Advances in mass spectrometry for the identification of pathogens

Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm

Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate identification of microorganisms from microbial isolates. However, one major hurdle that limits the deployment of this tool for routine clinical diagnosis, and other areas of research such as culturomics, is the instrument time required for the mass spectrometer to analyze a single sample, which can take ∼1 h per sample, when using mass spectrometers that are presently used in most institutes. To address this issue, in this study, we employed, for the first time, tandem mass tags (TMTs) in multiplex identifications of microorganisms from multiple TMT-labeled samples in one MS/MS experiment. A difficulty encountered when using TMT labeling is the presence of interference in the measured intensities of TMT reporter ions. To correct for interference, we employed in the proposed method a modified version of the expectation maximization (EM) algorithm that redistributes the signal from ion interference back to the correct TMT-labeled samples. We have evaluated the sensitivity and specificity of the proposed method using 94 MS/MS experiments (covering a broad range of protein concentration ratios across TMT-labeled channels and experimental parameters), containing a total of 1931 true positive TMT-labeled channels and 317 true negative TMT-labeled channels. The results of the evaluation show that the proposed method has an identification sensitivity of 93-97% and a specificity of 100% at the species level. Furthermore, as a proof of concept, using an in-house-generated data set composed of some of the most common urinary tract pathogens, we demonstrated that by using the proposed method the mass spectrometer time required per sample, using a 1 h LC-MS/MS run, can be reduced to 10 and 6 min when samples are labeled with TMT-6 and TMT-10, respectively. The proposed method can also be used along with Orbitrap mass spectrometers that have faster MS/MS acquisition rates, like the recently released Orbitrap Astral mass spectrometer, to further reduce the mass spectrometer time required per sample.

Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions

A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.

Fractionation of bacteria by electrophoresis as pre-separation method before MALDI-MS detection

The present study attempted to apply the capillary electrophoresis technique for the fractionation and separation of S. Staphylococcus hominis and Escherichia coli bacteria isolated from urine samples and the detection of migrated fraction with spectrometric method. This involved the selection of suitable conditions for separation as well as the identification of pathogens. The result of the research was the separation of Gram-negative and Gram-positive bacteria, as well as their subsequent identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using two different approaches (culture of fractions on an agar plate and direct analysis of the collected fractions). The preliminary results provide a solid basis for further research on the use of electromigration techniques with LDI detection to identify pathogens such as bacteria and viruses in biological samples.

Evaluation of the Limit of Detection of Bacteria by Tandem Mass Spectrometry Proteotyping and Phylopeptidomics

Shotgun proteomics has proven to be an attractive alternative for identifying a pathogen and characterizing the antimicrobial resistance genes it produces. Because of its performance, proteotyping of microorganisms by tandem mass spectrometry is expected to become an essential tool in modern healthcare. Proteotyping microorganisms that have been isolated from the environment by culturomics is also a cornerstone for the development of new biotechnological applications. Phylopeptidomics is a new strategy that estimates the phylogenetic distances between the organisms present in the sample and calculates the ratio of their shared peptides, thus improving the quantification of their contributions to the biomass. Here, we established the limit of detection of tandem mass spectrometry proteotyping based on MS/MS data recorded for several bacteria. The limit of detection for Salmonella bongori with our experimental set-up is 4 × 10⁴ colony-forming units from a sample volume of 1 mL. This limit of detection is directly related to the amount of protein per cell and therefore depends on the shape and size of the microorganism. We have demonstrated that identification of bacteria by phylopeptidomics is independent of their growth stage and that the limit of detection of the method is not degraded in presence of additional bacteria in the same proportion.

A Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Direct-from-Urine-Specimen Diagnostic for Gram-Negative Pathogens

