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

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.

Design and Implementation of Noble Metal Nanoparticle Cluster Arrays for Plasmon Enhanced Biosensing

Nanoparticle Cluster Arrays (NCAs) are a class of electromagnetic materials that comprise chemically defined nanoparticles assembled into clusters of defined size in an extended deterministic arrangement. NCAs are fabricated through integration of chemically synthesized building blocks into predefined patterns using a hybrid top-down/bottom-up fabrication approach that overcomes some of the limitations of conventional top-down fabrication methods with regard to minimum available feature size and structural complexity. NCAs can sustain near-field interactions between nanoparticles within individual clusters as well as between entire neighboring clusters. The availability of near-field interactions on multiple length scales - together with the ability to further enhance the coupled plasmon modes through photonic modes in carefully designed array morphologies - leads to a multiscale cascade electromagnetic field enhancement throughout the array. This feature article introduces the design and fabrication fundamentals of NCAs and characterizes the electromagnetic coupling mechanisms in the arrays. Furthermore, it reviews how the optical properties of NCAs can be tuned through the size and shape of the nanoparticle building blocks and the geometry, size, and separation of the assembled clusters. NCAs have potential applications in many different areas; this feature article focuses on plasmon enhanced biosensing and surface enhanced Raman spectroscopy (SERS), in particular.

Oxford nanopore sequencing in clinical microbiology and infection diagnostics

Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.