20 years of PulseNet: The national molecular subtyping network for foodborne disease surveillance

The U.S. Centers for Disease Control reports PulseNet is celebrating 20 years of public health achievements in transforming the way foodborne disease outbreaks are detected and investigated.

pulse-net-20-200PulseNet is a national surveillance network of federal, state, and local public health laboratories that work together to detect foodborne disease outbreaks by connecting DNA fingerprints of bacteria that cause illness. The network facilitates the early identification of common sources of foodborne outbreaks and helps regulatory agencies identify areas where implementation of new measures are likely to improve the safety of the food supply.

A recent economic evaluation of PulseNet activities suggests that the network prevents at least 270,000 illnesses from infection with Salmonella, E. coli, and Listeria and saves an estimated $500 million each year. In 2013, PulseNet began using whole genome sequencing (WGS) to detect outbreaks caused by Listeria, the most deadly foodborne pathogen. PulseNet is quickly expanding the use of WGS in state laboratories and has begun using WGS in investigations of other foodborne pathogens such as Campylobacter, E. coli, and Salmonella. With incorporation of WGS and other advanced molecular detection methods, PulseNet will continue to improve foodborne disease detection and identify outbreaks faster and with more accuracy.

Additional information regarding CDC’s Advanced Molecular Detection initiative is available at http://www.cdc.gov/amd/. Additional materials on the 20th anniversary of PulseNet, including success stories from state public health laboratories and fact sheets are available at the CDC PulseNet website.

Sporadic illnesses, outbreak illnesses, are similiar

Outbreak data have been used to estimate the proportion of illnesses attributable to different foods. Applying outbreak-based attribution estimates to non-outbreak foodborne illnesses requires an assumption of similar exposure pathways for outbreak and sporadic illnesses. This assumption cannot be tested, but other comparisons can assess its veracity.

vomit-FBOur study compares demographic, clinical, temporal, and geographic characteristics of outbreak and sporadic illnesses from Campylobacter, Escherichia coli O157, Listeria, and Salmonella bacteria ascertained by the Foodborne Diseases Active Surveillance Network (FoodNet). Differences among FoodNet sites in outbreak and sporadic illnesses might reflect differences in surveillance practices. For Campylobacter, Listeria, and Escherichia coli O157, outbreak and sporadic illnesses are similar for severity, sex, and age. For Salmonella, outbreak and sporadic illnesses are similar for severity and sex. Nevertheless, the percentage of outbreak illnesses in the youngest age category was lower.

Therefore, we do not reject the assumption that outbreak and sporadic illnesses are similar.

Comparing characteristics of sporadic and outbreak-associated foodborne illnesses, United States, 2004-2011

Emerging Infectious Diseases, Volume 22, Number 7, July 2016, DOI: 0.3201/eid2207.150833

E.D. Ebel, M.S. Williams, D. Cole, C.C. Travis, K.C. Klontz, N.J. Golden, R.M. Hoekstra


Typhoid fever spread from asymptomatic restaurant worker in Colorado

On September 11, 2015, a single case of typhoid fever, caused by Salmonella Typhi infection, was reported to the Colorado Department of Public Health and Environment (CDPHE).

symptoms_of_typhoid_feverBecause the patient (patient A) had symptom onset September 2 and had traveled internationally for 4 days 60 days before symptom onset, the case initially was thought to be travel-associated* (1,2).

On October 1, a second case of S. Typhi infection was reported in patient B, with symptom onset September 20. Patient B reported no international travel or contact with ill persons or known carriers. Patients A and B resided approximately 6 miles (10 kilometers) apart and had no discernible epidemiologic connection. Family members of patients A and B tested negative for S. Typhi. CDPHE and the Weld County Department of Public Health and Environment (WCDPHE) investigated to 1) determine whether these cases represented a larger outbreak, 2) identify common exposure sources, and 3) stop transmission. Investigators determined that the typhoid fever in both patients and in a third patient (patient C) was associated with eating in the same restaurant during a 5-day period.