Urinary tract infections (UTIs) pose a major public health burden. The vast majority of UTIs are caused by Gram-negative bacteria. Current culture-based pathogen identification methods may require up to 24 to 48 h of incubation. In this study, we developed and evaluated a method for Gram-negative pathogen identification direct from urine, without culture, via matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in approximately 1 h. Urine samples were collected (n = 137) from the University of Maryland Medical Center clinical microbiology laboratory. To identify bacteria direct from urine, two methods were evaluated. First, 1 μL of urine was directly spotted onto the MALDI target plate, and second, 1 mL of urine was centrifuged at 8,000 rpm for 5 min before processing using the fast lipid analysis technique (FLAT). Mass spectra were acquired on the Bruker MALDI Biotyper sirius system in the negative-ion mode. Results were compared to those of standard culture methods. When 1 μL of urine was directly spotted, positive agreement was 81.5% (101/124) and, after centrifugation, 94.4% (117/124) relative to that of standard culture methods. Negative agreement for both methods was 100% (13/13). The time to results for both of the specimen preparation methods using the FLAT extraction protocol was approximately 1 h, with minimal hands-on time required (<5 min). The ability to rapidly identify pathogens directly from urine, without the need for culture, allows for faster turnaround times and, potentially, improved patient outcomes. Overall, the FLAT extraction protocol, in combination with lipid A identification, provides a reproducible and accurate method to rapidly identify urinary pathogens. IMPORTANCE This study describes and evaluates a direct-from-urine extraction method that allows identification of Gram-negative bacteria via MALDI-TOF MS within 1 h. Currently, identification of urinary pathogens requires 24 h of culture prior to identification. While this method may not replace culture, we demonstrate its utility in screening for common urinary pathogens. By providing identifications in under 1 h, clinicians can potentially treat patients sooner with more-targeted antimicrobial therapy. In turn, earlier treatment can improve patient outcome and antimicrobial stewardship. Furthermore, MADLI-TOF MS is a readily available, easy-to-use diagnostic tool in clinical laboratories, making implementation of this method possible.

Advances in rapid detection of SARS-CoV-2 by mass spectrometry

COVID-19 has already been lasting for more than two years and it has been severely affecting the whole world. Still, detection of SARS-CoV-2 remains the frontline approach to combat the pandemic, and the reverse transcription polymerase chain reaction (RT-PCR)-based method is the well recognized detection method for the enormous analytical demands. However, the RT-PCR method typically takes a relatively long time, and can produce false positive and false negative results. Mass spectrometry (MS) is a very commonly used technique with extraordinary sensitivity, specificity and speed, and can produce qualitative and quantitative information of various analytes, which cannot be achieved by RT-PCR. Since the pandemic outbreak, various mass spectrometric approaches have been developed for rapid detection of SARS-CoV-2, including the LC-MS/MS approaches that could allow analysis of several hundred clinical samples per day with one MS system, MALDI-MS approaches that could directly analyze clinical samples for the detection, and efforts for the on-site detection with portable devices. In this review, these mass spectrometric approaches were summarized, and their pros and cons as well as further development were also discussed.

Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods

Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.

Nanomedicine as a promising strategy for the theranostics of infectious diseases

Infectious diseases caused by bacteria, viruses, and fungi and their global spread pose a great threat to human health. The 2019 World Health Organization report predicted that infection-related mortality will be similar to cancer mortality by 2050. Particularly, the global cumulative numbers of the recent outbreak of coronavirus disease (COVID-19) have reached 110.7 million cases and over 2.4 million deaths as of February 23, 2021. Moreover, the crisis of these infectious diseases exposes the many problems of traditional diagnosis, treatment, and prevention, such as time-consuming and unselective detection methods, the emergence of drug-resistant bacteria, serious side effects, and poor drug delivery. There is an urgent need for rapid and sensitive diagnosis as well as high efficacy and low toxicity treatments. The emergence of nanomedicine has provided a promising strategy to greatly enhance detection methods and drug treatment efficacy. Owing to their unique optical, magnetic, and electrical properties, nanoparticles (NPs) have great potential for the fast and selective detection of bacteria, viruses, and fungi. NPs exhibit remarkable antibacterial activity by releasing reactive oxygen species and metal ions, exerting photothermal effects, and causing destruction of the cell membrane. Nano-based delivery systems can further improve drug permeability, reduce the side effects of drugs, and prolong systemic circulation time and drug half-life. Moreover, effective drugs against COVID-19 are still lacking. Recently, nanomedicine has shown great potential to accelerate the development of safe and novel anti-COVID-19 drugs. This article reviews the fundamental mechanisms and the latest developments in the treatment and diagnosis of bacteria, viruses, and fungi and discusses the challenges and perspectives in the application of nanomedicine.

