{"id":"https://openalex.org/W7214587489","doi":"https://doi.org/10.1002/mbo3.70408","title":"Genomic Detection of Multidrug\u2010Resistant H58 ST1 Salmonella Typhi in a South African Urban Waterway Reveals Epidemiological Links With Clinical Isolates","display_name":"Genomic Detection of Multidrug\u2010Resistant H58 ST1 Salmonella Typhi in a South African Urban Waterway Reveals Epidemiological Links With Clinical Isolates","publication_year":2026,"publication_date":"2026-09-27","ids":{"openalex":"https://openalex.org/W7214587489","doi":"https://doi.org/10.1002/mbo3.70408","pmid":"https://pubmed.ncbi.nlm.nih.gov/42802586","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13617252"},"language":"en","primary_location":{"id":"doi:10.1002/mbo3.70408","doi":"https://doi.org/10.1002/mbo3.70408","is_oa":true,"landing_page_url":"https://doi.org/10.1002/mbo3.70408","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mbo3.70408","source":{"id":"https://openalex.org/S4210229223","display_name":"MicrobiologyOpen","issn_l":"2045-8827","issn":["2045-8827"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"MicrobiologyOpen","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mbo3.70408","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022048955","display_name":"Sanelisiwe Thinasonke Duze","orcid":"https://orcid.org/0000-0002-3909-4628","observed_orcids":["https://orcid.org/0000-0002-3909-4628"]},"institutions":[{"id":"https://openalex.org/I107920810","display_name":"National Health Laboratory Service","ror":"https://ror.org/00znvbk37","country_code":"ZA","type":"government","lineage":["https://openalex.org/I107920810"]},{"id":"https://openalex.org/I192619145","display_name":"University of the Witwatersrand","ror":"https://ror.org/03rp50x72","country_code":"ZA","type":"education","lineage":["https://openalex.org/I192619145"]}],"countries":["ZA"],"is_corresponding":true,"raw_author_name":"Sanelisiwe Thinasonke Duze","raw_affiliation_strings":["Department of Clinical Microbiology and Infectious Diseases, National Health Laboratory Service and Faculty of Health Sciences University of Witwatersrand Johannesburg South Africa"],"raw_orcid":"https://orcid.org/0000-0002-3909-4628","affiliations":[{"raw_affiliation_string":"Department of Clinical Microbiology and Infectious Diseases, National Health Laboratory Service and Faculty of Health Sciences University of Witwatersrand Johannesburg South Africa","institution_ids":["https://openalex.org/I107920810","https://openalex.org/I192619145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065460322","display_name":"Musa D. Marimani","orcid":"https://orcid.org/0000-0002-6007-586X","observed_orcids":["https://orcid.org/0000-0002-6007-586X"]},"institutions":[{"id":"https://openalex.org/I192619145","display_name":"University of the Witwatersrand","ror":"https://ror.org/03rp50x72","country_code":"ZA","type":"education","lineage":["https://openalex.org/I192619145"]}],"countries":["ZA"],"is_corresponding":false,"raw_author_name":"Musa Marimani","raw_affiliation_strings":["Department of Anatomical Pathology, Faculty of Health Science University of Witwatersrand Johannesburg South Africa"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Anatomical Pathology, Faculty of Health Science University of Witwatersrand Johannesburg South Africa","institution_ids":["https://openalex.org/I192619145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042127097","display_name":"Mrudula Patel","orcid":"https://orcid.org/0000-0002-8406-118X","observed_orcids":["https://orcid.org/0000-0002-8406-118X"]},"institutions":[{"id":"https://openalex.org/I107920810","display_name":"National Health Laboratory Service","ror":"https://ror.org/00znvbk37","country_code":"ZA","type":"government","lineage":["https://openalex.org/I107920810"]},{"id":"https://openalex.org/I192619145","display_name":"University of the Witwatersrand","ror":"https://ror.org/03rp50x72","country_code":"ZA","type":"education","lineage":["https://openalex.org/I192619145"]}],"countries":["ZA"],"is_corresponding":false,"raw_author_name":"Mrudula Patel","raw_affiliation_strings":["Department of Clinical Microbiology and Infectious Diseases, National Health Laboratory Service and Faculty of Health Sciences University of Witwatersrand Johannesburg South Africa"],"raw_orcid":"https://orcid.org/0000-0002-8406-118X","affiliations":[{"raw_affiliation_string":"Department of Clinical Microbiology and Infectious Diseases, National Health Laboratory Service and Faculty of Health Sciences University of Witwatersrand Johannesburg South