Transforming clinical microbiology with bacterial genome sequencing

By Xavier Didelot, R. Bowden, Daniel J. Wilson, T. Peto, D. Crook. Nature reviews genetics, 2012

780 citations recorded by the source corpus.

Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

Subfields: Clinical Biochemistry, Epidemiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/311fc6e5bc9c7745b7ae20d3c708555c9fd7c4e8

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Citations in the corpus

Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms (2014, background): “Microbial whole-genome sequencing using bench-top sequencing technologies holds great promises to enhance diagnostic and public health microbiology [1–3].”
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes (2015, positive): “Introduction Sequencing has become an indispensible tool in modern microbiology, dramatically changing the resolution and speed of studies of biodiversity [1], evolution [2–6], and molecular biology [7], and improving pathogen surveillance [8] and clinical diagnostics [9,10].”
Microplastic-Associated Biofilms: A Comparison of Freshwater and Marine Environments (2018, background): “This would result in important insights into the transfer of pathogens on plastics, provided that suitable databases are available for comparison [88, 89].”
PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data (2013, background): “PathogenFinder could be helpful in situations of possible bacterial outbreaks, in which a fast analysis of the unknown strain is important to save lives, and follows the direction modern clinical microbiology [32] and global epidemiology [33] are taking driven by the revolution brought by high throu”
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis (2015, background): “Microbial genome sequencing has the potential to substantially increase the speed of antibiotic resistance detection for many pathogens 2 and in addition provides valuable information on relatedness that could contribute to surveillance.”
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes (2015, background): “Following recent developments in sequencing technologies, both the time and cost required to sequence whole bacterial genomes have dropped to levels where it is now being applied in clinical and public health microbiology [1,2].”
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs (2014, background): “WGS has revolutionised pathogen research, and its potential to revolutionise the practice of public health epidemiology, surveillance and infection control has been recognised for some time [4-10].”
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes (2013, background): “Next-generation sequencing technologies have greatly reduced the cost for sequencing bacterial genomes and metagenomes and have increased the likelihood of rapid whole-bacterial-genome sequencing in clinical microbiology laboratories (1).”