CDPHE defined a case of typhoid fever as clinically compatible illness with isolation of S. Typhi during July 1–October 15 and identification of an isolate with one of two pulsed-field gel electrophoresis (PFGE) outbreak patterns that differed by one band. A carrier was defined as a person who had contact with patients, reported no recent illness, and had S. Typhi with either of the PFGE outbreak patterns in an isolate from a rectal swab or stool specimen. Case finding included searching PulseNet for other isolates that might have been associated with the Colorado cases (3). On October 13, CDPHE issued a health alert notification to clinicians, local public health authorities, and laboratories to be vigilant for additional cases and to encourage reporting. During October 1–9, CDPHE and WCDPHE used the Salmonella National Hypothesis Generating Questionnaire (4), credit card receipts, food recall, shopper card records, and social media to identify potential exposures shared by patients A and B during the 60 days preceding symptom onset. Investigators found that the two patients had fresh produce purchases from the same grocery stores and had six common restaurant exposures.

On October 19, CDPHE was notified of a third Weld Country resident who had tested positive for S. Typhi infection. Patient C had symptom onset September 15 and reported no recent travel or relation to patient A or B. Patient C was interviewed using the Salmonella questionnaire, and credit card receipts were reviewed. Patient C did not shop at the same grocery stores as patients A or B, but all three patients had eaten at restaurant A during August 16–20, 2015. Patients A and C were hospitalized. Isolates from patients B and C had indistinguishable PFGE patterns (pattern 2), and the isolate from patient A had a 1-band difference (pattern 1), which met the PFGE outbreak definition.

s.typhi.symptomsCDPHE hypothesized that a chronic S. Typhi carrier might be working in food service at restaurant A, where food is prepared using fresh ingredients. Possible transmission routes were investigated through environmental assessments and staff interviews; food service staff members were asked to be tested for S. Typhi. Environmental assessments performed on October 27 found no deficiencies in hand hygiene or other food handling issues. Administrators from restaurant A provided a list of all current and former employees who worked in food handling during August 10–August 20, 2015. These more conservative dates were chosen because food might have been served as many as 4 days after preparation, and because of concerns regarding the accuracy of credit card statement dates.

On October 28, current restaurant employees were confidentially interviewed at a local clinic by CDPHE and WCDPHE regarding international travel, symptoms, and work tasks. Because bacterial shedding can be intermittent, employees were requested to collect rectal swab specimens from themselves on October 28 and November 3 for culture and PFGE testing of isolates. All employees were allotted paid time to be interviewed and provide specimens. By October 29, a total of 28 (100%) current employees had responded and provided one or more rectal swab specimens. On October 30, CDPHE was notified by the state health laboratory that S. Typhi had been isolated from one employee. The isolate’s PFGE pattern was indistinguishable from outbreak pattern 1, the pattern of patient A.

Interviews with the infected restaurant worker revealed travel to a country with endemic typhoid fever 15 years earlier, but no recent symptoms, and no contact with any ill persons. The worker was excluded from food service work, treated with azithromycin for 28 days, and monitored with stool testing until three consecutive specimens obtained ≥1 month apart were negative for S. Typhi (2). Restaurant A agreed to keep the worker’s job open and allow him to return to work once he was no longer a carrier.

Typhi infection is a nationally notifiable condition; in Colorado, reporting is required within 24 hours of case detection. Notable clinical symptoms of typhoid fever include insidious onset of fever, and headache, constipation, chills, myalgia, and malaise (1). Unlike other Salmonella species, S. Typhi does not commonly cause diarrhea, and vomiting typically is not severe (1).

Typhi infection is endemic in many low-income countries; an estimated 22 million cases and 200,000 deaths occur each year (2). In the United States, approximately 5,700 cases of typhoid fever are reported annually; the majority occur among travelers (1). In Colorado during 2009–2014, on average, six cases of confirmed typhoid fever were reported annually; all cases were associated with international travel or attributed to a household member or close contact with a carrier. Humans are the only reservoir for S. Typhi; disease is transmitted via the fecal-oral route, typically by contaminated food or water. Chronic carriage occurs in 2%–5% of cases (1,2), and shedding of S. Typhi in chronic carrier stools can be intermittent.

This investigation highlights the potential for chronic S. Typhi carriers to cause illness in other persons, even years after infection. When cases of typhoid fever not associated with travel are detected, rapid and thorough interviewing is essential. Social media posts and credit card receipts to detect common exposures can be useful. The high cooperation rate among workers at the restaurant, which is rare in foodborne outbreak investigations, was attributed to the restaurant’s support and accommodation, demonstrating the importance of collaboration among local public health, state public health, public health laboratories, patients, and industry for successful investigations.

