Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii group in Taiwan

Acinetobacter, particularly the Acinetobacter baumannii group, is a major cause of nosocomial infections, and carbapenem-resistant Acinetobacter spp. are important human pathogens. We collected 492 Acinetobacter spp. strains from two hospitals in Taiwan and classified them using MALDI-TOF MS and blaOXA-51-like PCR; 94.5% were A. baumannii, and 5.5% were non-A. baumannii (NAB). We confirmed their identity by rpoB gene sequencing of 239 randomly selected A. baumannii strains and all 27 NAB strains. Our analysis revealed that the rpoB alleles of OXA51-like-negative strains matched those of two NAB species, A. seifertii and A. nosocomialis, while all OXA51-like-positive strains matched A. baumannii, as per the Pasteur MLST scheme database. Among the 492 strains, 240 exhibited carbapenem resistance, including 237 carbapenem-resistant A. baumannii (CRAB) strains and three CR-NAB strains. All CRAB strains were positive for blaOXA-51-like; 72.6% also carried blaOXA-23-like, 22.8% carried blaOXA-24-like, 3.4% co-carried blaOXA-23-like+blaOXA-24-like, and 1.27% carried blaOXA-51-like alone. Among the three CR-NAB strains, one carried blaNDM-1, and two co-carried blaOXA-58-like+blaIMP. We also established a new multiplex PCR method for rapid screening of common capsular types (KL), which showed a difference between CRAB and carbapenem-susceptible A. baumannii (CSAB). KL2, KL10, KL22, and KL52 accounted for 76.6% of CRAB strains, whereas about half of the CSAB strains were other KL types. Of the remaining CSAB strains, KL14 was the most predominant type at 10.3%. We further conducted MLST Pasteur typing for 262 isolates and found that the carbapenemase genes were correlated with either ST or KL types. Additionally, KL types showed correlations with ST types, carbapenem resistance, and certain clinical records. Whole-genome sequencing of a blaNDM-1-carrying A. seifertii strain revealed a plasmid transferable via in vitro conjugation, suggesting A. seifertii may be a reservoir for NDM-1 plasmids.IMPORTANCECarbapenem-resistant Acinetobacter spp. have been identified by the World Health Organization as a top priority for new antibiotic development. We established a rapid KL-typing method for efficient screening of Acinetobacter baumannii strains to enable epidemiological surveillance and provide a foundation for effective infection control. Our investigation of the molecular epidemiology of the A. baumannii group isolates revealed the prevalence of carbapenemase genes and major KL types among CR and CS strains of A. baumannii and NAB. We identified an A. seifertii strain carrying a Ti-type conjugative operon on a small plasmid that harbored genes encoding the NDM-1 carbapenemase alongside genes conferring resistance to aminoglycosides and bleomycin and closely resembled sequences detected in A. soli and A. pittii in Taiwan and China, respectively, suggesting its potential for transmitting multidrug resistance and contributing to the spread of antimicrobial resistance.

Rapid bacterial identification through volatile organic compound analysis and deep learning

BACKGROUND

The increasing antimicrobial resistance caused by the improper use of antibiotics poses a significant challenge to humanity. Rapid and accurate identification of microbial species in clinical settings is crucial for precise medication and reducing the development of antimicrobial resistance. This study aimed to explore a method for automatic identification of bacteria using Volatile Organic Compounds (VOCs) analysis and deep learning algorithms.

RESULTS

AlexNet, where augmentation is applied, produces the best results. The average accuracy rate for single bacterial culture classification reached 99.24% using cross-validation, and the accuracy rates for identifying the three bacteria in randomly mixed cultures were SA:98.6%, EC:98.58% and PA:98.99%, respectively.

CONCLUSION

This work provides a new approach to quickly identify bacterial microorganisms. Using this method can automatically identify bacteria in GC-IMS detection results, helping clinical doctors quickly detect bacterial species, accurately prescribe medication, thereby controlling epidemics, and minimizing the negative impact of bacterial resistance on society.

Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.

