Using MALDI Mass Spectrometry for Advanced Microbial Identification

October 2019 - Vol. 8 No. 9 - Page #14

A wide variety of pathogenic microorganisms cause disease in humans, with different microbial strains causing different levels of disease, from a common cold to potentially life-threatening infections such as tuberculosis (TB). Similarly, these different strains sit at various points along the antimicrobial susceptibility scale, with some strains entirely resistant to a multitude of drugs, some with intermediate susceptibility, and others that are completely susceptible to treatment. The combination of these elements results in myriad disease identification and treatment scenarios.

Antimicrobial resistance is a serious threat to global health and is placing a huge burden on health care systems worldwide. As an example, multidrug-resistant (MDR)-TB remains a public health crisis and a health security threat, particularly in countries such as India, Indonesia, and China. The World Health Organization (WHO) estimates that in 2017, there were 558,000 new TB cases with resistance to rifampicin (the most effective first-line drug), of which 82% (457,560 cases) had MDR-TB.1 As microbial species regularly evolve into new strains, there is great competition to discover and develop novel therapeutics to combat them, as well as innovative technologies to detect problematic microbes in the least amount of time.

The New Hanover Regional Medical Center (NHRMC) is a community hospital in Wilmington, North Carolina, and the microbiology laboratory maintains a special focus on microbial identification (ID). Accordingly, the laboratory has invested in sophisticated instrumentation to ensure NHRMC clinicians are able to deliver the most suitable treatment as quickly as possible, and to help fight antimicrobial resistance.

Moving to Mass Spectrometry

Many microbiology laboratories rely on traditional biochemical and culture techniques for microbial ID, which can hinder clinicians’ ability to access results in an expeditious timeframe. Previously at NHRMC, a typical microbiology ID could take 2-3 days using conventional methods. Antimicrobial susceptibility testing (AST) took up to 5 days. Furthermore, fastidious, slow-growing, non-viable or non-cultivable organisms can be a challenge to identify with traditional methods, requiring samples to be sent to a reference laboratory for further work up. In general, traditional biochemical methods are time consuming, and with re-testing not uncommon, that time can be stretched even further. In the interim, clinicians often place patients on precautionary broad-spectrum antibiotics, which is costly and has implications for the spread of antimicrobial resistance.

The introduction of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to NHRMC in 2016 dramatically improved turnaround time (TAT) for microbial ID in our lab. When tested during our instrument validation period, the percentage of identifications using MS proved superior to our traditional biochemical methods, which only properly identified 82% of samples compared to approximately 96% with MS. Using this technology for the ID and classification of bacteria and yeasts based on proteomic fingerprinting, these specialized MS instruments measure the highly abundant proteins found in all microorganisms. The characteristic spectrum pattern of these proteins is used to reliably and accurately ID a microorganism by matching against a library of 425 microbial species across 333 different groups, covering anaerobes, gram-positive and gram-negative bacteria, and yeasts.


Expedite ID and Resulting Patient Care

After implementing MALDI-TOF MS, the time to definitive ID in our microbiology lab reduced from a 3-5-day range to 1-2 days. In addition, shortly after this implementation, the microbiology lab became fully automated, which resulted in a further reduction in time of testing. The combination of these factors enabled significant workflow improvements, including next day turnaround on ID testing and expedited time to correct diagnosis, which enables our clinicians to better focus patient therapies much earlier in the process. For more information, see TABLE 1 indicating the time savings involving five organisms tested at NHRMC.


The introduction of MALDI-TOF MS and expedited ID of clinically significant organisms has led to a more active promotion of antibiotic stewardship by reducing the incidence of MDR organisms in our patient population and helping to rapidly initiate proper infection control measures. In addition, MALDI-TOF MS has enabled the laboratory to identify a greater number of organisms as compared to traditional microbiology instrumentation. For example, we have seen cases of patients receiving dental surgery and developing a post-procedure oral infection. Microorganisms responsible for oral infections can be difficult to ID, as many traditional biochemical ID panels do not include oral bacteria. Now the laboratory can identify sepsis contracted through oral infection, whereas in the past, such samples would have been sent to a reference laboratory, resulting in significant delays to targeted antibiotic therapy.

