Whole genome sequencing in clinical and public health microbiology

Pathology
J C KwongB P Howden

Abstract

Genomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology.The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology.Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories.As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future.Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.

References

Dec 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·F SangerA R Coulson
Jun 11, 1979·Nucleic Acids Research·R Staden
Jul 28, 1995·Science·R D FleischmannJ M Merrick
Feb 5, 1998·Journal of the National Cancer Institute·B Kuska
Aug 3, 2001·Nature Reviews. Genetics·E D Green
May 12, 2006·Proceedings of the National Academy of Sciences of the United States of America·Eric E SmithMaynard V Olson
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
May 13, 2010·Briefings in Bioinformatics·Heng Li, Nils Homer
Nov 13, 2010·Journal of Medical Microbiology·Kanokporn MongkolrattanothaiRavindra K Vegunta
Dec 15, 2010·The New England Journal of Medicine·Chen-Shan ChinMatthew K Waldor
May 3, 2011·Database : the Journal of Biological Databases and Curation·Daniel BlankenbergUNKNOWN Galaxy Team
Oct 7, 2011·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Silvana K RampiniErik C Böttger
Jan 13, 2012·Journal of Clinical Microbiology·Mette V LarsenOle Lund
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Apr 24, 2012·Nature Biotechnology·Nicholas J LomanMark J Pallen
Jul 12, 2012·The Journal of Antimicrobial Chemotherapy·Ea ZankariMette Voldby Larsen
Jul 26, 2012·BMC Genomics·Michael InouyeKathryn E Holt
Jul 26, 2012·Journal of Biomedicine & Biotechnology·Lin LiuMaggie Law
Aug 7, 2012·Nature Reviews. Microbiology·Nicholas J LomanMark J Pallen
Aug 24, 2012·Science Translational Medicine·Evan S SnitkinJulia A Segre
Oct 2, 2012·Bioinformatics·Ross LazarusUNKNOWN Galaxy Team
Jan 5, 2013·The Journal of Infectious Diseases·James R JohnsonEvgeni V Sokurenko
Jan 24, 2013·Briefings in Bioinformatics·Stephan PabingerZlatko Trajanoski
Feb 15, 2013·Journal of Clinical Microbiology·Norelle L SherryBenjamin P Howden
Apr 9, 2013·Nature Biotechnology·Sebastian JünemannDag Harmsen
Apr 11, 2013·JAMA : the Journal of the American Medical Association·Nicholas J LomanMark J Pallen
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach
May 10, 2013·PloS One·Tanya GolubchikRory Bowden
May 15, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Jodi A Lindsay
Jul 19, 2013·The New England Journal of Medicine·Claudio U KöserSharon J Peacock
Aug 9, 2013·The New England Journal of Medicine·Ami S BhattMatthew Meyerson
Aug 15, 2013·MBio·Benjamin P HowdenTimothy P Stinear
Sep 17, 2013·Genome Biology·Sergey KorenAdam M Phillippy
Sep 27, 2013·The New England Journal of Medicine·David W EyreA Sarah Walker
Oct 23, 2013·Antimicrobial Agents and Chemotherapy·Sushim Kumar GuptaJean-Marc Rolain
Dec 18, 2013·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·James R PriceMartin J Llewelyn

❮ Previous
Next ❯

Citations

Feb 20, 2016·Expert Review of Molecular Diagnostics·David R Murdoch
Oct 27, 2015·Frontiers in Microbiology·Md Habibur RahamanMunirul Alam
Apr 30, 2016·Expert Review of Molecular Diagnostics·Thomas ClavelAndreas Hiergeist
Jun 18, 2016·Health Security·Norman A DoggettSegaran Pillai
Apr 9, 2016·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·M FerdousJ W A Rossen
Sep 7, 2016·Expert Review of Proteomics·Maurizio Sanguinetti, Brunella Posteraro
Sep 15, 2016·Expert Review of Anti-infective Therapy·Stefano G GiulieriBenjamin P Howden
Sep 24, 2016·Journal of Clinical Medicine·Eamonn P Culligan, Roy D Sleator
Oct 22, 2016·Annals of the New York Academy of Sciences·Michael R GillingsSasha G Tetu
Oct 22, 2016·Annals of the New York Academy of Sciences·Boahemaa Adu-OppongGautam Dantas
Oct 30, 2016·Expert Review of Molecular Diagnostics·Teresa CimminoJean-Marc Rolain
Feb 6, 2017·American Journal of Infection Control·Sanchita DasMichael O Vernon
Feb 6, 2017·American Journal of Infection Control·Patrick TangLinda M Hoang
Jun 9, 2017·PLoS Computational Biology·Ryan R WickKathryn E Holt
Jun 6, 2017·Current Opinion in Infectious Diseases·Julia Johnson, Caroline Quach
Apr 2, 2016·Therapeutic Advances in Infectious Disease·Robyn S Lee, Marcel A Behr
Apr 6, 2018·Journal of Clinical Microbiology·Ryan R WickKelly L Wyres
Jan 10, 2018·Frontiers in Microbiology·Rafaela G FerrariCarlos A Conte-Junior
Apr 27, 2018·Journal of Clinical Microbiology·Eman AnisRebecca P Wilkes
Feb 23, 2018·Animal Health Research Reviews·Chitrita DebRoyElisabeth Roberts
Sep 14, 2018·Health Promotion International·Louis Rice, Rachel Sara
Nov 27, 2015·Journal of Clinical Microbiology·Jason C KwongBenjamin P Howden
Aug 12, 2016·Journal of Clinical Microbiology·Amy S GargisIra M Lubin
Jun 8, 2017·Clinical Microbiology Reviews·Tarah LynchGary Van Domselaar
Oct 29, 2018·Current Protocols in Microbiology·Brittni R KelleyJeremiah Johnson
Jan 4, 2019·Journal of Medical Microbiology·Attika RehmanIain L Lamont
Jan 28, 2018·Scientific Reports·Kazuhisa OkadaShigeyuki Hamada
Mar 12, 2019·Future Microbiology·Dongsheng HanJinming Li
Nov 28, 2017·Microbial Genomics·Ryan R WickKathryn E Holt
Jan 11, 2018·Microbial Genomics·Pedro FeijaoLeonid Chindelevitch
Aug 6, 2019·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Despina KotsanasRhonda L Stuart
May 28, 2019·Scientific Reports·Helen van AggelenBrian D Gross
Sep 16, 2017·Current Opinion in Infectious Diseases·Nenad MacesicNicholas P Tatonetti

❮ Previous
Next ❯

Methods Mentioned

BETA
electrophoresis
PCR

Software Mentioned

Galaxy
Illumina
wgMLST
UNIX
Linux
Basic Local Alignment Search Tool ( BLAST )
Applied
BLAST
Maths Bionumerics suite

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.