Pulsed field gel electrophoresis (PFGE) has been the standard way E. coli outbreaks are identified and traced to determine the source of outbreaks. Although PFGE tests can help investigators find the source of an E. coli outbreak, individual tests are time consuming and can only be performed by specially trained researchers. Also, PFGE results can be difficult to use for comparison between laboratories (which is the whole purpose in tracking E. coli outbreaks) partially because the banding patterns in PFGE are subjectively compared. A new technique to identify different strains of E. coli called multi-locus variable-number tandem repeat analysis (MLVA) is now being investigated by the CDC.
MLVA works by amplifying specific, highly variable DNA sequences that are formed from repeating units of 4-5 bases, or short tandem repeat, using PCR (Polymerase Chain Reaction: increases the amount of a certain sequence so it is easier to analyze). These units are repeated in varying amounts depending on the strain of E. coli. The number of units is measured using software that measures the sizes of the sequences.
For example, if two specific short tandem repeat sequence of E. coli O157:H7 DNA found in an infected individual and a potential source of infection, such as ground beef, and there is no difference in the number of units in the short tandem repeat sequence, there is a great likelihood that the two strains are either the same or extremely closely related. When multiple short tandem repeat sequences are compared (often 10 different sequences in the genome are compared) the probability that the strains are the same greatly increases.
MLVA is easier to reproduce and able to more easily distinguish between closely related strains of E. coli, potentially making it a better candidate to map sources of outbreaks that PFGE.
Sources
Cooley M, Carychao D, Crawford-Miksza L, Jay MT, Myers C, et al. (2007) Incidence and Tracking of Escherichia coli O157:H7 in a Major Produce Production Region in California. PLoS ONE 2(11): e1159. doi:10.1371/journal.pone.0001159
Noller AC, McEllistrem MC, Pacheco AGF, Boxrud DJ, Harrison LH (2003) Multilocus Variable-Number Tandem Repeat Analysis Distinguishes Outbreak and Sporadic Escherichia coli O157:H7 Isolates. Journal of Clinical Microbiology, 41:12 (2003) 5389-5397.
