Mike Kama

Ministry Of Health

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Conall Watson

UK Health Security Agency

Eric J. Nilles

Dana-Farber/Harvard Cancer Center

Kim Mulholland

London School of Hygiene & Tropical Medicine

Colleen L. Lau

University of Queensland

W. John Edmunds

London School of Hygiene & Tropical Medicine

Eric Rafai

Ministry Of Health

Catherine Satzke

Royal Children's Hospital

Fiona M. Russell

University of Melbourne

Eileen M. Dunne

University of Melbourne

Evelyn Tuivaga

Ministry Of Health

Cooperative Institutions

London School of Hygiene & Tropical Medicine

University of Melbourne

Centers for Disease Control and Prevention

University of Oxford

University of London

Ministry Of Health

Oxford University Clinical Research Unit

Murdoch Children's Research Institute

World Health Organization - Pakistan

University of Cambridge

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Lot quality assurance sampling to assess coverage and compliance following mass drug administration to eliminate lymphatic filariasis in Fiji: A methodological approach

PLoS ONE (2020)

Milika Rinamalo Lorenzo Pezzoli Mike Kama Eric Rafai Ilisapeci Kubuabola

Assessing the quality of mass drug administration (MDA) rounds is a key component of lymphatic filariasis (LF) elimination programs. Routine collection of administrative coverage is unreliable, especially when pockets with low program coverage exist. To address this gap, we used lot quality assurance sampling (LQAS) following the 10th annual LF-MDA round in Fiji to explore whether there was any area in which target coverage was not reached. We also assessed the level of drug compliance and satisfaction with the LF-MDA implementation strategy.We conducted a cross-sectional household survey in 3 divisions of Fiji. For LQAS, we defined 19 lots in 7 medical areas of the Suva sub-division and another 12 sub-divisions in the Central, Northern, and Eastern Divisions. A sample of 16 randomly selected household members was taken un each lot. We defined our decision rule as follows: if more than 1 person in a given lot did not swallow the medication, coverage was considered inadequate, i.e. less than 80%. Of the 7 lots in Suva sub-division and 12 lots in the 3 divisions, five and two lots, respectively, were identified as having inadequate coverage. The overall program coverage estimated from 304 samples was 92%, which was higher than the reported administrative coverage of 82%. About 98% of interviewees were offered the medication and 96% swallowed it. Non-participation arose from insufficient information on how to obtain the drugs. At least 92% were satisfied with the LF-MDA implementation strategy.Areas of low program coverage with results discordant with the reported administrative coverage existed in both urban and rural settings. Drug compliance and satisfaction were high, even after repeated rounds. We recommend increasing efforts to deliver the service in those areas with inadequate program coverage, as well as conducting timely coverage assessment through LQAS for corrective action.

Mass drug administration

Lymphatic Filariasis

10.1371/journal.pone.0238622

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Citations (2)

Epidemiological and Virological Characteristics of Influenza in the Western Pacific Region of the World Health Organization, 2006-2010

PLoS ONE (2012)

Ian Barr Aeron C. Hurt Anne Kelso Patrick C. Reading Sovann Ly

Source

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Factors associated with pneumococcal carriage and density in children and adults in Fiji, using four cross-sectional surveys

PLoS ONE (2020)

Eleanor Neal Cattram Nguyen F. Tupou Ratu Eileen M. Dunne Mike Kama

This study describes predictors of pneumococcal nasopharyngeal carriage and density in Fiji. We used data from four annual (2012–2015) cross-sectional surveys, pre- and post-introduction of ten-valent pneumococcal conjugate vaccine (PCV10) in October 2012. Infants (5–8 weeks), toddlers (12–23 months), children (2–6 years), and their caregivers participated. Pneumococci were detected and quantified using lytA qPCR, with molecular serotyping by microarray. Logistic and quantile regression were used to determine predictors of pneumococcal carriage and density, respectively. There were 8,109 participants. Pneumococcal carriage was negatively associated with years post-PCV10 introduction (global P<0.001), and positively associated with indigenous iTaukei ethnicity (aOR 2.74 [95% CI 2.17–3.45] P<0.001); young age (infant, toddler, and child compared with caregiver participant groups) (global P<0.001); urban residence (aOR 1.45 [95% CI 1.30–2.57] P<0.001); living with ≥2 children <5 years of age (aOR 1.42 [95% CI 1.27–1.59] P<0.001); low family income (aOR 1.44 [95% CI 1.28–1.62] P<0.001); and upper respiratory tract infection (URTI) symptoms (aOR 1.77 [95% CI 1.57–2.01] P<0.001). Predictors were similar for PCV10 and non-PCV10 carriage, except PCV10 carriage was negatively associated with PCV10 vaccination (0.58 [95% CI 0.41–0.82] P = 0.002) and positively associated with exposure to household cigarette smoke (aOR 1.21 [95% CI 1.02–1.43] P = 0.031), while there was no association between years post-PCV10 introduction and non-PCV10 carriage. Pneumococcal density was positively associated with URTI symptoms (adjusted median difference 0.28 [95% CI 0.16, 0.40] P<0.001) and toddler and child, compared with caregiver, participant groups (global P = 0.008). Predictors were similar for PCV10 and non-PCV10 density, except infant, toddler, and child participant groups were not associated with PCV10 density. PCV10 introduction was associated with reduced the odds of overall and PCV10 pneumococcal carriage in Fiji. However, after adjustment iTaukei ethnicity was positively associated with pneumococcal carriage compared with Fijians of Indian Descent, despite similar PCV10 coverage rates.

