This was originally published Oct. 1 on Maryn McKenna’s Superbug Blog, hosted by Wired Science.

“I know that we will not be conducting multi-state outbreak investigations. States may continue to find outbreaks, but we won’t be doing the cross-state consultation and laboratory work to link outbreaks that might cross state borders, such as a recent Hep A outbreak. We will not be doing rapid response for vaccine preventable disease cases or outbreaks, such as measles. We won’t be monitoring seasonal influenza activity in the U.S. as flu season begins. “Surveillance for other emerging infectious disease outbreaks, such as H7N9 and MERS, will be weakened. We won’t be doing routine inspections of BSL3 and BSL 4 labs as part of the select agent program. Our work to prevent HIV/STDs and TB in the states using molecular epidemiology will be discontinued.”

Let’s unpack that a little bit. In the U.S., the flu season is beginning. This year’s flu vaccine has been manufactured and is either already in the hands of state and local health departments or with doctors or on its way to them via the commercial middlemen who handle distribution for the manufacturers. (OnTwitter today, Jim Garrow of the Philadelphia Department of Public Health confirmed that they already have an inventory of flu vaccine.) So flu prevention won’t necessarily be harmed — except for those people who don’t get a flu shot unless CDC’s public health campaigns remind them because there won’t be any such campaigns. But flu surveillance, which CDC conducts and also assembles out of data sent to it by health departments and by networks of physicians, is on the shelf. Here’s what CDC’s flu-surveillance homepage looks like right now: (The original page is here.) And here is what that means: We are now at the start of flu season. If this season becomes a bad one — a rogue virus, an uneven epidemic, a concentration of cases in the elderly or the very young or in a particular city or state — we’ll have no way of knowing. And, for what it’s worth, we’ll have no way of directing additional public-health or research help because they’ve all been sent home. In tracking flu, one of the most unpredictable and mutable human-disease viruses around, we have been blinded. And, if the shutdown continues more than a few weeks, then that blindness will also blanket development of next year’s flu vaccine — because, within a few weeks, CDC researchers would start analyzing this year’s northern and southern hemisphere viruses to determine what ought to be included in next year’s vaccine mix. That blindness is not limited to the U.S. CDC loans scientists and sends money to the World Health Organization and to dozens of countries in the industrialized and developing worlds. One of its specialties is helping to track the emergence of new flu viruses that have pandemic potential. That global spyglass has just been shuttered. And, we are less than two weeks from the official beginning of the hajj, the worldwide pilgrimage of observant Muslims to the holy sites of Saudi Arabia — where, if you’ve been following along, MERS has been slowly growing for more than a year. Health planners have been quietly fretting for months that the hajj might allow the spread of MERS outside of the Middle East — a reasonable fear, as that has happened in past hajj seasons with other diseases. But with the shutdown, we lose some of the most accurate tools for finding that out. This enforced ignorance of disease spread isn’t hypothetical. Just this morning, the WHO tweeted that there is a three-country outbreak of more than 200 cases of polio in the Horn of Africa. The top polio-hunters in the worldwide eradication effort, the ones who developed the “molecular clock” that allows the eradication campaign to trace new cases back to their source, work at  — yup, CDC. The shutdown’s risks to health aren’t limited to what CDC does. The Food and Drug Administration has sent home 45 percent of its staff. The ones who remain can do so because they work in programs that receive user fees such as reviews of proposed new pharmaceuticals. Those can continue provided the application for review was already submitted. (New reviews, according to FDA’s statement today, are out of luck.) But food safety — always an underfunded mandate — is in real danger. HHS’s memo on shutdown staffing acknowledged this:

“FDA will be unable to support the majority of its food safety, nutrition, and cosmetics activities. FDA will also have to cease safety activities such as routine establishment inspections, some compliance and enforcement activities, monitoring of imports, notification programs (e.g., food contact substances, infant formula), and the majority of the laboratory research necessary to inform public health decision-making.”

