Wednesday, May 27, 2009

School closures

It turns out that I have not been alone in wondering about what to do if school children or staff appear to have the flu. The death of Mitchell Wiener, assistant principal at Intermediate School 238 here in New York City (NYC), sparked a wave of concern and much debate on when to close schools. NYC Health Commissioner (and soon-to-be head of the CDC), Dr. Frieden and school Chancellor Klein posted criteria that the city will use to close affected schools, following CDC's own guidelines. But these measures have not reduced the concerns as fear spreads faster than the virus.

As previously mentioned, the dilemma of whether or not to close a school would be greatly alleviated if a fast (overnight turnaround) accurate test was available. The majority of disease clusters will turn out not to be due to the swine flu virus. Conversely, true swine flu cases could be identified before the infection spreads within the school (hopefully, even before the child has attended school).



Thursday, May 21, 2009

Is that test necessary?: blood cultures in pneumonia

In response to a question in the American Society of Microbiology laboratory discussion group (DivC), I sent this message:

In fact, as Dr. Manasse suspects, blood cultures are the subject of the Joint Commission Core Measure PN-3b.

However, careful examination of the measure does not justify the use of blood culture tests in all Emergency Department patients with pneumonia.

Core Measure PN-3b "Blood Cultures Performed in the Emergency Department Prior to Initial Antibiotic Received in Hospital" is described at:
http://manual.jointcommission.org/bin/view/Manual/MIF0006



As you can see there, the measure is justified by "Published pneumonia treatment guidelines recommend performance of blood cultures for all inpatients to optimize therapy" and lists several published guidelines. The most recent citation is:

Mandell LA, Wunderink RG, Anzueto A, et al. Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults. Clin. Infect. Dis. 2007;44 Suppl 2:S27-72
(http://www.guideline.gov/summary/summary.aspx?ss=15&doc_id=10560
)

Mandell et al. write that "Recommendations for diagnostic testing remain controversial. The overall low yield and infrequent positive impact on clinical care argue against the routine use of common tests, such as blood and sputum cultures", however they add that "cultures may have a major impact on the care of an individual patient" and identify the individual patients for whom "pretreatment blood samples for culture...should be obtained" as those with:
  • Intensive care unit admission
  • Cavitary infiltrates
  • Leukopenia
  • Active alcohol abuse
  • Chronic severe liver disease
  • Asplenia (anatomic or functional)
  • Positive pneumococcal Urinary Antigen Test result
  • Pleural effusion
(Table 5 and Recommendation # 12)

Severe pneumonia that justifies blood culture testing, in addition to the criteria above, also includes patients with three or more of the following "minor" criteria:
  • Respiratory rate >=30 breaths/min
  • PaO2/FiO2 ratio =<250
  • Multilobar infiltrates
  • Confusion/disorientation
  • Uremia (BUN level, >=20 mg/dL)
  • Hypothermia (core temperature, <36>
  • Thrombocytopenia (platelet count, <100,000>
  • Hypotension requiring aggressive fluid resuscitation
  • Hypoglycemia (in nondiabetic patients)
  • Hyponatremia
  • Unexplained metabolic acidosis or elevated lactate level
For the rest of patients with less severe pneumonia, recommendation #11 applies: "Routine diagnostic tests to identify an etiologic diagnosis are optional for outpatients with Community Acquired Pneumonia".

Thus, Denise Jones' Emergency Department (ED) physicians are only 33.3% correct in requesting blood cultures in patients with low oxygen saturation, since hypoxia should be accompanied by two other minor criteria to justify the test, according to the authorities cited by the Joint Commission.

The criteria listed above require a basic patient assessment that can be completed quickly in the ED (problem-oriented patient history, measurement of blood pressure, temperature and respiration rate, chest x-ray, CBC, urine antigen tests and serum metabolic profile plus alcohol and lactic acid levels) so that they will only slightly delay administration of antibiotics.

For these reasons, and armed with the information above, the laboratory could argue convincingly against the need to obtain a sample before deciding whether a blood culture will be needed.

In addition to the unnecessary work imposed on usually overwhelmed ED and laboratory staffs, the invasive nature of the procedure and the cost of supplies and equipment, there is the problem of false negatives: in samples kept at room temperature, some organisms might grow to exceed the CO2 detection threshold so that their presence will not be detected by the continuous CO2 monitoring system when they are eventually placed in the blood culture incubator. BioMérieux sent a BacT/Alert system notification to that effect a couple of years ago.

False positive results could also be more frequent in these circumstances. I have noticed that often, blood culture contamination rates are higher in the ED than in in-patient services (is that also your experience?) and I wonder whether sterility precautions are observed as scrupulously when the person drawing the sample is not sure that it will, in fact, be used.

