Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

被引：73

作者：

Rizal, Nurnabila Syafiqah Muhamad ^{[1
]}

Neoh, Hui-min ^{[1
]}

Ramli, Ramliza ^{[2
]}

Periyasamy, Petrick Ramesh A. L. K. ^{[3
]}

Hanafiah, Alfizah ^{[2
]}

Samat, Muttaqillah Najihan Abdul ^{[2
]}

Tan, Toh Leong ^{[4
]}

Wong, Kon Ken ^{[2
]}

Nathan, Sheila ^{[5
]}

Chieng, Sylvia ^{[5
]}

Saw, Seow Hoon ^{[6
]}

Khor, Bee Yin ^{[7
]}

机构：

[1] Univ Kebangsaan Malaysia, UKM Med Mol Biol Inst UMBI, Kuala Lumpur 56000, Malaysia

[2] Univ Kebangsaan Malaysia, Fac Med, Dept Med Microbiol & Immunol, Kuala Lumpur 56000, Malaysia

[3] Univ Kebangsaan Malaysia, Fac Med, Dept Med, Kuala Lumpur 56000, Malaysia

[4] Univ Kebangsaan Malaysia, Fac Med, Dept Emergency Med, Kuala Lumpur 56000, Malaysia

[5] Univ Kebangsaan Malaysia, Fac Sci & Technol, Dept Biol Sci & Biotechnol, Bangi 43600, Selangor, Malaysia

[6] Univ Tunku Abdul Rahman, Fac Sci, Kampar 31900, Perak, Malaysia

[7] BioEasy Sdn Bhd, Shah Alam 40170, Selangor, Malaysia

来源：

DIAGNOSTICS | 2020年 / 10卷 / 10期

关键词：

bacterial pathogen identification; culture and biochemical testing; 16S rRNA next-generation sequencing; middle-income countries; diagnostic microbiology; CLINICAL MICROBIOLOGY; HIGH-RESOLUTION; CULTURE; BACTERIA; COMPLEX; IMPACT; MICROORGANISMS; MYCOBACTERIA; TECHNOLOGIES; ORGANISMS;

D O I：

10.3390/diagnostics10100816

中图分类号：

R5 [内科学];

学科分类号：

1002 ; 100201 ;

摘要：

Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.

引用

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