Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

Autor: Stephen Baker, Zamin Iqbal, Martin Hunt, Kate S. Baker, Timothy J. Dallman, Danielle J. Ingle, Rebecca J. Bengtsson, Louise Cerdeira, Jane Hawkey, Nicholas Thomson, Kathryn E. Holt, Claire Jenkins, Deborah A Williamson, Kalani Paranagama, François-Xavier Weill
Přispěvatelé: Hawkey, Jane [0000-0001-9661-5293], Weill, François-Xavier [0000-0001-9941-5799], Thomson, Nicholas R. [0000-0002-4432-8505], Baker, Stephen [0000-0003-1308-5755], Cerdeira, Louise [0000-0002-4495-2615], Iqbal, Zamin [0000-0001-8466-7547], Williamson, Deborah A. [0000-0001-7363-6665], Holt, Kathryn E. [0000-0003-3949-2471], Apollo - University of Cambridge Repository, IRAS OH Epidemiology Microbial Agents, Thomson, Nicholas R [0000-0002-4432-8505], Williamson, Deborah A [0000-0001-7363-6665], Holt, Kathryn E [0000-0003-3949-2471]
Rok vydání: 2020
Předmět:
0301 basic medicine
631/326/325/2482
Shigella sonnei/classification
Drug Resistance
Bacterial/genetics
General Physics and Astronomy
Drug resistance
Azithromycin
Global Health
631/114/1386
Ciprofloxacin
Azithromycin/pharmacology
Drug Resistance
Multiple
Bacterial
Shigella sonnei
631/181/757
692/308/174
Phylogeny
Genetics
education.field_of_study
Genome
Multidisciplinary
Geography
article
Single Nucleotide
Genomics
Anti-Bacterial Agents
England
Multiple
Shigellosis
Genotype
Science
Population
030106 microbiology
45/23
Microbial Sensitivity Tests
Biology
Polymorphism
Single Nucleotide
Ciprofloxacin/pharmacology
General Biochemistry
Genetics and Molecular Biology
Anti-Bacterial Agents/pharmacology
Dysentery
03 medical and health sciences
Antibiotic resistance
Bacillary/diagnosis
medicine
Humans
Polymorphism
education
Genotyping
Dysentery
Bacillary
Whole Genome Sequencing
Australia
Outbreak
Genome
Bacterial/genetics
General Chemistry
bacterial infections and mycoses
medicine.disease
United States
Genomics/methods
Drug Resistance
Multiple
Bacterial/genetics
ComputingMethodologies_PATTERNRECOGNITION
030104 developmental biology
Genetics
Population
Microbial Sensitivity Tests/methods
Dysentery
Bacillary/diagnosis
Genome
Bacterial
Zdroj: NATURE COMMUNICATIONS
Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)
Nature Communications, 12(1), 1. Nature Publishing Group
ISSN: 2041-1723
Popis: Funder: KEH is supported by a Senior Medical Research Fellowship from the Viertel Foundation of Australia RJB through a UKRI MRC New Investigator Research Grant (held by KSB, MR/R020787/1)
Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales.
Databáze: OpenAIRE
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