Routine identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: Success rate, economic analysis, and clinical outcome

Identification of herpes simplex virus type 1 infection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

This study aimed to investigate whether Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) could identify Herpes simplex virus type 1 (HSV1) infection in samples in vitro and in vivo. MS spectra of supernatants and suspensions from infected human cornea epithelial (HCE) cell culture samples and infected samples of BALB/c mouse corneas were obtained by a VITEK® mass spectrometer. The discriminating peaks between infected and non-infected samples were used to establish discriminating superspectra (DSPc for cells and DSPm for corneas) by SARAMIS™ software. Another infected cells with two viral titers and infected cornea samples were used for blind testing against two DSPs. The results showed that automatic matching by the SARAMIS system revealed 28 discriminating peaks in HSV1-infected cells and 17 discriminating peaks in HSV1 keratitis, generating two discriminating superspectra (DSPs). Blind testing of virus-infected samples demonstrated a high positive identification rate for both in vitro and in vivo DSPs. The positive identification rate varied with viral titers, with cell suspensions exhibiting significantly higher rates compared to supernatants. Cluster analysis based on MS spectra revealed that there were more obvious differences between in vivo and in vitro samples compared to the differences between infected and non-infected samples. These findings suggest that MALDI-TOF MS can directly identify HSV1 in vitro or in vivo infected specimens, with higher positivity rates achieved when using cellular suspensions directly. This is an attempt on the method of virus detection, which shows potential for using MS to detect HSV1 infection or other virus infection in humans.

Diagnosis Accuracy of Raman Spectroscopy in the Identification of Pathogenic Bacteria

As an emerging technology, Raman spectroscopy (RS) has been used to identify pathogenic bacteria with excellent performance. The aim of this study was to verify the diagnosis accuracy of RS in identification of pathogenic bacteria. This meta-analysis systematically evaluated the accuracy of RS for identification of pathogenic bacteria. We searched the electronic databases of PubMed and Web of Science to obtain relevant articles; STATA 15.1 was used to analyze all sensitivities, specificies, and their 95% confidence interval (CI). The summary receiver operating characteristic curves (SROC) and area under the curve (AUC) were used to display more performance of RS. Nineteen articles were included according to the inclusion and exclusion criteria. The pooled sensitivity and specificity of RS for the identification of pathogenic bacteria were 0.94 (95% CI, 0.89-0.96) and 0.99 (95% CI, 0.97-0.99). The diagnostic odds ratio (DOR) was 1209 (95% CI, 367-3980), and AUC of SROC was 0.99 (95% CI, 0.98-1.00). For gram-positive bacteria, the sensitivity and specificity of different species ranged from 0.00 to 1.00 and 0.96 to 1.00, with a pooled sensitivity and specificity of 0.96 (95% CI, 0.90-0.98) and 0.99 (95% CI, 0.98-1.00). For gram-negative bacteria, the sensitivity and specificity of different species ranged from 0.30 to 1.00 and 0.92 to 1.00, with a pooled sensitivity and specificity of 0.92 (95% CI, 0.76-0.98) and 0.99 (95% CI, 0.98-1.00). For acid-fast bacteria, the sensitivity and specificity of different species ranged from 0.83 to 1.00 and 0.96 to 1.00, with a pooled sensitivity and specificity of 0.96 (95% CI, 0.84-0.99) and 1.00 (95% CI, 0.96-1.00). RS provides a new method for pathogenic bacteria identification and demonstrates high sensitivity and specificity for most included species.

Accelerated Bacterial Identification with MALDI-TOF MS Leads to Fewer Diagnostic Tests and Cost Savings

INTRODUCTION

Rapid microbiology reporting can enhance both clinical and economic outcomes.

MATERIAL AND METHODS

This three-year, quasi-experimental study, single-group pretest-posttest study, conducted at a university medical center, aimed to evaluate the clinical and economic impact of rapid microbiological identification reporting using MALDI-TOF MS. A total of 363 consecutive hospitalized patients with bacterial infections were evaluated, comparing a historical control group (CG, n = 183) with an intervention group (IG, n = 180). In the CG, microbiological information (bacterial identification and antibiotic susceptibility) was provided between 18:00 and 22:00 h, while in the IG, bacterial identification was reported between 12:00 and 14:00 h, and antibiotic susceptibility was reported between 18:00 and 22:00 h.

RESULTS

The IG demonstrated a significant reduction in the number of patients undergoing Microbiology (p = 0.01), Biochemistry (p = 0.05), C-Reactive Protein (p = 0.02), Radiological Tests (p = 0.05), Computed Tomography Tests (p = 0.04), and Pathology (p = 0.01). However, no statistically significant reduction was observed in economic costs related to microbiological testing (p = 0.76) or antibiotic consumption (p = 0.59). The timely reporting of microbiological identification to clinicians resulted in fewer patients undergoing additional diagnostic tests, ultimately contributing to reduced healthcare resource utilization without adversely affecting clinical outcomes.

Predicting Pseudomonas aeruginosa drug resistance using artificial intelligence and clinical MALDI-TOF mass spectra

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used in clinical microbiology laboratories for bacterial identification but its use for detection of antimicrobial resistance (AMR) remains limited. Here, we used MALDI-TOF MS with artificial intelligence (AI) approaches to successfully predict AMR in Pseudomonas aeruginosa, a priority pathogen with complex AMR mechanisms. The highest performance was achieved for modern β-lactam/β-lactamase inhibitor drugs, namely, ceftazidime/avibactam and ceftolozane/tazobactam. For these drugs, the model demonstrated area under the receiver operating characteristic curve (AUROC) of 0.869 and 0.856, specificity of 0.925 and 0.897, and sensitivity of 0.731 and 0.714, respectively. As part of this work, we developed dynamic binning, a feature engineering technique that effectively reduces the high-dimensional feature set and has wide-ranging applicability to MALDI-TOF MS data. Compared to conventional feature engineering approaches, the dynamic binning method yielded highest performance in 7 of 10 antimicrobials. Moreover, we showcased the efficacy of transfer learning in enhancing the AUROC performance for 8 of 11 antimicrobials. By assessing the contribution of features to the model's prediction, we identified proteins that may contribute to AMR mechanisms. Our findings demonstrate the potential of combining AI with MALDI-TOF MS as a rapid AMR diagnostic tool for Pseudomonas aeruginosa.IMPORTANCEPseudomonas aeruginosa is a key bacterial pathogen that causes significant global morbidity and mortality. Antimicrobial resistance (AMR) emerges rapidly in P. aeruginosa and is driven by complex mechanisms. Drug-resistant P. aeruginosa is a major challenge in clinical settings due to limited treatment options. Early detection of AMR can guide antibiotic choices, improve patient outcomes, and avoid unnecessary antibiotic use. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid species identification in clinical microbiology. In this study, we repurposed mass spectra generated by MALDI-TOF and used them as inputs for artificial intelligence approaches to successfully predict AMR in P. aeruginosa for multiple key antibiotic classes. This work represents an important advance toward using MALDI-TOF as a rapid AMR diagnostic for P. aeruginosa in clinical settings.

Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers

Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.

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.

Microbiome of limb-threatening diabetic foot ulcers indicates the association of fastidious Stenotrophomonas and major amputation

BACKGROUND

Proper identification of the polymicrobial microorganisms in patients with limb-threatening diabetic foot ulcers (LTDFUs) using conventional culture is insufficient. This prospective study evaluates the potential value of adjuvant molecular testing assisting in identify fastidious micro-organisms in LTDFUs compared to standard treatment alone.

METHODS

Ninety patients with LTDFUs received interdisciplinary and standard antibiotic treatment in a referral diabetic foot center. A simultaneous 16S amplicon sequencing (16S AS) specimen along with conventional culture collected at admission was used to retrospectively evaluate the microbiological findings and its association with amputation outcomes.

RESULTS

The microorganism count revealed by 16S AS overwhelmed that of conventional culturing (17 vs. 3 bacteria/ulcer respectively). The Stenotrophomonas spp. revealed in 29 patients were highly correlated with major (above ankle) amputation (OR: 4.76, 95% CI 1.01-22.56), while only one had been concomitantly identified by conventional culturing. Thus, there were 27 cases without proper antibiotics coverage during treatment.

CONCLUSIONS

Adjuvant molecular testing assisted identification of fastidious pathogens such as Stenotrophomonas infection and might be associated with major amputation in patients with LTDFUs.

Detection and quantification of Plasmodium falciparum in human blood by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a proof of concept study

BACKGROUND

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) has revolutionized identification of bacteria and is becoming available in an increasing number of laboratories in malaria-endemic countries. The purpose of this proof-of-concept study was to explore the potential of MALDI-TOF as a diagnostic tool for direct detection and quantification of Plasmodium falciparum in human blood.

METHODS

Three different P. falciparum strains (3D7, HB3 and IT4) were cultured and synchronized following standard protocols. Ring-stages were diluted in fresh blood group 0 blood drawn in EDTA from healthy subjects to mimic clinical samples. Samples were treated with saponin and washed in PBS to concentrate protein material. Samples were analysed using a Microflex LT MALDI-TOF and resulting mass spectra were compared using FlexAnalysis software.

RESULTS

More than 10 peaks specific for P. falciparum were identified. The identified peaks were consistent among the three genetically unrelated strains. Identification was possible in clinically relevant concentrations of 0.1% infected red blood cells, and a close relationship between peak intensity and the percentage of infected red blood cells was seen.

CONCLUSION

The findings indicate that the method has the potential to detect and quantify P. falciparum at clinically relevant infection intensities and provides proof-of-concept for MALDI-TOF-based diagnosis of human malaria. Further research is needed to include other Plasmodium spp., wildtype parasite isolates and to increase sensitivity. MALDI-TOF may be a useful tool for mass-screening purposes and for diagnosis of malaria in settings where it is readily available.

Dermatophytosis caused by trichophyton mentagrophytes complex in organic pigs

BACKGROUND

Dermatophytosis (ringworm) caused by members of the Trichophyton mentagrophytes complex is rarely diagnosed in pigs but has been recognized as an increasingly common infection in humans. Further, resistance to antifungal drugs have been reported both in Asia and in Europe. This is the first scientific report of infection by the T. mentagrophytes complex in pigs in the Nordic countries.

CASE PRESENTATION

Skin lesions developed in grower pigs in an organic fattening pig farm with outdoor production and following laboratory analyses, dermatophytosis caused by members of the T. mentagrophytes complex was diagnosed. Infection was linked to poor hygiene, high humidity, and moderate outdoor temperatures, in combination with high pig density. A farm worker developed a skin lesion after close contact with affected pigs, which highlighted the zoonotic potential of porcine dermatophytosis. The dermatophytes may have originated from the herd supplying the growers where similar lesions occurred in pigs. Further, pigs from another organic fattening herd that received growers from the same supplier herd also developed dermatophytosis. The lesions healed without treatment as the housing conditions were improved. Isolation of affected pigs prevented spread to other pigs CONCLUSION: Members of the T. mentagrophytes complex can cause ringworm in pigs. The fungi probably persist in the haircoat and may cause overt disease when environmental conditions promote growth of mycelia.

Comparison of Autof Ms1000 and EXS3000 MALDI-TOF MS Platforms for Routine Identification of Microorganisms

Purpose

Matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF) has recently been widely used in clinical microbiology laboratories, with the advantages of being reliable, rapid, and cost-effective. Here, we reported the performance of two MALDI-TOF MS instruments, EXS3000 (Zybio, China) and Autof ms1000 (Autobio, China), which are commonly used in clinical microbiology field.

Methods

A total of 209 common clinical common isolates, including 70 gram-negative bacteria strains, 58 gram-positive bacteria strains, 33 yeast strains, 15 anaerobic bacteria strains, and 33 mold strains, and 19 mycobacterial strains were tested. All strains were identified by EXS3000 (Zybio, China) and Autof ms1000 (Autobio, China). Sequence analysis of 16S rRNA or ITS regions was used to verify all strains.

Results

Current study found that species-level discrimination was found to be 191 (91.39%) and 190 (90.91%) by EXS3000 and Autof ms1000, respectively. Genus-level discrimination was 205 (98.09%) by the EXS3000 and 205 (98.09%) by the Autof ms1000, respectively. The correct results at species level of the EXS3000 were 91.43% (64/70) for gram-negative bacteria, 93.1% (54/58) for gram-positive cocci, 93.94% (31/33) for yeast, 100% (15/15) for anaerobes and 81.82% (27/33) for filamentous fungi. The correct results at species level of the Autof ms1000 were 92.86% (65/70) for gram-negative bacteria, 91.38% (53/58) for gram-positive cocci, 93.94% (31/33) for yeast, 100% (15/15) for anaerobes and 78.79% (26/33) for filamentous fungi.

