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  • How many human pathogens are there in Laos? An estimate of national human pathogen diversity and analysis of historical trends

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Original research
How many human pathogens are there in Laos? An estimate of national human pathogen diversity and analysis of historical trends
  1. Madeleine Claire Clarkson1,2,
  2. Ricardo Aguas3,4,
  3. Kathryn Sweet5,
  4. Tamalee Roberts2,
  5. Michel Strobel6,
  6. Paul N Newton2,3
  1. 1Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
  2. 2Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
  3. 3Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
  4. 4Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
  5. 5Independant researcher, Vientiane, Lao People's Democratic Republic
  6. 6Independant researcher, Toulouse, France
  1. Correspondence to Madeleine Claire Clarkson; Madeleineclarkson{at}gmail.com

Abstract

Objective The emergence of infectious diseases pose major global health threats. Estimates of total in-country human pathogen diversity, and insights as to how and when species were described through history, could be used to estimate the probability of new pathogen discoveries. Data from the Lao People’s Democratic Republic (Laos) were used in this proof-of-concept study to estimate national human pathogen diversity and to examine historical discovery rate drivers.

Methods A systematic survey of the French and English scientific and grey literature of pathogen description in Laos between 1874 and 2017 was conducted. The first descriptions of each known human pathogen in Laos were coded according to the diagnostic evidence available. Cumulative frequency of discovery across time informed the rate of discovery. Four distinct periods of health systems development in Laos were identified prospectively and juxtaposed to the unmodelled rate of discovery. A model with a time-varying rate of discovery was fitted to these data using a Markov-Chain- Monte-Carlo technique.

Results From 6456 pathogen descriptions, 245 discoveries of known human pathogens in Laos, including repeat discoveries using different grades of evidence, were identified. The models estimate that the Laos human pathogen species diversity in 2017 is between 169 and 206. During the last decade, there has been a 33-fold increase in the discovery rate coinciding with the strengthening of medical research and microbiology.

Conclusion Discovery curves can be used to model and estimate country-level human pathogen diversity present in a territory. Combining this with historical assessment improves the understanding of the factors affecting local pathogen discovery.

PROSPERO registration number A protocol of this work was registered on PROSPERO (ID:CRD42016046728).

  • public health
  • health systems evaluation
  • mathematical modelling
  • epidemiology
https://creativecommons.org/licenses/by/4.0/

This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https://creativecommons.org/licenses/by/4.0/.

https://doi.org/10.1136/bmjgh-2020-002972

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    Footnotes

    • Handling editor Senjuti Saha

    • Contributors The paper was developed initially for MCC’s MSc thesis. Therefore, the literature search, figures, study design, data collection, data analysis, data interpretation and writing were all undertaken by her. The concept for the paper was developed by PN who advised on all components of this paper, contributing his personal libraries to the data collection, reviewing the data, offering consistent support and guidance, and editing the many iterations of this paper. RA supervised and was consulted throughout the model development, including coding, figures and design and revising the paper. KS was consulted throughout the development of the historical discussion. She also suggested appropriate archives and search terms. She made the appropriate introductions to the Lao National Archives, extended the use of her personal libraries and revised the paper. TR reviewed the database and provided microbiological insight for pathogen taxonomy and revised the paper. MS assisted with the translation of older and handwritten French medical papers and revised the paper.

    • Funding Wellcome Trust of Great Britain and London School of Hygiene and Tropical Medicine.

    • Disclaimer The funding source had no role in the design, conduct of the study or the decision to publish.

    • Competing interests None declared.

    • Patient consent for publication Not required.

    • Provenance and peer review Not commissioned; externally peer reviewed.

    • Data availability statement All data relevant to the study are included in the article or uploaded as online supplemental information. Name of pathogen, year and grade of evidence used in discovery are available in a table 1 in the online supplemental file.