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

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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.

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