Conclusion

Although the results show that the EXS3000 and Autof ms1000 systems are equally good choices in terms of analytical efficiency for routine procedures, the test result of EXS3000 is slightly better than Autof ms1000. It's worth mentioning that the target plate of the EXS 3000 instrument is reusable, but the target plate of the Autof ms1000 is disposable, making the EXS3000 more effective in reducing costs.

Current Limitations of Staph Infection Diagnostics, and the Role for VOCs in Achieving Culture-Independent Detection

Staphylococci are broadly adaptable and their ability to grow in unique environments has been widely established, but the most common and clinically relevant staphylococcal niche is the skin and mucous membranes of mammals and birds. S. aureus causes severe infections in mammalian tissues and organs, with high morbidities, mortalities, and treatment costs. S. epidermidis is an important human commensal but is also capable of deadly infections. Gold-standard diagnostic methods for staph infections currently rely upon retrieval and characterization of the infectious agent through various culture-based methods. Yet, obtaining a viable bacterial sample for in vitro identification of infection etiology remains a significant barrier in clinical diagnostics. The development of volatile organic compound (VOC) profiles for the detection and identification of pathogens is an area of intensive research, with significant efforts toward establishing breath tests for infections. This review describes the limitations of existing infection diagnostics, reviews the principles and advantages of VOC-based diagnostics, summarizes the analytical tools for VOC discovery and clinical detection, and highlights examples of how VOC biomarkers have been applied to diagnosing human and animal staph infections.

What is essential remains invisible to the eyes? Blood pressure cuffs colonized by bacterial diversity

Using sphygmomanometers to measure blood pressure is a common practice in the healthcare context. The disinfection and maintenance of these devices is essential in clinical practice to prevent the proliferation of microorganisms. The aim of this study was to determine the presence of pathogenic microorganisms in sphygmomanometer cuffs in the clinical setting. A cross-sectional study was carried out. Five types of healthcare centers, selected through convenience sampling, participated in this study. Samples were collected from the inside of sphygmomanometer cuffs, and labeled and delivered to the laboratory for analysis. The samples were incubated in an oven at 35.5 °C for 24 h. A total CFU count was carried out on the plates that were cataloged as positive. Colonies that showed growth were identified using the matrix-assisted laser desorption/ionization-mass spectrometry technology. Of the total sample, (N = 372), 69.1% were positive and were isolated. In 30.9% (n = 115), no bacterial development was found within 48 h. A total of 257 microorganisms were found. The mean number of colony-forming units was 29.62 (SD = 32.33). The socio-health centers had the highest amount of bacterial contamination in the cuffs. In regards to the type of microorganisms, 31.5% (n = 81) found were Bacillus cereus, followed by 26.8% (n = 69) of Staphylococcus hominis and 9.7% (n = 25) were Pantoea agglomerans, among others. Statistically significant differences were found between the type of microorganism and the hours elapsed since the last disinfection (X²(19) = 44.582; p = 0.001). Statistically significant differences were found between the time elapsed since the last disinfection and the type of sphygmomanometer (X² (2) = 117.752; p = 0.000). Despite the fact that most hospitals and health centers have established infection control policies and protocols, the results of this study indicate the presence of pathogenic microorganisms in blood pressure cuffs in the clinical setting.

A New Approach to Imaging and Rapid Microbiome Identification for Prostate Cancer Patients Undergoing Radiotherapy

(1) Background: Little is known about the impact of urinary microflora, in particular, its effects on side effects after radiotherapy. The use of mass spectrometry identification method (MALDI) may bring a new look at the issue of the composition and significance of the urinary microbiome. This study aimed to use the mass spectrometry identification method (MALDI) to identify the microbiome of urine samples collected from 50 irradiated prostate cancer patients. (2) Methods: Blood and urine samples were collected before gold marker implantation, at the start and last day of radiotherapy, 1, 4 months after. Patients do not always collect the urine from the midstream; therefore, samples were collected from the first void and midstream in 12 patients for MALDI analysis; in the remaining 38 patients—from the midstream void for MALDI and biochemical analysis. (3) Results: Microorganisms were present in 140/181 urine samples. We found 33 different species 3G(−) and 30G(+). The most frequently isolated strains were: Staphylococcus haemolyticus, Staphylococcus epidermidis, Staphylococcus hominis, Enterococcus faecalis, and Micrococcus luteus. When comparing the type of urine samples, bacteria were more common in samples from the first-void urine than from the midstream one. The absence of bacteria was found in 12.2% of samples from the first-void urine and in 24.7% from the midstream. There was no difference in the total incidence of species between streams (p = 0.85). Before fiducial implantation, the total number of detected bacterial species was significantly higher in comparison to the end of radiotherapy (p = 0.038), indicating that the administered therapy resulted in depleting the local microbiome. One month after radiotherapy, an increase in the number of isolated bacteria was observed. The number of bacterial species in urine did not correlate with blood parameters. The presence of leukocytes (p = 0.013) and proteins (p = 0.004) in urine was related to a greater variety of bacteria found in urine specimens. (4) Conclusions: We obtained a similar spectrum of bacteria from the initial and middle urine streams. We also showed that there is a change in bacteria species affected by the treatment of prostate cancer patients, with both antibiotics before gold fiducial implantation and radiotherapy.

An Overview of Healthcare Associated Infections and Their Detection Methods Caused by Pathogen Bacteria in Romania and Europe

Healthcare-associated infections can occur in different care units and can affect both patients and healthcare professionals. Bacteria represent the most common cause of nosocomial infections and, due to the excessive and irrational use of antibiotics, resistant organisms have appeared. The most important healthcare-associated infections are central line-associated bloodstream infections, catheter-associated urinary tract infections, surgical site, soft tissue infections, ventilator-associated pneumonia, hospital acquired pneumonia, and Clostridioides difficile colitis. In Europe, some hospitalized patients develop nosocomial infections that lead to increased costs and prolonged hospitalizations. Healthcare-associated infection prevalence in developed countries is lower than in low-income and middle-income countries such as Romania, an Eastern European country, where several factors contribute to the occurrence of many nosocomial infections, but official data show a low reporting rate. For the rapid identification of bacteria that can cause these infections, fast, sensitive, and specific methods are needed, and they should be cost-effective. Therefore, this review focuses on the current situation regarding healthcare-associated infections in Europe and Romania, with discussions regarding the causes and possible solutions. As a possible weapon in the fight against the healthcare-associated infections, the diagnosis methods and tests used to determine the bacteria involved in healthcare-associated infections are evaluated.