Selective Capture and Identification of Methicillin-Resistant Staphylococcus aureus by Combining Aptamer-Modified Magnetic Nanoparticles and Mass Spectrometry

A nucleic acid aptamer that specifically recognizes methicillin-resistant Staphylococcus aureus (MRSA) has been immobilized on magnetic nanoparticles to capture the target bacteria prior to mass spectrometry analysis. After the MRSA species were captured, they were further eluted from the nanoparticles and identified using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The combination of aptamer-based capture/enrichment and MS analysis of microorganisms took advantage of the selectivity of both techniques and should enhance the accuracy of MRSA identification. The capture and elution efficiencies for MRSA were optimized by examining factors such as incubation time, temperature, and elution solvents. The aptamer-modified magnetic nanoparticles showed a capture rate of more than 90% under the optimized condition, whereas the capture rates were less than 11% for non-target bacteria. The as-prepared nanoparticles exhibited only a 5% decrease in the capture rate and a 9% decrease in the elution rate after 10 successive cycles of utilization. Most importantly, the aptamer-modified nanoparticles revealed an excellent selectivity towards MRSA in bacterial mixtures. The capture of MRSA at a concentration of 10² CFU/mL remained at a good percentage of 82% even when the other two species were at 10⁴ times higher concentration (10⁶ CFU/mL). Further, the eluted MRSA bacteria were successfully identified using MALDI mass spectrometry.

Integrated on-site collection and detection of airborne microparticles for smartphone-based micro-climate quality control

The rapid emergence of air-mediated diseases in a micro-climate demands on-site monitoring of airborne microparticles. The on-site detection of airborne microparticles becomes more challenging as the particles are highly localized and change dynamically over time. However, most existing monitoring systems rely on time-consuming sample collection and centralized off-site analysis. Here, we report a smartphone-based integrated microsystem for on-site collection and detection that enables real-time detection of indoor airborne microparticles with high sensitivity. The collection device, inspired by the Venturi effect, was designed to collect airborne microparticles without requiring an additional power supply. Our systematic analysis showed that the collection device was able to collect microparticles with consistent negative pressure, regardless of the particle concentration in the air sample. By incorporating a microfluidic-biochip based on inertial force to trap particles and an optoelectronic photodetector into a miniaturized device with a smartphone, we demonstrate real-time and sensitive detection of the collected airborne microparticles, such as Escherichia coli, Bacillus subtilis, Micrococcus luteus, and Staphylococcus with a particle-density dynamic range of 103-108 CFU mL-1. Because of its capabilities of minimal-power sample collection, high sensitivity, and rapid detection of airborne microparticles, this integrated platform can be readily adopted by the government and industrial sectors to monitor indoor air contamination and improve human healthcare.

Identification of bacteria in juice/lettuce using magnetic nanoparticles and selected reaction monitoring mass spectrometry

Ensuring food safety requires a rapid and reliable method for detecting food-borne pathogens. Mass spectrometry has been demonstrated as a powerful tool to classify pure bacterial species. However, matrix interference from food backgrounds may lead to false results because of the suppression of microbial signals. It is useful to develop a method for bacterial enrichment and marker identification in food samples. Magnetic zirconia nanoparticles were used to concentrate spiked microorganisms from apple juice/lettuce under specific conditions (pH 4.5). Bacterial identification was achieved using nanoLC-MS. Selected reaction monitoring of bacteria-related peptides was applied for the first time to identify bacteria including Staphylococcus aureus and Escherichia coli. This study presents an accurate means for bacterial identification in food matrixes using MS. The analysis time is less than 90 min and the minimum concentration of E. coli detected was 5 × 103 CFU/mL. The interaction between bacteria and the magnetic nanoparticles was electrostatic and nonspecific, in contrast to immunoassays which require specific antibodies. The targeted peptide analysis focuses on the bacterial markers, thus significantly simplifying the analysis and leading to an accurate identification of bacteria.

Identification of Neisseria meningitidis by MALDI-TOF MS may not be reliable

OBJECTIVES

The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique is increasingly used in hospital laboratories for routine identification of microorganisms. However, its performance is variable, particularly for highly variable species such as Neisseria meningitidis. Reliable identification of N. meningitidis is crucial for the management of invasive meningococcal disease by rapid implementation of treatment and preventive measures among close contacts. We assessed and improved N. meningitidis identification by MALDI-TOF MS by enriching the databases with reference strains identified using whole genome sequencing (WGS) as a reference standard.

METHODS

We first built a collection of 24 strains from several species of the Neisseria genus that we characterized by WGS. This collection was added to the available database to test by MALDI-TOF MS another collection of 32 clinical isolates received between 2015 and 2017 at the French National Reference Laboratory for Meningococci.

