{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T15:27:02Z","timestamp":1772724422785,"version":"3.50.1"},"reference-count":34,"publisher":"American Society of Tropical Medicine and Hygiene","issue":"6","license":[{"start":{"date-parts":[[2023,12,6]],"date-time":"2023-12-06T00:00:00Z","timestamp":1701820800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,6]]},"abstract":"<jats:title>ABSTRACT.<\/jats:title>\n<jats:p>Infectious conjunctivitis outbreaks remain a public health burden. This study focuses on the pathogen and antimicrobial resistance (AMR) profiles identified in Niger. Sixty-two patients with acute infectious conjunctivitis who presented to health posts were enrolled from December 2021 to May 2022. Nasal and conjunctival swabs were obtained from each patient. Unbiased RNA deep sequencing (RNA-seq) was used to identify associated pathogens. A pathogen was identified in 39 patients (63%; 95% CI, 50\u201374). Of those, an RNA virus was detected in 23 patients (59%; 95% CI, 43\u201373). RNA viruses were diverse and included human coronaviruses (HCoVs): SARS-CoV-2, HCoV-229E, HCoV-HKU1, and HCoV-OC43. A DNA virus was identified in 11 patients (28%; 95% CI, 17\u201344). Of those, four patients had a coinfection with an RNA virus and two patients had a coinfection with both an RNA virus and a bacterium. DNA viruses were predominantly human herpesvirus (cytomegalovirus, Epstein\u2013Barr virus, human herpesvirus 8) and human adenovirus species B, C, and F. Eighteen patients (46%; 95% CI, 32\u201361) had a bacteria-associated infection that included <jats:italic>Haemophilus influenza<\/jats:italic>, <jats:italic>Haemophilus aegyptius<\/jats:italic>, <jats:italic>Staphylococcus aureus<\/jats:italic>, <jats:italic>Streptococcus pneumoniae<\/jats:italic>, and <jats:italic>Moraxella<\/jats:italic> spp. Antimicrobial resistance determinants were detected in either the conjunctiva or nasal samples of 20 patients (32%; 95% CI, 22\u201345) and were found to be more diverse in the nose (Shannon alpha diversity, 1.12 [95% CI, 1.05\u20131.26] versus 1.02 [95% CI, 1.00\u20131.05], <jats:italic>P<\/jats:italic> = 0.01). These results suggest the potential utility of leveraging RNA-seq to surveil pathogens and AMR for ocular infections.<\/jats:p>","DOI":"10.4269\/ajtmh.23-0498","type":"journal-article","created":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T18:57:16Z","timestamp":1699297036000},"page":"1333-1338","source":"Crossref","is-referenced-by-count":3,"title":["Comprehensive Profile of Pathogens and Antimicrobial Resistance in Conjunctivitis Cases from Niger"],"prefix":"10.4269","volume":"109","author":[{"given":"Abdou","family":"Amza","sequence":"first","affiliation":[{"name":"Programme Nationale de Sant\u00e9 Oculaire, Niamey, Niger;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beido","family":"Nassirou","sequence":"additional","affiliation":[{"name":"Programme Nationale de Sant\u00e9 Oculaire, Niamey, Niger;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boubacar","family":"Kadri","sequence":"additional","affiliation":[{"name":"Programme Nationale de Sant\u00e9 Oculaire, Niamey, Niger;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saley","family":"Ali","sequence":"additional","affiliation":[{"name":"Programme Nationale de Sant\u00e9 Oculaire, Niamey, Niger;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boubacar","family":"Mariama","sequence":"additional","affiliation":[{"name":"Programme Nationale de Sant\u00e9 Oculaire, Niamey, Niger;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ciss\u00e9 Mamadou","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"Programme Nationale de Sant\u00e9 Oculaire, Niamey, Niger;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lamine Aboubacar","family":"Roufaye","sequence":"additional","affiliation":[{"name":"Programme Nationale de Sant\u00e9 Oculaire, Niamey, Niger;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elodie","family":"Lebas","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emily","family":"Colby","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lina","family":"Zhong","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cindi","family":"Chen","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin","family":"Ruder","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danny","family":"Yu","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"YuHeng","family":"Liu","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Abraham","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aaron","family":"Chang","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lina","family":"Mai","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Armin","family":"Hinterwirth","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerami D.","family":"Seitzman","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"},{"name":"Department of Ophthalmology, University of California, San Francisco, California;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas M.","family":"Lietman","sequence":"additional","affiliation":[{"name":"Francis I. Proctor Foundation, University of California, San Francisco, California;"},{"name":"Department of Ophthalmology, University of California, San Francisco, California;"},{"name":"Department of Epidemiology and Biostatistics, University of California, San Francisco, California;"},{"name":"Institute for Global Health Sciences, University of California, San Francisco, California"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thuy","family":"Doan","sequence":"additional","affiliation":[{"name":"Francis I. 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