Cross-sectional study

Carriage

10.1371/journal.pone.0231041

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Citations (12)

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Nature Communications (2016)

Vanessa Wong Stephen Baker Thomas R. Connor Derek Pickard Andrew J. Page

The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations.

Salmonella enterica

10.1038/ncomms12827

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The utility of serology for elimination surveillance of trachoma

Nature Communications (2018)

Amy Pinsent Anthony W. Solomon Robin L. Bailey Rhiannon Bid Anaseini Cama

Robust surveillance methods are needed for trachoma control and recrudescence monitoring, but existing methods have limitations. Here, we analyse data from nine trachoma-endemic populations and provide operational thresholds for interpretation of serological data in low-transmission and post-elimination settings. Analyses with sero-catalytic and antibody acquisition models provide insights into transmission history within each population. To accurately estimate sero-conversion rates (SCR) for trachoma in populations with high-seroprevalence in adults, the model accounts for secondary exposure to Chlamydia trachomatis due to urogenital infection. We estimate the population half-life of sero-reversion for anti-Pgp3 antibodies to be 26 (95% credible interval (CrI): 21-34) years. We show SCRs below 0.015 (95% confidence interval (CI): 0.0-0.049) per year correspond to a prevalence of trachomatous inflammation-follicular below 5%, the current threshold for elimination of active trachoma as a public health problem. As global trachoma prevalence declines, we may need cross-sectional serological survey data to inform programmatic decisions.

Seroprevalence

10.1038/s41467-018-07852-0

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Social mixing in Fiji: Who-eats-with-whom contact patterns and the implications of age and ethnic heterogeneity for disease dynamics in the Pacific Islands

PLoS ONE (2017)

Conall Watson Jeremaia Coriakula Dung Tran Thi Ngoc Stefan Flasche Adam J. Kucharski

Empirical data on contact patterns can inform dynamic models of infectious disease transmission. Such information has not been widely reported from Pacific islands, nor strongly multi-ethnic settings, and few attempts have been made to quantify contact patterns relevant for the spread of gastrointestinal infections. As part of enteric fever investigations, we conducted a cross-sectional survey of the general public in Fiji, finding that within the 9,650 mealtime contacts reported by 1,814 participants, there was strong like-with-like mixing by age and ethnicity, with higher contact rates amongst iTaukei than non-iTaukei Fijians. Extra-domiciliary lunchtime contacts follow these mixing patterns, indicating the overall data do not simply reflect household structures. Inter-ethnic mixing was most common amongst school-age children. Serological responses indicative of recent Salmonella Typhi infection were found to be associated, after adjusting for age, with increased contact rates between meal-sharing iTaukei, with no association observed for other contact groups. Animal ownership and travel within the geographical division were common. These are novel data that identify ethnicity as an important social mixing variable, and use retrospective mealtime contacts as a socially acceptable metric of relevance to enteric, contact and respiratory diseases that can be collected in a single visit to participants. Application of these data to other island settings will enable communicable disease models to incorporate locally relevant mixing patterns in parameterisation.

