Sunday, October 15, 2017

Biosensors Detect Harmful Bugs in the Lungs of Cystic Fibrosis Patients

Pseudomonas aeruginosa are strains of bacteria that are widely found in the environment. Pseudomonas is a major cause of lung infections in people with cystic fibrosis. The bacteria thrive in moist environments and equipment, such as humidifiers and catheters in hospital wards, and in kitchens, bathrooms, pools, hot tubs and sinks.

Pseudomonas infections are known as opportunistic. This means the bacteria only cause infections when a person has CF or another condition that weakens the body's immune system.

Pseudomonas is one of the most common bacteria found in people with CF. About half of all people with CF have Pseudomonas. More than 60 percent of adults with CF have Pseudomonas.

The number of people with CF with the bacteria has been decreasing, however.Once Pseudomonas is established in the airways, it's very difficult to eliminate. But aggressive treatment can delay the development of long-term infection.

The rapid detection of Pseudomonas in CF patients is also paramount in treating patients. And scientists at the Imperial College London are doing just that. The following text provides an overview of their work.

Biosensors and the detection of Pseudomonas

A team of Imperial researchers has developed a tool which 'lights up' when it detects the chemical signature of harmful bacteria in the lung.

In a clinical first, the group from the Department of Medicine used the tools, called cell-free biosensors, to test samples of sputum (phlegm) from patients with cystic fibrosis (CF).

Biosensors are based on engineered DNA circuits, designed to detect changes in their environment, such as the presence of chemicals, or changes in pH or temperature.

These tools, which harness the biological machinery inside cells, can be used to quickly spot chemical traces of active microbial colonies in samples from the lung and could help to accurately diagnose bacterial infections in vulnerable patients.

In a small, proof-of-concept study, the team found that their biosensors could accurately detect markers of Pseudomonas bacteria – a leading cause of chest infections in people with weak immune systems or chronic conditions, such as CF – and were as sensitive as existing chemical diagnostic tests but could potentially be cheaper and easier to use.

Rapid diagnostic tests

The researchers are hopeful they could eventually develop their cell-free sensors into a range of rapid diagnostic tests which could be used either at home, GP surgeries or in hospital clinics or even in remote areas of the world with limited access to hospital diagnostics, at a fraction of the price of existing tests.

Professor Paul Freemont, co-founder and co-director of The Centre for Synthetic Biology and Innovation at Imperial, said: “The driving force behind this research is to show that these tools work and could be used to detect particular diagnostic markers associated with infection.”

He added: “By applying an engineering approach to biology, these systems could be altered to sense for any microbe we choose. The possibilities for public health and cost-savings for health systems could be considerable.”

Biosensors have emerged through the growing field of synthetic biology, with scientists tweaking living cells to respond to certain conditions, such as the presence of a chemical compound.

The engineered DNA circuit: when the bacterial molecules (AHL) are present they trigger the production of a coloured protein (GFP)

At the heart of the technique are lengths of engineered DNA which, when inserted into a living cell, act as a circuit. If the right signal – such as a specific chemical compound – is present, then the circuit is switched ‘on’ and the cell produces a signal in the form of a coloured output, in this case a green fluorescent protein. If the substrate is not present, then the circuit remains ‘off’ and there is no signal.

In the latest study, published this week in the journal ACS Synthetic Biology, researchers report on using a ‘cell-free’ form of sensor to test clinical samples for the first time. Instead of being contained within the membrane of a cell, the engineered DNA circuit and cellular machinery of their sensors are free-floating in a solution.

The team engineered their sensor’s circuit to respond to a molecule produced specifically by the bacterium Pseudomonas aeruginosa. These bacteria release a chemical signature in order to communicate with bacteria around them and to sense how many of them there are. As they replicate, more cells release the signature, and so the concentration of the signal increases, giving the bacteria an idea of the state of their population.