Typhoid fever outbreak associated with an asymptomatic carrier at a restaurant ― Weld County, Colorado, 2015

MMWR Morb Mortal Wkly Rep 2016;65:606–607. June 2016, DOI: http://dx.doi.org/10.15585/mmwr.mm6523a4.

Jessica Hancok-Allen, Alicia B. Cronquist, JoRene Peden, Debra Adamson, Nereida Corral, Kerri Brown


Better environmental control, less Legionnaires’ disease

Background: The number of reported cases of Legionnaires’ disease, a severe pneumonia caused by the bacterium Legionella, is increasing in the United States. During 2000–2014, the rate of reported legionellosis cases increased from 0.42 to 1.62 per 100,000 persons; 4% of reported cases were outbreak-associated. Legionella is transmitted through aerosolization of contaminated water. A new industry standard for prevention of Legionella growth and transmission in water systems in buildings was published in 2015. CDC investigated outbreaks of Legionnaires’ disease to identify gaps in building water system maintenance and guide prevention efforts.

legionaires.jun.16Methods: Information from summaries of CDC Legionnaires’ disease outbreak investigations during 2000–2014 was systematically abstracted, and water system maintenance deficiencies from land-based investigations were categorized as process failures, human errors, equipment failures, or unmanaged external changes.

Results: During 2000–2014, CDC participated in 38 field investigations of Legionnaires’ disease. Among 27 land-based outbreaks, the median number of cases was 10 (range = 3–82) and median outbreak case fatality rate was 7% (range = 0%–80%). Sufficient information to evaluate maintenance deficiencies was available for 23 (85%) investigations. Of these, all had at least one deficiency; 11 (48%) had deficiencies in ≥2 categories. Fifteen cases (65%) were linked to process failures, 12 (52%) to human errors, eight (35%) to equipment failures, and eight (35%) to unmanaged external changes.

Conclusions and Implications for Public Health Practice: Multiple common preventable maintenance deficiencies were identified in association with disease outbreaks, highlighting the importance of comprehensive water management programs for water systems in buildings. Properly implemented programs, as described in the new industry standard, could reduce Legionella growth and transmission, preventing Legionnaires’ disease outbreaks and reducing disease.

Deficiencies in environmental control identified in outbreaks of Legionnaires’ disease — North America, 2000–2014


L.E. Garrison, J.M. Kunz, L.A. Cooley, M.R. Moore, C. Lucas, S. Schrag, J. Sarisky, C.G. Whitney


More proof: Same E. coli O121 found in flour in sick consumer’s home

On June 10, 2016, U.S. Food and Drug Administration whole genome sequencing on E. coli O121 isolates recovered from an open sample of General Mills flour belonging to one of the consumers who was sickened was found to be closely genetically related the clinical isolates from human illnesses. The flour came from a lot that General Mills has recalled.

flour.e.coli.O121To date, 38 people infected with the outbreak strain of E. coli O121 have been reported from 20 states. Illnesses started on dates ranging from December 21, 2015 to May 3, 2016. Ten ill people have been hospitalized. In its investigation, CDC learned that some people who got sick had eaten or handled raw dough.

FDA’s traceback investigation determined that the raw dough eaten or handled by ill people or used in restaurant locations was made using General Mills flour that was produced in the same week in November 2015 at the General Mills facility in Kansas City, Missouri. Epidemiology and traceback evidence available at this time indicate that General Mills flour manufactured at this facility is the likely source of the outbreak.

On May 31, 2016, following a conference call among FDA, CDC and the firm, General Mills conducted a voluntary recall of flour products produced between November 14, 2015 and December 4, 2015. Recalled products are sold in stores nationwide or may be in consumers’ pantries and are sold under three brand names: Gold Medal flour, Signature Kitchens flour and Gold Medal Wondra flour. The varieties include unbleached, all-purpose, and self-rising flours.

General Mills also sells bulk flour to customers who use it to make other products. General Mills has contacted these customers directly to inform them of the recall. FDA is working with General Mills to ensure that the customers have been notified, and to evaluate the recall for effectiveness.

