{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T13:58:13Z","timestamp":1792677493690,"version":"4.5.0"},"reference-count":60,"publisher":"American Society of Tropical Medicine and Hygiene","issue":"4","license":[{"start":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T00:00:00Z","timestamp":1775001600000},"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":[[2026,4,1]]},"abstract":"<jats:title>ABSTRACT.<\/jats:title>\n                  <jats:p>\n                    Severe febrile illness (SFI), a major cause of child mortality in Sub-Saharan Africa (SSA), is frequently caused by bloodstream infections (BSI), increasingly caused by antimicrobial-resistant organisms. However, antimicrobial resistance (AMR) prevalence and patterns in this population are largely unknown. We conducted a prospective cohort study of children aged 28 days to 14 years with SFI at a referral hospital in Tanzania (July 2022\u2013September 2023) to determine the prevalence, pathogen profile, and AMR patterns of BSIs. Blood cultures were performed on all participants. Isolates underwent AMR testing and whole genome sequencing (WGS) to identify AMR genes and assess genetic relatedness. The association between BSI and mortality was assessed using logistic regression. Among the 392 enrolled children (median age 17.8 months), 5.2% (\n                    <jats:italic>n<\/jats:italic>\n                    = 20) had culture-confirmed BSI, with a case fatality rate of 45%. Gram-negative bacteria predominated (\n                    <jats:italic>Escherichia coli, Klebsiella pneumoniae<\/jats:italic>\n                    ), with 79% of isolates exhibiting phenotypic resistance to ceftriaxone, a first-line antimicrobial. WGS revealed extended\u2013spectrum \u03b2-lactamase genes (\n                    <jats:italic>CTX-M-15<\/jats:italic>\n                    ,\n                    <jats:italic>CTX-M-27<\/jats:italic>\n                    ) in most Enterobacterales isolates and identical isolates among 2\/4 patients with\n                    <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                    and 2\/3\n                    <jats:italic>Candida albicans<\/jats:italic>\n                    infections. Children with BSI had significantly higher mortality than those without BSI (adjusted odds ratio 3.9; 95% CI: 1.5\u201310.1,\n                    <jats:italic>P<\/jats:italic>\n                    &lt;0.01). These findings emphasize the urgent need for expanded AMR surveillance systems, empiric antibiotic regimens tailored to local AMR patterns, and culture-independent diagnostics in SSA. These data are critical for understanding the cause of severe infection and have the potential to guide policy aimed at reducing child mortality from BSI.\n                  <\/jats:p>","DOI":"10.4269\/ajtmh.25-0522","type":"journal-article","created":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T18:41:25Z","timestamp":1772131285000},"page":"767-773","source":"Crossref","is-referenced-by-count":2,"title":["Prospective Genomic Surveillance of Severe Febrile Illness in Tanzanian Children Identifies High Mortality and Resistance to First-Line Antibiotics in Bloodstream Infections"],"prefix":"10.4269","volume":"114","author":[{"given":"Teresa B.","family":"Kortz","sequence":"first","affiliation":[{"name":"University of California, San Francisco, California;"},{"name":"University of California San Francisco, Institute for Global Health Sciences, San Francisco, California;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria T.","family":"Chu","sequence":"additional","affiliation":[{"name":"University of California, San Francisco, California;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raya Y.","family":"Mussa","sequence":"additional","affiliation":[{"name":"Muhimbili National Hospital, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erasto M.","family":"Sunzula","sequence":"additional","affiliation":[{"name":"Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria M.","family":"Mlele","sequence":"additional","affiliation":[{"name":"Muhimbili National Hospital, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cecilia L.","family":"Msemwa","sequence":"additional","affiliation":[{"name":"Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lushona K.","family":"Mathias","sequence":"additional","affiliation":[{"name":"Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Namala P.","family":"Mkopi","sequence":"additional","affiliation":[{"name":"Muhimbili National Hospital, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan J.","family":"Ward","sequence":"additional","affiliation":[{"name":"University of California, San Francisco, California;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathleen S.","family":"Sun","sequence":"additional","affiliation":[{"name":"University of California, San Francisco, California;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jazmin M. Baez","family":"Maidana","sequence":"additional","affiliation":[{"name":"University of California, San Francisco, California;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anneka