bioRxiv (Cold Spring Harbor Laboratory) · 2021 · 10 citations · 59 references
Veterinary MedicineInfectious DiseasesMicrobiologyAntimicrobial Resistance EpidemiologyImmunology Of Infectious DiseasesInfectious Disease EpidemiologyBacterial InfectionsMolecular Epidemiology Of ResistanceSequence-based EpidemiologySusceptibility To InfectionTransmission DynamicsAcute Febrile IllnessAcute Infection PrevalenceAcute Intestinal InfectionCase-control Study DesignMultidrug-resistant OrganismsPhylogenetic Analysis Of Resistant IsolatesPhylogenetic Transmission InferenceWhole-genome Sequencing Analysis
Abstract Understanding the dynamics of infection and carriage of typhoid in endemic settings is critical to finding solutions to prevention and control. In a 3 year case-control study, we investigated typhoid among children aged <16 years (4,670 febrile cases and 8,549 age matched controls) living in an informal settlement, Nairobi, Kenya. 148 S . Typhi isolates from cases and 95 from controls (stool culture) were identified; a carriage frequency of 1%. Whole-genome sequencing showed 97% of cases and 88% of controls were genotype 4.3.1 (Haplotype58), with the majority of each (76% and 88%) being multidrug-resistant strains in 3 sublineages of H58 genotype (East Africa 1 (EA1), EA2, and EA3), with sequences from cases and carriers intermingled. The high rate of multidrug-resistant H58 S. Typhi, and the close phylogenetic relationships between carriers and controls, provides evidence for the role of carriers as a reservoir for the community spread of typhoid in this setting.
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The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations