{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T17:03:56Z","timestamp":1780333436240,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pntd.0007297","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T00:00:00Z","timestamp":1561420800000}}],"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2019,6,6]],"date-time":"2019-06-06T00:00:00Z","timestamp":1559779200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"DOI":"10.1371\/journal.pntd.0007297","type":"journal-article","created":{"date-parts":[[2019,6,6]],"date-time":"2019-06-06T17:29:43Z","timestamp":1559842183000},"page":"e0007297","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Genetic changes associated with the temporal shift in invasive non-typhoidal Salmonella serovars in Bamako Mali"],"prefix":"10.1371","volume":"13","author":[{"given":"Kristin","family":"Bornstein","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon M.","family":"Tennant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tracy H.","family":"Hazen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John D.","family":"Sorkin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milagritos D.","family":"Tapia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samba O.","family":"Sow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uma","family":"Onwuchekwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5721-5040","authenticated-orcid":true,"given":"Myron M.","family":"Levine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7337-7154","authenticated-orcid":true,"given":"David A.","family":"Rasko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,6,6]]},"reference":[{"issue":"8","key":"ref1","article-title":"Outbreak-associated Salmonella enterica Serotypes and Food Commodities, United States, 1998\u20132008","volume":"19","author":"B Jackson","year":"2013","journal-title":"Emerging Infectious Disease journal\u2014CDC"},{"issue":"2","key":"ref2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1086\/318457","article-title":"Nontyphoidal salmonellosis","volume":"32","author":"D Acheson","year":"2001","journal-title":"Clin Infect Dis"},{"issue":"4","key":"ref3","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1086\/427263","article-title":"Antimicrobial-resistant nontyphoidal Salmonella is associated with excess bloodstream infections and hospitalizations","volume":"191","author":"JK Varma","year":"2005","journal-title":"J Infect Dis"},{"issue":"12","key":"ref4","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"},{"issue":"3","key":"ref5","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1016\/S0035-9203(00)90337-7","article-title":"Clinical presentation of non-typhoidal Salmonella bacteraemia in Malawian children","volume":"94","author":"SM Graham","year":"2000","journal-title":"Trans R Soc Trop Med Hyg"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/1471-2334-10-95","article-title":"Salmonella enterica bacteraemia: a multi-national population-based cohort study","volume":"10","author":"KB Laupland","year":"2010","journal-title":"BMC Infect Dis"},{"issue":"4","key":"ref7","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1172\/JCI33998","article-title":"The neglected role of antibody in protection against bacteremia caused by nontyphoidal strains of Salmonella in African children","volume":"118","author":"CA MacLennan","year":"2008","journal-title":"J Clin Invest"},{"issue":"6","key":"ref8","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1086\/511437","article-title":"Bacteremia in Malawian children with severe malaria: prevalence, etiology, HIV coinfection, and outcome","volume":"195","author":"RN Bronzan","year":"2007","journal-title":"J Infect Dis"},{"issue":"3","key":"ref9","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":"Pediatr Infect Dis J"},{"issue":"7","key":"ref10","doi-asserted-by":"crossref","first-page":"e0003979","DOI":"10.1371\/journal.pntd.0003979","article-title":"Modelling the contributions of malaria, HIV, malnutrition and rainfall to the decline in paediatric invasive non-typhoidal Salmonella disease in Malawi","volume":"9","author":"NA Feasey","year":"2015","journal-title":"PLoS Negl Trop Dis"},{"issue":"3","key":"ref11","doi-asserted-by":"crossref","first-page":"e0003611","DOI":"10.1371\/journal.pntd.0003611","article-title":"Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa","volume":"9","author":"CK Okoro","year":"2015","journal-title":"PLoS Negl Trop Dis"},{"issue":"11","key":"ref12","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":"Nat Genet"},{"issue":"12","key":"ref13","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 Res"},{"issue":"9835","key":"ref14","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":"The Lancet"},{"key":"ref15","article-title":"Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings","author":"NA Feasey","year":"2016","journal-title":"Nat Genet"},{"issue":"3","key":"ref16","doi-asserted-by":"crossref","first-page":"e621","DOI":"10.1371\/journal.pntd.0000621","article-title":"Identification by PCR of non-typhoidal Salmonella enterica serovars associated with invasive infections among febrile patients in Mali","volume":"4","author":"SM Tennant","year":"2010","journal-title":"PLoS Negl Trop Dis"},{"issue":"6","key":"ref17","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1128\/CVI.00106-16","article-title":"Opsonophagocytic