Outsourced rep-PCR Technology Delivers Accurate, Affordable Microbial Identification

In recent years, contamination control has become a central topic in bio-security crisis management and within industries such as banking, insurance, and the public sector in preparation for potential pandemics and biohazards tied to terrorist attack. However, contamination control has long been an essential function in the pharmaceutical and life science markets, industrial kitchens and food services, and manufacturing where contamination poses a significant risk to technical processes of experiment or production. Unguarded proliferation of contamination can quickly lead to product damage, yield reduction, product recalls, and other outcomes highly detrimental to businesses and potentially dangerous to consumers.

THE POWER OF rep-PCR
With the use of a technique known as polymerase chain reaction (PCR) scientists can amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. PCR is a common and indispensable technique used in the functional analysis of genes; the diagnosis of hereditary diseases; the identification of genetic fingerprints; and the detection and diagnosis of infectious diseases.

rep-PCR is a modification of the PCR technique that makes use of DNA primers complementary to naturally occurring repetitive DNA sequences, present in multiple copies in the genomes of most Gram-negative and several Gram-positive bacteria. rep-PCR primers bind to specific repetitive sequences interspersed throughout the genome amplifying multiple fragments of various lengths. Fragments are separated using microfluidics electrophoresis. The technology follows traditional electrophoretic principles but requires only a small volume of sample. Inside the instrument, the DNA fragments are allowed to bind with an intercalating dye. As the fragments separate through the chip they pass over a laser thereby creating a graph of fluorescence intensity over time, yielding rep-PCR genomic fingerprint which resembles “bar code” patterns similar to UPC codes used in grocery stores. The rep-PCR genomic fingerprints generated from bacterial isolates permit differentiation to the species, subspecies, and strain level. With strain level identification accuracy, laboratories are able to introduce various industries to a new era of contamination control.

OVERCOMING THE HIGH PRICE OF ACCURACY
Equipment, reagents, and software components are required for microbial genotyping of bacteria and fungi. Commercially available systems offer unprecedented accurate identification of organisms at the genetic level using rep-PCR to amplify non-coding repetitive sequences interspersed throughout the bacterial genome. These systems employ a multi-step process to generate unique, reproducible fingerprints for each microbial sample and allow for real time data analysis and reports. However, steep acquisition costs make it cost-prohibitive for most companies to place a system within their own laboratory.

Recognizing that the use of rep-PCR was hampered by the high cost of ownership, the market responded with a solution that meets the needs of companies that occasionally or intermittently require highly accurate strain typing. Through outsourcing, genetic fingerprinting is now within the reach of companies, large and small, across industries through a qualified Current Good Manufacturing Practices contract services partner. A cGMP-certified partner can analyze samples in house and provide results via a secure, real-time, Web-based reporting process that is CFR Part 11 compliant and operated by an independent host for ultimate client confidentiality.