Flour has a long shelf life, and bags of flour may be kept in peoples’ homes for a long time. Consumers unaware of the recall could continue to eat these recalled flours and potentially get sick. If consumers have any of these recalled flours in their homes, they should throw them away.

(this is bad)

kids.cookie.doughPeople usually get sick from STEC O121 2-8 days (average of 3-4 days) after swallowing the bacteria. Most people develop diarrhea (often bloody) and abdominal cramps. Most people recover within a week.

Some illnesses last longer and can be more severe, resulting in a type of kidney failure called hemolytic uremic syndrome (HUS). HUS can occur in people of any age, but is most common in young children under 5 years, older adults, and people with weakened immune systems.

Restaurants and retailers should throw away any recalled General Mills flour. Some ill people reported handling raw dough at restaurants prior to eating their meal. Restaurants that allow their customers to handle raw dough should evaluate whether this practice is appropriate.

Restaurants and retailers should be aware that flour may be a source of pathogens and should control the potential for cross-contamination of food processing equipment and the food processing environment. They should follow the steps below:

Wash and sanitize display cases and refrigerators where potentially contaminated products were stored.

Wash and sanitize cutting boards, surfaces, and utensils used to prepare, serve, or store potentially contaminated products.

Wash hands with hot water and soap following the cleaning and sanitation process.

Retailers, restaurants, and other food service operators who have processed and packaged any potentially contaminated products need to be concerned about cross contamination of cutting surfaces and utensils through contact with the potentially contaminated products.

Regular frequent cleaning and sanitizing of food contact surfaces and utensils used in food preparation may help to minimize the likelihood of cross-contamination.

(this is bad)

kid-cookie3What Do Consumers Need To Do?

The recalled General Mills products have a long shelf-life, and they may be in peoples’ homes. Consumers unaware of the recall could continue to eat these products and potentially get sick.

If consumers have these products in their homes, they should throw it away. As a precaution, flour no longer stored in its original packaging should be discarded if it could be covered by this recall, and the containers used to store this flour should be thoroughly washed and sanitized.

Three people who became ill reported handling raw dough at restaurants prior to eating their meal. As a precaution, consumers, especially children, should not handle raw dough at home or at restaurant locations.

FDA warns against eating raw dough products made with any brand of flour or baking mix before cooking. Consumers should always practice safe food handling and preparation measures when handling flour. The FDA recommends following these safe food-handling practices to stay healthy:

Do not eat or play with any raw cookie dough or any other raw dough product made with flour that is intended to be cooked or baked.

Follow package directions on baking mixes and other flour-containing products for proper cooking temperatures and for specified times.

Wash hands, work surfaces, and utensils thoroughly after contact with raw dough products containing flour.

Keep raw foods separate from other foods while preparing them to prevent any contamination that might be present from spreading.

CDC continues to say no: Should you kiss chicks – 2016 edition

The U.S. Centers for Disease Control and Prevention, multiple states, and the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (USDA-APHIS) are investigating seven separate multistate outbreaks of human Salmonella infections linked to contact with live poultry in backyard flocks.

baby-chick-325pxIn the seven outbreaks, a total of 324 people infected with the outbreak strains of Salmonella were reported from 35 states.

Among people with available information, illnesses started on dates ranging from January 4, 2016 to May 11, 2016.

Sixty-six ill people were hospitalized, and one death was reported. Salmonella infection was not considered to be a contributing factor in the reported death.

Eighty-eight (27%) ill people were children 5 years of age or younger.

Epidemiologic, traceback, and laboratory findings linked the seven outbreaks to contact with live poultry such as chicks and ducklings from multiple hatcheries.

Regardless of where they were purchased, all live poultry can carry Salmonella bacteria, even if they look healthy and clean.

These outbreaks are a reminder to follow steps to enjoy your backyard flocks and keep your family healthy.

Always wash hands thoroughly with soap and water right after touching live poultry or anything in the area where the birds live and roam.

Do not let live poultry inside the house.

Do not let children younger than 5 years of age handle or touch chicks, ducklings, or other live poultry without supervision.

These outbreaks are expected to continue for the next several months since flock owners might be unaware of the risk of Salmonella infection from live poultry or participate in risky behaviors that can result in infection.