Previous studies have revealed levels of this same P. aeruginosa signature were higher in hospitalised patients than those with stable condition.

Samples taken from the lungs of patients, either with or without P. aeruginosa infection, were screened by adding them to tiny wells containing solutions of the biosensor. After four hours the samples were tested for green fluorescent protein – a sign that the bacterial signature was present.

Analysis revealed that the cell-free biosensor was able to detect the bacterial signature with the same accuracy as existing diagnostic tests, called liquid chromatography tandem mass spectrometry (LC-MS/MS). The biosensors were able to detect the concentration of the signal within a close range to LC-MS/MS.

Taking the technology forward

Currently, a major limitation for the cell-free sensors is the amount of time taken to prepare samples before testing, with lung sputum samples needing to be ‘cleaned up’ with the removal of biological materials which could interfere with the results.

In addition, as the DNA is synthetic – engineered in the lab – it would need to be disposed of carefully, with concerns around potential to contaminate the environment or pass to other organisms.

However, according to the researchers, the approach could offer significant cost-savings compared to the existing LC-MS/MS detection method. If suitably scaled up, using similar cell free biosensors could work out to be a fraction of the cost per sample.

Professor Jane Davies of the NHLI and an honorary consultant paediatrician at the Royal Brompton Hospital said: “Pseudomonas is the major infection in patients with cystic fibrosis and is closely linked to the severe lung disease which develops over time leading to premature death.

“At the moment, we only have opportunities to detect infection when patients come to clinics, perhaps every 2-3 months. A point of care test could transform the way in which we monitor patients, allowing us to treat early and personalise therapies.”

The group is now exploring how to take the technology forward and develop working prototypes, as well as a test to detect the signal in a patient’s urine. If the biosensor solution could be freeze-dried, this could even potentially take the form of a credit card-sized paper-based test, which would be affordable and ready for use in the field.

Loren Cameron, a PhD student in Freemont’s lab and one of the study authors, said: “Now we have shown these types of biosensors can be used with clinical samples, the next step is to refine our approach. We hope that in future, tools like this could be used to help test for the presence or severity of bacterial infections.” Ms Cameron is one of five postgraduate students funded as part of the Cystic Fibrosis Trust’s Strategic Research Centre for Pseudomonas infection.

Ke Yan Wen, a graduated PhD student from Freemont’s lab and also one of the lead authors, said: "We believe that cell-free systems are a promising platform for developing biosensors, since they are easy to use, produce a rapid response, and can be stored long-term in normal conditions.”

Source: Imperial College London

Thursday, September 14, 2017

My Opinions on Sage Products Rapid Method Warning Letter (and a reply to Tim Sandle's Blog)


Tim Sandle published a recent blog post concerning a (FDA) Warning Letter related to an inadequate validation of a rapid microbiological method by Sage Products Inc. Tim's post reviews the warning letter findings and poses a number of follow up questions.

My opinions are as follows. Tim's original blog post is reproduced after my opinion. Tim's blog on this topic may be viewed by clicking here.

The FDA warning letter may be viewed by clicking here.


MY OPINION

This was an unfortunate event that should, in no way, dissuade firms from implementing rapid methods. To support my opinion, I need to provide clarity around the warning letter points, which are presented below in quotation marks.

“Your firm failed to establish and document the accuracy, sensitivity, specificity, and reproducibility of its test methods. Specifically, you use the [redacted] method to screen for microbiological contamination in drugs produced entirely at your facility and those manufactured under contract. This [redacted] screening method [redacted] for microbiological examination of your liquid drug products is not adequate for its intended use. You attempted to validate your [redacted] microbial detection method, but were not able to demonstrate that it could reliably and repeatedly determine whether objectionable microorganisms were present in your drugs.”

This tells me two things. First the rapid method was not adequately validated to demonstrate equivalency to the compendial method, which is a requirement in USP and the other compendia.

