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

Guernier, Vanina; Diefenbach-Elstob, Tanya; Klotoe, Bernice J.; Burgess, Graham; Pelowa, Daniel; Dowi, Robert; Gula, Bisato; McBryde, Emma S.; Refrégier, Guislaine; Rush, Catherine M.; Sola, Christophe; Warner, Jeffrey

doi:10.1038/s41598-019-51892-5

Cited by 6 publications

(6 citation statements)

References 52 publications

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“…In contrast to HIV, TB-related qualitative research in PNG has been very limited (Diefenbach-Elstob et al, 2017; Marme, 2018; bib_Whittaker_et_al_2009Whittaker et al, 2009). Most of the formally collected and reported evidence that has informed the TB response in PNG has been clinical, biological or epidemiological in nature (Bainomugisa et al, 2018; Diefenbach-Elstob et al, 2018; Guernier-Cambert et al, 2019; Hapolo et al, 2019; Morris et al, 2019; Taune et al, 2019; Willie et al, 2021). Epidemiological and survey research offers important, relevant population-level information, and while the PNG National Department of Health is leading the response to address the biomedical and biological aspects of TB, this current study integrates a social and spatial dimension to this approach, a potentially critical aspect which to date has been largely neglected in PNG and elsewhere.…”

Section: Introductionmentioning

confidence: 99%

Exploring Tuberculosis Riskscapes in a Papua New Guinean ‘Hotspot’

et al. 2022

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This article explores socio-spatial dimensions of risk and how they can enhance understanding of a high burden tuberculosis (TB) context in the South Fly District of Papua New Guinea. We report on select findings from a qualitative study that included 128 semi-structured in-depth interviews and 10 focus group discussions with a wide range of South Fly District community members. Using the conceptual framework of ‘riskscapes’ to examine emic perspectives on risk, space and practice, we map key elements of TB riskscapes on Daru Island, South Fly District, along with solutions for navigating through these riskscapes. Overcrowding, lack of water, sanitation and hygiene, as well as food insecurity and undernutrition, were identified as common elements within participants’ riskscapes, that compounded upon each other to create the perception of an assemblage of risk favourable to TB transmission.

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Section: Introductionmentioning

confidence: 99%

Exploring Tuberculosis Riskscapes in a Papua New Guinean ‘Hotspot’

et al. 2022

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“…The high proportion of L1 is unique to Eastern Indonesia compared to Western and Central Indonesia where the proportion of L2 and L4 is higher [8–10]. This is also true in neighboring Papua New Guinea, where MTB L2 and L4 are the most dominant lineages [35]. However, the situation may be changing, as based on our sampling we observed probable transmissions of MTB from the rest of Indonesia to Papua.…”

Section: Discussionmentioning

confidence: 74%

A description of Lineage 1Mycobacterium tuberculosisfrom Papua, Indonesia

Djunaedy,

Febinia,

Hamers

et al. 2024

Preprint

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Indonesia has the third highest number of tuberculosis (TB) patients infected with Mycobacterium tuberculosis (MTB) Lineage 1 (L1). Most of these MTB L1 cases can be found in Indonesias remote easternmost province of Papua, one of Indonesias most underdeveloped provinces with a particularly high burden for TB. In this study, we sequenced and described 42 MTB L1 isolates from a well-characterized cohort of patients. We found a genetically diverse MTB L1 population with no association between pathogen genetic relatedness and place of residence or pathogen genetic relatedness and patient ethnicity, which could reflect mixing between different locales and ethnicities or our low sampling fraction. Only a small number showed genetic variants associated with drug resistance (5/42, 11.9%), probably due to a lack of effective treatment programs. The Papuan isolates showed similarities to other Island Southeast Asian Countries due to the high proportion of L1.2.1.2.1 (30/42, 71.4%), especially East Timor and the Philippines. This study fills a research gap of MTB L1 in Indonesian Papua and should serve as a stepping stone for further research in the region.

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“…Twenty (16.5%) publications reported using spoligotyping as one of the methods for detecting MSIs, with a majority employing one (Pavlic et al, 1999;Cox et al, 2005;García De Viedma et al, 2005;Umubyeyi et al, 2007;Furphy et al, 2012;Biffa et al, 2014;Chaoui et al, 2014;Lamine-Khemiri et al, 2014;Ssengooba et al, 2015;Wang et al, 2015;Egbe et al, 2017;Baffoe-Bonnie et al, 2019) or two (García De Viedma et al, 2003;Mokrousov et al, 2009;Huyen et al, 2012;Navarro et al, 2015;Silva-Pereira et al, 2019) additional methods ( Supplementary Table 2). Only three reports used spoligotyping as the sole genotyping method and reported MSIs at frequencies ranging from 11.8 to 57.1% (Andrews et al, 2008;Kamakoli et al, 2018;Guernier-Cambert et al, 2019). One significant limitation of spoligotyping is that it can underestimate MSIs as hybridization signals from multiple strains in a sample can overlap and appear as a single pattern (Kamakoli et al, 2018).…”

Section: Tuberculosis Complexmentioning

confidence: 99%

Methods for Detecting Mycobacterial Mixed Strain Infections–A Systematic Review

et al. 2020

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Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.

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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

Cited by 6 publications

References 52 publications

Exploring Tuberculosis Riskscapes in a Papua New Guinean ‘Hotspot’

Exploring Tuberculosis Riskscapes in a Papua New Guinean ‘Hotspot’

A description of Lineage 1Mycobacterium tuberculosisfrom Papua, Indonesia

Methods for Detecting Mycobacterial Mixed Strain Infections–A Systematic Review

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