It has excellent sanitation: Winter’s coming so people stop going to the heated pool

I miss the hot tub we had in Kansas.

Yet in the U.S., thousands of public pools, hot tubs are closed each year due to serious violations.

caddyshack.pool.poop-1The U.S. Centers for Disease Control and Prevention reports that inspections of public pools and other aquatic venues enforce standards that can prevent illness, drowning, and pool-chemical–associated injuries such as poisoning or burns.

“No one should get sick or hurt when visiting a public pool, hot tub, or water playground,” said Beth Bell, M.D., M.P.H., director of CDC’s National Center for Emerging and Zoonotic Infectious Diseases. “That’s why public health and aquatics professionals work together to improve the operation and maintenance of these public places so people will be healthy and safe when they swim.”

Inspection data were collected in 2013 in the five states with the most public pools and hot tubs: Arizona, California, Florida, New York and Texas. Researchers reviewed data on 84,187 routine inspections of 48,632 public aquatic venues, including pools, hot tubs, water playgrounds and other places where people swim in treated water.

Among the key findings:

Most inspections of public aquatic venues (almost 80 percent) identified at least one violation.

1 in 8 inspections resulted in immediate closure because of serious health and safety violations.

1 in 5 kiddie/wading pools were closed—the highest proportion of closures among all inspected venues.

The most common violations reported were related to improper pH (15 percent), safety equipment (13 percent), and disinfectant concentration (12 percent).

“Environmental health practitioners, or public health inspectors, play a very important role in protecting public health. However, almost one third of local health departments do not regulate, inspect, or license public pools, hot tubs, and water playgrounds,” said Michele Hlavsa, R.N., M.P.H., chief of CDC’s Healthy Swimming Program. “We should all check for inspection results online or on site before using public pools, hot tubs, or water playgrounds and do our own inspection before getting into the water.”

When visiting public or private pools, swimmers and parents of young swimmers can complete their own inspection using a short and easy checklist that will identify some of the most common health and safety problems:

Use a test strip (available at most superstores or pool-supply stores) to determine if the pH and free chlorine or bromine concentration are correct. CDC recommends:

diaper.poolFree chlorine concentration of at least 1 ppm in pools and at least 3 ppm in hot tubs/spas.

Free bromine concentration of at least 3 ppm in pools and at least 4 ppm in hot tubs/spas.

pH of 7.2–7.8.

Make sure the drain at the bottom of the deep end is visible. Clear water allows lifeguards and other swimmers to see swimmers underwater who might need help.

Check that drain covers appear to be secured and in good repair. Swimmers can get trapped underwater by a loose or broken drain cover.

Confirm that a lifeguard is on duty at public venues. If not, check whether safety equipment like a rescue ring with rope or pole is available.

If you find problems, do not get into the water and tell the person in charge so the problems can be fixed. For more information and other healthy and safe swimming steps, visit www.cdc.gov/healthywater/swimming.

Before CDC-led development of the Model Aquatic Health Code, there were no national standards for the design, construction, operation, and maintenance practices to prevent illness and injury at public treated recreational water venues. Now, local and state authorities can voluntarily adopt these science- and best practices–based guidelines to make swimming and other activities at public pools and other aquatic venues healthier and safer. The second edition of the code will be released during the 2016 swim season. For more information about the Model Aquatic Health Code, visitwww.cdc.gov/mahc.

hot.tubProblem/Condition: Aquatic facility–associated illness and injury in the United States include disease outbreaks of infectious or chemical etiology, drowning, and pool chemical–associated health events (e.g., respiratory distress or burns). These conditions affect persons of all ages, particularly young children, and can lead to disability or even death. A total of 650 aquatic facility–associated outbreaks have been reported to CDC for 1978–2012. During 1999–2010, drownings resulted in approximately 4,000 deaths each year in the United States. Drowning is the leading cause of injury deaths in children aged 1–4 years, and approximately half of fatal drownings in this age group occur in swimming pools. During 2003–2012, pool chemical–associated health events resulted in an estimated 3,000–5,000 visits to U.S. emergency departments each year, and approximately half of the patients were aged <18 years. In August 2014, CDC released the Model Aquatic Health Code (MAHC), national guidance that can be adopted voluntarily by state and local jurisdictions to minimize the risk for illness and injury at public aquatic facilities.

