In a new study, a team of California-based scientists shows that by targeting and analyzing a specific gene in Campylobacter, labs can screen dozens of isolates of the bacteria to find the handful most likely to be the source of an outbreak. Unlike other enteric bacteria, such as E. coli O157:H7, Campylobacter is so diverse in a farm environment that many different strains can be present in just a few samples. This genetic diversity makes it hard for scientists to link a human Campylobacter infection to its source, since the leading method of bacterial analysis — pulsed-field gel electrophoresis (PFGE) — is time-consuming and labor intensive, and therefore difficult to perform on more than a few isolates at a time. For this study, researchers zeroed in on one gene in Campylobacter, called porA, which has been suggested to be a good indicator of the uniqueness of a specific strain. The team collected samples from two different California dairies that were the sources of Campylobacter jejuni outbreaks linked to milk, and conducted porA sequencing on over 100 isolates found in cow feces and water runoff at these locations. Campylobacter outbreaks are rare. The majority of Campylobacter infections occur as sporadic cases, not linked to other illnesses; thus opportunities to study a Campylobacter outbreak are none too common. The first site from which the researchers took environmental samples was a dairy operated by inmates at a sate prison. Milk from that dairy sickened over 1,644 inmates at 11 correctional facilities in California in May of 2006, in what is still the largest recorded milk-related Campylobacter outbreak in the United States. Testing of samples of the pasteurized milk revealed no Campylobacter in the product — probably because the bacteria didn’t survive long enough in the milk, explained Michele Jay-Russell, lead author of the study. The research team visited the facility in August, three months after the outbreak, to see if they could find the outbreak strain in the environment using porA analysis. “We were looking for a needle in a haystack to go over to that prison dairy and take samples of feces and other farm samples and try to find the exact genetic match to the isolate that caused the human outbreak,” said Jay-Russell. They collected 25 samples from cow feces and waste water, finding a total of 70 C. jejuni isolates. Through porA analysis, the researchers narrowed this set down to a group of 8 most likely to match the outbreak strain. At the second farm, which was ground zero for a 2007 Campylobacter outbreak  raw milk that sickened 11 people, a total of 34 C. jejuni isolates were collected. These were narrowed down to a set of 17 likely candidates by porA sequencing.  “Our hypothesis was that if they had the same porA sequence then they were more likely to have the same PFGE pattern,” said Russell. Indeed, when the team submitted their pool of likely candidates to the state health lab for PFGE testing, several isolates were indistinguishable from the outbreak strain, said Jay-Russell. In other words, the strategy worked. “So what was new about [the study] was using this screening method to prioritize isolates, knowing that it was going to be too expensive for the state to test a hundred Campylobacter isolates using PFGE,” explained Jay-Russell. This study was conducted after the two outbreaks were over; however in the future, porA sequencing could help investigators take a large number of isolates and narrow them down to the few most likely to match the outbreak strain while an outbreak is still ongoing. “The public health lab is not going to be able to test hundreds of Campylobacter isolates using PFGE,” said Russell, noting that many health labs are already turning to genetic sequencing, at least for initial screening of pathogens. “This is the emerging technology. It’s kind of the way things are moving. So we wrote this paper to demonstrate that it worked in an outbreak setting, and that as health departments get sequencing machines to think about this kind of approach. You could do this with screening a lot of clinical isolates too if there was a huge outbreak.” The study was conducted by researchers at the University of California, Davis; the California Department of Public Health; USDA’s Agricultural Research Service and CDC’s Epidemic Intelligence Service. It appears in this month’s issue of the Journal of Clinical Microbiology.