Next step? The switch from stool culture to PCR

Dr. Alexander and his colleagues ultimately created four custom panels: one for bacteria (Salmonella, Shigella, Vibrio, and Y. enterocolitica as well as Shiga toxin 1 and 2 [enterohemorrhagic E. coli, or EHEC] and Campylobacter), one for viruses (including rotavirus and norovirus), and two separate panels testing for rotavirus and norovirus as single targets.

“We decided to offer the norovirus and rotavirus tests separately as single targets for our infection prevention team who might want to do a contact screening for patients with known norovirus or rotavirus, or for patients with diarrhea after more than three days of hospitalization who have been in contact with, or in close proximity to, a patient with norovirus or rotavirus,” Dr. Alexander explained. In this way, “the cost of the test for single target is less than for the entire panel.”

Depending on the PCR finding, Florida Hospital providers will, in collaboration with the microbiology laboratory, be able to follow up with a custom culture to more fully identify the organism and test for susceptibility. (See “Testing algorithm,” page 52.)

“And we are planning on submitting culture results to the state lab, which is very important, because moving from routine stool culturing to a molecular platform without collaborating with the public health department can have a negative impact. It’s very important that you communicate with them and they know you plan to move to a different platform.”

To provide clinical guidance while pathogens are undergoing susceptibility testing, the laboratory creates an enteric pathogen antibiogram every year. “Having the background data from the antibiogram can help the physician decide whether or not to treat the patient and which antibiotic to use,” he said. “I think it’s a good idea to go back into your system and develop a specific antibiogram for those organisms included in the panel.”

Dr. Alexander used the Verigine instrument when he worked at Marin General Hospital in Greenbrae, Calif. He and his colleagues there compared the prevalence of enteric pathogens identified from stool cultures in 2014 and by PCR testing in 2015 after they switched to the molecular platform. They had tested inpatients and outpatients with diarrhea and found PCR identified notably more of several pathogens.

“A striking thing we found was that the number of Campylobacter-positive isolates almost quadrupled, from 14 to 55 with PCR,” he said. “More Shigella cases were also identified [seven compared with two], and we detected the first and only Y. enterocolitica at the institution.”

The number of Vibrio-positive samples also increased from two to six, but “the most interesting data came for results from Shiga toxin E. coli,” Dr. Alexander said. PCR detected 16 isolates with Shiga toxin genes, including four O157 organisms, six O26 organisms, and six Shiga toxin-producing organisms that did not react with antigen O during stool testing. In addition, nine organisms with PCR-detected Shiga toxin genes did not produce Shiga toxin despite having the gene.

“If you’re only relying on culture-based methods in your facility right now, you’re only identifying O157 and Shiga toxin E. coli that produce toxin, which means you might be reporting false-negatives,” he said.

There are public health implications. “We’ve been told for many years that O157 is the most common type of E. coli in the United States, but the problem is that if a clinical lab is only screening for O157 or Shiga toxin-producing organisms, only those data will be reported to the state, so the data could be skewed,” he said.

Patients in the Marin General ER presenting with diarrhea previously often went home while a stool culture was in progress, he said, whereas with PCR many of the patients received results while still in the ER. “That means some patients can go home with a targeted antibiotic if required.”

Providers need to understand the advantages and limitations of PCR and have results interpreted for them as much as possible, Dr. Alexander said. “Make sure that in the description of the test results you indicate all the species that were screened for in the panel.”

And avoid reporting only “Shiga toxin.”

“Simply writing that you’ve found Shiga toxin 1 or 2 is probably not the most useful way to report your findings. If the patient has enterohemorrhagic E. coli, we emphasize that, as well as mention the type of Shiga toxin found.”

Providers should also be aware of what types of tests can be performed for stool and the laboratory requirements for specimen collection and transport, he added.

“And let physicians know what kind of testing will be done after a specific pathogen is found. Make it clear that after a positive Campylobacter finding, you will not be performing additional tests, or that when a specimen is positive for Shiga toxin, it will be sent to the public health department for further testing.”

He offers the following common questions:

• How many samples must a lab accept, and when is it appropriate to retest? “At Florida Hospital we plan to accept one sample per person to be submitted to the laboratory. We are still working with our infection prevention and infectious disease groups to determine when it would be appropriate to receive a second sample for retesting.”
• Can PCR for enteric pathogens be performed stat? “This is probably the most common question you would receive from emergency department providers. When they find out you have a rapid identification method for identifying enteric pathogens and the results can be back while the patient is still in the ED, they’ll be asking about stat testing. We will have 24-hour turnaround but plan to go down to six hours or maybe less.”
• Should the targets be offered separately or by group? “We don’t think the bacterial targets should be offered separately. They should be grouped just as we do with cultures. The viral targets can be offered along with the bacterial targets and/or as a single target in case norovirus or rotavirus is the suspected agent,” to decrease the cost of the test.
• Should bacterial, viral, and parasite targets be performed all at once? “Parasites have different conditions for epidemiological purposes, which is something your infection prevention and infectious disease groups need to consider, particularly when working with your outpatient providers. Parasite testing volume is mainly from outpatient settings, since some of the infections can be subclinical and/or chronic.” Infection prevention and ID physicians, along with pharmacy, should always be involved and able to provide feedback and recommendations, he says.
• What do you do with a positive result? “I think the best thing to do is to work with the public health department and enter information about susceptibility if you have previous data, for empirical treatment or if a physician needs that information. At the same time, you want to be able to identify the pathogen and submit that information to the public health department and as part of your quality assurance process for the system.”
• Would it be necessary to continue with a limited stool culture? “We will not be offering physicians the option of single or standalone stool culture. However, if a provider believes a culture is needed, they will be able to discuss the case with the laboratory and we may proceed with a culture if it’s appropriate.”

David Wild is a writer in Toronto.