MALDI-Based Mass Spectrometry in Clinical Testing: Focus on Bacterial Identification

The term “proteome” refers to the total of all proteins expressed in an organism. The term “proteomics” refers to the field of research that includes not only information on the expression levels of individual proteins, but also their higher-order structures, intermolecular interactions, and post-translational modifications. The core technology, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), is available for protein analysis thanks to the work of Koichi Tanaka and John Fenn, who were awarded the Nobel Prize in Chemistry in 2002. The most successful proteome analysis in clinical practice is rapid microbial identification. This method determines the bacterial species by comparing the proteome profile of the bacteria obtained by matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS) with a database. MS is superior in simplicity, speed, and accuracy to classic speciation by staining and phenotyping. In clinical microbiology, MS has had a large impact on the diagnosis and treatment of infectious disease. Early diagnosis and treatment of infectious disease are important, and rapid identification by MALDI-TOF MS has made a major contribution to this field.

Combination of MALDI-TOF Mass Spectrometry and Machine Learning for Rapid Antimicrobial Resistance Screening: The Case of Campylobacter spp

While MALDI-TOF mass spectrometry (MS) is widely considered as the reference method for the rapid and inexpensive identification of microorganisms in routine laboratories, less attention has been addressed to its ability for detection of antimicrobial resistance (AMR). Recently, some studies assessed its potential application together with machine learning for the detection of AMR in clinical pathogens. The scope of this study was to investigate MALDI-TOF MS protein mass spectra combined with a prediction approach as an AMR screening tool for relevant foodborne pathogens, such as Campylobacter coli and Campylobacter jejuni. A One-Health panel of 224 C. jejuni and 116 C. coli strains was phenotypically tested for seven antimicrobial resistances, i.e., ciprofloxacin, erythromycin, tetracycline, gentamycin, kanamycin, streptomycin, and ampicillin, independently, and were submitted, after an on- and off-plate protein extraction, to MALDI Biotyper analysis, which yielded one average spectra per isolate and type of extraction. Overall, high performance was observed for classifiers detecting susceptible as well as ciprofloxacin- and tetracycline-resistant isolates. A maximum sensitivity and a precision of 92.3 and 81.2%, respectively, were reached. No significant prediction performance differences were observed between on- and off-plate types of protein extractions. Finally, three putative AMR biomarkers for fluoroquinolones, tetracyclines, and aminoglycosides were identified during the current study. Combination of MALDI-TOF MS and machine learning could be an efficient and inexpensive tool to swiftly screen certain AMR in foodborne pathogens, which may enable a rapid initiation of a precise, targeted antibiotic treatment.

Markers for discriminating Campylobacter concisus genomospecies using MALDI-TOF analysis

Strains identified as Campylobacter concisus may belong to one of at least two biochemically indistinguishable, but genomically distinct, groups referred to as "genomospecies" that may differ in their pathogenic and zoonotic potential. Reliable, affordable and available identification methods are required to improve understanding of their significance in human illness. We examined the potential for MALDI-TOF MS, increasingly used in routine laboratories, for this task. Nineteen well-characterised strains were examined using a widely used MALDI-TOF MS commercial system, however only one strain confidently identified using their database. Data mining of the spectra obtained revealed a number of markers that could be used to help discriminate these genomospecies. We conclude that careful application of MALDI-TOF analysis could be useful to determine the role and significance of diverse C. concisus genomospecies in human disease.

The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS

Bacterial pathogens that cannot be identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) are occasionally encountered in clinical laboratories. The 16S rRNA gene is often used for sequence-based analysis to identify these bacterial species. Nevertheless, traditional Sanger sequencing is laborious, time-consuming and low-throughput. Here, we compared two commercially available 16S rRNA gene sequencing tests, which are based on Illumina and Nanopore sequencing technologies, respectively, in their ability to identify the species of 172 clinical isolates that failed to be identified by MALDI-TOF MS. Sequencing data were analyzed by respective built-in programs (MiSeq Reporter Software of Illumina and Epi2me of Nanopore) and BLAST+ (v2.11.0). Their agreement with Sanger sequencing on species-level identification was determined. Discrepancies were resolved by whole-genome sequencing. The diagnostic accuracy of each workflow was determined using the composite sequencing result as the reference standard. Despite the high base-calling accuracy of Illumina sequencing, we demonstrated that the Nanopore workflow had a higher taxonomic resolution at the species level. Using built-in analysis algorithms, the concordance of Sanger 16S with the Illumina and Nanopore workflows was 33.14% and 87.79%, respectively. The agreement was 65.70% and 83.14%, respectively, when BLAST+ was used for analysis. Compared with the reference standard, the diagnostic accuracy of Nanopore 16S was 96.36%, which was identical to Sanger 16S and was better than Illumina 16S (69.07%). The turnaround time of the Illumina workflow and the Nanopore workflow was 78h and 8.25h respectively. The per-sample cost of the Illumina and Nanopore workflows was US$28.5 and US$17.7, respectively.

An eco-friendly solvent-free reaction based on peptide probes: design an extraction-free method for analysis of acrylamide under microliter volume

Acrylamide is a group 2A carcinogen and potential endocrine disruptor that can enter the ecosystem by various routes and has recently become a dangerous pollutant. This widely used chemical can enter the human body via air inhalation, food or water consumption, or skin contact. In this study, we developed a peptide probe for the detection of acrylamide by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) after its micro-tagging with a peptide. Direct detection of acrylamide by MALDI-TOF MS is not feasible due to its poor ionization in the MALDI interface, which hinders its analysis by the technique. After microwave irradiation for 2 min, the formed acrylamide-peptide derivative was detected easily by MALDI-TOF MS without the need for extraction procedures. The procedure does not involve organic solvents and a water-soluble peptide that allows detection of acrylamide in small sample volumes with a limit of detection (LOD) of 0.05 ng/μL. The relative standard deviation (RSD) and relative error (RE) of the measurements were < 6.7% for intra- and inter-day assays. Gel-washing solutions from a polyacrylamide gel experiment were used as a model to study the efficiency of the developed method. Finally, we used the proposed method for the detection of free acrylamide in small volumes of lung epithelial cells (a model to test the air inhalation of acrylamide under a tiny volume of sample) and human urine. The developed method will enable rapid acrylamide detection in environmental and biological samples via a green approach based on microwave-assisted derivatization in water alongside the use of a less toxic derivatization reagent, reusable target plate, and miniaturization protocols.

Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories

Early diagnosis of severe infections requires of a rapid and reliable diagnosis to initiate appropriate treatment, while avoiding unnecessary antimicrobial use and reducing associated morbidities and healthcare costs. It is a fact that conventional methods usually require more than 24–48 h to culture and profile bacterial species. Mass spectrometry (MS) is an analytical technique that has emerged as a powerful tool in clinical microbiology for identifying peptides and proteins, which makes it a promising tool for microbial identification. Matrix assisted laser desorption ionization–time of flight MS (MALDI–TOF MS) offers a cost- and time-effective alternative to conventional methods, such as bacterial culture and even 16S rRNA gene sequencing, for identifying viruses, bacteria and fungi and detecting virulence factors and mechanisms of resistance. This review provides an overview of the potential applications and perspectives of MS in clinical microbiology laboratories and proposes its use as a first-line method for microbial identification and diagnosis.

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.

Liquid Extraction Surface Analysis Mass Spectrometry of ESKAPE Pathogens

The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) represent clinically important bacterial species that are responsible for most hospital-acquired drug-resistant infections; hence, the need for rapid identification is of high importance. Previous work has demonstrated the suitability of liquid extraction surface analysis mass spectrometry (LESA MS) for the direct analysis of colonies of two of the ESKAPE pathogens (Staphylococcus aureus and Pseudomonas aeruginosa) growing on agar. Here, we apply LESA MS to the remaining four ESKAPE species (E. faecium E745, K. pneumoniae KP257, A. baumannii AYE, and E. cloacae S11) as well as E. faecalis V583 (a close relative of E. faecium) and a clinical isolate of A. baumannii AC02 using an optimized solvent sampling system. In each case, top-down LESA MS/MS was employed for protein identification. In total, 24 proteins were identified from 37 MS/MS spectra by searching against protein databases for the individual species. The MS/MS spectra for the identified proteins were subsequently searched against multiple databases from multiple species in an automated data analysis workflow with a view to determining the accuracy of identification of unknowns. Out of 24 proteins, 19 were correctly assigned at the protein and species level, corresponding to an identification success rate of 79%.

Tissue microbiota in nasopharyngeal adenoid and its association with pneumococcal carriage

The microbial colonization in the nasopharynx is a prerequisite for the onset of infectious diseases. For successful infection, pathogens should overcome host defenses as well as compete effectively with the resident microbiota. Hence, elucidating the richness and diversity of the microbiome at the site of pathogen colonization is pivotal. Here, we investigated the adenoidal tissue microbiota collected through adenoidectomy to evaluate the impact of Streptococcus pneumoniae. Prospectively, children with sleep-disordered breathing (SDB) and otitis media with effusion (OME) were enrolled. During adenoidectomy, the nasopharyngeal swab and adenoid tissues were collected to determine the pneumococcal carriage and tissue microbiota, using multiplex PCR and 16S ribosomal RNA (16S rRNA) pyrosequencing. A total of 66 pediatric patients comprising 38 children with SDB and 28 children with OME were enrolled. There was no difference between the bacterial cultures from the surface of the nasopharyngeal adenoid in the SDB and OME groups. Thirty-four samples (17 SDB and 17 OME) underwent 16S rRNA pyrosequencing and fulfilled the criteria for further analysis. The Shannon diversity index for the samples from the SDB patients was found to be higher than that observed for the samples from OME patients, although the difference was not significant (p = 0.095). The Shannon diversity index for the samples negative for the pneumococcal carriage was significantly higher than that for the samples positive for pneumococcal carriage (p = 0.038). Alloprevotella, Staphylococcus, Moraxella, and Neisseriaceae were significantly dominant in the samples positive for the pneumococcal carriage. Dialister was significantly less present in the adenoid tissue positive for the pneumococcal carriage. Streptococcus pneumoniae, one of the most common pathogens of the airway, significantly influences the composition and diversity of the microbiota in the nasopharyngeal adenoid. Thus, bacterial community analysis based on 16S rRNA pyrosequencing allows for better understanding of the relationship between the adenoidal microbial communities.

Moraxella osloensis infection among adults and children: A pediatric case and literature review

Moraxella osloensis has been reported in the literature as a human pathogen, particularly among immunocompromised adults. In contrast to the adult population, most pediatric cases are among patients with no underlying immunological defect; however, no patient underwent further investigation and no data about the long-term follow-up are available. We report the case of a 2-month-old previously healthy girl infected with Moraxella osloensis. Here, we review case reports and case series of children and adults with Moraxella osloensis infection and compare them with our experience. On the basis of our findings, we recommend further investigations (immunological or other underlying diseases) when a child is found to be infected with these bacteria.

The Influence of Metabolic Inhibitors, Antibiotics, and Microgravity on Intact Cell MALDI-TOF Mass Spectra of the Cyanobacterium Synechococcus Sp. UPOC S4

The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp. UPOC S4 and to check the impact on reliability of identification. Defining the limits of this method is important for its use in biology and applied science. The compounds included inhibitors of respiration, glycolysis, citrate cycle, and proteosynthesis. They were used at 1–10 μM concentrations and different periods of up to 3 weeks. Cells were also grown without inhibitors in a microgravity because of expected strong effects. Mass spectra were evaluated using controls and interpreted in terms of differential peaks and their assignment to protein sequences by mass. Antibiotics, azide, and bromopyruvate had the greatest impact. The spectral patterns were markedly altered after a prolonged incubation at higher concentrations, which precluded identification in the database of reference spectra. The incubation in microgravity showed a similar effect. These differences were evident in dendrograms constructed from the spectral data. Enzyme inhibitors affected the spectra to a smaller extent. This study shows that only a long-term presence of antibiotics and strong metabolic inhibitors in the medium at 10⁻⁵ M concentrations hinders the correct identification of cyanobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF).

The Use of MALDI-TOF Mass Spectrometry to Analyze Commensal Oral Yeasts in Nursing Home Residents

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate method to identify microorganisms in clinical laboratories. This study isolates yeast-like microorganisms in the oral washes that are collected from non-bedridden nursing home residents, using CHROMagar Candida plates, and identifies them using Bruker MALDI-TOF MS. The ribosomal DNA sequences of the isolates are then examined. Three hundred and twenty yeast isolates are isolated from the oral washes. Candida species form the majority (78.1%), followed by Trichosporon/Cutaneotrichosporon species (8.8%). Bruker MALDI-TOF MS gives a high-level confidence, with a log(score) value of ≥1.8, and identifies 96.9% of the isolates. There are six inconclusive results (1.9%), and those sequences are verified as rare clinical species, including Candida ethanolica, Cutaneotrichosporon jirovecii, Exophiala dermatitidis, and Fereydounia khargensis. Almost all of the isolates have a regular color on the CHROMagar Candida plates. If the colonies are grouped by color on the plates, a specific dominant yeast species is present in each color group, except for purple or orange isolates. In conclusion, MALDI-TOF MS is verified as a fast, accurate and practical method to analyze oral yeasts in elderly subjects.