RESULTS

Using the commercially available library of mass spectrometry profiles, only 67% (95% confidence interval (CI), 47-82) concordance was observed at the species level between MALDI-TOF MS and WGS characterization. However, when the new enriched reference collection was used on the second subset of isolates, the identification of N. meningitidis was significantly improved (p 0.0016), showing 92% (95% CI, 75-98) specificity while that of the manufacturer's database alone was 52% (95% CI, 34-70).

CONCLUSIONS

Our data highlight the need to update the available MALDI-TOF MS database with high-quality references to enhance the identification of N. meningitidis and avoid unwarranted preventive measures or missing identification.

Characterization of microbial mixtures by mass spectrometry

MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.

Direct detection of carbapenemase-associated proteins of Acinetobacter baumannii using nanodiamonds coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The appearance and spread of carbapenem-resistant Acinetobacter baumannii (CRAB) pose a challenge for optimization of antibiotic therapies and outbreak preventions. The carbapenemase production can be detected through culture-based methods (e.g. Modified Hodge Test-MHT) and DNA based methods (e.g. Polymerase Chain Reaction-PCR). The culture-based methods are time-consuming, whereas those of PCR assays need only a few hours but due to its specificity, can only detect known genetic targets encoding carbapenem-resistance genes. Therefore, new approaches to detect carbapenemase-producing A. baumannii are of great importance. Here, we have developed a rapid and novel method using detonation nanodiamonds (DNDs) as a platform for concentration and extraction of A. baumannii carbapenemase-associated proteins prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS) analysis. To concentrate and extract the A. baumannii carbapenemase-associated proteins, we tested several protein precipitation conditions and found a 0.5% trifluoroacetic acid (TFA) solution within the bacterial suspension could result in strong ion signals with DNDs. A total of 66 A. baumannii clinical-isolates including 51 carbapenem-resistant strains and 15 carbapenem-susceptible strains were tested. Our result showed that among the 51 carbapenem-resistant strains 49 strains had a signal at m/z ~40,279 (±87); among the 15 carbapenem-susceptible strains, 4 strains showed a signal at m/z ~40,279. With on-diamond digestion, we confirmed that the captured protein at m/z ~40,279 was related to ADC family extended-spectrum class C beta-lactamase, from A. baumannii. Using this ADC family protein as a biomarker (m/z ~ 40,279) for carbapenem susceptibility testing of A. baumannii, the sensitivity and the specificity could reach 96% and 73% as compared to traditional imipenem susceptibility testing (MIC results). However, the sensitivity and specificity of this method reached 100% as compared to polymerase chain reaction (PCR) result. Our approach could directly detect the carbapenemase-associated proteins of A. baumannii within 90 min and does not require addition of carbapenemase substrate which is required in the MHT or other mass spectrometric methods. For future applications, our method could be efficiently used in the detection of other carbapenemase-producing bacteria.

The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives

The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012

This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.

Affinity capture using peptide-functionalized magnetic nanoparticles to target Staphylococcus aureus

Staphylococcus aureus, a commonly found pathogen, can cause food poisoning and infections. Thus, it is necessary to develop analytical methods for the rapid screening of S. aureus in suspicious samples. Magnetic nanoparticles (MNPs) are widely used as affinity probes to selectively enrich target species from complex samples because of their high specific surface area and magnetic properties. The MNP surface should be functionalized to have the capability to target specific species. We herein propose a straightforward method to functionalize aluminum oxide-coated iron oxide (Fe3O4@Al2O3) MNPs with the peptide HHHHHHDEEGLFVD (D). The peptide D was comprised of three domains: polyhistidine (H6) used as the linker, DEE added as the spacer, and GLFVD used for targeting S. aureus. D was immobilized on the surface of Fe3O4@Al2O3 MNPs through H6-Al chelation. Our results showed that the D-functionalized Fe3O4@Al2O3 MNPs (D-Fe3O4 MNPs) possess the capability to target S. aureus. The selective trapping experiments were conducted under microwave-heating for only 60 s, and sufficient bacterial cells were trapped by the MNPs to be identified by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We demonstrated that the D-Fe3O4@Al2O3 MNPs combined with MALDI-MS can be used to rapidly characterize trace amounts of S. aureus in complex juice and egg samples.

Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple 'fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html . Graphical Abstract ᅟ.

Mass Spectrometry in Clinical Laboratory: Applications in Biomolecular Analysis

Mass spectrometry (MS) is a technique that can identify analytes on the basis of mass-to-charge (m/z) ratio. Although this technique has been used in research and specialized clinical laboratories for decades, however, in recent years, MS has been increasingly used in routine clinical laboratories. MS, especially when coupled to gas chromatography or liquid chromatography, provides very specific and often sensitive analysis of many analytes. Other advantages of MS include simultaneous analysis of multiple analytes (>100) and generally without need for specialized reagents. Commonly measured analytes by MS include drugs, hormones, and proteins.