“After receiving three consumer complaints for discoloration of this product, you initiated testing of your retains using both the modified U.S. Pharmacopeia (USP) microbiological limits method and the [redacted] method. Both analyses found microbial contamination. Notably, the USP modified method [redacted] found an exceedingly high microbial count of over 57,000 CFU/ml, and also identified Burkholderia cepacia, an objectionable microorganism, in this product lot.”

“Had your firm been utilizing a screening method capable of consistently detecting B. cepacia, these products may not have been released in the first instance.”

Obviously! It appears the “validated” rapid method did not detect the presence of microorganisms in the original sample (which is why it was apparently released) and as such, there was no positive response to illicit confirmatory testing of an objectionable, such as B. cepacia.

“FDA informed you that your [redacted] method [redacted] has not been adequately validated for detecting the presence of microorganisms, including the presence of B. cepacia. In a subsequent meeting on November 30, 2016, FDA advised you to use a verified compendial method for all bulk drug solutions and finished product microbiological testing until you could further assess the suitability of the [redacted] method.”

This statement could mean a number of things. An alternative method, including a rapid method, must be equivalent to the compendial method. For nonsterile drugs, which I assume is the case with this warning letter, you must demonstrate the finished product is within aa appropriate quantitative specification (the reason why we perform USP 61) and does not contain any objectionable or specified microorganisms (which is why we perform USP 62 and additional tests for organisms that may not be specifically covered in the compendia). Some of the reasons why the rapid method could not detect microorganisms, including B. cepacia, could be fond in the next FDA statement.

“It specifies a [redacted] dilution factor. USP <62> requires a 1:10 dilution factor. Your dilution factor is [redacted] times greater than the USP method and provides insufficient detectability to rule out the presence of objectionable microorganisms and unacceptable total counts.”

Well, this is an issue regardless of whether the method used was USP 62 or an alternative method. Diluting out the test sample more than what is prescribed in the compendia may dilute out organisms that could be present. This was a mistake that should have been avoided.

Furthermore the rapid method it not account for the enrichment step called for in USP <62>. Also “it does not include the scraping step during sample preparation, which your submitted laboratory data indicates is required to validate organism recovery.”

Again, the same sample preparation steps must be performed in an alternative method, unless you can show a different procedure gives equivalent results to the compendial or original sampling and sample preparation strategy.

There was also a comment about the use of stressed organism as part of method validation (a controversial point within pharmaceutical microbiology): “it lacks evidence that small numbers of various microorganisms, including those that are injured and stressed, can be reliably recovered. Specifically, sample effect (defined by your firm as the inhibitory effect of a sample on the growth of various microorganisms) data for B. cepacia was collected using a fresh-grown culture, not a stressed organism.”

This was an interesting finding. The use of stressed organisms fueling the validation of rapid methods has been suggesting in PDA Technical Report #33 (TR33) and up until recently, the prior version of Ph. Eur. 5.1.6. Obviously, the FDA continues to require the use of stressed organisms when validating an alternative or rapid microbiological method because organisms normal found in finished product, especially if the product is preserved, will be stressed to some extent.

The final charge was that the method validation did not “establish potential sample interference factors (e.g., enhancing or quenching) for each product formulation.”

This tells me the firm did not perform method suitability on the product to eliminate the potential for false positives and false negatives. This is a current requirement in the USP, Ph. Eur. and TR33 and if Sage did not perform these tests during their rapid method validation studies, this is a significant issue.

There was also concern that the replacement method, unlike the USP method, did “not provide for potential speciation of the detected microbial contamination in the [redacted] initial screening test.”

Some rapid methods are based on the growth of microorganisms and may provide CFUs for subsequent analysis, including confirmation of an objectionable organisms and/or microbial identification. However, other rapid methods may not be based on growth and as such, follow up analysis of positive results may not be possible unless a separate sample was tested specifically for this purpose. Because eh exact rapid method under dispute is not disclosed in the warning letter, it is not possible to conclude the capabilities of the alternative method at this time.