Reporting Period Covered: 2013.

Description of System: The Network for Aquatic Facility Inspection Surveillance (NAFIS) was established by CDC in 2013. NAFIS receives aquatic facility inspection data collected by environmental health practitioners when assessing the operation and maintenance of public aquatic facilities. This report presents inspection data that were reported by 16 public health agencies in five states (Arizona, California, Florida, New York, and Texas) and focuses on 15 MAHC elements deemed critical to minimizing the risk for illness and injury associated with aquatic facilities (e.g., disinfection to prevent transmission of infectious pathogens, safety equipment to rescue distressed bathers, and pool chemical safety). Although these data (the first and most recent that are available) are not nationally representative, 15.7% of the estimated 309,000 U.S. public aquatic venues are located in the 16 reporting jurisdictions.

Results: During 2013, environmental health practitioners in the 16 reporting NAFIS jurisdictions conducted 84,187 routine inspections of 48,632 public aquatic venues. Of the 84,187 routine inspection records for individual aquatic venues, 78.5% (66,098) included data on immediate closure; 12.3% (8,118) of routine inspections resulted in immediate closure because of at least one identified violation that represented a serious threat to public health. Disinfectant concentration violations were identified during 11.9% (7,662/64,580) of routine inspections, representing risk for aquatic facility–associated outbreaks of infectious etiology. Safety equipment violations were identified during 12.7% (7,845/61,648) of routine inspections, representing risk for drowning. Pool chemical safety violations were identified during 4.6% (471/10,264) of routine inspections, representing risk for pool chemical–associated health events.

Interpretation: Routine inspections frequently resulted in immediate closure and identified violations of inspection items corresponding to 15 MAHC elements critical to protecting public health, highlighting the need to improve operation and maintenance of U.S. public aquatic facilities. These findings also underscore the public health function that code enforcement, conducted by environmental health practitioners, has in preventing illness and injury at public aquatic facilities.

Public Health Action: Findings from the routine analyses of aquatic facility inspection data can inform program planning, implementation, and evaluation. At the state and local level, these inspection data can be used to identify aquatic facilities and venues in need of more frequent inspections and to select topics to cover in training for aquatic facility operators. At the national level, these data can be used to evaluate whether the adoption of MAHC elements minimizes the risk for aquatic facility–associated illness and injury. These findings also can be used to prioritize revisions or updates to the MAHC. To optimize the collection and analysis of aquatic facility inspection data and thus application of findings, environmental health practitioners and epidemiologists need to collaborate extensively to identify public aquatic facility code elements deemed critical to protecting public health and determine the best way to assess and document compliance during inspections.

Immediate Closures and Violations Identified During Routine Inspections of Public Aquatic Facilities — Network for Aquatic Facility Inspection Surveillance, Five States, 2013

Surveillance Summaries / May 20, 2016 / 65(5);1–26

Michele C. Hlavsa, MPH; Taryn R. Gerth, MPH; Sarah A. Collier, MPH; Elizabeth L. Dunbar, MPH; Gouthami Rao, MPH; Gregory Epperson; Becky Bramlett; David F. Ludwig, MPH; Diana Gomez, MPH; Monty M. Stansbury; Freeman Miller; Jeffrey Warren; Jim Nichol; Harry Bowman; Bao-An Huynh, MPH; Kara M. Loewe; Bob Vincent; Amanda L. Tarrier, MPH; Timothy Shay; Robert Wright; Allison C. Brown, PhD; Jasen M. Kunz, MPH; Kathleen E. Fullerton, MPH; James R. Cope, PhD; Michael J. Beach, PhD


Who ya gonna call? MicrobeNet, CDC’s disease identification tool

MicrobeNet, an innovative online tool designed by the U.S. Centers for Disease Control and Prevention (CDC) has, since 2013, has helped laboratorians and doctors get the information they need to accurately diagnose causes of disease faster and save lives.

ghostbusters-imageMicrobeNet provides laboratorians with unprecedented access to CDC’s virtual microbe library of more than 2,400 rare and emerging infectious bacteria and fungi at no cost. The recent multi-state outbreak of Elizabethkingia in Wisconsin, Illinois and Michigan underscores the need for a tool like MicrobeNet in diagnostic laboratories. Hospitals and health departments using MicrobeNet can identify rare bacteria like Elizabethkingia quicker, and know they’re comparing their results to the most comprehensive and accurate disease database available.