Markedly Enhanced Analysis of Mass Spectrometry Images Using Weakly Supervised Machine Learning

Supervised and unsupervised machine learning algorithms are routinely applied to time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging data and, more broadly, to mass spectrometry imaging (MSI). These algorithms have accelerated large-scale, single-pixel analysis, classification, and regression. However, there is relatively little research on methods suited for so-called weakly supervised problems, where ground-truth class labels exist at the image level, but not at the individual pixel level. Unsupervised learning methods are usually applied to these problems. However, these methods cannot make use of available labels. Here a novel method specifically designed for weakly supervised MSI data is presented. A dual-stream multiple instance learning (MIL) approach is adapted from computational pathology that reveals the spatial-spectral characteristics distinguishing different classes of MSI images. The method uses an information entropy-regularized attention mechanism to identify characteristic class pixels that are then used to extract characteristic mass spectra. This work provides a proof-of-concept exemplification using printed ink samples imaged by ToF-SIMS. A second application-oriented study is also presented, focusing on the analysis of a mixed powder sample type. Results demonstrate the potential of the MIL method for broader application in MSI, with implications for understanding subtle spatial-spectral characteristics in various applications and contexts.

Lytic activity of phages against bacterial pathogens infecting diabetic foot ulcers

Complications of diabetes, such as diabetic foot ulcers (DFUs), are common, multifactorial in origin, and costly to treat. DFUs are the cause of nearly 90% of limb amputations among persons with diabetes. In most chronic infections such as DFU, biofilms are involved. Bacteria in biofilms are 100-1000 times more resistant to antibiotics than their planktonic counterparts. Multidrug-resistant (MDR) Staphylococcus aureus and Pseudomonas aeruginosa infections in DFUs may require alternative therapeutic agents such as bacteriophages ("phages"). This study describes the lytic activity of phage cocktails AB-SA01 (3-phage cocktail) and AB-PA01 (4-phage cocktail), which target S. aureus and P. aeruginosa, respectively. The host range and lytic effect of AB-SA01 and AB-PA01 on a planktonic culture, single-species biofilm, and mixed-species biofilm were evaluated. In vitro testing showed that 88.7% of S. aureus and 92.7% of P. aeruginosa isolates were susceptible to AB-SA01 and AB-PA01, respectively, in the planktonic state. The component phages of AB-SA01 and AB-PA01 infected 66% to 94.3% of the bacterial isolates tested. Furthermore, AB-SA01 and AB-PA01 treatment significantly (p < 0.05) reduced the biofilm biomass of their hosts, regardless of the antibiotic-resistant characteristics of the isolates and the presence of a non-susceptible host. In conclusion, the strong lytic activity, broad host range, and significant biofilm biomass reduction of AB-SA01 and AB-PA01 suggest the considerable potential of phages in treating antibiotic-resistant S. aureus and P. aeruginosa infections alone or as coinfections in DFUs.

Imported Toxigenic Corynebacterium Diphtheriae in Refugees with Polymicrobial Skin Infections, Germany, 2022

During August-December 2022, toxigenic Corynebacterium diphtheriae was isolated from 25 refugees with skin infections and 2 refugees with asymptomatic throat colonization at a refugee reception center in Germany. None had systemic toxin-mediated illness. Of erosive/ulcerative skin infections, 96% were polymicrobial. Erosive/ulcerative wounds in refugees should undergo testing to rule out cutaneous diphtheria.

A Method to Directly Identify Cronobacter sakazakii in Liquid Medium by MALDI-TOF MS

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry has been widely used as an emerging technology for the rapid identification of microorganisms. Cronobacter sakazakii (C. sakazakii) is a food-borne pathogen of particular importance to the powdered infant formula (PIF) processing environment due to its high lethality in infants. However, the traditional solid spotting detection method of pretreating samples for MALDI-TOF MS leads only to qualitative detection of C. sakazakii. We developed a new, low-cost, robust liquid spotting pretreatment method and used a response surface methodology to optimize its parameters. The applicability, accuracy, and quantitative potential were measured for different types of samples. The optimal parameters of this method were as follows: a volume of 70% formic acid of 25 μL, treatment with ultrasound at 350 W for 3 min, and a volume of acetonitrile added of 75 μL. These conditions led to the highest identification score for C. sakazakii (1926.42 ± 48.497). This method was found to detect bacteria accurately and reproducibly. When 70 strains of C. sakazakii isolates were analyzed with this method, the identification accuracy was 100%. The detection limit of C. sakazakii in environmental and PIF samples was 4.1 × 10¹ cfu/mL and 2.72 × 10³ cfu/mL, respectively.

