Custom database development and biomarker discovery methods for MALDI-TOF mass spectrometry-based identification of high-consequence bacterial pathogens

Rapid Detection of Salmonella Enteritidis, Typhimurium, and Thompson by Specific Peak Analysis Using Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

Rapid detection of Salmonella serovars is important for the effective control and monitoring of food industries. In this study, we evaluate the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid detection of three serovars, Enteritidis, Typhimurium, and Thompson, that are epidemiologically important in Korea. All strains were identified at the genus level, with a mean score of 2.319 using the BioTyper database, and their protein patterns were confirmed to be similar by principal component analysis and main spectrum profile dendrograms. Specific peaks for the three serovars were identified by analyzing 65 reference strains representing 56 different serovars. Specific mass peaks at 3018 ± 1 and 6037 ± 1, 7184 ± 1, and 4925 ± 1 m/z were uniquely found in the reference strains of serovars Enteritidis, Typhimurium, and Thompson, respectively, and they showed that the three serovars can be differentiated from each other and 53 other serovars. We verified the reproducibility of these mass peaks in 132 isolates, and serovar classification was achieved with 100% accuracy when compared with conventional serotyping through antisera agglutination. Our method can rapidly detect a large number of strains; hence, it will be useful for the high-throughput screening of Salmonella serovars.

A MALDI-TOF MS database for fast identification of Vibrio spp. potentially pathogenic to marine mollusks

In mollusk aquaculture, a large number of Vibrio species are considered major pathogens. Conventional methods based on DNA amplification and sequencing used to accurately identify Vibrio species are unsuitable for monitoring programs because they are time-consuming and expensive. The aim of this study was, therefore, to develop the MALDI-TOF MS method in order to establish a rapid identification technique for a large panel of Vibrio species. We created the EnviBase containing 120 main spectra projections (MSP) of the Vibrio species that are potentially responsible for mollusk diseases, comprising 25 species: V. aestuarianus, V. cortegadensis, V. tapetis and species belonging to the Coralliilyticus, Harveyi, Mediterranei, and Orientalis clades. Each MSP was constructed by the merger of raw spectra obtained from three different media and generated by three collaborating laboratories to increase the diversity of the conditions and thus obtain a good technique robustness. Perfect discrimination was obtained with all of the MSP created for the Vibrio species and even for very closely related species as V. europaeus and V. bivalvicida. The new EnviBase library was validated through a blind test on 100 Vibrio strains performed by our three collaborators who used the direct transfer and protein extraction methods. The majority of the Vibrio strains were successfully identified with the newly created EnviBase by the three laboratories for both protocol methods. This study documents the first development of a freely accessible database exclusively devoted to Vibrio found in marine environments, taking into account the high diversity of this genus. KEY POINTS: • Development of a MALDI-TOF MS database to quickly affiliate Vibrio species. • Increase of the reactivity when faced with Vibrio associated with mollusk diseases. • Validation of MALDI-TOF MS as routine diagnostic tool.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification of security-sensitive bacteria: Considerations for Canadian Bruker users

Background

The use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) systems for bacterial identification has rapidly become a front line tool for diagnostic laboratories, superseding classical microbiological methods that previously triggered the identification of higher risk pathogens. Unknown Risk Group 3 isolates have been misidentified as less pathogenic species due to spectral library availability, content and quality. Consequently, exposure to higher risk pathogens has been reported within Canadian laboratory staff following the implementation of MALDI-TOF MS. This overview aims to communicate the potential risk to laboratory staff of inaccurate identification of security-sensitive biological agents (SSBA) bacteria and to provide suggestions to mitigate.

Methods

Cultures were manipulated in a Biosafety Level 3 laboratory, prepared for MALDI-TOF MS analysis via full chemical extraction and analysed on a Bruker Microflex LT instrument. Data were analyzed with Biotyper software; comparing raw spectra against MS profiles in three libraries: Bruker Taxonomy; Bruker Security-Restricted; and National Microbiology Laboratory (NML) SSBA libraries. Four years of Bruker MALDI-TOF MS data acquired in-house were reviewed.

Results

In general, the Bruker MS spectral libraries were less successful in identifying the SSBA bacteria. More successful was the NML library. For example, using a high score cut-off (greater than 2.0), the Bruker SR library was unable to identify 52.8% of our Risk Group 3 agents and near neighbours to the species-level with confidence, whereas the custom NML library was unable to identify only 20.3% of the samples.