Tim Sandle poses the following questions in his original post on this subject, based on the Sage warning letter. I will answer each in turn:

Q. Does the validation of methods require the use “stressed” organisms?

A. Depending on the application, the use of stressed organisms should be considered. Firms do not have to test dozens of stressed organisms but should select relevant strains and use a stressing condition that is defendable. Novartis published a number of papers on stressing organisms when they validated a rapid sterility test (see the reference page at rapidmicromethods.com for downloads or links to the papers). IN any case, firms should discuss their validation plans with the relevant regulatory authority to understand if the use of stressed organisms is expected.

Q. Does validation always need to be against each product formulation (not just the strongest concentration of the most inhibitory ingredient)?

A. If method suitability testing takes into consideration the greatest (and least) challenge to the alternative method, then you may be able to justify bracketing formulations to support these studies. But this will depend on the actual formulations intended for testing. Again, discuss your strategy with the regulators up front.

Q. How are representative samples built into the validation process?

A. Samples should be selected for validation studies identical to what will be tested routinely (by the rapid method). Consideration for sample preparation, dilutions, etc. should also be noted and as required by the compendia or regulatory expectations.

Q. Does a list of objectionable organisms need to be prepared ahead of the method validation? Or is this just a B cepacia issue?

A. Firms should understand what organisms should be detected by the method, based on a product’s intended use and patient population. This should be done regardless of whether an alternative method will be validated or if the standard compendial method is utilized.

TIM'S ORIGINAL POST

In July 2017 Sage Products Inc. received a warning letter from the U.S. Food and Drug Administration (FDA). Within the warning letter was a concern about the implementation of rapid microbiological method, where the method had been used to replace a compendial method.

In the warning letter, the FDA state “Your firm failed to establish and document the accuracy, sensitivity, specificity, and reproducibility of its test methods.” This relates to the use of a rapid method.

Specifically: “You use the (b)(4) method to screen for microbiological contamination in drugs produced entirely at your facility and those manufactured under contract. This (b)(4) screening method (b)(4) for microbiological examination of your liquid drug products is not adequate for its intended use. You attempted to validate your (b)(4) microbial detection method, but were not able to demonstrate that it could reliably and repeatedly determine whether objectionable microorganisms were present in your drugs.”

The FDA are concerned about the comparative findings from the USP method and the replacement rapid method: “After receiving three consumer complaints for discoloration of this product, you initiated testing of your retains using both the modified U.S. Pharmacopeia (USP) microbiological limits method and the (b)(4) method. Both analyses found microbial contamination. Notably, the USP modified method (b)(4) found an exceedingly high microbial count of over 57,000 CFU/ml, and also identified Burkholderia cepacia, an objectionable microorganism, in this product lot.”

It seems that the firm elected to run with the results from the alternative method, despite the USP method finding an objectionable microorganism. This led the FDA to state: “Had your firm been utilizing a screening method capable of consistently detecting B. cepacia, these products may not have been released in the first instance.” Part of the reason was “because [the company] failed to include B. cepacia on the list of objectionable organisms.”

The use of the alternative method had also gone against FDA advice: “FDA informed you that your (b)(4) method (b)(4) has not been adequately validated for detecting the presence of microorganisms, including the presence of B. cepacia. In a subsequent meeting on November 30, 2016, FDA advised you to use a verified compendial method for all bulk drug solutions and finished product microbiological testing until you could further assess the suitability of the (b)(4) method.”

The concerns the FDA had with the rapid method were:

“It specifies a (b)(4) dilution factor. USP <62> requires a 1:10 dilution factor. Your dilution factor is (b)(4) times greater than the USP method and provides insufficient detectability to rule out the presence of objectionable microorganisms and unacceptable total counts.”

Furthermore the rapid method it not account for the enrichment step called for in USP <62>. Also “it does not include the scraping step during sample preparation, which your submitted laboratory data indicates is required to validate organism recovery.”

