Methods for Whole Cell Detection of Microorganisms

Abstract

Microbes are ubiquitous, and can be found occupying nearly every imaginable niche on Earth. These include organic and inorganic surfaces, interfacial boundaries and within macroscopically solid matrices, such as the pore space of rocks. Because phylogenetically divergent microbes may be visually indistinguishable, understanding the species distribution and ecological significance of environmental microbes requires diagnostic tools that extend beyond simple phenotypic description. Methods for microbial diagnostics can be divided into two broad categories: cellular and acellular. Acellular techniques, such as the polymerase chain reaction or certain immunoassay formats may be effective at detecting molecular, structural or biochemical targets associated with specific cell types, but this information is provided out of its "natural", and arguably most meaningful context -that of the individual microbial cell. In contrast, cellular methods have the potential to preserve an abundance of valuable information. Apart from molecular identity, this includes information regarding cell morphology and other physiological characteristics, cell number and distribution within a sample, and physical or spatial associations with other cell types. The aim of this chapter is to provide an overview of whole cell methods for microbial detection, including both existing approaches and those still in development. The tools described here are expected to find wide application for the detection of microbes on surfaces or within complex matrices across a number of parallel or allied fields, including environmental, food and clinical microbiologies.

Detection of Microbiological Content in Water as Indicator of Its Ecological State − Mini‐Review

“…Use of nucleic acid probing plays a noticeable role in microbial assays: there are fluorescence in situ hybridization, FISH, with fluorescent‐labeled DNA probe of the known sequence, DNA microarray with fluorescently labeled mRNAs or DNA from the specimens . As a result, numerous amounts of target genes could be detected.…”

“…) . For instance, light emission signal is received by whole cell biosensor where, in the presence of gene‐inducing environmental pollutants, cells react with production of fluorescent proteins . Biosensor prototype based on modified bacteriophage carrying gene of fluorescent reporter protein was successfully tested for the detection of E. coli in sea water samples .…”

Instrumental analytical tools for mycobacteria characterisation

“…Owing to the increased availability of modern genetic techniques and instrumentation, it is nowadays possible to detect and accurately identify a large number of species of the Mycobacterium genus (Tortoli 2006). Molecular techniques used for mycobacteria detection typically test for deoxyribonucleic acid (DNA) sequence on a chromosome and predominantly include polymerase chain reaction (PCR), fluorescence in situ hybridisation (FISH) or rolling circle amplification (Brehm-Stecher 2008;Schopf et al 2011;Sevilla et al 2015;Baliga et al 2018).…”

Advances in single-cell approaches in the study of foodborne pathogens

“…Although a wide variety of tools and technologies for analysis of microbial cells at the single-cell level have been previously reviewed (Brehm-Stecher and Johnson, 2004;Brehm-Stecher, 2007, 2008, the fi eld is continually expanding, with the introduction of new approaches or improvement of existing methods.…”