Conclusion

The last four years of data demonstrated both the importance of library selection and the limitations of the various spectral libraries. Enhanced standard operating procedures are advised to reduce laboratory exposure to SSBAs when using MALDI-TOF MS as a front line identification tool.

Novel specific peaks for differentiating the Lactobacillus plantarum group using matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Identifying the Lactobacillus plantarum group using conventional taxonomic methods such as biochemical analysis and 16S rRNA gene sequencing is inaccurate, expensive, and time-consuming. In this study, for the first time, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to identify the L. plantarum group and develop a classification method for species level differentiation with specific peaks based on mass spectra. Furthermore, from the mass spectra of 131 isolates aligned with the biotyper database, 131 isolates (100%) were correctly identified at the species level with a mean score of 2.316. However, commercial databases could not accurately differentiate some isolates of L. plantarum group species because the same colony was identified as different species with similar score values. Moreover, these two species showed a similar mass pattern in the main spectrum profiles-dendrogram and Principal component analysis clustering generated by the mass peak of the reference strains and isolates. Specific peaks to each species were investigated from the analyzed mass peak, and they clearly showed that three species could be differentiated. These peaks were verified by re-identifying 131 isolates, and it demonstrated 100% specificity and accuracy. Also, using a specific peak, isolates that were undifferentiated from the biotyper database were clearly identified as one species, similar to species-specific polymerase chain reaction. Our data demonstrate that the specific peaks accurately differentiate the L. plantarum group and enable high-resolution identification at the species level; this methodology can be used to rapidly and easily identify them and determine their nomenclature.

MALDI-TOF Mass Spectrometry and Specific Biomarkers: Potential New Key for Swift Identification of Antimicrobial Resistance in Foodborne Pathogens

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is today the reference method for direct identification of microorganisms in diagnostic laboratories, as it is notably time- and cost-efficient. In the context of increasing cases of enteric diseases with emerging multi-drug resistance patterns, there is an urgent need to adopt an efficient workflow to characterize antimicrobial resistance (AMR). Current approaches, such as antibiograms, are time-consuming and directly impact the "patient-physician" workflow. Through this mini-review, we summarize how the detection of specific patterns by MALDI-TOF MS, as well as bioinformatics, become more and more essential in research, and how these approaches will help diagnostics in the future. Along the same lines, the idea to export more precise biomarker identification steps by MALDI-TOF(/TOF) MS data towards AMR identification pipelines is discussed. The study also critically points out that there is currently still a lack of research data and knowledge on different foodborne pathogens as well as several antibiotics families such as macrolides and quinolones, and many questions are still remaining. Finally, the innovative combination of whole-genome sequencing and MALDI-TOF MS could be soon the future for diagnosis of antimicrobial resistance in foodborne pathogens.

A MALDI-TOF MS database with broad genus coverage for species-level identification of Brucella

Brucella are highly infectious bacterial pathogens responsible for a severely debilitating zoonosis called brucellosis. Half of the human population worldwide is considered to live at risk of exposure, mostly in the poorest rural areas of the world. Prompt diagnosis of brucellosis is essential to prevent complications and to control epidemiology outbreaks, but identification of Brucella isolates may be hampered by the lack of rapid and cost-effective methods. Nowadays, many clinical microbiology laboratories use Matrix-Assisted Laser Desorption Ionization–Time Of Flight mass spectrometry (MALDI-TOF MS) for routine identification. However, lack of reference spectra in the currently commercialized databases does not allow the identification of Brucella isolates. In this work, we constructed a Brucella MALDI-TOF MS reference database using VITEK MS. We generated 590 spectra from 84 different strains (including rare or atypical isolates) to cover this bacterial genus. We then applied a novel biomathematical approach to discriminate different species. This allowed accurate identification of Brucella isolates at the genus level with no misidentifications, in particular as the closely related and less pathogenic Ochrobactrum genus. The main zoonotic species (B. melitensis, B. abortus and B. suis) could also be identified at the species level with an accuracy of 100%, 92.9% and 100%, respectively. This MALDI-TOF reference database will be the first Brucella database validated for diagnostic and accessible to all VITEK MS users in routine. This will improve the diagnosis and control of brucellosis by allowing a rapid identification of these pathogens.