There was also a comment about the use of stressed organism as part of method validation (a controversial point within pharmaceutical microbiology): “it lacks evidence that small numbers of various microorganisms, including those that are injured and stressed, can be reliably recovered. Specifically, sample effect (defined by your firm as the inhibitory effect of a sample on the growth of various microorganisms) data for B. cepacia was collected using a fresh-grown culture, not a stressed organism.”

The final charge was that the method validation did not “establish potential sample interference factors (e.g., enhancing or quenching) for each product formulation.”

There was also criticism about the sampling and sample plan used to ensure the tested sample was representative of the lot. There was also concern that the replacement method, unlike the USP method, did “not provide for potential speciation of the detected microbial contamination in the (b)(4) initial screening test.”

The implications from the FDA letter, as well as signaling a pertinent lesson when implementing a rapid method that needs to be equivalence to or better than the rapid method, are:

  • Does the validation of methods require the use “stressed” organisms?
  • Does validation always need to be against each product formulation (not just the strongest concentration of the most inhibitory ingredient)?
  • How are representative samples built into the validation process?
  • Does a list of objectionable organisms need to be prepared ahead of the method validation? Or is this just a B cepacia issue?

If you have views on this, please add a comment.

Thanks to Nigel Halls for the heads-up about this warning letter and its considerable implications.

Friday, August 4, 2017

Longitude Prize Bacterial Dx Competition Announces Seed Funding Winners

On average antibiotics add 20 years to each person’s life. The development of antibiotics has been vital to our survival, yet the rise of antimicrobial resistance is threatening to make them ineffective in the future. The World Health Organization estimates that antibiotics treatments add an average of 20 years to all of our lives. But in the 80 years since the discovery of penicillin, our overuse of antibiotics has put pressure on bacteria to evolve resistance, leading to the emergence of untreatable superbugs that threaten the basis of modern medicine.

Clinicians often prescribe broad spectrum antibiotics to sick patients because doctors have to act quickly on imperfect information. These methods put selective pressure on microbes to evolve resistance to antibiotics. Prescriptions from clinicians are just one way in which people access antibiotics, however. There are many routes to these drugs and they vary around the world.

Radical change is needed to address the global problem of growing anti-microbial resistance, to ensure a healthcare system that can sustainably control and treat infections.

We cannot outpace microbial evolution. A new broad-spectrum antibiotic, if applied with current methods, would eventually meet new forms of resistance. The overall solution involves a long-term path towards a more intelligent use of antibiotics enabling a future of more effective prevention, targeted treatments and smart clinical decision support systems.

The Longitude Prize is a £10m prize fund that will reward a competitor that can develop a point–of–care diagnostic test that will conserve antibiotics for future generations and revolutionise the delivery of global healthcare. The test must be accurate, rapid, affordable and easy to use anywhere in the world.

Run by Nesta and supported by Innovate UK as funding partner, the Longitude Prize competition recently announced 13 winners for the second round of seed funding.

Each winning team received awards between £10,000 ($13,210) and £25,000 ($37,927) for their research proposals. Funding for the second round draws on a £250,000 grant from Merck & Company. The groups come from Australia, Belgium, India, Israel, The Netherlands, the US, and the UK.

Teams are at various stages in test developments, ranging from proof of concept to initial clinical validation to fabrication of components for prototypes. They are attempting to diagnose infections including Escherichia coli, urinary tract infections, and sepsis.

Many teams are working on technology that will detect the susceptibility of bacteria to antibiotics, which will support specific antibiotic treatments for bacterial infections and minimize the spread of drug resistance.