In partnership with Bruker Corp., CDC has recently added a new module to MicrobeNet that allows labs to search the protein signatures of the bacteria and compare them to the rare pathogens in CDC’s MicrobeNet library by using Bruker’s MALDI Biotyper systems. Using MALDI to test is extremely fast and cheaper to run than many other types of testing, making the technology increasingly popular among labs. The new MicrobeNet module will be immediately available to laboratorians and clinicians using the Bruker system in labs nationwide. Until the addition of the MALDI library, MicrobeNet offered two ways to search pathogens: by DNA sequence or biochemical tests (chemical reactions caused by the bacteria).

MicrobeNet can dramatically improve the health of people in the United States and around the world by cutting the time for testing from about a week to a few hours.

“MicrobeNet has the potential to revolutionize public health,” said John R. McQuiston, PhD, team lead for CDC’s Special Bacteriology Reference Laboratory and CDC’s lead for MicrobeNet. “This system helps public health labs and hospitals quickly identify some of the most difficult pathogens to grow and detect. In turn, MicrobeNet will help treat patients faster and allow health departments to respond to public health emergencies more effectively.”

Traditionally, clinicians or laboratorians who needed to identify a rare bacteria or fungi or to confirm an infectious disease diagnosis with one of these organisms needed to send a sample to CDC and await test results. With MicrobeNet, they can access the information they need immediately.

One of MicrobeNet’s greatest advantages lies in allowing two-way communications between users and CDC staff who are experts in the diseases that users are searching. MicrobeNet allows state public health experts to monitor disease trends in their state in real time and recognize when those trends might indicate an outbreak. It also provides public health agencies with a valuable snapshot of nationwide disease trends and will help CDC identify multistate outbreaks and provide information to public health partners in the affected states.

In addition to being faster, using the MALDI module in MicrobeNet offers dramatic cost savings for clinical and public health laboratories because they no longer will need to develop their own pathogen libraries. These laboratories will also have the assurance that their information has been confirmed by CDC experts. In addition, for many germs, MicrobeNet provides doctors with information about which antibiotics the bacteria are resistant to. By quickly identifying the species of bacteria, lab staff can pass this critical information to the doctors who can use it to help make a diagnosis and select the right treatment, thus reducing the risk of their patients developing drug-resistant infections.

MicrobeNet was launched in 2013 by the Division of High-Consequence Pathogens and Pathology’s Special Bacteriology Reference Laboratory as a way to help state public health laboratories and other diagnostic labs rapidly identify rare and emerging infections, with the goal of saving time, money, and lives. MicrobeNet initially had a DNA sequence search module. Since then, MicrobeNet has added a phenotypic and biochemical search tool and, through a partnership with ThermoFisher, a DNA sequence editing tool, MicrobeBridge. CDC has also entered pages of information, including contact information for the subject matter expert for every species.

Funded in part by CDC’s Advanced Molecular Detection initiative, MicrobeNet currently includes information about more than 2,400 bacteria and fungi, including images and information about growing these organisms. Every month, CDC adds information on as many as 100 new species to MicrobeNet to aid in detection, diagnosis, and planning treatment for sick patients.

For more information on MicrobeNet, please visit: http://www.cdc.gov/microbenet/. Labs wishing to join MicrobeNet can request an account by visiting https://microbenet.cdc.gov or emailing MicrobeNet@cdc.gov.

Stop kissing small turtles: 133 sick from four multistate outbreaks of human Salmonella

Since 2015, the U.S. Centers for Disease Control, multiple states, U.S Fish and Wildlife Service, the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (USDA-APHIS), and the U.S. Food and Drug Administration (FDA) Center for Veterinary Medicine have investigated four separate multistate outbreaks of human Salmonella infections linked to contact with small turtles.

turtle.kissIn the four outbreaks, a total of 133 people infected with the outbreak strains of Salmonella were reported from 26 states between January 16, 2015 and April 8, 2016:

  • 38 ill people were hospitalized, and no deaths were reported;
  • 41% of ill people were children 5 years of age or younger; and,
  • epidemiologic and laboratory findings linked the four outbreaks of human Salmonella infections to contact with small turtles or their environments, such as water from a turtle habitat.

