The Future of PulseNet

How does PulseNet adapt to changing technology?

PulseNet is committed to finding and using the best techniques to identify outbreaks. Currently, PulseNet is undergoing many changes because the network has added whole genome sequencing (WGS) to its toolbox. Using WGS will enhance PulseNet’s ability to detect and solve outbreaks faster and with more accuracy. 

PulseNet is also adapting to the increasing use of culture-independent diagnostic tests (CIDT). Clinical laboratories use these tests to detect and identify disease-causing bacteria as part of patient diagnosis (see CIDT section). As these new technologies are adopted, PulseNet will continue to create rapid and standardized methods for PulseNet participants.

How Culture-Independent Diagnostic Testing (CIDT) presents a challenge

Culture-independent diagnostic testing (CIDT) is rapidly changing the way that clinical laboratories diagnose patients with foodborne illness. A new generation of CIDTs is becoming available that can simultaneously test patient samples (such as stool) for illness-causing bacteria and have results within hours, without having to grow the bacteria. This allows doctors to rapidly determine the cause of a patient’s illness but does not produce the bacterial isolates that are the raw material needed by PulseNet for DNA fingerprinting. 

Why does the use of CIDT endanger the PulseNet system?

The use of CIDT instead of culture-based diagnosis could endanger the PulseNet system for the following reasons:

• A shift toward CIDTs means that many clinical laboratories will stop isolating or collecting bacterial isolates from patients with foodborne illness. 
• PulseNet’s most important information comes from the bacteria that are found in samples from sick people and are then sent to public health laboratories for DNA fingerprinting and other testing. 
• PulseNet needs these bacterial isolates to get a DNA fingerprint. Without a DNA fingerprint of the bacteria, CDC and public health labs will not be able to find, monitor, and prevent foodborne disease outbreaks, track antibiotic resistance, or follow trends to know if prevention policies are working.

One approach to maintaining isolates for PulseNet is for public health laboratories to assume the burden of culturing, or obtaining bacterial isolates, from CIDT-positive patient samples. While this may be necessary in the short run, this process is slow, expensive, and not likely to be sustainable.

What is being done about the CIDT challenge?

CDC is working closely with the Association of Public Health Laboratories (APHL), public health officials, regulatory agencies, diagnostic laboratories, CIDT kit manufacturers, and clinicians to ensure that when a CIDT result is positive, samples are collected and isolates are recovered locally or provided to state public health laboratories. Researchers are identifying the best methods to store and culture samples to recover bacterial isolates from patient samples.

PulseNet is also exploring a variety of new testing methods that work directly on patient samples without the need for a bacterial isolate. These methods include metagenomics approaches and other strategies using next generation sequencing technology (NGS). Metagenomics is a way to determine the genetic code in some or all of the microorganisms in a patient sample. 

Next generation sequencing (NGS) is a fast, relatively cheap way to perform whole genome sequencing (a laboratory procedure that determines the genetic material, or the genome, of an organism in one process).

These innovations are in the early stages of development. Researchers hope that the use of these methods will eliminate the need for collecting bacterial isolates for PulseNet and thus solve the CIDT problem and speed up the process of detecting and solving outbreaks.

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