We are all compelled to avoid waste and error in health care, especially now that the prospect of real reform is on the horizon. Laboratory efforts to fine-tune accreditation demands so that they make sense, are a valuable contribution. Denise: go ahead and fight that battle using the information above.

Friday, May 15, 2009

In preparation for the Fall


As the number of confirmed cases seems to be decreasing (as shown by the May 4th CDC figure) and severity appears not to exceed that of seasonal influenza, public attention to the 2009 H1N1 flu wanes. Laboratorian's attention should not: as mentioned earlier, parallels with the 1918 pandemic predict worse outbreaks in the Fall. In my opinion, the following laboratory diagnostic tools should be in place in the U.S. by then: (1) a sensitive molecular test for virus detection and (2) a specific serum/plasma antibody test for retroactive diagnosis.

The CDC developed the amplified RNA test in an amazingly short time. However, it has been limited to local Public Health laboratories. Despite those laboratories' heroic efforts, this limitation precludes its widespread use. The first test offered outside Public Health labs, was only made available by Quest Diagnostics two days ago. However, this test is only offered in one location in the U.S. and still requires confirmation by local Public Health laboratories. Further, important details of sample collection and estimates for the clinical sensitivity of the molecular test are not yet available.

I was personally involved in two potential school events which begged a rapid sensitive test. I described the first experience below (another teacher in that school's district has since been confirmed as suffering from the swine flu). Last Friday, I was asked advice in a third-grade incidence, where six out of 30 students in a single classroom in a school in New York City fell ill with suggestive symptoms. On Monday half of the students in the class, including five of the six, were absent. The symptoms (fever, malaise, headache, muscle aches) of the sixth, a nine year old girl whose pediatrician prescribed Tamiflu (oseltamivir) on Saturday, resolved within hours of starting treatment. Today, a week later, most of the sick children have returned, and the whole class is visiting the local Zoo. If the incident was, in fact, due to the flu, this group of students has disseminated the virus widely. Had one of the sick students been tested within the first day and found to host the H1N1 virus, the school might have decided to take containing measures, including possible closure, despite the CDC advise of not to close "unless there is a magnitude of faculty or student absenteeism that interferes with the school's ... ability to function."

While we should no longer worry that the children who fell ill last week could spread the virus, others in the incubation phase of this potential H1N1 outbreak, might. In this scenario, the finding of specific antibodies in the blood of convalescent students, could help with containment efforts and in the diagnosis of contacts. Such antibody test would also be used as an important epidemiological tool.

Thursday, May 7, 2009

Method and sample collection for the '09 H1N1 confirmation test

Dan Jernigan from the CDC is quoted by GenomeWeb, as informing that the CDC's rRT-PCR Swine Flu Panel has been distributed to 78 qualified labs throughout all 50 states in the US, as well as labs in 130 countries, and 10 Department of Defense labs in the US. Because of the shortage of reagents, the CDC is working with other vendors to get new molecular assays cleared.

The current CDC rRT-PCR test uses TaqMan probes designed by the CDC and is run on Applied Biosystems' 7500 Fast Dx Real-Time PCR instrument (the brochure is a 31.4Mb download). Last October, this instrument/CDC rRT-PCR Flu Panel combination received 510(k) clearance for sub-typing of influenza viruses in qualified laboratories.

The "flocked swab" recommended for sample collection is explained in Copan's web site, which also offers a Twit, a set of video instructions and an animation explaining nasopharingeal sample collection.

Dr. E. J. Baron, Director of the Clinical Microbiology and Virology Laboratories at Stanford U. Med. Center, informed that these Copan swabs are available from Copan (Cat # 503CS01), Becton Dickinson (Cat # 220252) and Diagnostic Hybrids (which offers several configurations).

Tuesday, May 5, 2009

More links

New web-based resources addressing the 2009 H1N1 virus pandemic are available:

PubMed added useful links to its homepage, including one to publications recently added and another to GeneBank's H1N1 sequences. An FDA page devoted to testing reiterates that "no influenza tests are sufficiently sensitive to rule out an influenza infection, and clinicians must consider clinical and epidemiological criteria along with laboratory testing results."

The CDC's page devoted to clinical laboratory issues, lists links to other pages in the CDC site as well as a link to the Association of Public Health Laboratories' homepage, from where you can access their H1N1 page. Three links to pages in the WHO site ("Protocol for Antiviral Susceptibility Testing by PyrosequencingExternal Web Site Policy", "Sequencing Primers and Protocol" and "CDC Protocol of Realtime RTPCR for Swine Influenza A(H1N1)"), refer to sequencing and molecular testing.