Investigating Unfavorable Factors That Impede MALDI-TOF-Based AI in Predicting Antibiotic Resistance

The combination of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) spectra data and artificial intelligence (AI) has been introduced for rapid prediction on antibiotic susceptibility testing (AST) of Staphylococcus aureus. Based on the AI predictive probability, cases with probabilities between the low and high cut-offs are defined as being in the “grey zone”. We aimed to investigate the underlying reasons of unconfident (grey zone) or wrong predictive AST. In total, 479 S. aureus isolates were collected and analyzed by MALDI-TOF, and AST prediction and standard AST were obtained in a tertiary medical center. The predictions were categorized as correct-prediction group, wrong-prediction group, and grey-zone group. We analyzed the association between the predictive results and the demographic data, spectral data, and strain types. For methicillin-resistant S. aureus (MRSA), a larger cefoxitin zone size was found in the wrong-prediction group. Multilocus sequence typing of the MRSA isolates in the grey-zone group revealed that uncommon strain types comprised 80%. Of the methicillin-susceptible S. aureus (MSSA) isolates in the grey-zone group, the majority (60%) comprised over 10 different strain types. In predicting AST based on MALDI-TOF AI, uncommon strains and high diversity contribute to suboptimal predictive performance.

Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques: A large-scale benchmarking study

Today machine learning methods are commonly deployed for bacterial species identification using MALDI-TOF mass spectrometry data. However, most of the studies reported in literature only consider very traditional machine learning methods on small datasets that contain a limited number of species. In this paper we present benchmarking results on an unprecedented scale for a wide range of machine learning methods, using datasets that contain almost 100,000 spectra and more than 1000 different species. The size and the diversity of the data allow to compare three important identification scenarios that are often not distinguished in literature, i.e., identification for novel biological replicates, novel strains and novel species that are not present in the training data. The results demonstrate that in all three scenarios acceptable identification rates are obtained, but the numbers are typically lower than those reported in studies with a more limited analysis. Using hierarchical classification methods, we also demonstrate that taxonomic information is in general not well preserved in MALDI-TOF mass spectrometry data. For the novel species scenario, we apply for the first time neural networks with Monte Carlo dropout, which have shown to be successful in other domains, such as computer vision, for the detection of novel species.

Sample preparation and culture condition effects on MALDI-TOF MS identification of bacteria: A review

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an excellent tool for bacterial identification. It allows high throughput, sensitive and specific applications in clinical diagnostics and environmental research. Currently, there is no optimal standardized protocol for sample preparation and culture conditions to profile bacteria. The performance of MALDI-TOF MS is affected by several variables, such as sample preparation, culture media and culture conditions, incubation time/growth stage, incubation temperature, high salt content, blood in the culture media, and others. This review thus aims to clarify why a uniformed protocol is not plausible, to assess the effects these factors have on MALDI-TOF MS identification score, and discuss possible optimizations for its methodology, in relation to specific bacterial representatives and strain requirements.

Current Scenario and Challenges in the Direct Identification of Microorganisms Using MALDI TOF MS

MALDI TOF MS-based microbial identification significantly lowers the operational costs because of minimal requirements of substrates and reagents for extraction. Therefore, it has been widely used in varied applications such as clinical, food, military, and ecological research. However, the MALDI TOF MS method is laced with many challenges including its limitation of the reference spectrum. This review briefly introduces the background of MALDI TOF MS technology, including sample preparation and workflow. We have primarily discussed the application of MALDI TOF MS in the identification of microorganisms. Furthermore, we have discussed the current trends for bioaerosol detection using MALDI TOF MS and the limitations and challenges involved, and finally the approaches to overcome these challenges.

Association of capsular types with carbapenem resistance, disease severity, and mortality in Acinetobacter baumannii

Acinetobacter baumannii emerged as one of the most important pathogens that causes nosocomial infections due to its increased multidrug resistance. Identifying capsular epidemiology in A. baumannii can aid in the development of effective treatments and preventive measures against this emerging pathogen. Here we established a wzc-based method, and combined it with wzy-PCR to determine capsular types of A. baumannii causing nosocomial bacteraemia collected at two medical centres in Taiwan from 2015 to 2017. Among the 237 patients with A. baumannii bacteraemia, 98 (41.4%) isolates were resistant to carbapenems. Four prevalent capsular types (KL2, KL10, KL22, and KL52) accounted for 84.7% of carbapenem-resistant A. baumannii (CRAB) and 12.2% of non-CRAB. The rate of pneumonia, intensive care unit admission, APACHE II score, and Pitt bacteraemia score were higher in patients with KL2/10/22/52 infection than in those with non-KL2/10/22/52 infection. Patients with KL2/10/22/52 infection and patients with CRAB infection have a higher cumulative incidence of attributable and all-cause in-hospital 30-day mortality. On multivariate analysis, appropriate empirical antimicrobial therapy within 24 h was associated with a lower risk of 30-day attributable mortality in the KL2/10/22/52 isolates (odds ratio = 0.19, 95% CI: 0.06–0.66, p = 0.008) but not in non-KL2/10/22/52 isolates. Early recognition of carbapenem resistance-associated capsular types may help clinicians to promptly implement appropriate antimicrobial therapy for improving the outcomes in patients with CRAB bacteraemia.

MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology

There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS's crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.

Comparison of the culture method with multiplex PCR for the confirmation of Legionella spp. and Legionella pneumophila

AIMS

The detection and enumeration of Legionella spp. in water samples are typically performed via a cultural technique standardized in ISO 11731. This method is time-consuming (up to 15 days), and the specificity of the confirmation step is questionable. This study proposes the use of multiplex polymerase chain reaction (PCR) to confirm presumptive Legionella colonies directly from the culture plate; this shortens the response time by 2-5 days while still reporting results in colony forming units (CFU).

METHODS AND RESULTS

Two laboratories analysed a total of 290 colonies to compare the confirmation step of Legionella spp. and Legionella pneumophila in accordance with ISO 11731 by culture growth and agglutination vs multiplex PCR. Discordant results were resolved by the swiss national reference laboratory. The data were evaluated following ISO 16140 and showed that the PCR-technique had higher specificity.

CONCLUSIONS

The confirmation of Legionella spp., L. pneumophila and L. pneumophila serogroup 1 by multiplex PCR allows detection of positive colonies more rapidly and with higher specificity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study highlights a possibility to shorten the response time significantly during the enumeration of Legionella spp. and achieving a higher specificity while adhering to the legally recognized reporting in CFU.

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.

Fast Pathogen Identification Using Single-Cell Matrix-Assisted Laser Desorption/Ionization-Aerosol Time-of-Flight Mass Spectrometry Data and Deep Learning Methods

In diagnostics of infectious diseases, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) can be applied for the identification of pathogenic microorganisms. However, to achieve a trustworthy identification from MALDI-TOF MS data, a significant amount of biomass should be considered. The bacterial load that potentially occurs in a sample is therefore routinely amplified by culturing, which is a time-consuming procedure. In this paper, we show that culturing can be avoided by conducting MALDI-TOF MS on individual bacterial cells. This results in a more rapid identification of species with an acceptable accuracy. We propose a deep learning architecture to analyze the data and compare its performance with traditional supervised machine learning algorithms. We illustrate our workflow on a large data set that contains bacterial species related to urinary tract infections. Overall we obtain accuracies up to 85% in discriminating five different species.

Ribopeaks: a web tool for bacterial classification through m/z data from ribosomal proteins

Summary

MALDI-TOF MS is a rapid, sensitive and economic tool for bacterial identification. Highly abundant bacterial proteins are detected by this technique, including ribosomal proteins (r-protein), and the generated mass spectra are compared with a MALDI-TOF MS spectra database. Currently, it allows mainly the classification of clinical bacteria due to the limited number of environmental bacteria included in the spectra database. We present a wide-ranging bacterium classifier tool, called Ribopeaks, which was created based on r-protein data from the Genbank. The Ribopeaks database has more than 28 500 bacterial taxonomic records. It compares the incoming m/z data from MALDI-TOF MS analysis with models stored in the Ribopeaks database created by machine learning and then taxonomically classifies the bacteria.

Availability and implementation

The software is available at http://www.ribopeaks.com.

Supplementary information

Supplementary data are available at Bioinformatics online.

