ArticleJournal of biological methods2019
A step-by-step beginner's protocol for whole genome sequencing of human bacterial pathogens.
Article in Journal of biological methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- First comprehensive whole genome sequencing report of a multidrug-resistantNew microbes and new infections · 2026Article
- Whole-genome and pan-genome analyses reveal genomic differences among nontypeableFrontiers in cellular and infection microbiology · 2026Article
- Review
- Leveraging illumina iSeq100 for whole genome sequencing of Salmonella Typhi for a resource-limited setting.Scientific reports · 2025Article
- Study of epidemiological and molecular characteristics of Brucella strains circulating in Kazakhstan.Veterinary research communications · 2025Article
- Genome resequencing and comparative analysis of Streptococcus mutans in adults with high and low caries risk.Scientific data · 2025Article
- The Evolution of Next-Generation Sequencing Technologies.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Rapid assessment of clinical severity for salmonellosis cases via protein family domain analysis and machine learning.Academia molecular biology and genomics · 2025Article
- Genomic analysis of Salmonella Heidelberg isolated from the Brazilian poultry farms.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Implementation of a high-throughput whole genome sequencing approach with the goal of maximizing efficiency and cost effectiveness to improve public health.Microbiology spectrum · 2024Article
- Isoniazid resistance-conferring mutations are associated with highly variable phenotypic resistance.Journal of clinical tuberculosis and other mycobacterial diseases · 2023Article
- Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques.Cureus · 2023Review
- Complete genome sequence analysis of the multidrug resistantJournal of advanced veterinary and animal research · 2023Article
- The Genome of a Pigeonpea Compatible Rhizobial Strain '10ap3' Appears to Lack Common Nodulation Genes.Genes · 2023Article
- Whole-genome sequencing ofFrontiers in microbiology · 2023Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
- Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology.Current genetics · 2022Article
- Whole genome sequencing of the multidrug-resistantFrontiers in medicine · 2022Article
- Draft genome sequence of a nontypeable Haemophilus influenzae strain used in the study of human respiratory infection.BMC research notes · 2021Article
- Whole-genome analyses reveal gene content differences between nontypeableMicrobial genomics · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial whole genome sequencing (WGS) is becoming a widely-used technique in research, clinical diagnostic, and public health laboratories. It enables high resolution characterization of bacterial pathogens in terms of properties that include antibiotic resistance, molecular epidemiology, and virulence. The introduction of next-generation sequencing instrumentation has made WGS attainable in terms of costs. However, the lack of a beginner's protocol for WGS still represents a barrier to its adoption in some settings. Here, we present detailed step-by-step methods for obtaining WGS data from a range of different bacteria (Gram-positive, Gram-negative, and acid-fast) using the Illumina platform. Modifications have been performed with respect to DNA extraction and library normalization to maximize the output from the laboratory consumables invested. The protocol represents a simplified and reproducible method for producing high quality sequencing data. The key advantages of this protocol include: simplicity of the protocol for users with no prior genome sequencing experience and reproducibility of the protocol across a wide range of bacteria.
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