Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics

Séverine Matheus; Charlotte Balière; Véronique Hourdel; Jean-Michel Thiberge; Olivia Cheny; Magalie Demar; Stéphanie Houcke; Didier Hommel; Jean-Claude Manuguerra; Valérie Caro; Hatem Kallel

doi:10.5455/JMID.20240903122758

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Research Article
Online Published: 30 Dec 2024

J Microbiol Infect Dis. 2024; 14(4): 178-185

doi: 10.5455/JMID.20240903122758

Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics

Séverine Matheus, Charlotte Balière, Véronique Hourdel, Jean-michel Thiberge, Olivia Cheny, Magalie Demar, Stéphanie Houcke, Didier Hommel, Jean-claude Manuguerra, Valérie Caro, Hatem Kallel.

Abstract
Background:
Tropical infectious diseases pose a significant burden on global public health, exacerbated by the emergence of new pathogens. French Guiana (FG), a French overseas department in northeastern South America, presents favorable conditions for the emergence of zoonotic pathogens due to its tropical climate and diverse ecosystems. Over the past two decades, various emerging zoonotic pathogens have been detected in patients with severe infections, though, many other severe human infectious diseases remain undocumented.

Aim:
This prospective pilot study aims to identify infectious pathogens responsible for severe infections in French Guiana using routine diagnostic tests and metagenomic approach.

Methods:
This study was conducted from July 2013 to December 2015. It included consenting patients of all ages and sexes admitted to the ICU for severe infections in FG. Biological samples were collected based on clinical presentation (plasma, serum, nasopharyngeal swab, broncho-alveolar liquid, cerebrospinal fluid). All samples were collected in duplicate for routine microbiological tests and potential metagenomic sequencing when initial investigations proved negative.

Results:
During the study period, 10.9% (89/813) of ICU admissions were due to community-acquired sepsis. Of these, 22/89 (24.7%) were enrolled. Routine diagnosis tests identified a causal pathogen in 54.5% (12/22) of cases, including arboviruses, influenza virus, Trypanosoma cruzi, Coxiella burnetti, enterovirus, Histoplasma sp, and Leptospira sp. Five of the 22 patients had an unfavorable outcome. Genomic sequence analyses allowed identification of the first human case of Leptospira santarosai in the region.

Conclusion:
This pilot study underscores the array of pathogens causing severe infections in French Guiana. It emphasizes the need to investigate sepsis of unknown origin in a region susceptible to pathogen emergence or reemergence.

Key words: Infectious diseases, ICU, Diagnostic, First-line tests, Metagenomic approach

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How to Cite this Article

Pubmed Style

Matheus S, Balière C, Hourdel V, Thiberge J, Cheny O, Demar M, Houcke S, Hommel D, Manuguerra J, Caro V, Kallel H. Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics. J Microbiol Infect Dis. 2024; 14(4): 178-185.

doi:10.5455/JMID.20240903122758

Web Style

Matheus S, Balière C, Hourdel V, Thiberge J, Cheny O, Demar M, Houcke S, Hommel D, Manuguerra J, Caro V, Kallel H. Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics. https://www.jmidonline.org/?mno=218584 [Access: June 27, 2026].

doi:10.5455/JMID.20240903122758

AMA (American Medical Association) Style

Matheus S, Balière C, Hourdel V, Thiberge J, Cheny O, Demar M, Houcke S, Hommel D, Manuguerra J, Caro V, Kallel H. Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics. J Microbiol Infect Dis. 2024; 14(4): 178-185.

doi:10.5455/JMID.20240903122758

Vancouver/ICMJE Style

doi:10.5455/JMID.20240903122758

Harvard Style

Matheus, S., Balière, . C., Hourdel, . V., Thiberge, . J., Cheny, . O., Demar, . M., Houcke, . S., Hommel, . D., Manuguerra, . J., Caro, . V. & Kallel, . H. (2024) Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics. J Microbiol Infect Dis, 14 (4), 178-185.

doi:10.5455/JMID.20240903122758

Turabian Style

Matheus, Séverine, Charlotte Balière, Véronique Hourdel, Jean-michel Thiberge, Olivia Cheny, Magalie Demar, Stéphanie Houcke, Didier Hommel, Jean-claude Manuguerra, Valérie Caro, and Hatem Kallel. 2024. Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics. Journal of Microbiology and Infectious Diseases, 14 (4), 178-185.

doi:10.5455/JMID.20240903122758

Chicago Style

Matheus, Séverine, Charlotte Balière, Véronique Hourdel, Jean-michel Thiberge, Olivia Cheny, Magalie Demar, Stéphanie Houcke, Didier Hommel, Jean-claude Manuguerra, Valérie Caro, and Hatem Kallel. "Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics." Journal of Microbiology and Infectious Diseases 14 (2024), 178-185.

doi:10.5455/JMID.20240903122758

MLA (The Modern Language Association) Style

Matheus, Séverine, Charlotte Balière, Véronique Hourdel, Jean-michel Thiberge, Olivia Cheny, Magalie Demar, Stéphanie Houcke, Didier Hommel, Jean-claude Manuguerra, Valérie Caro, and Hatem Kallel. "Microbiological investigations of severe tropical infections in French Amazonia: A prospective pilot study of first-line tests and metagenomics." Journal of Microbiology and Infectious Diseases 14.4 (2024), 178-185. Print.

doi:10.5455/JMID.20240903122758

APA (American Psychological Association) Style

doi:10.5455/JMID.20240903122758

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