Mass Spectrometry in Clinical Laboratory: Applications in Therapeutic Drug Monitoring and Toxicology

Mass spectrometry (MS) has been used in research and specialized clinical laboratories for decades as a very powerful technology to identify and quantify compounds. In recent years, application of MS in routine clinical laboratories has increased significantly. This is mainly due to the ability of MS to provide very specific identification, high sensitivity, and simultaneous analysis of multiple analytes (>100). The coupling of tandem mass spectrometry with gas chromatography (GC) or liquid chromatography (LC) has enabled the rapid expansion of this technology. While applications of MS are used in many clinical areas, therapeutic drug monitoring, drugs of abuse, and clinical toxicology are still the primary focuses of the field. It is not uncommon to see mass spectrometry being used in routine clinical practices for those applications.

Applications of MALDI Mass Spectrometry in Clinical Chemistry

BACKGROUND

MALDI-TOF mass spectrometry (MS) is set to make inroads into clinical chemistry because it offers advantages over other analytical platforms. These advantages include low acquisition and operating costs, ease of use, ruggedness, and high throughput. When coupled with innovative front-end strategies and applied to important clinical problems, it can deliver rapid, sensitive, and cost-effective assays.

CONTENT

This review describes the general principles of MALDI-TOF MS, highlights the unique features of the platform, and discusses some practical methods based upon it. There is substantial potential for MALDI-TOF MS to make further inroads into clinical chemistry because of the selectivity of mass detection and its ability to independently quantify proteoforms.

SUMMARY

MALDI-TOF MS has already transformed the practice of clinical microbiology and this review illustrates how and why it is now set to play an increasingly important role in in vitro diagnostics in particular, and clinical chemistry in general.

Biomarker Characterization by MALDI-TOF/MS

Mass spectrometric techniques frequently used in clinical diagnosis, such as gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, ambient ionization mass spectrometry, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF/MS), are discussed. Due to its ability to rapidly detect large biomolecules in trace amounts, MALDI-TOF/MS is an ideal tool for characterizing disease biomarkers in biologic samples. Clinical applications of MS for the identification and characterization of microorganisms, DNA fragments, tissues, and biofluids are introduced. Approaches for using MALDI-TOF/MS to detect various disease biomarkers including peptides, proteins, and lipids in biological fluids are further discussed. Finally, various sample pretreatment methods which improve the detection efficiency of disease biomarkers are introduced.

Detection of Staphylococcus aureus by functional gold nanoparticle-based affinity surface-assisted laser desorption/ionization mass spectrometry

Staphylococcus aureus is one of the common pathogenic bacteria responsible for bacterial infectious diseases and food poisoning. This study presents an analytical method based on the affinity nanoprobe-based mass spectrometry that enables detection of S. aureus in aqueous samples. A peptide aptamer DVFLGDVFLGDEC (DD) that can recognize S. aureus and methicillin-resistant S. aureus (MRSA) was used as the reducing agent and protective group to generate DD-immobilized gold nanoparticles (AuNPs@DD) from one-pot reactions. The thiol group from cysteine in the peptide aptamer, i.e., DD, can interact with gold ions to generate DD-immobilized AuNPs in an alkaline solution. The generated AuNPs@DD has an absorption maximum at ∼518 nm. The average particle size is 7.6 ± 1.2 nm. Furthermore, the generated AuNPs@DD can selectively bind with S. aureus and MRSA. The conjugates of the target bacteria with AuNPs were directly analyzed by surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS). The gold ions generated from the AuNPs@DD anchored on the target bacteria were monitored. Gold ions (m/z 197 and 394) were only generated from the conjugates of the target bacterium-AuNP@DD in the SALDI process. Thus, the gold ions could be used as the indicators for the presence of the target bacteria. The detection limit of S. aureus using this method is in the order of a few tens of cells. The low detection limit is due to the ease of generation of gold cluster ion derived from AuNPs under irradiation with a 355 nm laser beam. Apple juice mixed with S. aureus was used as the sample to demonstrate the suitability of the method for real-world application. Because of its low detection limit, this approach can potentially be used to screen the presence of S. aureus in complex samples.

