Abstract
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.
Highlights
Diagnostic microbiology laboratories in Malaysia are divided into three categories: laboratories located in government hospitals, university laboratories in teaching hospitals, and laboratories in private medical centers or private testing laboratories [6]
The term “metagenomics” was first used by Handelsman et al over 20 years ago, where it refers to the study of genetic material from a sample without the need for isolation and culturing of the the microorganisms contained in the sample itself [39,40]
Used to study microbial community community diversity within samples from the environment and organisms, diagnostic microbiology diversity within samples from the environment and organisms, diagnostic microbiology laboratories were built on the metagenome concept to sequence only the 16S rRNA gene of laboratories were built on the metagenome concept to sequence only the 16S rRNA gene of bacterial bacterial populations within clinical specimens to identify infecting pathogens [23,41]
Summary
The current gold standard for bacterial pathogen identification in diagnostic microbiology laboratories involves culture and biochemical testing (CBtest); this workflow is widely available in hospitals of most middle-income countries where in-house microbiologists are available [1,2,3]. This includes Malaysia, a middle-income country situated in Southeast Asia. Identification of common medically important bacterial pathogens via CBtest can be technically easy and relatively affordable; standardization of CBtest workflows has led to wide-spread use of this identification method in diagnostic microbiology laboratories of middle- and higher-income countries, including Malaysia [2,3,6]
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