The U.S. Government Pandemic Flu site now addresses the 2009 H1N1 virus.

Sunday, May 3, 2009

Rapid influenza antigen testing recommendations

On Friday, the CDC posted recommendations for the use of rapid influenza testing in the assessment of patients suspected of having the SOIV H1N1 virus.

The Festschrift Symposium in Honor of Peter Jatlow, MD takes place in New Haven, CT. today. Dr. Jatlow, former Chairman of the Department of Laboratory Medicine at YaleUniversity, Director of Laboratories at Yale-New Haven Hospital, and an authority on the clinical chemistry of addiction, presided over the training of numerous promotions of clinical pathologists, many of whom will be attending.

Guidance on Specimen Collection and Rapid Testing

Roberta Carey, Acting Director of the Division of Laboratory Systems at the CDC made available an interim draft list of answers to Frequently Asked Questions from laboratories on May 1st. Since I could not find a link to this letter, I include a copy below:

Frequently Asked Questions on Swine Flu (H1N1) from the Laboratories

1. What specimens are acceptable for the recovery of swine flu?

The preferred respiratory specimens include: nasopharyngeal swab/aspirate or nasal wash/aspirate. If these specimens cannot be collected, a combined nasal swab with an oropharyngeal swab is acceptable. For patients who are intubated, an endotracheal aspirate should also be collected. Specimens should be placed into sterile viral transport media (VTM) and immediately placed on ice or cold packs or at 4°C (refrigerator) for transport to the laboratory.

2. If swabs are used to collect a specimen, which ones are acceptable?

There are a variety of swabs with a synthetic tip shown to have superior recovery of viruses, such as the flocked swabs. Avoid cotton tipped swabs, calcium-alginate swabs and those with a wooden shaft, which would inhibit the recovery of the virus, and may not be approved for use with the rapid testing kits.

3. If I receive a swab for rapid testing, I have nothing left to send for confirmation. What should I do?

You may ask your clinicians to collect two swabs. If your rapid test is positive for influenza A, then send the second swab to the public health lab for testing. Ideally the second swab should be immersed in viral transport media during transport. If only one swab is received, you may have leftover diluent where the cells from the swab were extracted that could be suitable for further testing. It is unknown at this time if these diluents or saline are compatible with the confirmatory tests.

4. I don’t have access to dry ice, how can I ship specimens to my public health lab?

It is acceptable to place the specimens in appropriately sealed shipping container (Styrofoam box) with cold packs if the specimens will be delivered within 24 hr. These specimens should be shipped according to category B packing since these are primary diagnostic specimens and do not contain known biothreat agents.

5. Will my rapid flu test detect swine flu?

The sensitivity and specificity of rapid influenza kits for the novel Swine H1N1 virus is not known. CDC is evaluating capabilities of rapid test methods to detect the swine flu strains. Until that evaluation is complete, interpretation of results from the rapid flu tests may be unreliable. If there is clinical evidence of disease and strong suspicion of a “suspected case” with a negative test result, a specimen should be sent to the state public health lab. Contact your public health lab for what specimen criteria must be met before shipping to them.

6. Will my rapid shell vial tissue culture recover swine flu?

The sensitivity of the cell lines and mixed cell lines in shell vials and the immunofluorescent antisera used to detect swine flu H1N1 is not known. Contact the provider of your cells for documentation of the performance of their product. If there is clinical evidence of disease and strong suspicion of a “suspected case” with a negative test result, the specimen may be sent to the state public health lab. Contact your public health lab for what specimen criteria must be met before shipping to them.

7. Can rapid flu testing be done in our point of care labs?

Wherever possible manipulation of the specimen for testing should take place in a BSL-2 laboratory in a biosafety cabinet. Where that is not possible, such as a physician's office lab, then appropriate personal protective equipment (lab coat, gloves, masks, eye protection)should be worn when performing the test.

8. What precautions must be used in my viral lab?

CDC safety guidelines for labworkers states that diagnostic work for culture and typing of clinical samples from patients suspected to have swine flu virus should be conducted in a BSL-2 laboratory and testing performed in a biosafety cabinet. Similar precautions should be observed when preparing the specimen for diagnostic molecular testing.

9. Do all laboratory personnel need to wear enhanced personal protective equipment?

Personal protective equipment (PPE) is recommended based on risk. It would be prudent for laboratorians to wear the recommended respiratory protection, shoe covers, gown, eye protection and gloves if they are manipulating these specimens for diagnostic testing where aerosols may be created. Other personnel in the laboratory who are not handling these specimens would not require this level of PPE unless they are performing high risk activities such as mycobacterial culture.