Use of rapid diagnostic techniques in ICU patients with infections

Background

Infection is a common complication seen in ICU patients. Given the correlation between infection and mortality in these patients, a rapid etiological diagnosis and the determination of antimicrobial resistance markers are of paramount importance, especially in view of today's globally spread of multi drug resistance microorganisms. This paper reviews some of the rapid diagnostic techniques available for ICU patients with infections.

Methods

A narrative review of recent peer-reviewed literature (published between 1995 and 2014) was performed using as the search terms: Intensive care medicine, Microbiological techniques, Clinical laboratory techniques, Diagnosis, and Rapid diagnosis, with no language restrictions.

Results

The most developed microbiology fields for a rapid diagnosis of infection in critically ill patients are those related to the diagnosis of bloodstream infection, pneumonia -both ventilator associated and non-ventilator associated-, urinary tract infection, skin and soft tissue infections, viral infections and tuberculosis.

Conclusions

New developments in the field of microbiology have served to shorten turnaround times and optimize the treatment of many types of infection. Although there are still some unresolved limitations of the use of molecular techniques for a rapid diagnosis of infection in the ICU patient, this approach holds much promise for the future.

Detection of strep throat causing bacterium directly from medical swabs by touch spray-mass spectrometry

Strep throat causing Streptococcus pyogenes was detected in vitro and in simulated clinical samples by performing touch spray ionization-mass spectrometry. MS analysis took only seconds to reveal characteristic bacterial and human lipids. Medical swabs were used as the substrate for ambient ionization. This work constitutes the initial step in developing a non-invasive MS-based test for clinical diagnosis of strep throat. It is limited to the single species, S. pyogenes, which is responsible for the vast majority of cases. The method is complementary to and, with further testing, a potential alternative to current methods of point-of-care detection of S. pyogenes.

Oligopeptides as biomarkers of cyanobacterial subpopulations. Toward an understanding of their biological role

Cyanobacterial oligopeptides comprise a wide range of bioactive and/or toxic compounds. While current research is strongly focused on exploring new oligopeptide variants and their bioactive properties, the biological role of these compounds remains elusive. Oligopeptides production abilities show a remarkably patchy distribution among conspecific strains. This observation has prompted alternative approaches to unveil their adaptive value, based on the use of cellular oligopeptide compositions as biomarkers of intraspecific subpopulations or chemotypes in freshwater cyanobacteria. Studies addressing the diversity, distribution, and dynamics of chemotypes in natural systems have provided important insights into the structure and ecology of cyanobacterial populations and the adaptive value of oligopeptides. This review presents an overview of the fundamentals of this emerging approach and its most relevant findings, and discusses our current understanding of the role of oligopeptides in the ecology of cyanobacteria.

Recent advances in bacteria identification by matrix-assisted laser desorption/ionization mass spectrometry using nanomaterials as affinity probes

Identifying trace amounts of bacteria rapidly, accurately, selectively, and with high sensitivity is important to ensuring the safety of food and diagnosing infectious bacterial diseases. Microbial diseases constitute the major cause of death in many developing and developed countries of the world. The early detection of pathogenic bacteria is crucial in preventing, treating, and containing the spread of infections, and there is an urgent requirement for sensitive, specific, and accurate diagnostic tests. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is an extremely selective and sensitive analytical tool that can be used to characterize different species of pathogenic bacteria. Various functionalized or unmodified nanomaterials can be used as affinity probes to capture and concentrate microorganisms. Recent developments in bacterial detection using nanomaterials-assisted MALDI-MS approaches are highlighted in this article. A comprehensive table listing MALDI-MS approaches for identifying pathogenic bacteria, categorized by the nanomaterials used, is provided.

Gram-stain plus MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry) for a rapid diagnosis of urinary tract infection

