We're 11 days now into the federal shutdown and four days since the announcement of a major foodborne outbreak in chicken that is challenging the shutdown-limited abilities of the food-safety and disease-detective personnel at the Centers for Disease Control and Prevention, Food and Drug Administration and Department of Agriculture. Here's an update.

The CDC has been able to bring back a few personnel to work on this – but only a few. Meanwhile, the Salmonella causing the outbreak has been shown to be multiple strains, several of which are resistant to multiple families of antibiotics.

I spoke to Dr. Chris Braden, director of the CDC's division of foodborne, waterborne and environmental diseases, and here is what he said:

Under normal circumstances, his division totals 300 workers.

Once people were sent home by the shutdown, he was left with 40 people to operate that entire division. Crucially, that includes the program PulseNet, which is possibly the most important component of foodborne-illness investigation in the entire US government; it compares the molecular fingerprints of organisms sent in by state health labs to see whether an outbreak is making people sick in multiple places at once.

The CDC were required to send those workers home, even though the agency was aware at the time of more than 30 different outbreaks of foodborne illness, including the first signals of the Salmonella outbreak.

After some discussion with the Department of Health and Human Services – and after realizing that the shutdown would be not days, but possibly weeks – the CDC was able to wangle the return of 30 additional personnel. (That is, 30 additional people were declared "essential.") Those 30 were distributed across the CDC, to influenza (it is flu season) and to polio (as part of the stressed global eradication program).

To cover all the programs in his division – not just this massive Salmonella outbreak – Braden got 10 people. Some, not all, have returning to working on PulseNet.

"There wasn't a number that says, 'You're only allowed this many people,'" he told me. "The judgment was that we have to protect life and property during the shutdown. We knew that most of the routine stuff that we were going to do was not going to function, that there were a lot of things that could happen out there that we may not know about, but we did have to address what we knew were risks that were identified."

>'We may be missing something out there that could be a problem... We have a blind spot.'

With the few additional people that they now have, here is what is known (numbers as of Oct. 10):

The official case count still stands at 278, but no one believes the numbers will stop there.

The breakdown by state – 17 states, not 18 as we heard the other day – is: Alaska (2), Arkansas (1), Arizona (11), California (213), Colorado (4), Connecticut (1), Florida (1), Hawaii (1), Idaho (2), Michigan (2), North Carolina (1), Nevada (8), Oregon (8), Texas (5), Utah (2), Washington (15) and Wisconsin (1).

Out of the 278, the CDC has some data for 274 of them. Those people range in age from less than a year old to 93 years old. The median age is 20. (NB: The median is not the average of all the ages; it's the middle of the range of all of them. That it is low suggests there may be lots of teen and child cases.)

Out of the 278, the CDC has medical information for 183 of them. Of those, 76, or 42 percent, have been admitted to hospitals – which, Braden said, is about double what the CDC usually expects.

Illnesses in this outbreak have been occurring since March 1. But, Braden said, CDC analysts don't believe this is just a continuation of the earlier outbreak that Foster Farms was involved in last summer; rather, they think it is a different one. More on that lower down.

A statistically significant proportion of the people whom state health departments have managed to interview seem to have been made ill by chicken which they bought raw and cooked at home – which is to say, not chicken that was bought cooked, and not chicken from a restaurant or food-service provider.

Now, the organism itself: This is interesting and troubling.

There are seven strains of Salmonella circulating within this outbreak.

Within the limited testing they have been able to do, the CDC has determined that four of the seven strains are drug-resistant.

Two of the four are resistant to many antibiotics.

The antibiotics to which the strains are resistant are: ampicillin, chloramphenicol, gentamicin, kanamycin, streptomycin, sulfisoxazole, and tetracycline.

This complex resistance pattern "is probably contributing to the high hospitalization rate," Braden told me.