Brucella are bacteria that mainly infect animals. They can also be transmitted to humans and cause a serious disease called brucellosis. Half the world's population is considered exposed, especially in the poorest rural areas. Experts agree that prompt identification of Brucella isolates is essential to provide appropriate treatment to patients and to control epidemiological outbreaks. Mis-identification of these highly infectious pathogens may lead to delays in diagnosis, but also to increased risks of accidental exposure for laboratory workers. MALDI-TOF mass spectrometry is now the first line of bacterial identification in many routine diagnostic laboratories. However, not all clinical mass spectrometers can identify Brucella. In this work, we updated a database with Brucella spectra to improve the performance of MALDI-TOF mass spectrometers. These instruments will now be able to identify accurately Brucella isolates. This will greatly improve the diagnosis of brucellosis.

Misidentification of Risk Group 3/Security Sensitive Biological Agents by MALDI-TOF MS in Canada: November 2015-October 2017

Background

Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a technology increasingly used in diagnostic identification of microorganisms. However, anecdotal evidence suggests that this technology is associated with misidentification of Risk Group 3 (RG3)/Security Sensitive Biological Agents (SSBA) resulting in exposure risks to laboratory personnel.

Objective

To investigate and characterize incidents related to the use of MALDI-TOF MS in Canada between November 6, 2015, and October 10, 2017.

Methods

Cases were identified from laboratory incident reports in the national Laboratory Incident Notification Canada (LINC) surveillance system. Eligible cases referred directly to MALDI-TOF MS or one of three RG3/SSBA organisms, Brucella species, Francisella tularensis and Burkholderia pseudomallei. A questionnaire was developed to identify potential risk factors leading to the exposure. Reporters from organizations with selected incidents were interviewed using the questionnaire. Data were entered into an Excel spreadsheet and standard descriptive statistical analysis performed to assess common characteristics and identify possible risk factors.

Results

There were eight eligible incidents and a total of 39 laboratory workers were exposed to RG3/SSBA organisms. In five (out of eight) of the incidents, the reporters indicated that their device was equipped with both clinical and research reference libraries. For six incidents where reporters knew the type of library used, only the clinical library was employed at the time of the incident even though both libraries were available in five of these incidents. In all eight cases, the exposure occurred during the sample preparation stage with analyses performed on an open bench and directly from the specimen. And in all eight cases, patient specimens were received without information regarding potential risk.

Conclusion

This first national study characterizing the nature and extent of laboratory incidents involving RG3/SSBA that are related to the use of MALDI-TOF MS identifies risk factors and provides baseline data that can inform mitigation strategies.

MALDI-TOF mass spectrometry and high-consequence bacteria: safety and stability of biothreat bacterial sample testing in clinical diagnostic laboratories

We considered the application of MALDI-TOF mass spectrometry for BSL-3 bacterial diagnostics, with a focus on the biosafety of live-culture direct-colony testing and the stability of stored extracts. Biosafety level 2 (BSL-2) bacterial species were used as surrogates for BSL-3 high-consequence pathogens in all live-culture MALDI-TOF experiments. Viable BSL-2 bacteria were isolated from MALDI-TOF mass spectrometry target plates after 'direct-colony' and 'on-plate' extraction testing, suggesting that the matrix chemicals alone cannot be considered sufficient to inactivate bacterial culture and spores in all samples. Sampling of the instrument interior after direct-colony analysis did not recover viable organisms, suggesting that any potential risks to the laboratory technician are associated with preparation of the MALDI-TOF target plate before or after testing. Secondly, a long-term stability study (3 years) of stored MALDI-TOF extracts showed that match scores can decrease below the threshold for reliable species identification (<1.7), which has implications for proficiency test panel item storage and distribution.

Traditional approaches versus mass spectrometry in bacterial identification and typing

Biochemical methods such as metabolite testing and serotyping are traditionally used in clinical microbiology laboratories to identify and categorize microorganisms. Due to the large variety of bacteria, identifying representative metabolites is tedious, while raising high-quality antisera or antibodies unique to specific biomarkers used in serotyping is very challenging, sometimes even impossible. Although serotyping is a certified approach for differentiating bacteria such as E. coli and Salmonella at the subspecies level, the method is tedious, laborious, and not practical during an infectious disease outbreak. Mass spectrometry (MS) platforms, especially matrix assisted laser desorption and ionization-time of flight mass spectrometry (MALDI-TOF-MS), have recently become popular in the field of bacterial identification due to their fast speed and low cost. In the past few years, we have used liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based approaches to solve various problems hindering serotyping and have overcome some insufficiencies of the MALDI-TOF-MS platform. The current article aims to review the characteristics, advantages, and disadvantages of MS-based platforms over traditional approaches in bacterial identification and categorization.