I hope not, but this response to a case where microbial genomics was used to determine the source of a Listeria monocytogenes outbreak isn’t encouraging (boldface mine):

Last month, when health officials reported they discovered a pathogenic connection between raw milk from a Pennsylvania dairy and two illnesses in 2014 — one in California and the other in Florida — a wave of disbelief and condemnation began rippling out from the raw milk community.

News stories about the announcement from the Centers for Disease Control and Prevention sparked a flurry of online comments from raw milk drinkers and producers who disparaged the government’s science and scientists.

A common thread through many of the posts was disbelief that laboratory analysis could actually prove the pathogen samples from the two patients and the dairy were the same strain of Listeria monocytogenes.

Raw milk advocates questioned why the CDC said only that the samples were “closely related genetically” and that Miller’s Organic Farm in Pennsylvania was the “likely source.” Conspiracy theories about a big government agenda to destroy the raw milk industry emerged as fans of unpasteurized raw dairy products questioned why a specific dairy was being targeted when the CDC would not definitively state their lab analysis was 100 percent correct.

The CDC used whole genome sequencing (WGS) to analyze the DNA of the Listeria from a sample of Miller’s Organic Farm raw milk. That DNA fingerprint of “about 2 million base pairs” was then fed into the PulseNet database, said Matthew Wise, the Outbreak Response Team Lead in CDC’s Division of Foodborne, Waterborne, and Environmental Diseases.

The database already included the DNA fingerprints from the Listeria monocytogenes that sickened the California and Florida patients. When the CDC scientists added the database and ran a search for matches, the connection was discovered.

Microbial genomics, it’s ‘just a theory’:

“As scientists, we couch it with a little uncertainty, though,” Wise said. “Because we are scientists we know new information can be discovered on Wednesday that we didn’t have on Tuesday.”

Wise said when CDC scientists say something is the “likely source” of an outbreak it has much stronger meaning than the general public probably realizes.

“When we say ‘a likely source’ it means we have two different lines of evidence showing the same result. It means we are very, very confident we know the source,” Wise said.

Similarly, when the CDC reports a pathogen isolate from sick people is “closely related genetically” to a pathogen isolate from a specific food source, the agency isn’t talking about a shirt-tail relative situation.

“Closely related genetically for us means in the realm of identical twins,” Wise said.

Actually, it’s closer than identical twins–they’re essentially clones, but I won’t quibble over the analogy.

It’s worth noting that L. monocytogenes outbreaks can be incredibly dangerous, with mortality rates about one in six; among infants, it’s can be higher*. So stopping these outbreaks early is critical.

Without microbial genomics, what look like isolated cases occurring in different parts of the country can be tracked back to a single facility, and, with Listeria, that saves lives.

So this raw milkie ‘teach the controversy’ crap isn’t helping. That said, there should be more transparency in methods, so these claims can be analyzed by independent groups (some agencies embrace this, others do not). Not only will that build trust (though not among the raw milkies), but it would improve the methods, which can only help.

This is something people who build microbial informatics ‘pipelines’ and sequencing systems increasingly are going to have to confront: as microbial genomics becomes more applied, ‘bespoke’ pipelines and sequencing methods aren’t going to cut it. Failure rates will have to be even lower, and sequencing and analysis standards will have to be higher.

*As with many infectious diseases, we probably overestimate mortality since we underestimate the denominator. That said, L. monocytogenes is really bad news.