Usefulness of matrix-assisted laser desorption ionization/time of flight mass spectrometry for the identification of Streptococcus mutans

This study evaluated the reliability of MALDI-TOF MS coupled with statistical tools for the identification of Streptococcus mutans in comparison with PCR-based techniques. Bacterial isolates were identified and serotyped by conventional PCR, using S. mutans species and serotype-specific primers. For bacterial identification, mass spectra data from S. mutans and other streptococci were compared with Biotyper V 3.1 database and the mass peak lists were examined by cluster and principal component (PCA) analysis. Identification of potential biomarkers was performed using UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases and BLAST tool of the NCBI database. PCR identified 100% of the isolates as S. mutans. S. mutans strains were typed as serotypes c (85.6%), e (8.6%), k (4.8%), and f (0.9%). Although only the 70% of the strains tested were identified at species level by the Biotyper database, PCA and cluster analysis of mass peaks allowed the identification of 100% S. mutans isolates and its differentiation from the other oral and non-oral streptococci. One mass peak at m/z value of 9572.73 was identified as species-specific biomarker for S. mutans. No biomarkers were identified for S. mutans serotypes. KEY POINTS: • MALDI-TOF MS coupled with statistical tools for the identification of S. mutans. • Detection of species identifying biomarkers by MALDI-TOF MS. • PCR identification and serotyping of S. mutans from saliva samples.

Study on Molecular Profiles of Staphylococcus aureus Strains: Spectrometric Approach

Staphylococcus aureus remains a major health problem responsible for many epidemic outbreaks. Therefore, the development of efficient and rapid methods for studying molecular profiles of S. aureus strains for its further typing is in high demand. Among many techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) represents a timely, cost-effective, and reliable strain typing approach, which is still rarely used due to insufficient knowledge about the impact of sample preparation and analysis conditions on the molecular profiles and strain classification efficiency of S. aureus. The aim of this study was to evaluate the effect of the culture conditions and matrix type on the differentiation of molecular profiles of various S. aureus strains via the MALDI TOF MS analysis and different computational methods. The analysis revealed that by changing the culture conditions, matrix type, as well as a statistical method, the differentiation of S. aureus strains can be significantly improved. Therefore, to accelerate the incorporation of the MALDI-based strain typing in routine laboratories, further studies on the standardization and searching of optimal conditions on a larger number of isolates and bacterial species are of great need.

Advances in automated techniques to identify Acinetobacter calcoaceticus-Acinetobacter baumannii complex

Acinetobacter species, particularly those within Acinetobacter calcoaceticus-A. baumannii complex (ACB complex), have emerged as clinically relevant pathogens in hospital environments worldwide. Early and quick detection and identification of Acinetobacter infections is challenging, and traditional culture and biochemical methods may not achieve adequate levels of speciation. Moreover, currently available techniques to identify and differentiate closely related Acinetobacter species are insufficient. The objective of this review is to recapitulate the current evolution in phenotypic and automated techniques used to identify the ACB complex. Compared with other automated or semiautomated systems of bacterial identification, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) demonstrates a high level of Acinetobacter species identification and discrimination, including newly discovered species A. seifertii and A. dijkshoorniae.

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.

Proteomic fingerprinting of Neotropical hard tick species (Acari: Ixodidae) using a self-curated mass spectra reference library

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry is an analytical method that detects macromolecules that can be used for proteomic fingerprinting and taxonomic identification in arthropods. The conventional MALDI approach uses fresh laboratory-reared arthropod specimens to build a reference mass spectra library with high-quality standards required to achieve reliable identification. However, this may not be possible to accomplish in some arthropod groups that are difficult to rear under laboratory conditions, or for which only alcohol preserved samples are available. Here, we generated MALDI mass spectra of highly abundant proteins from the legs of 18 Neotropical species of adult field-collected hard ticks, several of which had not been analyzed by mass spectrometry before. We then used their mass spectra as fingerprints to identify each tick species by applying machine learning and pattern recognition algorithms that combined unsupervised and supervised clustering approaches. Both Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) classification algorithms were able to identify spectra from different tick species, with LDA achieving the best performance when applied to field-collected specimens that did have an existing entry in a reference library of arthropod protein spectra. These findings contribute to the growing literature that ascertains mass spectrometry as a rapid and effective method to complement other well-established techniques for taxonomic identification of disease vectors, which is the first step to predict and manage arthropod-borne pathogens.

MASS SPECTROMETRY-BASED PERSONALIZED DRUG THERAPY

Personalized drug therapy aims to provide tailored treatment for individual patient. Mass spectrometry (MS) is revolutionarily involved in this area because MS is a rapid, customizable, cost-effective, and easy to be used high-throughput method with high sensitivity, specificity, and accuracy. It is driving the formation of a new field, MS-based personalized drug therapy, which currently mainly includes five subfields: therapeutic drug monitoring (TDM), pharmacogenomics (PGx), pharmacomicrobiomics, pharmacoepigenomics, and immunopeptidomics. Gas chromatography-MS (GC-MS) and liquid chromatography-MS (LC-MS) are considered as the gold standard for TDM, which can be used to optimize drug dosage. Matrix-assisted laser desorption ionization-time of flight-MS (MALDI-TOF-MS) significantly improves the capability of detecting biomacromolecule, and largely promotes the application of MS in PGx. It is becoming an indispensable tool for genotyping, which is used to discover and validate genetic biomarkers. In addition, MALDI-TOF-MS also plays important roles in identity of human microbiome whose diversity can explain interindividual differences of drug response. Pharmacoepigenetics is to study the role of epigenetic factors in individualized drug treatment. MS can be used to discover and validate pharmacoepigenetic markers (DNA methylation, histone modification, and noncoding RNA). For the emerging cancer immunotherapy, personalized cancer vaccine has effective immunotherapeutic activity in the clinic. MS-based immunopeptidomics can effectively discover and screen neoantigens. This article systematically reviewed MS-based personalized drug therapy in the above mentioned five subfields. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Electrochemical sensors for rapid diagnosis of pathogens in real time