Here is an overview of the Discovery Award Winning Teams:
  • ID Genomics, a Seattle-based company, is developing "bacterial fingerprinting" technology that will reduce prescription errors and overuse of broad-spectrum antibiotics by improving the speed and accuracy of the antibiotic prescribing process. ID's Clonet rapid diagnostic test determines the bacterial fingerprint of different strains of the main pathogens in urinary tract infections (UTIs) in less than 30 minutes, which is then matched against the company's reference database of thousands of bacterial strains and their profiles. A clinician can then prescribe the antibiotic best suited to their infection.   
  • Coris BioConcept, a Belgium-based company, specializes in developing, manufacturing, and marketing rapid diagnostic tests based on strip chromatography with the use of colloidal gold particles, latex microspheres, or fluorescent dyes (ICT). The ICT range detects infectious disease including enteric and respiratory pathogens, and could potentially be used to confirm if a bacteria is resistant or sensitive to carbapenem antibiotics.  
  • Drug and Diagnostics for Tropical Disease is developing a test to determine if an antibiotic can still bind to its targeted protein or not, providing an answer within minutes without specialized equipment and allowing a doctor to test a patient in the office.
  • A consortium called EPDAL:Bradford and Lincoln plans to design an efficient and inexpensive diagnostic test to identify the most significant gram-negative pathogens. On the premise that protein chemistry is the same in the structure of gram-negative bacteria (GNB) or proteins, the company will exploit the ability of protein elements to select different color complexing molecules and use differential staining to organize bacteria into separate categories based on their protein elements and color complex-elution properties.
  • Embryyo, an Indian company, is working on a diagnostic device that will facilitate in early detection of bacterial or viral infection on the bloodstream, at the onset of a pathogenic infection when pathogen counts are very low. Based on microfluidic cell separation and flow focusing microdevices, the device will potentially aid in the differential diagnosis of bacterial versus viral infections.
  • Encompass Consortium, based in Australia, is developing a method to determine antimicrobial susceptibility with the accuracy and speed needed to influence a physician's initial choice of antibiotics. The company aims to miniaturize and automate its first-generation flow cytometry-assisted antimicrobial susceptibility tests (FAST) for near point-of-care use.
  • Going Against the Flow, another Australian company, is working on a point-of-care test that will detect the activation of neutrophils to allow early detection and treatment of sepsis. Instead of detecting infection directly, the test will rely on the body's sensitive and quick response to bacterial infections using original yet simple methods to detect the early response to neutrophils.
  • Microplate-Strathclyde Biomedical Engineer and SIPBS's approach will bring together expertise to develop a rapid diagnostic test for antimicrobial susceptibility.
  • Module Innovations, an Indian company, is developing USense, a diagnostic platform based on color changing polymers for rapid microbial detection.
  • OxTB, Cambridge and Oxford, is working on a bedside test that uses whole-genome sequencing (WGS) to determine the presence of Mycobacterium tuberculosis in a clinical sample, predict drug susceptibility, and inform disease surveillance by demonstrating the genetic relationships to previously witnessed strains.
  • Prismatix, an Israeli-based company, has developed a method of phase-shift reflectometric interference spectroscopic measurements (PRISM) that monitor bacterial activity silicon-based microstructures in real time.
  • RAPDIF, based out of The Netherlands, plans to improve the diagnosis of febrile diseases in sub-Saharan Africa. It aims to develop a diagnostic tool that can identify bacterial infections.
  • Rapid AMR Detection Team, from the University of Bristol, is developing an optical technique to quickly detect whether bacteria are alive or not, relying on optical detection of the state of bacteria after injecting antibiotics and not relying on bacterial growth.
Source: The Longitude Prize Challenge

Sunday, April 23, 2017

Inclusion of Rapid Test Results Leaves Gaps in CDC Foodborne Illness Data

For the first time, the CDC’s yearly report on foodborne illnesses in the U.S. included infections that were identified only with rapid diagnostic tests, which can speed up treatment for patients but lead to important gaps in data, researchers said.

