{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T23:41:11Z","timestamp":1788306071036,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.pntd.0006156","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,1,25]],"date-time":"2018-01-25T00:00:00Z","timestamp":1516838400000}}],"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2018,1,12]],"date-time":"2018-01-12T00:00:00Z","timestamp":1515715200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100006090","name":"Center for Global Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006090","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI090882"],"award-info":[{"award-number":["AI090882"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HD054314-06"],"award-info":[{"award-number":["HD054314-06"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["Grant. HD054314-06"],"award-info":[{"award-number":["Grant. HD054314-06"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"DOI":"10.1371\/journal.pntd.0006156","type":"journal-article","created":{"date-parts":[[2018,1,12]],"date-time":"2018-01-12T13:29:31Z","timestamp":1515763771000},"page":"e0006156","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":50,"title":["Multi-drug resistant non-typhoidal Salmonella associated with invasive disease in western Kenya"],"prefix":"10.1371","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8247-2172","authenticated-orcid":true,"given":"Adam","family":"Akullian","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel M.","family":"Montgomery","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4301-1573","authenticated-orcid":true,"given":"Grace","family":"John-Stewart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel I.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hillary S.","family":"Hayden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew C.","family":"Radey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyle R.","family":"Hager","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer R.","family":"Verani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John Benjamin","family":"Ochieng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Juma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Katieno","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barry","family":"Fields","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Godfrey","family":"Bigogo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allan","family":"Audi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judd","family":"Walson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,1,12]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"2489","DOI":"10.1016\/S0140-6736(11)61752-2","article-title":"Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa","volume":"379","author":"NA Feasey","year":"2012","journal-title":"Lancet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1056\/NEJMoa040275","article-title":"Bacteremia among Children Admitted to a Rural Hospital in Kenya","volume":"352","author":"JA Berkley","year":"2005","journal-title":"New England Journal of Medicine"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1086\/603553","article-title":"Invasive non-Typhi Salmonella disease in Africa","volume":"49","author":"SC Morpeth","year":"2009","journal-title":"Clin Infect Dis"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/0140-6736(90)92096-Z","article-title":"Life-threatening bacteraemia in HIV-1 seropositive adults admitted to hospital in Nairobi, Kenya","volume":"336","author":"CF Gilks","year":"1990","journal-title":"The Lancet"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1097\/00002030-200208160-00009","article-title":"Non-typhoidal salmonella bacteraemia among HIV-infected Malawian adults: high mortality and frequent recrudescence","volume":"16","author":"MA Gordon","year":"2002","journal-title":"Aids"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1177\/004947550403400404","article-title":"Non-typhoidal salmonella bacteraemia\u2014an under-recognized feature of AIDS in African adults","volume":"34","author":"AM Kankwatira","year":"2004","journal-title":"Tropical doctor"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.jinf.2008.03.012","article-title":"Salmonella infections in immunocompromised adults","volume":"56","author":"MA Gordon","year":"2008","journal-title":"The Journal of infection"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1001\/archinte.1985.00360040092021","article-title":"Salmonella infections in patients with acquired immunodeficiency syndrome","volume":"145","author":"S Profeta","year":"1985","journal-title":"Archives of internal medicine"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1520","DOI":"10.1128\/IAI.00887-09","article-title":"Both hemolytic anemia and malaria parasite-specific factors increase susceptibility to Nontyphoidal Salmonella enterica serovar typhimurium infection in mice","volume":"78","author":"CM Roux","year":"2010","journal-title":"Infection and immunity"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e10568","DOI":"10.1371\/journal.pone.0010568","article-title":"A decline in the incidence of invasive non-typhoidal Salmonella infection in The Gambia temporally associated with a decline in malaria infection","volume":"5","author":"G Mackenzie","year":"2010","journal-title":"PloS one"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1093\/infdis\/155.6.1319","article-title":"Plasmodium falciparum malaria and Salmonella infections in Gambian children","volume":"155","author":"DC Mabey","year":"1987","journal-title":"The Journal of infectious diseases"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1097\/00006454-200012000-00016","article-title":"Nontyphoidal Salmonella infections of children in tropical Africa","volume":"19","author":"SM Graham","year":"2000","journal-title":"The Pediatric infectious disease journal"},{"key":"ref13","article-title":"Malaria-associated L-Arginine deficiency