Assay To Evaluate Immunogenicity of Nontyphoidal Salmonella Vaccines","volume":"23","author":"G Ramachandran","year":"2016","journal-title":"Clin Vaccine Immunol"},{"issue":"11","key":"ref18","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1099\/jmm.0.47416-0","article-title":"Molecular epidemiology of community-acquired invasive non-typhoidal Salmonella among children aged 2\u201329 months in rural Gambia and discovery of a new serovar, Salmonella enterica Dingiri","volume":"56","author":"UN Ikumapayi","year":"2007","journal-title":"J Med Microbiol"},{"issue":"suppl 4","key":"ref19","doi-asserted-by":"crossref","first-page":"S332","DOI":"10.1093\/cid\/civ729","article-title":"Invasive nontyphoidal Salmonella infections among children in Mali, 2002\u20132014: microbiological and epidemiologic features guide vaccine development","volume":"61","author":"MD Tapia","year":"2015","journal-title":"Clin Infect Dis"},{"issue":"4","key":"ref20","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1007\/BF01719658","article-title":"Salmonella typhimurium andSalmonella enteritidis: Changing epidemiology from 1973 until 1992","volume":"10","author":"F Le Bacq","year":"1994","journal-title":"Eur J Epidemiol"},{"issue":"2","key":"ref21","first-page":"e00929","article-title":"Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut","volume":"5","author":"S-P Nuccio","year":"2014","journal-title":"MBio"},{"issue":"3","key":"ref22","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1073\/pnas.1423499112","article-title":"Reconstructing pathogen evolution from the ruins","volume":"112","author":"S-P Nuccio","year":"2015","journal-title":"Proc Natl Acad Sci"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/1471-2105-12-356","article-title":"CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing","volume":"12","author":"SV Angiuoli","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"ref24","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"D Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"ref25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-6-2","article-title":"Visualization of comparative genomic analyses by BLAST score ratio","volume":"6","author":"DA Rasko","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e332","DOI":"10.7717\/peerj.332","article-title":"The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.","volume":"2","author":"JW Sahl","year":"2014","journal-title":"PeerJ"},{"issue":"3","key":"ref27","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1093\/bioinformatics\/btq665","article-title":"Mugsy: fast multiple alignment of closely related whole genomes","volume":"27","author":"SV Angiuoli","year":"2011","journal-title":"Bioinformatics"},{"key":"ref28","article-title":"bx-python","author":"J Taylor","year":"2016","journal-title":"bx-python"},{"issue":"23","key":"ref29","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"PD Schloss","year":"2009","journal-title":"Appl Environ Microbiol"},{"issue":"9","key":"ref30","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"A Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"ref31","article-title":"FigTree","year":"2007","journal-title":"Molecular Evolution, Phylogenetics and Epidemiology"},{"issue":"12","key":"ref32","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"M Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"ref33","article-title":"Resistance Index of Penicillin-Resistant Bacteria to Various Physicochemical Agents","author":"M Kazemi","year":"2012","journal-title":"ISRN Microbiol"},{"key":"ref34","article-title":"Disk Diffusion Supplemental Tables","year":"2011"},{"issue":"6","key":"ref35","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":"DCW Mabey","year":"1987","journal-title":"J Infect Dis"},{"issue":"4","key":"ref36","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":"Infect Immun"},{"issue":"1","key":"ref37","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/nm.2601","article-title":"Malaria impairs resistance to Salmonella through heme- and heme oxygenase-dependent dysfunctional granulocyte mobilization","volume":"18","author":"AJ Cunnington","year":"2012","journal-title":"Nat Med"},{"issue":"1","key":"ref38","doi-asserted-by":"crossref","first-page":"108","DOI":"10.4269\/ajtmh.1992.47.108","article-title":"Quinine with tetracycline for the treatment of drug-resistant falciparum malaria in Thailand","volume":"47","author":"G Watt","year":"1992","journal-title":"Am J Trop Med Hyg"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0007297","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T00:00:00Z","timestamp":1561420800000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pntd.0007297","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T11:57:57Z","timestamp":1589025477000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0007297"}},"subtitle":[],"editor":[{"given":"Thomas C.","family":"Darton","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,6,6]]},"references-count":38,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2019,6,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0007297","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pntd.0007297","asserted-by":"object"}]},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,6,6]]}}}