One bug or prix fixe? Respiratory pathogen testers weigh in
William Check, PhD
February 2017—With the number of rapid, accurate molecular assays for respiratory pathogens growing, microbiology laboratories have more options than ever. They include, among others, Meridian Bioscience’s Illumigene assays for group A Streptococcus and pertussis and its newest assay, Mycoplasma Direct, as well as Alere’s assays for influenza A/B, respiratory syncytial virus, and Streptococcus on its i molecular platform. No longer are laboratories limited to inaccurate rapid antigen tests, weeks-long culture, or multi-pathogen panels.
Laboratories with different test volumes and patient populations will make different choices.
“I think there is a place for both targeted testing and panel testing,” Beverly B. Rogers, MD, chief of pathology at Children’s Healthcare of Atlanta, says. “I feel strongly that when you admit someone to the hospital with respiratory symptoms, panel testing is far and away the best thing to do. You’d be surprised to see what comes up.”
Holy Cross Hospital in Taos, NM, has chosen single-organism tests. “We looked at a respiratory panel. We had BioFire in to do a demo,” says laboratory director Susan Romansky, BS, MLS(ASCP). Because of the higher cost for the panel, she and colleagues opted for single-organism assays. “We didn’t want the shotgun approach,” she says.
A particular point of divergence is testing for Mycoplasma pneumoniae in patients with respiratory symptoms. This organism, which causes what is often referred to as “walking pneumonia,” is associated with up to 40 percent of community-acquired pneumonias and occurs in children and adults. Its characteristic symptom is a dry, paroxysmal cough. Some say this justifies a single-organism test, others that it makes an organism-specific test less urgent.
Romansky favors a single-organism test for this pathogen. “Mycoplasma has specific clinical manifestations,” she says. “We are not going to be looking for pertussis or viruses in those patients.”
Romansky’s laboratory started using Meridian Mycoplasma Direct in September 2016, three months after the FDA cleared it. Her laboratory had previously been using Meridian Mycoplasma ImmunoCard. “Our reasons for switching were twofold,” Romansky says. First, interpretation of the serology method was too subjective. “On the ImmunoCard you are looking for a blue color. It is somewhat subjective. You can overcall or undercall it,” she says.
Second, compared with ImmunoCard, “There is increased sensitivity and specificity with Mycoplasma Direct.”
Holy Cross was already using other Meridian Illumigene assays in the laboratory. “This has been one of the simplest Illumigene assays we’ve brought in,” she says of Mycoplasma Direct. “It has only a very few steps. We did the validation quickly and had it up and running.” Turnaround time is less than one hour.
Romansky wants to do follow-up studies with the molecular assay. It uses a throat swab, as opposed to the serology with ImmunoCard. She would like to see whether Mycoplasma Direct detects Mycoplasma sooner than serology.
In keeping with the single-organism testing philosophy, Romansky’s laboratory is using Alere i tests for flu and respiratory syncytial virus.
Sarah Drenning, C-PNP, a nurse practitioner at the Taos Clinic for Children and Youth, orders tests from Holy Cross. Drenning says she likes the new test because she can get a swab in the office and have a result quickly, often the same day, which works well for children and families.
Drenning has ordered Mycoplasma Direct for patients who have clinical symptoms and exam findings consistent with Mycoplasma pneumoniae or pneumonia generally. “It is a worthwhile test to do since Mycoplasma pneumoniae can be a prolonged illness if it’s not treated,” she says. She uses rapid antigen tests for flu and RSV in the office. “If those are negative, I might look for Mycoplasma,” Drenning adds. So far she has sent only a handful of samples for the new test, all of which have been negative. “We haven’t used antibiotics in those patients and they have all gotten better,” she says.
At Cabell Huntington (W.Va.) Hospital, microbiology manager Russ Gaskins, MT(ASCP), replaced an IgM card test with Mycoplasma Direct. “There is no doubt that this Mycoplasma test is 100 percent better than what we were using before,” Gaskins says.
Converting was not difficult from a methodologic point of view. However, Gaskins says, “We had to communicate to physicians and nursing units that we had a new test that required a new type of specimen.” They sent a message via the computer ordering system that the old test was being replaced. “Also, now when you put in Mycoplasma test, the only source that comes up is throat swab,” Gaskins says.
In addition to Mycoplasma Direct, Cabell Huntington offers the BioFire FilmArray respiratory panel, which includes Mycoplasma. “Respiratory panels are making a huge difference in patient care,” Gaskins notes. “We are finding things we didn’t see or even look for. It helps to rule in or rule out.” They have five instruments to run the panel throughout the 24-hour cycle, whereas Mycoplasma Direct has a cutoff time for submission of specimens. “We just can’t do everything all day long,” Gaskins explains.