induces mast cell-associated disruption to intestinal barrier defenses against non-typhoidal Salmonella bacteremia","author":"JY Chau","year":"2013","journal-title":"Infection and immunity"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1097\/01.inf.0000202066.02212.ff","article-title":"Salmonella bacteremia in Kenyan children","volume":"25","author":"AJ Brent","year":"2006","journal-title":"The Pediatric infectious disease journal"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1891","DOI":"10.1016\/j.micinf.2005.12.020","article-title":"The clonal spread of multidrug-resistant non-typhi Salmonella serotypes","volume":"8","author":"P Butaye","year":"2006","journal-title":"Microbes and infection \/ Institut Pasteur"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"2279","DOI":"10.1101\/gr.091017.109","article-title":"Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype","volume":"19","author":"RA Kingsley","year":"2009","journal-title":"Genome research"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1086\/529146","article-title":"Epidemics of invasive Salmonella enterica serovar enteritidis and S. enterica Serovar typhimurium infection associated with multidrug resistance among adults and children in Malawi","volume":"46","author":"MA Gordon","year":"2008","journal-title":"Clin Infect Dis"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"585","DOI":"10.3855\/jidc.549","article-title":"Genotypic and demographic characterization of invasive isolates of Salmonella Typhimurium in HIV co-infected patients in South Africa","volume":"3","author":"KH Keddy","year":"2009","journal-title":"Journal of infection in developing countries"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.ijantimicag.2004.08.015","article-title":"Increasing prevalence of multidrug-resistant non-typhoidal salmonellae, Kenya, 1994\u20132003","volume":"25","author":"S Kariuki","year":"2005","journal-title":"International journal of antimicrobial agents"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1086\/500320","article-title":"Outbreak of multidrug-resistant Salmonella enterica serotype Typhimurium Definitive Type 104 infection linked to commercial ground beef, northeastern United States, 2003\u20132004","volume":"42","author":"AM Dechet","year":"2006","journal-title":"Clin Infect Dis"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e42085","DOI":"10.1371\/journal.pone.0042085","article-title":"Genotypic homogeneity of multidrug resistant s. Typhimurium infecting distinct adult and childhood susceptibility groups in Blantyre, Malawi","volume":"7","author":"CL Msefula","year":"2012","journal-title":"PloS one"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1038\/ng.2423","article-title":"Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa","volume":"44","author":"CK Okoro","year":"2012","journal-title":"Nature genetics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1099\/jmm.0.46375-0","article-title":"Invasive multidrug-resistant non-typhoidal Salmonella infections in Africa: zoonotic or anthroponotic transmission?","volume":"55","author":"S Kariuki","year":"2006","journal-title":"J Med Microbiol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e2487","DOI":"10.1371\/journal.pntd.0002487","article-title":"Invasive non-typhoidal Salmonella typhimurium ST313 are not host-restricted and have an invasive phenotype in experimentally infected chickens","volume":"7","author":"BN Parsons","year":"2013","journal-title":"PLoS Negl Trop Dis"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1186\/1471-2180-6-101","article-title":"Characterisation of community acquired non-typhoidal Salmonella from bacteraemia and diarrhoeal infections in children admitted to hospital in Nairobi, Kenya","volume":"6","author":"S Kariuki","year":"2006","journal-title":"BMC microbiology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"633","DOI":"10.4314\/eamj.v79i12.8670","article-title":"Non-typhi salmonella in children with severe malaria","volume":"79","author":"JO Oundo","year":"2002","journal-title":"East African medical journal"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/S1473-3099(10)70072-4","article-title":"Community-acquired bloodstream infections in Africa: a systematic review and meta-analysis","volume":"10","author":"EA Reddy","year":"2010","journal-title":"The Lancet infectious diseases"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e31237","DOI":"10.1371\/journal.pone.0031237","article-title":"Differing burden and epidemiology of non-Typhi Salmonella bacteremia in rural and urban Kenya, 2006\u20132009","volume":"7","author":"C Tabu","year":"2012","journal-title":"PloS one"},{"issue":"01","key":"ref29","doi-asserted-by":"crossref","DOI":"10.3855\/jidc.3080","article-title":"Using next generation sequencing to tackle non-typhoidal Salmonella infections","volume":"7","author":"J Wain","year":"2013","journal-title":"The Journal of Infection in Developing Countries"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1093\/ije\/dyp374","article-title":"Evaluation of the optimal recall period for disease symptoms in home-based morbidity surveillance in rural and urban Kenya","volume":"39","author":"DR Feikin","year":"2010","journal-title":"International journal of epidemiology"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.4269\/ajtmh.2005.73.1151","article-title":"Health and demographic surveillance in rural western Kenya: a platform for evaluating interventions to reduce morbidity and mortality from infectious diseases","volume":"73","author":"K Adazu","year":"2005","journal-title":"The American journal of tropical medicine and hygiene"},{"key":"ref32","article-title":"zscore06: Stata command for the calculation of anthropometric z-scores using the 2006 WHO child growth standards","author":"JL Leroy","year":"2011"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1086\/505866","article-title":"Surveillance for bacterial diarrhea and