Whole genome sequencing in clinical and public health microbiology

被引:217
作者
Kwong, J. C. [1 ,2 ]
McCallum, N. [3 ,4 ,5 ]
Sintchenko, V. [3 ,4 ,5 ]
Howden, B. P. [1 ,2 ,6 ]
机构
[1] Univ Melbourne, Doherty Inst Infect & Immun, Dept Microbiol & Immunol, Microbiol Diagnost Unit,Publ Hlth Lab, Melbourne, Vic 3000, Australia
[2] Austin Hlth, Dept Infect Dis, Heidelberg, Vic, Australia
[3] Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Sydney, NSW 2006, Australia
[4] Univ Sydney, Sydney Med Sch, Sydney, NSW 2006, Australia
[5] Westmead Hosp, Inst Clin Pathol & Med Res, Ctr Infect Dis & Microbiol Publ Hlth, Sydney, NSW, Australia
[6] Monash Univ, Dept Microbiol, Clayton, Vic 3168, Australia
基金
澳大利亚国家健康与医学研究理事会; 英国医学研究理事会;
关键词
Clinical microbiology; genomics; public health microbiology; sequencing; WGS; whole genome sequencing; RESISTANT STAPHYLOCOCCUS-AUREUS; ESCHERICHIA-COLI; MYCOBACTERIUM-TUBERCULOSIS; ANTIMICROBIAL RESISTANCE; PATHOGEN IDENTIFICATION; BACTERIAL GENOME; CYSTIC-FIBROSIS; ARG-ANNOT; GENES; READ;
D O I
10.1097/PAT.0000000000000235
中图分类号
R36 [病理学];
学科分类号
100104 ;
摘要
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.
引用
收藏
页码:199 / 210
页数:12
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