Since 1975, the FDA has banned the sale and distribution of turtles with a shell length of less than 4 inches in size as pets because they are often linked to Salmonella infections, especially in young children.

Small turtles should not be purchased as pets or given as gifts.

All turtles, regardless of size, can carry Salmonella bacteria even if they look healthy and clean. These outbreaks are a reminder to follow simple steps to enjoy pet reptiles and keep your family healthy.

It’s not simple or so many people wouldn’t get sick – so many little kids.

The outbreak is expected to continue at a low level for the next several months since consumers might be unaware of the risk of Salmonella infection from small turtles. If properly cared for, turtles have a long life expectancy.

Change the law, name the supplier: Salmonella in seed transfers to sprouts in Kansas and sickens 26

They’re probably still eating sprout-laden sandwiches at science-based faculty meetings at Kansas State University.

jimmy.john's.sproutsFollowing an initial announcement of eight people sick with Salmonella from sprouts in Kansas and Missouri – followed by surveillance silence – the U.S. Centers for Disease Control now reports that 26 people were infected with the outbreak strains of Salmonella Muenchen (25 people), or Salmonella Kentucky (1 person), as reported from 12 states. Eight people were hospitalized and no deaths were reported.

In February 2016, state and local health and regulatory officials in several states traced back the source of the sprouts from multiple restaurant locations where ill people ate them, and identified Sweetwater Farms of Inman, Kansas, as a supplier of alfalfa sprouts to all of these locations. The FDA collected and tested irrigation water and alfalfa sprout samples from Sweetwater Farms LLC and found Salmonella Kentucky and Salmonella Cubana. Salmonella Muenchen was not isolated.

On February 19, 2016, FDA and other federal, state, and local agencies briefed Sweetwater Farms LLC on their findings, and the firm voluntarily recalled alfalfa sprouts grown from a specific seed lot.

On February 26, 2016, Sweetwater Farms informed the FDA that it would recall all of its sprout products from the market.

After the recalls by Sweetwater Farms were completed, Salmonella Muenchen illnesses were still reported by people who reported eating alfalfa sprouts before they got sick. FDA traceback investigations indicated that several sprouters other than Sweetwater Farms produced the alfalfa sprouts these ill people ate. All of these sprouters, as well as Sweetwater Farms, used the same seed lot.

FDA tested samples of seeds from this lot and isolated Salmonella Cubana with the same DNA fingerprint of the Salmonella Cubana isolated in irrigation water from Sweetwater Farms. FDA contacted the seed supplier, who then called for the return of the contaminated seed lot from growers. The seed supplier is not named here because FDA is prohibited by law from releasing certain information about supply chains, which may constitute confidential commercial information. However, FDA has been able to confirm that all domestic sprouters who received contaminated seeds either returned or destroyed the seeds, and the shelf life of all sprouts grown from this seed lot has expired. Therefore, no sprouts from the contaminated seed lot are expected to be on the market.

sprout.santa.barf.xmasOn May 13, 2016, CDC reports that this outbreak appears to be over. FDA has provided the sprouters with information on reducing microbial food safety hazards for sprouted seeds and complying with new standards for growing, harvesting, packing, and holding of produce for human consumption under the Produce Safety Rule, which beings to go into effect for sprouters in January 2017 with additional time for small and very small operations. In particular, covered sprouters will now be required to comply with sprout-specific requirements such as treating seeds to reduce the presence of microorganisms of public health significance, testing the growing environment for Listeria as well as testing each production batch of spent sprout irrigation water or sprouts for E. coli O157:H7, Salmonella species and, under certain conditions, other pathogens. In addition, sprouters would be expected to comply with all other applicable requirements of the Produce Safety Rule, such as requirements related to worker health and hygiene, agricultural water and buildings, tools and equipment.

An updated table of raw sprout related outbreaks is available at: http://barfblog.com/wp-content/uploads/2016/04/Sprout-associated-outbreaks-4-27-16.xlsx