Translated, that means: No foodborne outbreak tracking; no inspection of food imports; no lab research; no publishing of guidance documents. (Food Safety News and Regulatory Focus have more.) At the U.S. Department of Agriculture — which attends to about 15 percent of the U.S. food supply, including meat, compared to FDA’s 85 percent — things are a bit better. Eighty-seven percent of its staff have been retained, including most of the Food Safety and Inspection Service. In its shutdown memo, USDA says FSIS falls under an Office of Management and Budget shutdown category described as “necessary to perform activities necessarily implied by law” (for wonks, that’s No. 3 of the five categories). Thus, they can continue to conduct meat, poultry and egg inspections on-site; that is, at plants and packing houses. However, the agency loses personnel as follows:

“The following headquarters staffs performing the central program guidance, coordination, direction and planning functions described will be furloughed except as minimally required in direct support of Agency field operations:

• Inspection Operations (Office of Field Operations): Responsible for planning, coordinating and directing the Meat, Poultry, and Egg Products Inspection programs. Due to the large numbers of in plant inspection personnel who support excepted activities, most individuals in this area would be excepted and on duty.
• Public Health Science (Office of Public Health Science): The Public Health Science Program is responsible for planning, coordinating and directing all scientific guidance and support in chemistry, epidemiology, pathology, toxicology, nutrition, and parasitological. The Public Health Science Program also performs Agency risk assessments, directs the residue testing program, and also performs activities that address zoonotic diseases. With the exception of the laboratory function within Public Health Science, designations for these functions would be non-excepted, with limited individuals being identified as excepted and on duty. The majority of all Laboratory functions will be excepted.
• International Programs (Office of Field Operations, Office of Policy and Program Development, and Office of Investigation, Enforcement and Audit): The International Programs are responsible for ensuring that meat, poultry, and egg products from foreign countries are safe and wholesome. Program personnel also confer with foreign governments on issues involving imports and exports of meat, poultry and egg products and international food safety standards. A substantial number of these programs other than inspection of imports and certifying products for export would not be excepted.”

I know other Wired colleagues are going to tackle the shutdown’s effect on the rest of the government science apparatus. There is no question, though, that public and global health and food safety are experiencing great impact. Better hope there are no major outbreaks brewing and that no food producer or manufacturer — or food importer in a country with lower standards — decides that now is the time to try to slip something by government-funded detection and response. As of this morning, the protections we rely on are no longer there.

December 23, 2011 / 60(50);1701-1704:

…In 2010, a total of 787 FTEs were working as foodborne disease epidemiologists in state, regional, and local health departments in the United States. Of these, 616.5 (78%) had an epidemiology-related degree or had completed some coursework in epidemiology; 170.5 (22%) had only on-the-job training or no formal epidemiology training (Table).

Formal education in epidemiology was highest at the state level, where most (73%) foodborne disease epidemiologists had an epidemiology degree. The proportion of personnel working as foodborne epidemiologists who had a nursing degree was substantially higher at the local level (19%) than at the regional (5%) or state (4%) level. States reported the need for an additional 304 FTEs to reach full program capacity, with the greatest demand (50% of need) for master’s-level epidemiologists…

Although states investigate foodborne disease outbreaks caused by numerous pathogens, they were more likely to investigate outbreaks associated with some pathogens than others. For specific pathogens, a history of investigating >75% of outbreaks was reported by the highest proportion of states for E. coli (86% of states), followed by Listeria (81%), Salmonella (78%), Campylobacter (73%), other foodborne pathogens (68%), and norovirus (55%). Conversely, a small but substantial proportion of states reported investigating <25% of outbreaks caused by these same pathogens:Campylobacter (16% of states), Listeria (13%), E. coli (10%), norovirus (7%) and Salmonella (4%).

States were more likely to obtain stool specimens than food samples as part of foodborne outbreak investigations. Relatively few states reported always collecting either stool specimens (five states) or food (one state) samples associated with foodborne disease outbreaks; 33 states collected stool specimens in 50%-99% of outbreaks, and 36 states collected food samples in <50% of outbreaks. Thirty-nine states reported having performed 1-10 tracebacks of commercial products during the past 3 years; relatively few (seven states) had conducted ≥11 tracebacks, and three states completed no tracebacks of commercial products during that period.

All respondents reported barriers to investigating foodborne or enteric outbreaks. Barriers reported as either moderate or substantial by states included delayed notification of the outbreak (reported by 41 states), lack of sufficient number of foodborne safety staff members (29), lower prioritization of investigations (27), lack of ability to pay overtime (20), lack of adequate epidemiology expertise (12), difficulties working with in-state agencies (eight), constraints related to administrative support (eight), and difficulties working with other state or federal agencies (five)…

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“CDC: Whether your food-related illness gets investigated depends on which state you live in (MMWR)” was first posted on Maryn McKenna’s blog, The Further Adventures of Germ Girl, on Dec. 22, 2011. 

