Identification of Rare Pathogenic Bacteria in a Clinical Microbiology Laboratory: Impact of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

Abstract

bDuring the past 5 years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories.

RETRACTED ARTICLE: Culture of previously uncultured members of the human gut microbiota by culturomics

“…This analysis was performed using a Microflex LT system (Bruker Daltonics). For each spectrum, a maximum of 100 peaks was used and these peaks were compared with those of previous samples in the computer database of the Bruker Base and our homemade database, including the spectra of the bacterial species identified in previous works 28,29 . An isolate was labelled as correctly identified at the species level when at least one of the colonies' spectra had a score ≥1.9 and another of the colonies' spectra had a score ≥1.…”

The Ongoing Revolution of MALDI-TOF Mass Spectrometry for Microbiology Reaches Tropical Africa

“…1,6,7,18,21 Thus, conventional biochemical techniques, such as S. pneumoniae latex agglutination and indole tests, are sometimes still necessary for accurate identification. Other misidentifications rarely observed but also previously reported were within the genera Achromobacter, Burkholderia, and Aeromonas.…”

“…Currently, the estimated wait for one bacterial identification is reported to be from 1 minute and 46 seconds to 2 minutes per sample. 6,16 The use and necessity of this new system were quickly shown by the fact that traditional phenotypic systems were abandoned on the arrival of the MALDI-TOF MS in the laboratory. The rapid and accurate identification of routinely encountered bacterial and fungal species as well as those that are rare and difficult to identify using phenotypic methods provides a promising way to improve the care of patients with infectious diseases in Africa.…”

“…The required reagents are not expensive and do not require specific storage conditions if they are prepared in the laboratory. 1,6 Overall, it has been clearly shown that MALDI-TOF MS is less expensive than traditional methods, even when taking into account the costs of reagents, labor, performance measurements, waste disposal, microorganism prevalence, and instrument maintenance expenses as well as multiple runs and additional tests needed to maximize accuracy. 6,18,21,22 Moreover, several studies have shown the clinical benefits of using MALDI-TOF MS.…”

“…5 Thus, its use has become widespread in many clinical laboratories, first primarily in Europe and Asia. 1,2,[5][6][7][8][9][10][11] Currently, the specific identification of microorganisms in Africa raises several issues, including that there are no regulations governing pathogen identification in many countries. Although culturing capabilities are available in major hospitals in Africa, performance limitations of the biochemical identification methods may still be encountered.…”