Journal
DIAGNOSTICS
Volume 10, Issue 10, Pages -Publisher
MDPI
DOI: 10.3390/diagnostics10100816
Keywords
bacterial pathogen identification; culture and biochemical testing; 16S rRNA next-generation sequencing; middle-income countries; diagnostic microbiology
Categories
Funding
- Geran Universiti Penyelidikan (GUP) of Universiti Kebangsaan Malaysia [GUP-2017-003]
- Universiti Kebangsaan Malaysia [GP-2019-K016842]
- Dana Pecutan Penerbitan 2020 from Universiti Kebangsaan Malaysia
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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.
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