Microbiological confirmation of a urinary tract infection (UTI) takes 24–48 h. In the meantime, patients are usually given empirical antibiotics, sometimes inappropriately. We assessed the feasibility of sequentially performing a Gram stain and MALDI-TOF MS mass spectrometry (MS) on urine samples to anticipate clinically useful information. In May-June 2012, we randomly selected 1000 urine samples from patients with suspected UTI. All were Gram stained and those yielding bacteria of a single morphotype were processed for MALDI-TOF MS. Our sequential algorithm was correlated with the standard semiquantitative urine culture result as follows: Match, the information provided was anticipative of culture result; Minor error, the information provided was partially anticipative of culture result; Major error, the information provided was incorrect, potentially leading to inappropriate changes in antimicrobial therapy. A positive culture was obtained in 242/1000 samples. The Gram stain revealed a single morphotype in 207 samples, which were subjected to MALDI-TOF MS. The diagnostic performance of the Gram stain was: sensitivity (Se) 81.3%, specificity (Sp) 93.2%, positive predictive value (PPV) 81.3%, negative predictive value (NPV) 93.2%, positive likelihood ratio (+LR) 11.91, negative likelihood ratio (−LR) 0.20 and accuracy 90.0% while that of MALDI-TOF MS was: Se 79.2%, Sp 73.5, +LR 2.99, −LR 0.28 and accuracy 78.3%. The use of both techniques provided information anticipative of the culture result in 82.7% of cases, information with minor errors in 13.4% and information with major errors in 3.9%. Results were available within 1 h. Our serial algorithm provided information that was consistent or showed minor errors for 96.1% of urine samples from patients with suspected UTI. The clinical impacts of this rapid UTI diagnosis strategy need to be assessed through indicators of adequacy of treatment such as a reduced time to appropriate empirical treatment or earlier withdrawal of unnecessary antibiotics.

Recovery and identification of bacterial DNA from illicit drugs

Bacterial infections, including Bacillus anthracis (anthrax), are a common risk associated with illicit drug use, particularly among injecting drug users. There is, therefore, an urgent need to survey illicit drugs used for injection for the presence of bacteria and provide valuable information to health and forensic authorities. The objectives of this study were to develop a method for the extraction of bacterial DNA from illicit drugs and conduct a metagenomic survey of heroin and methamphetamine seized in the Australian Capital Territory during 2002-2011 for the presence of pathogens. Trends or patterns in drug contamination and their health implications for injecting drug users were also investigated. Methods based on the ChargeSwitch(®)gDNA mini kit (Invitrogen), QIAamp DNA extraction mini kit (QIAGEN) with and without bead-beating, and an organic phenol/chloroform extraction with ethanol precipitation were assessed for the recovery efficiency of both free and cellular bacterial DNA. Bacteria were identified using polymerase chain reaction and electrospray ionization-mass spectrometry (PCR/ESI-MS). An isopropanol pre-wash to remove traces of the drug and diluents, followed by a modified ChargeSwitch(®) method, was found to efficiently lyse cells and extract free and cellular DNA from Gram-positive and Gram-negative bacteria in heroin and methamphetamine which could then be identified by PCR/ESI-MS. Analysis of 12 heroin samples revealed the presence of DNA from species of Comamonas, Weissella, Bacillus, Streptococcus and Arthrobacter. No organisms were detected in the nine methamphetamine samples analysed. This study develops a method to extract and identify Gram-positive and Gram-negative bacteria from illicit drugs and demonstrates the presence of a range of bacterial pathogens in seized drug samples. These results will prove valuable for future work investigating trends or patterns in drug contamination and their health implications for injecting drug users as well as enabling forensic links between seizures to be examined.

Lysozyme-encapsulated gold nanocluster-based affinity mass spectrometry for pathogenic bacteria

RATIONALE

Bacterial infections can be difficult to treat and can lead to irreversible damage to patients if proper treatment is not provided in time. Additionally, the emerging threat from antibiotic-resistant bacterial strains makes medical treatment even more difficult. Thus, rapid identification of infected bacterial strains is essential to assist diagnostics and medical treatment.

METHODS

Lysozymes are glycoside hydrolases that can bind with peptidoglycans on bacterial cell walls. In this work, we demonstrated that lysozyme-encapsulated gold nanoclusters (lysozyme-AuNCs) with red photoluminescence can be used as affinity probes to concentrate pathogenic bacteria. After bacteria had been probed by the lysozyme-AuNCs in a sample solution, the lysozyme-AuNC-bacteria conjugates were readily spun down at a low centrifugation speed. The red emission from the AuNCs on the conjugates could be visualized with the naked eye under illumination of ultraviolet light. The bacteria in the conjugates can be identified by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with principal component analysis (PCA).

RESULTS

We demonstrated that pathogenic bacteria including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, pandrug-resistant Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecalis, and vancomycin-resistant Enterococcus faecalis (VRE) can be readily concentrated by the lysozyme-AuNCs and distinguished by the results combining MALDI-MS and PCA. Additionally, the possibility of using the current approach to differentiate E. faecalis from VRE was also demonstrated. The lowest detection concentration for E. coli using the current approach is ~10(6) cells/mL.