antimicrobial resistance in rural western Kenya, 1997\u20132003","volume":"43","author":"JT Brooks","year":"2006","journal-title":"Clin Infect Dis"},{"key":"ref34","article-title":"Performance standards for antimicrobial susceptibility testing; seventeenth informational supplement","year":"2007"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e1002776","DOI":"10.1371\/journal.ppat.1002776","article-title":"Multilocus sequence typing as a replacement for serotyping in Salmonella enterica","volume":"8","author":"M Achtman","year":"2012","journal-title":"PLoS Pathog"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e81760","DOI":"10.1371\/journal.pone.0081760","article-title":"When whole-genome alignments just won&apos;t work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes","volume":"8","author":"SN Gardner","year":"2013","journal-title":"PloS one"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PloS one"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1093\/sysbio\/sys062","article-title":"Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks","volume":"61","author":"DH Huson","year":"2012","journal-title":"Systematic biology"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e00154","DOI":"10.1128\/mBio.00154-16","article-title":"Genomic Analysis of Salmonella enterica Serovar Typhimurium Characterizes Strain Diversity for Recent U.S. Salmonellosis Cases and Identifies Mutations Linked to Loss of Fitness under Nitrosative and Oxidative Stress","volume":"7","author":"HS Hayden","year":"2016","journal-title":"mBio"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"438","DOI":"10.3855\/jidc.158","article-title":"Invasive salmonellosis in Malawi","volume":"2","author":"MA Gordon","year":"2008","journal-title":"Journal of infection in developing countries"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"S363","DOI":"10.1093\/cid\/civ691","article-title":"Three Epidemics of Invasive Multidrug-Resistant Salmonella Bloodstream Infection in Blantyre, Malawi, 1998\u20132014","volume":"61","author":"NA Feasey","year":"2015","journal-title":"Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/ng.3644","article-title":"Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings","volume":"48","author":"NA Feasey","year":"2016","journal-title":"Nature genetics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/cid\/cir1032","article-title":"High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease","volume":"54","author":"CK Okoro","year":"2012","journal-title":"Clin Infect Dis"},{"key":"ref45","first-page":"107","article-title":"Microbial Surface Components and Toxins in Relation to Pathogenesis","volume":"51","author":"M Rhen","year":"1991"},{"key":"ref46","first-page":"177","article-title":"The virulence plasmids of Salmonella","volume":"2","author":"R Rotger","year":"1999","journal-title":"International microbiology: the official journal of the Spanish Society for Microbiology"},{"issue":"Suppl 4","key":"ref47","doi-asserted-by":"crossref","first-page":"S317","DOI":"10.1093\/cid\/civ711","article-title":"Epidemiology and Genomics of Invasive Nontyphoidal Salmonella Infections in Kenya","volume":"61","author":"S Kariuki","year":"2015","journal-title":"Clin Infect Dis"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1097\/01.aids.0000174449.32756.c7","article-title":"Cotrimoxazole prophylaxis by HIV-infected persons in Uganda reduces morbidity and mortality among HIV-uninfected family members","volume":"19","author":"J Mermin","year":"2005","journal-title":"Aids"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"3756","DOI":"10.1128\/AAC.01409-09","article-title":"Impact of cotrimoxazole on carriage and antibiotic resistance of Streptococcus pneumoniae and Haemophilus influenzae in HIV-infected children in Zambia","volume":"54","author":"DM Mwenya","year":"2010","journal-title":"Antimicrobial agents and chemotherapy"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"320","DOI":"10.4269\/ajtmh.2008.79.320","article-title":"Does Cotrimoxazole Prophylaxis for the Prevention of HIV-Associated Opportunistic Infections Select for Resistant Pathogens in Kenyan Adults?","volume":"79","author":"MJ Hamel","year":"2008","journal-title":"The American journal of tropical medicine and hygiene"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"859","DOI":"10.3201\/eid1106.041017","article-title":"International Salmonella Typhimurium DT104 infections, 1992\u20132001","volume":"11","author":"M Helms","year":"2005","journal-title":"Emerging infectious diseases"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"490","DOI":"10.3201\/eid0805.010267","article-title":"Excess mortality associated with antimicrobial drug-resistant Salmonella typhimurium","volume":"8","author":"M Helms","year":"2002","journal-title":"Emerging infectious diseases"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1111\/nyas.12380","article-title":"Antibacterial resistance in sub-Saharan Africa: an underestimated emergency","volume":"1323","author":"S Kariuki","year":"2014","journal-title":"Annals of the New York Academy of Sciences"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0006156","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,1,25]],"date-time":"2018-01-25T00:00:00Z","timestamp":1516838400000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pntd.0006156","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,9]],"date-time":"2019-10-09T05:28:58Z","timestamp":1570598938000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0006156"}},"subtitle":[],"editor":[{"given":"Nicholas","family":"Feasey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,1,12]]},"references-count":53,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,1,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0006156","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pntd.0006156","asserted-by":"object"}]},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,12]]}}}