Africa","institution_ids":["https://openalex.org/I107920810","https://openalex.org/I192619145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5022048955"],"corresponding_institution_ids":["https://openalex.org/I107920810","https://openalex.org/I192619145"],"apc_list":{"value":3540,"currency":"USD","value_usd":3540},"apc_paid":{"value":3540,"currency":"USD","value_usd":3540},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.62084947,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"15","issue":"5","first_page":"e70408","last_page":"e70408"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/salmonella-enterica-serovar-typhi","display_name":"Salmonella typhi","score":0.9829999804496765},{"id":"https://openalex.org/keywords/multidrug-resistance","display_name":"multidrug resistance","score":0.890999972820282},{"id":"https://openalex.org/keywords/st1","display_name":"ST1","score":0.9039999842643738},{"id":"https://openalex.org/keywords/st2","display_name":"ST2","score":0.7440000176429749},{"id":"https://openalex.org/keywords/urban-waterways","display_name":"urban waterways","score":0.9160000085830688},{"id":"https://openalex.org/keywords/environmental-reservoirs","display_name":"environmental reservoirs","score":0.8220000267028809},{"id":"https://openalex.org/keywords/antimicrobial-resistance-genes","display_name":"antimicrobial resistance genes","score":0.847000002861023},{"id":"https://openalex.org/keywords/mercury-resistance-genes","display_name":"mercury resistance genes","score":0.7360000014305115},{"id":"https://openalex.org/keywords/qacedelta1","display_name":"qacE\u03941","score":0.9390000104904175},{"id":"https://openalex.org/keywords/salmonella-pathogenicity-islands","display_name":"Salmonella pathogenicity islands","score":0.878000020980835},{"id":"https://openalex.org/keywords/phylogenetic-affinities","display_name":"phylogenetic relatedness","score":0.9100000262260437},{"id":"https://openalex.org/keywords/typhoid-fever","display_name":"typhoid fever","score":0.6990000009536743},{"id":"https://openalex.org/keywords/one-health-surveillance","display_name":"One Health surveillance","score":0.8190000057220459},{"id":"https://openalex.org/keywords/south-africa","display_name":"South Africa","score":0.6420000195503235}],"concepts":[{"id":"https://openalex.org/C2994552716","wikidata":"https://www.wikidata.org/wiki/Q21600865","display_name":"Salmonella typhi","level":4,"score":0.7811999917030334},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6772000193595886},{"id":"https://openalex.org/C62130838","wikidata":"https://www.wikidata.org/wiki/Q5196163","display_name":"Pathogenicity island","level":4,"score":0.6424999833106995},{"id":"https://openalex.org/C10389963","wikidata":"https://www.wikidata.org/wiki/Q848328","display_name":"Serotype","level":2,"score":0.545199990272522},{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.5333999991416931},{"id":"https://openalex.org/C2781065037","wikidata":"https://www.wikidata.org/wiki/Q150839","display_name":"Salmonella","level":3,"score":0.519599974155426},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5174999833106995},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4431000053882599},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.4381999969482422},{"id":"https://openalex.org/C520601542","wikidata":"https://www.wikidata.org/wiki/Q83319","display_name":"Typhoid fever","level":2,"score":0.4343999922275543},{"id":"https://openalex.org/C97669555","wikidata":"https://www.wikidata.org/wiki/Q4118435","display_name":"Molecular epidemiology","level":4,"score":0.4101000130176544},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.4009999930858612},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.38670000433921814},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.38199999928474426},{"id":"https://openalex.org/C133936738","wikidata":"https://www.wikidata.org/wiki/Q643839","display_name":"Multiple drug resistance","level":3,"score":0.38089999556541443},{"id":"https://openalex.org/C77434933","wikidata":"https://www.wikidata.org/wiki/Q4043440","display_name":"Multilocus sequence typing","level":4,"score":0.3603000044822693},{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.34940001368522644},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.33719998598098755},{"id":"https://openalex.org/C2779607309","wikidata":"https://www.wikidata.org/wiki/Q2264864","display_name":"Salmonella enterica","level":4,"score":0.32089999318122864},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3183000087738037},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.31189998984336853},{"id":"https://openalex.org/C2780258820","wikidata":"https://www.wikidata.org/wiki/Q5195454","display_name":"Genomic