Mixing patterns

Social contact

10.1371/journal.pone.0186911

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Citations (9)

Unravelling infectious disease eco-epidemiology using Bayesian networks and scenario analysis: A case study of leptospirosis in Fiji

Environmental Modelling & Software (2017)

Colleen L. Lau Helen J. Mayfield John H. Lowry Conall Watson Mike Kama

Causality

10.1016/j.envsoft.2017.08.004

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Citations (24)

Discovery of a Streptococcus pneumoniae serotype 33F capsular polysaccharide locus that lacks wcjE and contains a wcyO pseudogene

PLoS ONE (2018)

Sam Manna Eileen M. Dunne Belinda D. Ortika Casey L. Pell Mike Kama

As part of large on-going vaccine impact studies in Fiji and Mongolia, we identified 25/2750 (0.9%) of nasopharyngeal swabs by microarray that were positive for Streptococcus pneumoniae contained pneumococci with a divergent 33F capsular polysaccharide locus (designated ‘33F-1’). We investigated the 33F-1 capsular polysaccharide locus to better understand the genetic variation and its potential impact on serotyping results. Whole genome sequencing was conducted on ten 33F-1 pneumococcal isolates. Initially, sequence reads were used for molecular serotyping by PneumoCaT. Phenotypic typing of 33F-1 isolates was then performed using the Quellung reaction and latex agglutination. Genome assemblies were used in phylogenetic analyses of each gene in the capsular locus to investigate genetic divergence. All ten pneumococcal isolates with the 33F-1 cps locus typed as 33F by Quellung and latex agglutination. Unlike the reference 33F capsule locus sequence, DNA microarray and PneumoCaT analyses found that 33F-1 pneumococci lack the wcjE gene, and instead contain wcyO with a frameshift mutation. Phylogenetic analyses found the wzg, wzh, wzd, wze, wchA, wciG and glf genes in the 33F-1 cps locus had higher DNA sequence similarity to homologues from other serotypes than to the 33F reference sequence. We have discovered a novel genetic variant of serotype 33F, which lacks wcjE and contains a wcyO pseudogene. This finding adds to the understanding of molecular epidemiology of pneumococcal serotype diversity, which is poorly understood in low and middle-income countries.

Pseudogene

10.1371/journal.pone.0206622

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Citations (8)

Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji

Nature Communications (2021)

Alasdair D Henderson Mike Kama Maïté Aubry Stéphane Hué Anita Teissier

Abstract Zika virus (ZIKV) has caused large, brief outbreaks in isolated populations, however ZIKV can also persist at low levels over multiple years. The reasons for these diverse transmission dynamics remain poorly understood. In Fiji, which has experienced multiple large single-season dengue epidemics, there was evidence of multi-year transmission of ZIKV between 2013 and 2017. To identify factors that could explain these differences in dynamics between closely related mosquito-borne flaviviruses, we jointly fit a transmission dynamic model to surveillance, serological and molecular data. We estimate that the observed dynamics of ZIKV were the result of two key factors: strong seasonal effects, which created an ecologically optimal time of year for outbreaks; and introduction of ZIKV after this optimal time, which allowed ZIKV transmission to persist over multiple seasons. The ability to jointly fit to multiple data sources could help identify a similar range of possible outbreak dynamics in other settings.

Zika Virus

Transmissibility (structural dynamics)

Flavivirus

10.1038/s41467-021-21788-y

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Citations (3)

Real-time qPCR improves meningitis pathogen detection in invasive bacterial-vaccine preventable disease surveillance in Fiji

Scientific Reports (2016)

Eileen M. Dunne Silivia Mantanitobua Shalini P. Singh Rita Reyburn Evelyn Tuivaga

Abstract As part of the World Health Organization Invasive Bacterial-Vaccine Preventable Diseases (IB-VPD) surveillance in Suva, Fiji, cerebrospinal fluid (CSF) samples from suspected meningitis patients of all ages were examined by traditional methods (culture, Gram stain, and latex agglutination for bacterial antigen) and qPCR for Streptococcus pneumoniae, Neisseria meningitidis , and Haemophilus influenzae . Of 266 samples tested, pathogens were identified in 47 (17.7%). S. pneumoniae was the most common pathogen detected (n = 17) followed by N. meningitidis (n = 13). The use of qPCR significantly increased detection of IB-VPD pathogens (P = 0.0001): of 35 samples that were qPCR positive for S. pneumoniae, N. meningitidis , and H. influenzae , only 10 were culture positive. This was particularly relevant for N. meningitidis , as only 1/13 cases was culture positive. Molecular serotyping by microarray was used to determine pneumococcal serotypes from 9 of 16 (56%) of samples using DNA directly extracted from CSF specimens. Results indicate that qPCR significantly increases detection of S. pneumoniae, N. meningitidis , and H. influenzae in CSF, and that application of molecular diagnostics is a feasible way to enhance local and global surveillance for IB-VPD.

Latex fixation test

Streptococcus suis

10.1038/srep39784

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Citations (15)