Identification performance of MALDI-ToF-MS upon mono- and bi-microbial cultures is cell number and culture proportion dependent

Biotyping using matrix-assisted laser desorption ionization-time of flight (MALDI-ToF) mass spectroscopy (MS) has revolutionized microbiology by allowing clinicians and scientists to rapidly identify microbes at genus and species levels. The present study extensively assesses the suitability and reliability of MALDI-ToF biotyping of 14 different aerobic and anaerobic bacterial species as pure and mixed cultures. Reliable identification at species level was possible from biomaterial of older colonies and even frozen biomaterial, although this was species dependent. Using standard instrument settings and direct application of biomaterial onto the MALDI-ToF target plates, it was determined that the cell densities necessary for completely reliable identification of pure cultures varied between 2.40 × 10⁸ and 1.10 × 10¹⁰ viable cell counts (VCCs) per mL, depending on the species. Evaluation of the mixed culture algorithm of the Bruker Biotyper^® software showed that the performance of the algorithm depends greatly on the targeted species, on their phylogenetic distance, and on their ratio of VCC per mL in the mixed culture. Hence, the use of MALDI-ToF-MS with incorporation of the mixed culture algorithm of the software is a useful pre-screening tool for early identification of contaminants, but due to the great variability in performance between different species and the usually unknown percentage of the possible contaminant in the mixture, it is advisable to combine this method with other microbiology methods.

Acceleration of the identification of sepsis-inducing bacteria in cultures of dog and cat blood

OBJECTIVES

To evaluate matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-TOF MS) combined with the Sepsityper kit (Bruker Daltoniks GmbH, Bremen) for the direct detection of bacterial species from inoculated blood cultures from dogs and cats.

MATERIALS AND METHODS

Canine and feline blood samples were inoculated with typical sepsis-causing bacteria such as Staphylococcus intermedius, Staphylococcus aureus, Streptococcus canis, Enterococcus faecalis, Escherichia coli and Pseudomonas aeruginosa at two distinct concentrations (each in triplicate), resulting in 72 blood culture bottles incubated at 37°C. Samples were comparatively analysed with MALDI-TOF MS after preparation with the Sepsityper kit and also by standard bacteriology (culturing and biochemical characterisation).

RESULTS

Bacterial species identified from agar plates and by MALDI-TOF MS from blood culture bottles were identical for all samples. The MALDI Biotyper software (Bruker Daltoniks) correctly identified all bacterial strains from inoculated canine and feline blood with analysis indicating very good precision.

CLINICAL SIGNIFICANCE

MALDI-TOF MS analysis combined with the Sepsityper kit is a reliable tool for a quick detection of veterinary-relevant bacterial species directly from blood culture bottles. This approach could reduce the time for identification of critical species to only 24 hours.

Current status of MALDI-TOF mass spectrometry in clinical microbiology

Mass spectrometry (MS) is a type of analysis used to determine what molecules make up a sample, based on the mass spectrum that are created by the ions. Mass spectrometers are able to perform traditional target analyte identification and quantitation; however, they may also be used within a clinical setting for the rapid identification of bacteria. The causative agent in sepsis is changed over time, and clinical decisions affecting the management of infections are often based on the outcomes of bacterial identification. Therefore, it is essential that such identifications are performed quickly and interpreted correctly. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer is one of the most popular MS instruments used in biology, due to its rapid and precise identification of genus and species of an extensive range of Gram-negative and-positive bacteria. Microorganism identification by Mass spectrometry is based on identifying a characteristic spectrum of each species and then matched with a large database within the instrument. The present review gives a contemporary perspective on the challenges and opportunities for bacterial identification as well as a written report of how technological innovation has advanced MS. Future clinical applications will also be addressed, particularly the use of MALDI-TOF MS in the field of microbiology for the identification and the analysis of antibiotic resistance.

Intelligence Algorithms for Protein Classification by Mass Spectrometry

Mass spectrometry (MS) is an important technique in protein research. Effective classification methods by MS data could contribute to early and less-invasive diagnosis and also facilitate developments in the bioinformatics field. As MS data is featured by high dimension, appropriate methods which can effectively deal with the large amount of MS data have been widely studied. In this paper, the applications of methods based on intelligence algorithms have been investigated. Firstly, classification and biomarker analysis methods using typical machine learning approaches have been discussed. Then those are followed by the Ensemble strategy algorithms. Clearly, simple and basic machine learning algorithms hardly addressed the various needs of protein MS classification. Preprocessing algorithms have been also studied, as these methods are useful for feature selection or feature extraction to improve classification performance. Protein MS data growing with data volume becomes complicated and large; improvements in classification methods in terms of classifier selection and combinations of different algorithms and preprocessing algorithms are more emphasized in further work.