Microbial infections remain the principal cause for high morbidity and mortality rates. While approximately 1400 human pathogens have been recognized, the majority of healthcare-associated infectious diseases are caused by only a few opportunistic pathogens (e.g., Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli), which are associated with increased antibiotic and antimicrobial resistance. Rapid detection, reliable identification and real-time monitoring of these pathogens remain not only a scientific problem but also a practical challenge of vast importance, especially in tailoring effective treatment strategies. Although the development of vaccinations and antibacterial drug treatments are the leading research, progress, and implementation of early warning, quantitative systems indicative of confirming pathogen presence are necessary. Over the years, various approaches, such as conventional culturing, straining, molecular methods (e.g., polymerase chain reaction and immunological assays), microscopy-based and mass spectrometry techniques, have been employed to identify and quantify pathogenic agents. While being sensitive in some cases, these procedures are costly, time-consuming, mostly qualitative, and are indirect detection methods. A great challenge is therefore to develop rapid, highly sensitive, specific devices with adequate figures of merit to corroborate the presence of microbes and enable dynamic real-time measurements of metabolism. As an alternative, electrochemical sensor platforms have been developed as powerful quantitative tools for label-free detection of infection-related biomarkers with high sensitivity. This minireview is focused on the latest electrochemical-based approaches for pathogen sensing, putting them into the context of standard sensing methods, such as cell culturing, mass spectrometry, and fluorescent-based approaches. Description of the latest, impactful electrochemical sensors for pathogen detection will be presented. Recent breakthroughs will be highlighted, including the use of micro- and nano-electrode arrays for real-time detection of bacteria in polymicrobial infections and microfluidic devices for pathogen separation analysis. We will conclude with perspectives and outlooks to understand shortcomings in designing future sensing schemes. The need for high sensitivity and selectivity, low-cost implementation, fast detection, and screening increases provides an impetus for further development in electrochemical detectors for microorganisms and biologically relevant targets.

Integrating Bacterial Identification and Susceptibility Testing: A Simple and Rapid Approach to Reduce the Turnaround Time in the Management of Blood Cultures

We evaluated a rapid bacterial identification (rID) and a rapid antimicrobial susceptibility testing by disk diffusion (rAST) from positive blood culture to overcome the limitations of the conventional methods and reduce the turnaround time in bloodstream infection diagnostics. The study included hemocultures flagged as positive by bacT/ALERT®, identification by MALDI-TOF MS, and rAST. The results were compared to identification and antimicrobial susceptibility testing (AST) results by current standard methods, after 24 h incubation. For rAST categorical agreement (CA), very major errors (VME), major errors (ME), and minor errors (mE) were calculated. A total of 524 bacterial samples isolated from blood cultures were obtained, including 246 Gram-negative (GN) and 278 Gram-positive (GP) aerobes. The overall concordance of rID was 88.6%, and it was highest among GN (96%). A total of 2196 and 1476 antimicrobial agent comparisons were obtained for GN and GP, respectively. Evaluation of rAST, CA, VME, ME, and mE disclosed 97.7, 0.7, 0.5, and 1.1% for GN and 98.0, 0.5, 0.7, and 0.8% for GP, respectively. Meropenem CA, VME, and ME were 98.3, 0.5, and 0.5%, respectively; mE was not observed. Oxacillin CA, ME, and mE were 97.4, 1.6, and 0.6%, respectively; VME was not observed. Overall, kappa scores of the results of the comparisons demonstrated the high agreement between rAST and the standard method. Identification and AST of aerobic bacteria from positive blood cultures after a short period of incubation on solid blood agar is a fast and reliable method that may improve the management of bloodstream infections.

Evaluation of filter paper as a means to transport inactivated bacteria for identification using the MALDI-TOF MS system

A novel approach to transport inactivated bacteria in filter paper for identification in the MALDI-TOF MS was evaluated. Seventy four bacterial isolates were evaluated and the approach presented sensitivity of 97.3% and specificity of 100%. Inactivated bacteria in filter paper are a safer alternative to transport bacteria for MALDI-TOF MS identification.

Evaluation of Staphylococcus aureus Subtyping Module for Methicillin-Resistant Staphylococcus aureus Detection Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

A recently developed S. aureus subtyping module for rapidly differentiate methicillin-resistant Staphylococcus aureus (MRSA) from methicillin-susceptible S. aureus (MSSA) had been introduced into China. The principle of this method was to identify the methicillin resistance through detection of a specific phenol soluble modulin-mec peak (PSM-mec) by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). A total of 347 non-duplicated S. aureus strains were collected from the Second Affiliated Hospital of Zhejiang University School of Medicine during January 2014 to February 2019. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the automated subtyping module in identifying MRSA were evaluated. The specificity and PPV of this method were both 100%, and the sensitivity was 60.2%. PSM-bearing MRSA was reported with different prevalence from different parts of the world, our sample collection has the highest percentage so far. The repeatability showed that 1.7% (6/347) and 18.4% (64/347) were reported differently in the intra- and inter-batch analysis, respectively, which demonstrated that the threshold of this method could be further optimized to increase the sensitivity of MRSA detection. Overall, Bruker^™ MALDI Biotyper can detect S. aureus isolates with a quite high specificity and expedite the identification of MRSA isolates without using extra reagent, labor, or time. The reduced turnaround time of MRSA identification is essential for appropriate therapeutic management and timely intervention for infection control.

Accurate identification of clinically important Acinetobacter spp.: an update

Acinetobacter species have emerged as one of the most clinically important pathogens. The phenotypic techniques which are currently available are insufficient in accurately identifying and differentiating the closely related and clinically important Acinetobacter species. Here, we discuss the advantages and limitations of the conventional phenotypic methods, automated identification systems, molecular methods and MALDI-TOF in the precise identification and differentiation of Acinetobacter species. More specifically, several species of this genus are increasingly reported to be of high clinical importance. Molecular characterization such as of bla_OXA-51-like PCR together with rpoB sequencing has high discriminatory power over the conventional methods for Acinetobacter species identification, especially within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex.

Acinetobacter species are considered to be one of the most important pathogens and associated with increased mortality. The species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex have emerged as high priority pathogens, especially in intensive care units, thereby posing a challenge to infection management practices. However, identification of Acinetobacter to the species level is difficult. Clear differentiation among various Acinetobacter species with available standard biochemical methods and automated systems is challenging. Although various molecular methods are available, they are not regularly used in diagnostic laboratories. The advantages and disadvantages of different methods useful in the accurate identification of Acinetobacter species are discussed in this review.