island","level":4,"score":0.29829999804496765},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.296999990940094},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29109999537467957},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.2897999882698059},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.2775000035762787},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27730000019073486},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.26109999418258667},{"id":"https://openalex.org/C17757408","wikidata":"https://www.wikidata.org/wiki/Q4135516","display_name":"genomic DNA","level":3,"score":0.25609999895095825}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008826","descriptor_name":"Microbial Sensitivity Tests","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010957","descriptor_name":"Plasmids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012485","descriptor_name":"Salmonella typhi","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D012485","descriptor_name":"Salmonella typhi","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D012485","descriptor_name":"Salmonella typhi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012485","descriptor_name":"Salmonella typhi","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":true},{"descriptor_ui":"D013019","descriptor_name":"South Africa","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D014435","descriptor_name":"Typhoid Fever","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D014435","descriptor_name":"Typhoid Fever","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024901","descriptor_name":"Drug Resistance, Multiple, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D037521","descriptor_name":"Virulence Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D045483","descriptor_name":"Rivers","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1002/mbo3.70408","doi":"https://doi.org/10.1002/mbo3.70408","is_oa":true,"landing_page_url":"https://doi.org/10.1002/mbo3.70408","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mbo3.70408","source":{"id":"https://openalex.org/S4210229223","display_name":"MicrobiologyOpen","issn_l":"2045-8827","issn":["2045-8827"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"MicrobiologyOpen","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13617252","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13617252/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13617252/pdf/MBO3-15-e70408.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Microbiologyopen","raw_type":"Text"},{"id":"pmid:42802586","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42802586","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"MicrobiologyOpen","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:0a795939da7a4b35b113412d8a264e16","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/0a795939da7a4b35b113412d8a264e16","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"MicrobiologyOpen, Vol 15, Iss 5, Pp n/a-n/a (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1002/mbo3.70408","doi":"https://doi.org/10.1002/mbo3.70408","is_oa":true,"landing_page_url":"https://doi.org/10.1002/mbo3.70408","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mbo3.70408","source":{"id":"https://openalex.org/S4210229223","display_name":"MicrobiologyOpen","issn_l":"2045-8827","issn":["2045-8827"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-70","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"MicrobiologyOpen","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.9763000011444092,"id":"https://metadata.un.org/sdg/3"},{"display_name":"Clean water and sanitation","score":0.6618000268936157,"id":"https://metadata.un.org/sdg/6"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G7546543188","display_name":null,"funder_award_id":"138302","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"},{"id":"https://openalex.org/G992447086","display_name":null,"funder_award_id":"138279","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214587489.pdf","grobid_xml":"https://content.openalex.org/works/W7214587489.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1779315825","https://openalex.org/W2024519563","https://openalex.org/W2032519858","https://openalex.org/W2040974259","https://openalex.org/W2107772251","https://openalex.org/W2117043113","https://openalex.org/W2120902911","https://openalex.org/W2142678478","https://openalex.org/W2143325926","https://openalex.org/W2158084007","https://openalex.org/W2164868452","https://openalex.org/W2394763400","https://openalex.org/W2460333423","https://openalex.org/W2470052926","https://openalex.org/W2587454028","https://openalex.org/W2768017947","https://openalex.org/W2884207653","https://openalex.org/W2891078715","https://openalex.org/W2902905086","https://openalex.org/W2917067204","https://openalex.org/W2941864079","https://openalex.org/W2982645296","https://openalex.org/W2990618091","https://openalex.org/W3003482753","https://openalex.org/W3046229