Dataset Information

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

ABSTRACT: There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa.

SUBMITTER: Park SE

PROVIDER: S-EPMC6269545 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Publications

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Park Se Eun SE Pham Duy Thanh DT Boinett Christine C Wong Vanessa K VK Pak Gi Deok GD Panzner Ursula U Espinoza Ligia Maria Cruz LMC von Kalckreuth Vera V Im Justin J Schütt-Gerowitt Heidi H Crump John A JA Breiman Robert F RF Adu-Sarkodie Yaw Y Owusu-Dabo Ellis E Rakotozandrindrainy Raphaël R Soura Abdramane Bassiahi AB Aseffa Abraham A Gasmelseed Nagla N Keddy Karen H KH May Jürgen J Sow Amy Gassama AG Aaby Peter P Biggs Holly M HM Hertz Julian T JT Montgomery Joel M JM Cosmas Leonard L Olack Beatrice B Fields Barry B Sarpong Nimako N Razafindrabe Tsiriniaina Jean Luco TJL Raminosoa Tiana Mirana TM Kabore Leon Parfait LP Sampo Emmanuel E Teferi Mekonnen M Yeshitela Biruk B El Tayeb Muna Ahmed MA Sooka Arvinda A Meyer Christian G CG Krumkamp Ralf R Dekker Denise Myriam DM Jaeger Anna A Poppert Sven S Tall Adama A Niang Aissatou A Bjerregaard-Andersen Morten M Løfberg Sandra Valborg SV Seo Hye Jin HJ Jeon Hyon Jin HJ Deerin Jessica Fung JF Park Jinkyung J Konings Frank F Ali Mohammad M Clemens John D JD Hughes Peter P Sendagala Juliet Nsimire JN Vudriko Tobias T Downing Robert R Ikumapayi Usman N UN Mackenzie Grant A GA Obaro Stephen S Argimon Silvia S Aanensen David M DM Page Andrew A Keane Jacqueline A JA Duchene Sebastian S Dyson Zoe Z Holt Kathryn E KE Dougan Gordon G Marks Florian F Baker Stephen S

Nature communications 20181130 1

There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4 ...[more]

PMID: 30504848

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Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.

Dataset Information

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Publications

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Similar Datasets

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