Program Cost Savings

One key driver behind the move to MS (and overall automation) was the potential to save money on ID and AST, and our laboratory has realized substantial benefits since the incorporation of the MALDI-TOF MS instrumentation and workflow. Antibiotic therapy has been narrowed in 60% of patients, with a correlated estimated savings of $200,000, simply by providing a definitive ID quicker, and then de-escalating or stopping antibiotics.

The overall costs of conducting biochemical tests also has been reduced. In the first year of using MALDI-TOF MS, the hospital reduced the cost of ancillary testing by approximately $100,000 and minimized administrative work for technical staff by approximately 70%. The projected savings for year 2 include an expected reduction of $30,000-$40,000 in ancillary costs of reagents in the laboratory. A definitive identification via MALDI-TOF MS costs approximately $1.90 per ID, whereas the previous biochemical ID method cost $8.57; yielding a savings of $6.67 per ID.

Moving Forward

The implementation of sophisticated technology, such as MALDI-TOF MS, helps arm our laboratorians and clinicians with the tools necessary to effectively combat the most challenging pathogens. Without a confirmed ID of the infecting organism, clinicians can only provide broad-spectrum antimicrobials, which, in addition to being an expensive treatment strategy, also poses a higher risk for the spread of antimicrobial resistance. By informing clinicians on the exact ID of an organism in a shorter timeframe, patients can be administered specific, narrowed antibiotics sooner, saving money, reducing hospital length of stay, and helping to combat the ongoing threat of MDR organisms.


  1. World Health Organization (WHO). Global Tuberculosis Report 2018. Accessed 9.1.2019.


Kevin McNabb, PhD, MBA, MT(ASCP), is the director of microbiology, immunology, and molecular testing in the Department of Pathology and Laboratory Services at New Hanover Regional Medical Center in Wilmington, North Carolina. Having joined NHRMC in 2012, his prior experience as a Colonel in the US Army Medical Service Corps for 28 years paved the way toward leadership of the microbiology laboratory at NHRMC. Kevin’s areas of expertise include immunology, allergy testing, autoimmune diseases, initiation of immune response, vaccine development, molecular diagnostic testing, antimicrobial therapy, and susceptibility testing.

One example of the impact that MALDI-TOF MS has had on patient outcomes at NHRMC involved a 21-year-old male who presented to the ED with a fever and headache. The patient had Graves disease (autoimmune disorder affecting the thyroid) and a history of hypertension, with no other outstanding health issues.

The patient was admitted, blood specimens were sent to the laboratory for culture, and urinalysis, chemistry, and hematology profiles were created. A meningitis panel and other laboratory tests returned negative, but a blood culture was positive at 20 hours after admission (both anaerobic bottles). A Gram stain showed gram-negative long thin rods and was sub-cultured for reading at 2 days. The physician called the next day and requested to look at the culture, which was growing anaerobically at 18 hours (38 hours from admission).

Through MALDI-TOF MS ID, the microbiology lab found the organism to be Fusobacterium necrophorum—the causative bacterial species of Lemierre’s syndrome, which can lead to serious complications, including sepsis. The physician was immediately notified and patient therapy was changed to ceftriaxone and metronidazole, at a higher than standard dosing. The patient had already been on ceftriaxone therapy since admission, but at a much lower dose. Within 6 hours of the change in therapy, the patient was responding and was transferred from the ICU to a regular bed, 44 hours after admission. Without relatively rapid identification, the change in therapy would likely have taken much longer, resulting in an extended ICU stay, longer overall length of stay, and the potential for a poor clinical outcome.


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