The poisoning appears to be due to ethylene glycol; the vinegar had been stored in barrels that previously contained antifreeze. According to the AP, investigators haven’t yet been able to say whether the vinegar was put in the barrels out of ignorance, making it a problem of accidental contamination, or deliberately by an unscrupulous producer seeking to cut corners.

It’s the second vinegar scandal in China this month. Two weeks ago, an official of the association that oversees vinegar production in Shanxi province claimed that 95 percent of its highly regarded “aged” vinegar is dosed with industrial acid in order to cut fermentation time and turn out batches faster.

And those are just the latest. They follow the meat that glowed in the dark; the tainted buns; the exploding watermelons; the 40 tons of bean sprouts containing antibiotics and carcinogens; the rice contaminated with heavy metals; the mushrooms imbued with bleach; and the pork so dosed with banned stimulants that athletes attending an international meet in Shanghai had to be told which restaurants were safe to eat at.

Three years after the melamine-in-milk scandal that made 300,000 children sick, and two years after China passed its first-ever food safety law in response, the country is still struggling to keep its food supply healthy. The Chinese government recently cracked down, closing almost 5,000 food-producing businesses and arresting 2,000 people — but China experts say a needlessly complex bureaucracy and ferocious determination to turn a profit mean the contamination will keep coming. (On forums where expats chat, Westerners living in China wonder whether there is anything safe to eat.) (Update: Commenters at the China Law Blog, many of them apparently resident in China, reflect the same anxiety.)

It’s tempting to view these Chinese food scandals as interesting but remote, the learning curve of a society that pushes unfettered capitalism but never experienced the kind of progressive movement that led to food-safety reform in the United States. Except for one small detail: Chinese products don’t stay in China. They are traded around the world, and increasingly they are sold here.

The permeability of the US marketplace to Chinese goods of uncertain origin should have been clear in 2007, when melamine contamination was found not only in milk sold in China but in pet food sold in the U.S. (Up to 4,000 pets are believed to have died.)

But a report published in June by the Food and Drug Administration makes it clear that imports from China are increasing in the US — and that the FDA is underfunded and under-equipped to deal with it. The unusual “special report,” called Pathway to Global Product Safety and Quality, said imports include:

— 10-15 percent of all food eaten in US households

— 60 percent of fruits and vegetables

— 80 percent of seafood

— 50 percent of medical devices

— 80 percent of the active pharmaceutical ingredients in medications.

China is the major player in that market growth, with India a close second:

Import lines from emerging markets, including Mexico, India, China, and Thailand, increased faster between 2002 and 2009 than lines from developed markets, and this disparity is likely to continue. China and India are each expected to see a more than 400% increase in their product exports between now and 2020, with China accounting for nearly 20% of all global product exports by that time… China and India are each expected to see 9% annual growth in food exports between 2010 and 2020.

And with surprising frankness, the FDA admitted that it cannot keep up:

FDA does not — nor will it — have the resources to adequately keep pace with the pressures of globalization. In 2008 the Government Accountability Office recommended that FDA increase inspections of foreign drug establishments and improve information it receives to manage overseas inspections. But at current rates, it would take an estimated nine years for FDA to inspect every high- priority pharmaceutical facility just once. The same holds for food products. [The 2011 Food Safety Modernization Act] directs the agency to inspect at least 600 foreign food facilities within the next year and double those inspections every year for the next five. While the goal may be attainable in the first year, it would be impossible for FDA to complete 19,200 foreign food inspections in year six without a substantial increase in resources or a complete overhaul in the way it operates.

(Just to be clear, the FDA is not getting “a substantial increase in resources.” As Food Safety News reported after the budget deal was struck, the agency initially faced deep cuts and now at best will have flat funding.)

The FDA isn’t alone in thinking it isn’t up to the job of policing imported food. The Office of the Inspector General in its parent department, Health and Human Services, said in June that the agency is performing erratically in policing recalls of imported foods. In April, the Government Accountability Office said that, even given its limited resources, the FDA needs to do a better job policing imported seafood specifically.

China, the GAO report said,is the largest single supplier of seafood imported to the US. But in the past 6 years, the FDA has inspected 41 — 1.5 percent — of the 2,744 Chinese seafood processors selling to the U.S.

Maryn McKenna is a journalist for national magazines and the author of SUPERBUG and BEATING BACK THE DEVIL. Follow @marynmck on Twitter.

This post originally appeared Aug. 23, 2011, at Wired Science’s Superbug.