Perhaps because of the value of the respiratory panel, Gaskins says, “We are really not doing the numbers we thought we would” with Mycoplasma Direct. “I think it’s due to the availability of the rapid panel.” He cites the dry cough, where mucus stays in the lungs, as a particular feature of Mycoplasma pneumoniae that might tip the clinician to order a single-pathogen test. “However,” he notes, “even if clinicians suspect Mycoplasma, they are better off ordering the respiratory panel because if the patient also has coronavirus, for example, they will find out at the same time.”
Physicians find it hard to pass on tests they get back as easily and as fast as a panel, Gaskins notes. “It is more expensive, but it can save hospital days. And compared to the cost of a hospital day, a panel is not much expense.”
The laboratory at Orange Park (Fla.) Medical Center uses the Mycoplasma Direct kit. “Prior to this, we were using the Illumigene Mycoplasma, which had a separate extraction phase with the Qiagen DNA extraction kit,” says microbiology supervisor Michael Ibuoye, MS, MT(AMT). “The Mycoplasma Direct kit bypasses this extraction phase, which makes life much easier for us as a hospital diagnostic microbiology lab.” With the first kit, extraction required 19 steps and tied up a technologist for two hours, Ibuoye says.
Illumigene Mycoplasma Direct incorporates an integral extraction step and uses LAMP (loop-mediated isothermal amplification) technology. In a three-institution comparison reported at the 2016 meeting of the American Society for Microbiology, investigators found that, among the 465 specimens tested, the original Mycoplasma kit detected 25 specimens as positive while the Mycoplasma Direct detected 34 positive specimens. There was no gold standard method so it can’t be determined whether the new assay is more sensitive or less specific.
In the Orange Park laboratory, Mycoplasma is ordered on all patients who come in for bronchoscopy. That’s three to four patients per day, Ibuoye says. “It is done on almost all BALs, except where there is a known cause.”
For more typical flu symptoms, Ibuoye’s laboratory performs flu A/B and RSV rapid enzyme immunoassay screens. They don’t do a respiratory panel in-house; if a clinician orders it, they send it out.
In addition to Children’s Healthcare of Atlanta hospital laboratories, where Dr. Rogers is chief of pathology, the system has six urgent care walk-in clinics with high-complexity labs in the Atlanta area. In these clinics, clinical pathologist Elizabeth Weinzierl, MD, PhD, has brought on the Alere rapid molecular strep and flu A/B molecular amplification assays. The Alere rapid strep assay has been validated and will be in the clinics soon, after which the laboratory will eliminate strep culture.
“I don’t feel it’s worth it to put in a specific Mycoplasma test. We don’t see it as a frequently requested test in our population,” says Dr. Rogers, an adjunct professor of pathology and pediatrics at Emory University School of Medicine.
At Children’s Healthcare of Atlanta, the primary testing mode is the BioFire respiratory panel. Mycoplasma is on the panel. “There is such a high prevalence of people in the community who are walking around without symptoms and are Mycoplasma positive. So you have to be cautious when you get a positive result back and interpret it within the clinical context,” Dr. Rogers points out.
It is not uncommon to have multiple positive reactions on the panel—perhaps RSV with adenovirus or flu. “Those are really sick kids,” she says.
“If there was an adult patient with fever, dry cough, and shortness of breath that didn’t resolve, there would be a tendency to treat them as an outpatient with a Z pack,” she says. To Dr. Rogers, this is not a hypothetical situation. “Several years ago, I had persistent nonproductive cough and shortness of breath. My husband said, ‘You’ve got Mycoplasma.’ He’s a pathologist but he’s also boarded in internal medicine and a good clinician. So I wrote a prescription for a Z pack and got better in two days.”
She and microbiologists Robert Jerris, PhD, and Mark Gonzalez, PhD, are having a conversation with the clinical team about whether during flu season they want to bring into the hospital laboratories a flu-only molecular test for patients seen in the emergency department. “We put in the panel first. Now that there are really good single-organism tests, we may end up having a hybrid for outpatients,” she says.
Dr. Rogers would also see a role for a panel in the outpatient setting, mostly to reassure parents, when a clinician sends home a patient with respiratory symptoms. But the current charge to the patient or insurance for a large panel is very high, so the cost of the panel outweighs the benefit, and therefore the panel is not performed in practice. With panel results in these scenarios, “You could say, ‘Your child has an RSV viral infection and these are the typical symptoms. There is no need for antibiotics.’ ” This could lessen the demand for antibiotics and decrease the development of antibiotic resistance. “If the charge weren’t so high, if you could do a panel and charge maybe $200, that is what I would do for outpatients,” she says.
Of the expense of a respiratory panel, Dr. Rogers says: “Medical economics is interesting. When we say the panel costs are high, does that mean the cost to perform the test or the cost that is charged to the patient? They often differ by a factor of 10 or higher. Therefore, the clinicians and patients see the test as very expensive, when it may not be terribly expensive to run.”
William Check is a writer in Ft. Lauderdale, Fla.