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Microbiology turnaround times & how to improve your workflow

Beyond providing a STAT result, improving TAT can likely improve antimicrobial stewardship, infection control practices and healthcare costs associated with CNS infections.1

They say a watched pot never boils. It’s as true in the microbiology lab as it is in the kitchen. And yet, despite many microbiology technologies requiring multiple days to report comprehensive results, the pressure to treat patients with evident symptoms of infection and the temptation to prescribe antibiotics empirically because “I have seen this before and it sure looks like strep, staph, listeria, etc…” are out of line with best practices in antibiotic stewardship and best standards of patient care. There is a delicate balance here and how best to navigate it is the question.

There are specific requirements for the technical supervisor directly related to microbiology testing, including specific training for 6 to 12 months in microbiology unless the technical supervisor is an MD or equivalent with a certification in clinical pathology. This position as well as the clinical consultant can be the most daunting ones to staff in the smaller community.

In our article, “Microbiology & Staffing Issues in the Community Hospital,” we reviewed three factors that affect the mix of tests, including automation, what infectious agents are in the community and antibiotic stewardship program specifications.

The Optimal Solution

The optimal solution will balance tests needed in the facility or community when the patient is not referred to a tertiary care facility, capabilities of the staff and laboratory to perform these tests, knowledge of the technology choices available, and the courage to send out tests best performed elsewhere, and to make the decision of when the patient’s condition dictates transportation to a facility with more advanced technology and facilities.

While it was once true that result quality, especially specific identification of an organism from the myriad of possibilities, was dependent on culture followed by sub-culture techniques on plated media, and each step required at least one day, advances in technology, particularly molecular techniques, have changed the picture significantly. Some sexually transmitted diseases were first performed on molecular testing systems more than 10 years ago.

Respiratory infections have also undergone a revolution from fast (<20 minutes) visually read tests for influenza, strep, RSV and others to improved sensitivity and reduction in subjectivity by using readers with lateral flow assays. Even more recently, molecular assays have improved sensitivity, specificity and predictive value to an exceptional degree, with test times for some assays of one hour or less. In addition, since molecular assays amplify the signal beyond what is collected on the swab, they reduce false negatives and uncertainty that often results in repeat testing which delays reporting of results and patient treatment decisions.

As the menu of molecular tests continues to increase, and panels combining common pathogens become increasingly available, the choices for microbiology testing in the community hospital have improved greatly.

Respiratory tests and STDs have been the “tip of the spear” in market availability, options for gastrointestinal infection, urogenital infection, blood culture and meningitis are becoming more widely available and have changed the equation from “Can we afford to wait for the test to be done, are we sure the result is right, do we have the patience to hold off treatment until we KNOW” to “which tests do we truly need in our community, which manufacturer offers the range of test panels we want, how do we compare options for new molecular technologies with unfamiliar names like PCR and single strand displacement and can we afford to invest in new technologies, lab and staff training and the on-going costs of providing the tests in our community?”

While some tests will continue to require multiple days for some time to come, and the decision to upgrade current technology to newer, faster and more accurate/specific technology is a challenging one, turnaround time for many microbiology tests and the leveling of the playing field on interpretive skill of the operator through automation of reading and reporting results means many microbiology tests can be done in a single lab shift and can be done with more confidence in results and less concern about staff irrespective of the setting in a well-managed lab.

Thus, now the decision criteria are more linked to improving outcomes and at what cost. As time goes on, there is an expectation that the number of tests will continue to expand, technology choices will widen for a period and finally the market will select the best few manufacturers and technologies to bring them the range of tests their community, patients and medical staff need and demand.

The community hospital has exciting microbiology testing options available, and resources such as the new wave of molecular system manufacturers, trusted distribution companies, laboratory consultants and the peer group of “early adopters” of these emerging technologies in other hospitals can provide guidance to help with the decision-making process.

Time to result in microbiology testing will continue to decrease and create an ever-increasing opportunity to provide critical tests on time, improve confidence in diagnosis and speed needed treatment in communities across the country and the world.

1: Hemmert, Andrew C. & Gilbreath, Jeremy J. (2016, June 22). The Current State of Diagnostics for Meningitis and Encephalitis. Medical Laboratory Observer. Retrieved from

2: Pettit, N.N. PharmD, Matushek, S. MS, Charnot-Katsikas, A. MD, Tesic, V. MD, MS, Boonlayangour, S. MS, Brielmaier, B. PharmD, Pisano, J. MD. Comparison of Turnaround Time (TAT) and Time to Oseltamivir Discontinuation between Two Respiratory Viral Panel Testing (RVP) Methodologies. University of Chicago Medicine. Retrieved from