Application of polymerase chain reaction (PCR) and TaqMan PCR techniques to the detection and identification of Rhodococcus coprophilus in faecal samples.

This study presents an improved approach for detecting and identifying Rhodococcus coprophilus – an organism found in herbivore faeces – as an indicator of faecal contamination, by using Polymerase Chain Reaction (PCR) and TaqMan PCR techniques. The devised methods significantly reduce detection time from 21 days to merely 2-3 days, thereby enhancing the ability to distinguish farmed herbivore faecal pollution from human contamination.

Introduction

• Rhodococcus coprophilus is a type of bacteria that typically resides in the faeces of herbivorous animals. It can be used as an indicator to identify whether faecal contamination in water bodies is of animal or human origin.
• Traditional methods for detecting R. coprophilus are time-consuming and require up to 21 days to yield results, which restricts their effectiveness.

Innovative Detection Method

• The researchers have introduced a novel and time-efficient procedure for identifying R. coprophilus by extracting its DNA from faecal samples.
• Two PCR techniques – conventional PCR and TaqMan PCR – were optimised to not only detect this bacterium within 2-3 days, but also estimate its quantity in the faecal specimens.
• Both methods revolved around amplifying the 16S rRNA gene of the bacteria, generating a particular amplicon (fragment of DNA resulting from amplification) that is exclusively characteristic to R. coprophilus.

Efficiency and Specificity

• While conventional PCR required a minimum sample of 60 bacterial cells to produce a detectable result, TaqMan PCR could accomplish it even with a single cell.
• The TaqMan PCR approach demonstrated a perfectly linear response for quantitative estimation over an extensive range, both with bacterial cells and isolated DNA.

Test Outcomes and Relevance

• Successful DNA amplification was observed in faecal samples of cows, sheep, horses, and deer. However, the samples derived from humans, pigs, possums, ducks, and rabbits yielded no positive results.
• This differential response underlines the strength of the proposed PCR methods in distinguishing between faecal residues of farmed herbivores and humans, thus serving a significant role in environmental pollution studies.