396","https://openalex.org/W3048398081","https://openalex.org/W3084522719","https://openalex.org/W3088851683","https://openalex.org/W3092401661","https://openalex.org/W3093231752","https://openalex.org/W3119057451","https://openalex.org/W3126718151","https://openalex.org/W3157626993","https://openalex.org/W3162760699","https://openalex.org/W4225685907","https://openalex.org/W4368358104","https://openalex.org/W4376645810","https://openalex.org/W4381430972","https://openalex.org/W4384208044","https://openalex.org/W4387208463","https://openalex.org/W4389742051","https://openalex.org/W4390704263","https://openalex.org/W4392316399","https://openalex.org/W4392378426","https://openalex.org/W4392913558","https://openalex.org/W4394785938","https://openalex.org/W4402067667","https://openalex.org/W4402917587","https://openalex.org/W4404332439","https://openalex.org/W4404516304","https://openalex.org/W4406428242","https://openalex.org/W4407319135","https://openalex.org/W4408092452","https://openalex.org/W4408673885","https://openalex.org/W4410287244","https://openalex.org/W4412417229","https://openalex.org/W4414515854","https://openalex.org/W4414936133","https://openalex.org/W4417025398"],"related_works":["https://openalex.org/W4293242413","https://openalex.org/W3116372659","https://openalex.org/W2277245754","https://openalex.org/W7095781347","https://openalex.org/W4400959514","https://openalex.org/W2129452342","https://openalex.org/W1998020486","https://openalex.org/W4408046970","https://openalex.org/W4410810995","https://openalex.org/W2133152152"],"abstract_inverted_index":{"ABSTRACT":[0],"Typhoid":[1],"fever":[2],"remains":[3,30],"a":[4,127,252],"major":[5],"public":[6],"health":[7],"concern":[8],"in":[9,46,191,241],"South":[10,48,242],"Africa.":[11],"However,":[12],"the":[13,24,43,60,116,137,201,230,248,262],"role":[14],"of":[15,26,233,256],"urban":[16],"waterways":[17],"as":[18,93,126,251],"environmental":[19,254],"reservoirs":[20],"and":[21,57,65,79,104,140,157,223,246],"contributors":[22],"to":[23,115,187],"spread":[25],"resistant":[27,141,257],"Salmonella":[28,85,183],"Typhi":[29,39,238],"poorly":[31],"understood.":[32],"This":[33,227],"study":[34,228],"characterized":[35],"four":[36],"S":[37,94,236,258],".":[38,95,159,181,237,259],"isolates":[40,90,113,133,161,177,206],"recovered":[41],"from":[42],"Jukskei":[44,249],"River":[45,250],"Johannesburg,":[47],"Africa,":[49],"using":[50,82],"whole\u2010genome":[51],"sequencing.":[52],"Genomic":[53],"DNA":[54],"was":[55],"extracted":[56],"sequenced":[58],"on":[59],"Illumina":[61],"NextSeq.":[62],"2000":[63],"platform,":[64],"assembled":[66],"genomes":[67,86],"were":[68,91,134,189],"analyzed":[69],"for":[70,87,264],"sequence":[71],"types":[72],"(STs),":[73],"AMR":[74],"determinants,":[75],"plasmids,":[76],"virulence":[77],"factors,":[78],"phylogenetic":[80],"relatedness":[81],"124":[83],"clinical":[84,217],"comparison.":[88],"All":[89,160,204],"confirmed":[92],"Typhi,":[96,260],"comprising":[97],"ST1":[98,112,132,176,192],"(":[99,106,166],"n":[100,107],"=":[101,108],"2":[102,109],")":[103],"ST2":[105],").":[110],"The":[111,131],"belonged":[114],"H58":[117,235],"lineage":[118],"(genotype":[119],"4.3.1.1),":[120],"with":[121,213],"isolate":[122],"BRSA001":[123],"further":[124],"classified":[125],"sublineage":[128],"4.3.1.1.":[129],"EA1.":[130],"multidrug\u2010resistant,":[135],"carrying":[136,239],"IncQ1":[138],"plasmid":[139],"genes,":[142],"including":[143],"aph(6)\u2010Id":[144],",":[145,147,150,152,154,156,168,170,172],"aph(3\u2033)\u2010Ib":[146],"bla":[148],"TEM\u20101B":[149],"catA1":[151],"sul1":[153],"sul2":[155],"dfrA7":[158],"possessed":[162],"mercury":[163],"resistance":[164],"genes":[165],"merR":[167],"merT":[169],"merP":[171],"merC":[173],"),":[174],"while":[175],"additionally":[178],"harbored":[179],"qacE\u03941":[180,240],"Ten":[182],"Pathogenicity":[184],"Islands":[185],"(SPI\u20101":[186],"SPI\u201010)":[188],"identified":[190],"isolates.":[193,203],"Phylogenetic":[194],"analysis":[195],"revealed":[196],"notable":[197],"genetic":[198],"diversity":[199],"among":[200],"river":[202,205],"clustered":[207],"tightly":[208],"(\u2264":[209],"5":[210],"allele":[211],"differences)":[212],"at":[214],"least":[215],"two":[216],"isolates,":[218],"indicating":[219],"shared":[220],"epidemiological":[221],"links":[222],"possible":[224],"localized":[225],"transmission.":[226],"provides":[229],"first":[231],"report":[232],"multidrug\u2010resistant":[234],"African":[243],"surface":[244],"water":[245],"highlights":[247],"potential":[253],"source":[255],"reinforcing":[261],"need":[263],"strengthened":[265],"One":[266],"Health":[267],"genomic":[268],"surveillance.":[269]},"counts_by_year":[],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2026-09-29T00:00:00"}