M.","family":"Hooft","sequence":"additional","affiliation":[{"name":"University of California, San Francisco, California;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juma A.","family":"Mfinanga","sequence":"additional","affiliation":[{"name":"Muhimbili National Hospital, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph L.","family":"DeRisi","sequence":"additional","affiliation":[{"name":"University of California, San Francisco, California;"},{"name":"Chan Zuckerberg Biohub, San Francisco, California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hendry R.","family":"Sawe","sequence":"additional","affiliation":[{"name":"Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel P.","family":"Manyahi","sequence":"additional","affiliation":[{"name":"Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles R.","family":"Langelier","sequence":"additional","affiliation":[{"name":"University of California, San Francisco, California;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2795","reference":[{"key":"b1","series-title":"Lancet","first-page":"3027","article-title":"Global, regional, and national causes of under-5 mortality in 2000\u201315: An updated systematic analysis with implications for the sustainable development goals","volume":"388","author":"Liu","year":"2016"},{"key":"b2","series-title":"Front Pediatr","first-page":"278","article-title":"Clinical presentation and outcomes among children with sepsis presenting to a public tertiary hospital in Tanzania","volume":"5","author":"Kortz","year":"2017"},{"key":"b3","series-title":"Front Microbiol","first-page":"2118","article-title":"Bacteraemia, malaria, and case fatality among children hospitalized with fever in Dar es Salaam, Tanzania","volume":"11","author":"Moyo","year":"2020"},{"key":"b4","series-title":"Antimicrob Agents Chemother","article-title":"A systematic review and meta-analysis of the prevalence of community-onset bloodstream infections among hospitalized patients in Africa and Asia","volume":"64","author":"Marchello","year":"2019"},{"key":"b5","series-title":"PLoS One","first-page":"e0127962","article-title":"Etiology of severe febrile illness in low- and middle-income countries: A systematic review","volume":"10","author":"Prasad","year":"2015"},{"key":"b6","series-title":"J Pediatric Infect Dis Soc","first-page":"11","article-title":"Systematic review of antibiotic resistance rates among gram-negative bacteria in children with sepsis in resource-limited countries","volume":"4","author":"Le Doare","year":"2015"},{"key":"b7","series-title":"Lancet","first-page":"1199","article-title":"Global burden of bacterial antimicrobial resistance 1990\u20132021: A systematic analysis with forecasts to 2050","volume":"404","year":"2024"},{"key":"b8","series-title":"Lancet Infect Dis","first-page":"e33","article-title":"Antimicrobial resistance among children in sub-Saharan Africa","volume":"18","author":"Williams","year":"2018"},{"key":"b9","article-title":"Emergency Triage Assessment and Treatment (ETAT) Manual for Participants. Geneva, Switzerland: World Health Organization.","year":"2005"},{"key":"b10","series-title":"Saudi J Anaesth","first-page":"S31","article-title":"The STROBE guidelines","volume":"13","author":"Cuschieri","year":"2019"},{"key":"b11","series-title":"CLSI Supplement M100","year":"2021"},{"key":"b12","series-title":"Gigascience","first-page":"giaa111","article-title":"IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring","volume":"9","author":"Kalantar","year":"2020"},{"key":"b13","series-title":"Nucleic Acids Res","first-page":"D517","article-title":"CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020"},{"key":"b14","series-title":"Antimicrob Agents Chemother","first-page":"3348","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013"},{"key":"b15","series-title":"Clin Infect 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tertiary care hospital in Tanzania","volume":"9","author":"Smith","year":"2021"},{"key":"b25","series-title":"J Racial Ethn Health Disparities","first-page":"1308","article-title":"Antibiotic use among hospitalized patients in Africa: A systematic review of point prevalence studies","volume":"11","author":"Abubakar","year":"2024"},{"key":"b26","series-title":"JAC Antimicrob Resist","first-page":"dlab092","article-title":"Extended-spectrum \u03b2-lactamases: An update on their characteristics, epidemiology and detection","volume":"3","author":"Castanheira","year":"2021"},{"key":"b27","series-title":"Infect Genet Evol","first-page":"185","article-title":"Current epidemiology, genetic evolution and clinical impact of extended-spectrum \u03b2-lactamase-producing Escherichia coli and Klebsiella pneumoniae.","volume":"61","author":"Chong","year":"2018"},{"key":"b28","series-title":"Trop Med Int Health","first-page":"855","article-title":"ESBL-producing Enterobacteriaceae in a rural Rwandan community: Carriage among community members, livestock, farm products and environment","volume":"28","author":"Geuther","year":"2023"},{"key":"b29","series-title":"Nat Rev Microbiol","first-page":"355","article-title":"Streptococcus pneumoniae: Transmission, colonization