r = 0.28, P < 0.01) and the FFQ-estimated animal protein intake significantly correlated with the hair δ(15) N (Spearman's r = 0.34, P < 0.001). The limits of agreement were ±2.39 Z-score residuals for total protein intake and ±2.19 Z-score for animal protein intake, and intra-individual differences increased as protein intake increased. The classification into the same and adjacent quartiles was 66.0% for total protein intake and 73.6% for animal protein intake. Median daily total and animal protein intake estimates from the FFQ and the 3-day WFR showed a good agreement with differences of 0.2 and 4.9 g, respectively. None of the studied communities in the PNG Highlands met the biologically required protein intake; although the community closer to an urban center showed higher protein intake than the more remote communities. CONCLUSIONS: The newly developed 32-item FFQ for PNG Highlanders is applicable for evaluation of protein intake at the individual level. Am. J. Hum. Biol. 27:349-357, 2015. © 2014 Wiley Periodicals, Inc.

Evaluation of a rapid immunochromatographic assay for the detection of rotavirus, norovirus and adenovirus from children hospitalized with acute watery diarrhea.

We evaluated the IP-Triple I immunochromatographic rapid test for the detection of rotavirus, norovirus and adenovirus using stool samples from children with diarrhoea. The detection of norovirus and adenovirus was poor compared to polymerase chain reaction assays. However, high sensitivity (92%) and specificity (99%) were obtained for the detection of rotavirus.

Diarrhoeal disease surveillance in Papua New Guinea: findings and challenges.

Diarrhoeal diseases are among the leading causes of morbidity and mortality in the Western Pacific Region. However, data on the major causes of infectious diarrhoea are limited in many countries within the Region, including Papua New Guinea. In 2013-2014, we conducted surveillance for acute diarrhoeal illness in four provinces in Papua New Guinea. One rural health clinic from each province participated in the surveillance activity. Samples were sent to central laboratories and batch analysed for bacterial and viral gastrointestinal pathogens that are commonly associated with diarrhoea. Across the four sites, the most commonly detected pathogens were Shigella spp., Campylobacter spp. and rotavirus. In this paper, we report the results of the surveillance activity and the challenges that we faced. The lessons learnt may be applicable to other parts of the Region with a similar socioeconomic status.

A High Burden of Asymptomatic Gastrointestinal Infections in Traditional Communities in Papua New Guinea.

Stool samples were collected from 148 healthy adults living a traditional subsistence lifestyle in Papua New Guinea and screened for enteric pathogens using real-time RT-PCR/PCR assays. Enteric pathogens were detected in a high proportion (41%) of individuals. Clear differences were observed in the detection of pathogens between highland and lowland communities. In particular, there was a marked difference in detection rates of norovirus GII (20% and 0%, respectively) and Shigella sp. (15% and 0%, respectively). Analysis of the relationship between enteric pathogen carriage and microbial community composition of participants, using box plots to compare specific normal flora population numbers, did not suggest that gut microbial composition was directly associated with pathogen carriage. This study suggests that enteric pathogens are common in healthy individuals in Papua New Guinean highland communities, presumably acting as a reservoir of infection and thus contributing to a high burden of gastrointestinal illnesses.

Characterization of the gut microbiota of Papua New Guineans using reverse transcription quantitative PCR.

There has been considerable interest in composition of gut microbiota in recent years, leading to a better understanding of the role the gut microbiota plays in health and disease. Most studies have been limited in their geographical and socioeconomic diversity to high-income settings, and have been conducted using small sample sizes. To date, few analyses have been conducted in low-income settings, where a better understanding of the gut microbiome could lead to the greatest return in terms of health benefits. Here, we have used quantitative real-time polymerase chain reaction targeting dominant and sub-dominant groups of microorganisms associated with human gut microbiome in 115 people living a subsistence lifestyle in rural areas of Papua New Guinea. Quantification of Clostridium coccoides group, C. leptum subgroup, C. perfringens, Bacteroides fragilis group, Bifidobacterium, Atopobium cluster, Prevotella, Enterobacteriaceae, Enterococcus, Staphylococcus, and Lactobacillus spp. was conducted. Principle coordinates analysis (PCoA) revealed two dimensions with Prevotella, clostridia, Atopobium, Enterobacteriaceae, Enterococcus and Staphylococcus grouping in one dimension, while B. fragilis, Bifidobacterium and Lactobacillus grouping in the second dimension. Highland people had higher numbers of most groups of bacteria detected, and this is likely a key factor for the differences revealed by PCoA between highland and lowland study participants. Age and sex were not major determinants in microbial population composition. The study demonstrates a gut microbial composition with some similarities to those observed in other low-income settings where traditional diets are consumed, which have previously been suggested to favor energy extraction from a carbohydrate rich diet.

Detection of enteric viral and bacterial pathogens associated with paediatric diarrhoea in Goroka, Papua New Guinea.

OBJECTIVES: The aim of this study was to investigate the viral and bacterial causes of acute watery diarrhoea in hospitalized children in Papua New Guinea. METHODS: A retrospective analysis was conducted on stool samples collected from 199 children (age <5 years) admitted to the paediatric ward of Goroka General Hospital from August 2009 through November 2010. A large range of viral and bacterial enteric pathogens were targeted using real-time PCR/RT-PCR assays. RESULTS: Young children were much more likely to be admitted with acute gastroenteritis, with 62.8% of patients aged <1 year and 88.4% aged <2 years. An enteric pathogen was detected in 69.8% (n=138) of patients. The most commonly detected pathogens were Shigella spp (26.6%), rotavirus (25.6%), adenovirus types 40/41 (11.6%), enterotoxigenic Escherichia coli (11.1%), enteropathogenic E. coli (8.5%), norovirus G2 (6.0%), and Campylobacter spp (4.0%). Norovirus G1, sapovirus, and Salmonella spp were also detected, but below our statistical limit of detection. Vibrio cholerae and astrovirus were not detected in any patients. Mixed infections were detected in 22.1% of patients, with Shigella and rotavirus most commonly detected in co-infections with other pathogens. CONCLUSIONS: This study demonstrates that Shigella and rotavirus are the major pathogens associated with acute paediatric gastroenteritis in this setting.

Evaluation of colorimetric detection methods for Shigella, Salmonella, and Vibrio cholerae by loop-mediated isothermal amplification.

We evaluated loop-mediated isothermal amplification end-point detection methods for Salmonella, Shigella, and Vibrio cholerae. Detection sensitivities were comparable to real-time PCR methods. The colorimetric dyes hydroxynaphthol blue and SYBR Green I showed increased sensitivity when compared to visual and automated turbidity readings. End-point colorimetric dyes promise great utility in developing settings.