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A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases
Jeanna Ray
Posted: Monday, July 15, 2013 12:14 PM
Joined: 6/6/2011
Posts: 4

The critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Read full text recommendations.

Feedback welcome.  Please send us your comments here.

Phillip Tarr
Posted: Tuesday, September 3, 2013 11:59 AM
Joined: 8/23/2011
Posts: 1

We have read the exceptionally comprehensive IDSA/ASM Guidelines on laboratory diagnosis (Clin Infect Dis. 2013 Aug;57(4):485-8 ).  The microbiology laboratory-provider interface is an area of effort that is under-appreciated in patient care systems, and your outstanding work will help bridge that gap.

However, as individuals who care for many children with bacterial enteric infections, and as investigators in the field of gastrointestinal illnesses, we are very concerned about the recommendation for stool specimen submission. Briefly, we strongly believe that the acutely ill patient with diarrhea who warrants testing for a bacterial enteric infection should undergo such evaluation as a matter of priority. We also believe that a policy that encourages specimens submitted in cups hinders that process.

Here are our thoughts:

1.      Cup specimens are notoriously difficult to obtain, even among the presumably motivated group of patients who visit emergency facilities. Figure 1 in demonstrates just how difficult it is to obtain stool specimens in cups, if left to patient/parent preference.

2.      There are important specimen custody issues: If a patient can't produce specimen on site, it is very cumbersome to return it to a facility for culture.  Questions that arise include: where in the institution should it go?  Is the doctor's office open?  Are there drop off issues?  Did it really come from the patient?  Will the right paperwork accompany the specimen? 

Also, if a patient is admitted from an emergency facility, there are frequent hand-off glitches, and it is often unclear if a test is truly pending, or has merely been ordered. There is no value in delaying taking possession of a specimen that could contain a bacterial pathogen, and considerable value in accelerating the time to result (even if negative).

3.      It is difficult to state with certainty, but biohazard control might be easier to implement using a contained swab culture system than a patient - managed cup specimen. Specifically, the sheathed swab system seems more hygienic.

4.      The "rectum to plate" interval is shorter using a swab-based protocol than a cup from home to an institution or office to a laboratory pathway.  A few hours gained by sending a swab on presentation could result in a day earlier time to result.

5.      If a patient with diarrhea presents to an ER, the organisms that are traditionally the most important to find (i.e., bacterial enteric pathogens) are not those best diagnosed in cup specimens (though we do acknowledge access issues play a role in choice of place of presentation of less than acute illnesses to acute care facilities).

6.     The references cited in the Guidelines as supporting the superiority of cup stool specimens do not demonstrate the inferiority of swab cultures. Reference 106 (Diagn Microbiol Infect Dis 2006;56:123-6) pertains only to Salmonella, and, in fact, finds merit in testing both cups and swabs. Reference 107 (J Clin Microbiol 2007;45:1278-83) reports that bulk stool and swabs have equivalent yields for bacterial enteric pathogens.  

Phillip I. Tarr, M.D.
Melvin E. Carnahan Professor of Pediatrics
Professor of Molecular Microbiology
Director, Division of Pediatric Gastroenterology, Hepatology and Nutrition
Co-Leader, Pathobiology Research Unit, Washington University School of Medicine


Lori Holtz, M.D.                                                                                                        

Assistant Professor of Pediatrics, Division of Gastroenterology, Hepatology & Nutrition

Washington University School of Medicine


Ryan McKee, M.D.

Clinical Fellow, Division of Pediatrics Emergency Medicine

Washington University School of Medicine


David Schnadower, M.D., M.P.H.
Fellowship Director, Division of Pediatric Emergency Medicine
Washington University School of Medicine


Rebecca Stolle, R.N.

St. Louis Children's Hospital


Donna M. Denno, M.D., M.P.H.

Associate Professor of Pediatrics

Adjunct Associate Professor, Health Services Departments of Pediatrics and Global Health

University of Washington


Eileen J. Klein, MD, MPH

Professor, Pediatrics

Fellowship Director, Pediatric Emergency Medicine

Co-Director, Emergency Department Research

University of Washington and Seattle Children's Hospital


Stephen B. Freedman, .M.D.C.M., M.S.c.

Associate Professor of Pediatrics

Sections of Pediatric Emergency Medicine and Gastroenterology

Alberta Children's Hospital and University of Calgary



File Attachment(s):
2013-9-3 IDSA-ASM Letter.doc (120320 bytes)


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