and invasion","volume":"16","author":"Weiser","year":"2018"},{"key":"b30","series-title":"Antimicrob Agents Chemother","first-page":"561","article-title":"Candida bloodstream infections: Comparison of species distributions and antifungal resistance patterns in community-onset and nosocomial isolates in the SENTRY Antimicrobial Surveillance Program, 2008\u20132009","volume":"55","author":"Pfaller","year":"2011"},{"key":"b1","series-title":"Lancet","first-page":"3027","article-title":"Global, regional, and national causes of under-5 mortality in 2000\u201315: An updated systematic analysis with implications for the sustainable development 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Geneva, Switzerland: World Health Organization.","year":"2005"},{"key":"b10","series-title":"Saudi J Anaesth","first-page":"S31","article-title":"The STROBE guidelines","volume":"13","author":"Cuschieri","year":"2019"},{"key":"b11","series-title":"CLSI Supplement M100","year":"2021"},{"key":"b12","series-title":"Gigascience","first-page":"giaa111","article-title":"IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring","volume":"9","author":"Kalantar","year":"2020"},{"key":"b13","series-title":"Nucleic Acids Res","first-page":"D517","article-title":"CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020"},{"key":"b14","series-title":"Antimicrob Agents Chemother","first-page":"3348","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"McArthur","year":"2013"},{"key":"b15","series-title":"Clin Infect Dis","first-page":"1179","article-title":"Investigating transfusion-related sepsis using culture-independent metagenomic sequencing","volume":"71","author":"Crawford","year":"2020"},{"key":"b16","article-title":"SPID: SNP Pipeline for Infectious Disease","year":"2024"},{"key":"b17","series-title":"Bioinformatics","first-page":"3094","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018"},{"key":"b18","series-title":"Bioinformatics","first-page":"1312","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014"},{"key":"b19","series-title":"J Biomed Inform","first-page":"377","article-title":"Research electronic data capture (REDCap) \u2013 A metadata-driven methodology and workflow process for providing translational research informatics support","volume":"42","author":"Paul","year":"2009"},{"key":"b20","series-title":"J Infect Dis","first-page":"1834","article-title":"The Lambarene Organ Dysfunction Score (LODS) is a simple clinical predictor of fatal malaria in African children","volume":"200","author":"Helbok","year":"2009"},{"key":"b21","series-title":"BMJ","first-page":"361","article-title":"Prognostic indicators of early and late death in children admitted to district hospital in Kenya: Cohort study","volume":"326","author":"Berkley","year":"2003"},{"key":"b22","series-title":"Ministry of Health CD, Gender, Elderly and Children","year":"2021"},{"key":"b23","series-title":"PLoS Med","first-page":"e1004179","article-title":"Patterns of antibiotic use, pathogens, and prediction of mortality in hospitalized neonates and young infants with sepsis: A global neonatal sepsis observational cohort study (NeoOBS)","volume":"20","author":"Russell","year":"2023"},{"key":"b24","series-title":"Front Pediatr","first-page":"764163","article-title":"Delayed presentation and mortality in children with sepsis in a public tertiary care hospital in Tanzania","volume":"9","author":"Smith","year":"2021"},{"key":"b25","series-title":"J Racial Ethn Health Disparities","first-page":"1308","article-title":"Antibiotic use among hospitalized patients in Africa: A systematic review of point prevalence studies","volume":"11","author":"Abubakar","year":"2024"},{"key":"b26","series-title":"JAC Antimicrob Resist","first-page":"dlab092","article-title":"Extended-spectrum \u03b2-lactamases: An update on their characteristics, epidemiology and detection","volume":"3","author":"Castanheira","year":"2021"},{"key":"b27","series-title":"Infect Genet Evol","first-page":"185","article-title":"Current epidemiology, genetic evolution and clinical impact of extended-spectrum \u03b2-lactamase-producing Escherichia coli and Klebsiella pneumoniae.","volume":"61","author":"Chong","year":"2018"},{"key":"b28","series-title":"Trop Med Int Health","first-page":"855","article-title":"ESBL-producing Enterobacteriaceae in a rural Rwandan community: Carriage among community members, livestock, farm products and environment","volume":"28","author":"Geuther","year":"2023"},{"key":"b29","series-title":"Nat Rev Microbiol","first-page":"355","article-title":"Streptococcus pneumoniae: Transmission, colonization and invasion","volume":"16","author":"Weiser","year":"2018"},{"key":"b30","series-title":"Antimicrob Agents Chemother","first-page":"561","article-title":"Candida bloodstream infections: Comparison of species distributions and antifungal resistance patterns in community-onset and nosocomial isolates in the SENTRY Antimicrobial Surveillance Program, 2008\u20132009","volume":"55","author":"Pfaller","year":"2011"}],"container-title":["The American Journal of Tropical Medicine and 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