CONCLUSIONS

The results indicated that the lysozyme-AuNCs are effective affinity probes for Gram-positive and Gram-negative bacteria. By combining the results from MALDI-MS and PCA, different bacteria can be easily distinguished. The current approach can be potentially used to assist the identification of bacteria from biological fluids.

Non-phenotypic tests to detect and characterize antibiotic resistance mechanisms in Enterobacteriaceae

In the past 2 decades, we have observed a rapid increase of infections due to multidrug-resistant Enterobacteriaceae. Regrettably, these isolates possess genes encoding for extended-spectrum β-lactamases (e.g., blaCTX-M, blaTEM, blaSHV) or plasmid-mediated AmpCs (e.g., blaCMY) that confer resistance to last-generation cephalosporins. Furthermore, other resistance traits against quinolones (e.g., mutations in gyrA and parC, qnr elements) and aminoglycosides (e.g., aminoglycosides modifying enzymes and 16S rRNA methylases) are also frequently co-associated. Even more concerning is the rapid increase of Enterobacteriaceae carrying genes conferring resistance to carbapenems (e.g., blaKPC, blaNDM). Therefore, the spread of these pathogens puts in peril our antibiotic options. Unfortunately, standard microbiological procedures require several days to isolate the responsible pathogen and to provide correct antimicrobial susceptibility test results. This delay impacts the rapid implementation of adequate antimicrobial treatment and infection control countermeasures. Thus, there is emerging interest in the early and more sensitive detection of resistance mechanisms. Modern non-phenotypic tests are promising in this respect, and hence, can influence both clinical outcome and healthcare costs. In this review, we present a summary of the most advanced methods (e.g., next-generation DNA sequencing, multiplex PCRs, real-time PCRs, microarrays, MALDI-TOF MS, and PCR/ESI MS) presently available for the rapid detection of antibiotic resistance genes in Enterobacteriaceae. Taking into account speed, manageability, accuracy, versatility, and costs, the possible settings of application (research, clinic, and epidemiology) of these methods and their superiority against standard phenotypic methods are discussed.

Rapid characterization of microorganisms by mass spectrometry--what can be learned and how?

Strategies for the rapid and reliable analysis of microorganisms have been sought to meet national needs in defense, homeland security, space exploration, food and water safety, and clinical diagnosis. Mass spectrometry has long been a candidate technique because it is extremely rapid and can provide highly specific information. It has excellent sensitivity. Molecular and fragment ion masses provide detailed fingerprints, which can also be interpreted. Mass spectrometry is also a broad band method--everything has a mass--and it is automatable. Mass spectrometry is a physiochemical method that is orthogonal and complementary to biochemical and morphological methods used to characterize microorganisms.

Establishing drug resistance in microorganisms by mass spectrometry

A rapid method to determine drug resistance in bacteria based on mass spectrometry is presented. In it, a mass spectrum of an intact microorganism grown in drug-containing stable isotope-labeled media is compared with a mass spectrum of the intact microorganism grown in non-labeled media without the drug present. Drug resistance is determined by predicting characteristic mass shifts of one or more microorganism biomarkers using bioinformatics algorithms. Observing such characteristic mass shifts indicates that the microorganism is viable even in the presence of the drug, thus incorporating the isotopic label into characteristic biomarker molecules. The performance of the method is illustrated on the example of intact E. coli, grown in control (unlabeled) and (13)C-labeled media, and analyzed by MALDI TOF MS. Algorithms for data analysis are presented as well.

Human serum albumin stabilized gold nanoclusters as selective luminescent probes for Staphylococcus aureus and methicillin-resistant Staphylococcus aureus

In this work, human serum albumin (HSA) stabilized gold nanoclusters (HSA-AuNCs) with reddish photoluminescence were used as sensing probes for pathogenic bacteria including Enterobacter cloacae, Escherichia coli J96, Pseudomonas aeruginosa, pandrug-resistant Acinetobacter baumannii (PDRAB), Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), Streptococcus pyogenes, and vancomycin-resistant Enterococcus faecalis (VRE). We discovered that HSA-AuNCs have unique affinity with S. aureus and MRSA. In addition to demonstrating the selective sensing ability of HSA-AuNCs toward S. aureus and MRSA, the binding peptide motifs identified from HSA-AuNCs were characterized by mass spectrometry. The identified binding peptides were further used as the reducing and stabilizing agents for generation of peptide-bound AuNCs (Pep-AuNCs). The generated Pep-AuNCs were demonstrated to have the binding affinities with S. aureus and MRSA.