Culture-independent diagnostic tests (CIDTs) are increasingly being used by clinicians to detect enteric infections because they produce results more quickly than traditional culture methods, researchers from the CDC and other public health facilities across the country wrote in MMWR. However, used alone, these tests tell only part of the story, leaving out important information on pathogen subtypes and antimicrobial resistance, and making it difficult to monitor trends or link infections to outbreaks, the researchers said.

Such information can be obtained only if a reflex culture is performed on the CIDT-positive specimen, the researchers said. But according to their report, which compared surveillance data for 15% of the U.S. population from 2013 to 2016, a large proportion of positive CIDT results do not receive these much-needed cultures.

“We need foodborne-illness trend data to monitor progress toward making our food supply safer,” Robert Tauxe, MD, MPH, director of the CDC’s Division of Foodborne, Waterborne, and Environmental Diseases, said in a statement. “It’s important that laboratories continue to do follow-up cultures on CIDT-positive patients so public health officials can get the information needed to protect people from foodborne illness.”

Potential for false-positive results

Including CIDT results in the CDC data for 2016 raised the incidence rates for six of the most reported bacterial foodborne illnesses. However, interpreting these increases is complicated, the researchers said.

As an example, they noted that the incidence of culture-confirmed infections with Campylobacter — the most commonly reported bacterial foodborne illness — was “significantly lower” in 2016 compared with the average over the previous 3 years. However, a “slight but not significant” increase occurred when infections that were diagnosed only through CIDTs were included.

Further, Campylobacter is one of the pathogens for which antigen-based CIDTs are often used. These tests can produce a large number of false-positive results, leading to skewed estimates of incidence, the researchers said.

“When interpreting incidence and trends in light of changing diagnostic testing, considering frequency of testing, sensitivity, and specificity of these tests is important,” they wrote. “The observed increases in incidence of confirmed or CIDT positive–only infections in 2016 compared with 2013 to 2015 could be caused by increased testing, varying test sensitivity, an actual increase in infections, or a combination of these reasons.”

FoodNet data

The researchers looked at preliminary 2016 data from the CDC’s Foodborne Disease Active Surveillance Network, also called FoodNet, which monitors cases of nine foodborne disease at 10 sites in Connecticut, Georgia, Maryland, Minnesota, New Mexico, Oregon, Tennessee and certain counties in California, Colorado and New York, and compared the incidence rates with data from 2013 to 2015.

The sites reported 24,029 foodborne infections in 2016, including 5,512 hospitalizations and 98 deaths. Campylobacter was the leading cause of bacterial foodborne illness with 8,547 reported infections, followed by Salmonella (8,172), Shigella (2,913), Shiga toxin-producing Escherichia coli (1,845), Cryptosporidium (1,816), Yersinia (302), Vibrio (252), Listeria (127) and Cyclospora (55).
Salmonella typhimurium infections, which often are linked to beef and poultry, decreased 18% in 2016 compared with the average incidence for 2013 to 2015. The reduction is possibly due to regulatory action by the USDA to reduce Salmonella contamination in poultry and vaccination of chicken flocks, according to a CDC news release.

The CDC said increases in Yersinia, Cryptosporidium, and Shiga toxin-producing E. coli infections were likely due to the increased use of CIDTs.

“This report provides important information about which foodborne germs are making people sick in the United States,” Tauxe said. “It also points out changes in the ways clinicians are testing for foodborne illness and gaps in information as a result.”

The researchers said previous analyses have indicated that the number of foodborne infections in the U.S. “far exceeds those diagnosed” and that CIDTs might be making them “more visible.” But they said more tools are needed to accurately interpret FootNet surveillance data in light of these changes to testing practices.

“FoodNet is collecting more data and developing these tools,” they wrote. “With these, FoodNet will continue to track the needed progress toward reducing foodborne illness.” – by Gerard Gallagher

Reference

Marder EP, et al. MMWR Morb Mortal Wkly Rep. 2017;doi:10.15585/mmwr.mm6615a1