If you've been hanging around here for a while, you'll know that I'm interested in drug resistance in food, because it distributes drug-resistant infection more broadly through the world, and because it often indicates that the resistance arose from antibiotic use in agriculture. If you're new to this topic, start with this: When people with a foodborne illness go to the doctor, they are often treated "empirically" – that is, they are given what is widely agreed to be the right drug for the organism most likely to be causing what is making them sick. But they often are not tested to see what the actual bacterial cause is, and it is even less likely that the bacterial cause, once cultured, will be tested for drug susceptibility. What all that comes down to: If someone is given a drug to which their organism is resistant, they will not get better – and the longer the infection lasts, the more likely they are to suffer serious long-term consequences down the road.

>'This outbreak... is outstripping our understanding.'

The pattern of resistance in these isolates is different from that in the earlier Foster Farms outbreak; there also was just one strain in that outbreak compared to seven in this one. In addition, that outbreak was centered on Foster Farms slaughterhouses in Washington State; this one appears to be centered in California.

"Presumably there is something (in the Foster Farms production chain) that is feeding into multiple facilities," Braden said. And then he added something that made my heart skip a little:

The information that we're getting from this outbreak – with so many strains, the fact that a number of them are multi-drug resistant, the fact that there's some overlap with the previous outbreak, but there's some new ones – is outstripping our understanding of what's happening in those facilities and what's happening in the production farms back upstream.

I asked Braden to talk about that a bit more, and what he said next made my jaw drop. The data that the strains in this outbreak are multi-drug resistant was achieved before the shutdown occurred. The program that achieved it, the CDC's portion of the National Antimicrobial Resistance Monitoring System, or NARMS, remains shut down. At the moment, the CDC cannot do any more resistance analysis related to this outbreak, or any other one:

We were able to do that testing in NARMS before the furlough. We had four retail samples from Foster Farms chicken, and five human isolates from ill persons connected to this outbreak. We saw clinically relevant resistance in all four of the retail chicken samples and in four of the five human isolates. And that was done before the furlough. This is specialized testing. We have a special laboratory that does it and we have people with specialized training that work in that laboratory. All that testing has stopped. There is no staff doing that type of testing, so that even if there were isolates coming in that might be associated with an outbreak, we wouldn't know it and we wouldn't know that they're antibiotic resistant.

I asked Braden if that worried him.

There are other types of surveillance both in my division and around CDC that is not occurring now. So it has a number of us concerned that we may be missing something out there that could be a problem, but due to the fact that we have people furloughed and those systems are not functioning, we may be missing something. That's a concern of mine. All that stuff that we would normally do with the isolates that are normally sent to us, oftentimes because there's something unusual or rare about what they're seeing, those isolates are not being tested at this point. So we have a blind spot.

Updates from elsewhere in the outbreak:

Consumers Union has an ongoing project on meat safety. When they went into their stored samples, they found one came from one of the Foster Farms lots that have been associated with this outbreak. They tested it and found the outbreak strain of Salmonella. Consumer Reports, their magazine arm, has urged its readers not to buy – or use, if they have already bought – any Foster Farms chicken.

Under the US food-safety system, recalls are voluntary and the responsibility of the company. According to a statement posted yesterday, Foster Farms has not implemented a recall. But according to NPR's food blog The Salt, the USDA has sent the company a "Notice of Intended Enforcement" telling the company that it will withdraw its onsite Food Safety and Inspection Service personnel if a plan to correct the problem is not submitted.

On Capitol Hill today, Congresswoman Louise Slaughter (D-NY) – a public health microbiologist and persistent champion of regulating overuse of antibiotics in agriculture – joined with Congresswoman Rosa DeLauro (D-CT), who has pressed for better food labelling, to make sure people understand how directly the continuing outbreak is tied to the shutdown.

"This outbreak should galvanize lawmakers to end the GOP shutdown and finally curb the overuse of antibiotics on the farm, a practice which is destroying the effectiveness of our most precious medical tool, the antibiotic," Slaughter said. DeLauro added: "We need to re-open the government to address this and other potential outbreaks before more people end up in the hospital, and we need to stop shortchanging the agencies that protect the public health, and give them the resources they need to do their jobs."