Rapid separation and identification of beer spoilage bacteria by inertial microfluidics and MALDI-TOF mass spectrometry

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS), in combination with Biotyper software, is a rapid, high-throughput, and accurate method for the identification of microbes. Microbial outbreaks in a brewery present a major risk for companies as it can lead to cost-intensive recalls and damage to the brand reputation. MALDI-TOF MS has been implemented into a brewery setting for quality control practices and the identification of beer spoilage microorganisms. However, the applicability of this approach is hindered by compatibility issues associated with mixed cultures, requiring the use of time-consuming selective cultivation techniques prior to identification. We propose a novel, low-cost approach based on the combination of inertial microfluidics and secondary flows in a spiral microchannel for high-throughput and efficient separation of yeasts (Saccharomyces pastorianus and Saccharomyces cerevisiae) from beer spoilage microorganisms (Lactobacillus brevis and Pediococcus damnosus). Flow rates were optimised using S. pastorianus and L. brevis, leading to separation of more than 90% of the L. brevis cells from yeast. The microorganisms were then identified to the species level using the MALDI-TOF MS platform using standard sample preparation protocols. This study shows the high-throughput and rapid separation of spoilage microorganisms (0.3-3 μm) from background yeast (5 μm) from beer, subsequent identification using MALDI Biotyper, and the potential applicability of the approach for biological control in the brewing industry.

Infective endocarditis caused by Cardiobacterium hominis endocarditis: A case report and review of the literature

BACKGROUND

While it has been increasing cases of C. hominis endocarditis in the past decades due to advances of diagnostic methods, the epidemiology and clinical manifestations of IE caused by C. hominis is still unknown.

CASE PRESENTATION

A 62-year old man was admitted to our institute with fever, anorexia and general fatigue for the preceding one month. He had a past medical history of both aortic and mitral valves replacement due to cardiac diseases. He was diagnosed as IE caused by C. hominis according to the modified duke criteria. The patient received 2 weeks of combination therapy of intravenous ceftriaxone (CTRX) 2g and gentamycin 180mg daily followed by 4 weeks CTRX 2g daily alone. Oral moxifloxacin 400mg once daily was given for an additional 4 weeks. After the antibiotic therapy was discontinued, disease recurrence was not observed. We reviewed previously reported C. hominis IE cases in 60 publications including ours. Of 73 patients enrolled, 53 were male, the mean age was 52 years. The most common risk factor of IE was past history of cardiac diseases in 44/73 (60%). As for antibiotics initially prescribed, third-generation cephalosporins was most frequently used in 28/69 (41%). While the cure rate was 67/73 (93%), 31/73 patients (43%) received a surgical intervention. Embolic lesions to the central nervous system and vertebrae were seen in 16/72 (22%) and 5/72 (7%).

CONCLUSION

IE caused by C. hominis has a favorable prognosis, showing the cure rate of 93%. Physicians should recognize the possible occurrence of emboli among IE patients.

Identification of Burkholderia pseudomallei by Use of the Vitek Mass Spectrometer

Burkholderia pseudomallei is the causative agent of melioidosis. This condition most often presents as pneumonia and bacteremia, with mortality rates of 9% to 70%. Therefore, early identification of this organism may aid in directing appropriate management. This study aimed to use the Vitek matrix-assisted laser desorption ionization-time of flight mass spectrometer to create a spectrum for the rapid identification of B. pseudomallei Spectra from 85 isolate cultures were acquired using the Vitek mass spectrometer research mode. A SuperSpectrum was created using peak matching and subsequently activated for analysis of organism identification. All 85 isolates were correctly identified as B. pseudomallei A total of 899 spectra were analyzed and demonstrated a specificity of 99.8%. Eighty-one clinical isolates were used, of which 10 were neuromelioidosis, and no discernible spectrum difference was appreciated. Spectrum acquisition from a single spot was only successful in 374/899 (41%) of isolates. This increased to 100% when 3 spots of the same extract were analyzed. The Vitek mass spectrometer can be used for the rapid identification of B. pseudomallei with a high level of specificity.

Matrix-Assisted Laser Desorption Time of Flight Mass Spectrometry

Matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS), adapted for use in clinical microbiology laboratories, challenges current standards of microbial detection and identification. This article summarizes the capabilities of MALDI-TOF MS in diagnostic clinical microbiology laboratories and describes the underpinnings of the technology, highlighting topics such as sample preparation, spectral analysis, and accuracy. The use of MALDI-TOF MS in the clinical microbiology laboratory is growing, and, when properly deployed, can accelerate diagnosis and improve patient care.

Evaluation of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card for identification of Bacteroides fragilis group isolates and antimicrobial susceptibilities of these isolates in a Chinese university hospital

BACKGROUND AND PURPOSE

Bacteroides fragilis group isolates are most frequently isolated anaerobic pathogens. This study aimed to evaluate the accuracy of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card on the identification of clinical B. fragilis group isolates, as well as to determine their antimicrobial susceptibilities.

METHODS

A total of 138 isolates of B. fragilis group isolates were identified with the three MALDI-TOF MS systems and VITEK 2 ANC cards. 16S rRNA gene sequencing was used as the reference identification method for comparison. Antimicrobial susceptibilities were determined by agar dilution method to 19 antimicrobial agents recommended by Clinical and Laboratory Standards Institute (CLSI).

RESULTS

Hundred thirty three isolates of Bacteroides spp. and 5 isolates of Parabacteroides spp. were identified by 16S rRNA sequencing. The rates of accurate identification at species level of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card were 94.2%, 94.2%, 98.6% and 94.9%, respectively, while that at genus level were 99.3%, 100%, 100% and 97.8%, respectively. Metronidazole and chloramphenicol were the most susceptible agents (99.3% and 92.8%, respectively), followed by meropenem, ertapenem, imipenem and piperacillin/tazobactam to which the susceptible rates ranged from 76.8% to 79.0%. The susceptible rates to carbapenems decreased 12.4-15.3% from 2010-2013 to 2014-2017.

CONCLUSION

All the four systems provided high accurate rate on the identification of B. fragilis group isolates. Metronidazole showed highest activity against these isolates. Attention should be paid to the higher resistant rates to carbapenems, clindamycin, moxifloxacin and tigecycline than the other countries.

A Moldy Application of MALDI: MALDI-ToF Mass Spectrometry for Fungal Identification

As a result of its being inexpensive, easy to perform, fast and accurate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) is quickly becoming the standard means of bacterial identification from cultures in clinical microbiology laboratories. Its adoption for routine identification of yeasts and even dimorphic and filamentous fungi in cultures, while slower, is now being realized, with many of the same benefits as have been recognized on the bacterial side. In this review, the use of MALDI-ToF MS for identification of yeasts, and dimorphic and filamentous fungi grown in culture will be reviewed, with strengths and limitations addressed.