Direct MALDI-TOF MS Identification of Bacterial Mixtures

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now widely used to characterize bacterial samples for clinical diagnosis, food safety control, environmental monitoring, and so on. However, existing standard approaches are only applied to analyze single colonies purified by plate culture, which limits the approaches to cultivable bacteria and makes the whole approaches time-consuming. In this work, we propose a new framework to analyze MALDI-TOF spectra of bacterial mixtures and to directly characterize each component without purification procedures. The framework is a combination of a synthetic mixture model based on a non-negative linear combination of candidate reference spectra and a statistical assessment by in silico generated spectra via a jackknife resampling. Ninety-seven model bacterial mixture samples and 8 cocultured blind-coded bacterial mixture samples, containing up to 6 strains in varied ratios in each sample, together with a reference database containing the mass spectra of 1081 strains, were used to validate the framework. High sensitivity (>80%, with error rate <5%) was achieved for balanced binary and ternary mixtures. The sensitivity was >60% for balanced quaternary and pentabasic mixtures, and 48%-71% for asymmetric situation, with error rate <5%. The work can facilitate rapid and reliable characterization of bacterial mixtures without purification procedures, which is of practical value in clinical diagnosis, food safety control, environmental monitoring, and so on. The framework can be further applied to many other spectroscopy-based analytics to interpret spectra from mixed samples.

Phenotypic typing and epidemiological survey of antifungal resistance of Candida species detected in clinical samples of Italian patients in a 17 months' period

INTRODUCTION

Yeast pathogens are emerging agents of nosocomial as well as community-acquired infections and their rapid and accurate identification is crucial for a better management of high-risk patients and for an adequate treatment.

METHODS

We performed a retrospective review of 156 yeast isolates collected during a 17 months' period of regular clinical practice at the Microbiology Department of San Camillo Hospital in Treviso, Italy and analyzed by the traditional culture-based method combined with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

RESULTS

Out of all the samples collected MALDI-TOF MS was able to characterize with a MT score ≥1.7 (accurate result at species level) 12 different yeast and yeast-like species from 140 samples: Candida albicans (63.7%), Candida glabrata (13.6%), Saccharomyces cerevisiae (6.5%), Candida parapsilosis (5.7%), Candida tropicalis (2.1%), Candida pararugosa (2.1%), Candida guilliermondii (2.1%), Candida kefyr (1.4%), Candida lusitaniae (0.7%), Candida palmioleophila (0.7%), Geotrichum silvicola (0.7%), Rhodotorula mucilaginosa (0.7%). Susceptibility testing toward seven common antifungal agents showed a characteristic MIC distribution of C. albicans isolates for echinocandins: particularly we noticed that 72% and 46% of C. albicans showed an MIC value close to clinical breakpoint as defined by EUCAST, respectively for anidulafungin and micafungin.

CONCLUSION

Accurate identification of microorganisms and the study of their antifungal susceptibility allow to understand the epidemiology of a particular area, permitting the choice of the most appropriate early antifungal treatment.

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues?

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement.

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.

Rapid phenotypic methods to improve the diagnosis of bacterial bloodstream infections: meeting the challenge to reduce the time to result

BACKGROUND

Administration of appropriate antimicrobial therapy is one of the key factors in surviving bloodstream infections. Blood culture is currently the reference standard for diagnosis, but conventional practices have long turnaround times while diagnosis needs to be faster to improve patient care. Phenotypic methods offer an advantage over genotypic methods in that they can identify a wide range of taxa, detect the resistance currently expressed, and resist genetic variability in resistance detection.

AIMS

We aimed to discuss the wide array of phenotypic methods that have recently been developed to substantially reduce the time to result from identification to antibiotic susceptibility testing.

SOURCES

A literature review focusing on rapid phenotypic methods for improving the diagnosis of bloodstream infection was the source.

CONTENT

Rapid phenotypic bacterial identification corresponds to Matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF), and rapid antimicrobial susceptibility testing methods comprised of numerous different approaches, are considered and critically assessed. Particular attention is also paid to emerging technologies knocking at the door of routine microbiology laboratories. Finally, workflow integration of these methods is considered.

IMPLICATIONS

The broad panel of phenotypic methods currently available enables healthcare institutions to draw up their own individual approach to improve bloodstream infection diagnosis but requires a thorough evaluation of their workflow integration. Clinical microbiology will probably move towards faster methods while maintaining a complex multi-method approach as there is no all-in-one method.

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Use with Positive Blood Cultures: Methodology, Performance, and Optimization

Early initiation of effective antibiotics for septic patients is essential for patient survival. Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized clinical microbiology for isolate identification and has the possibility to impact how blood culture testing is performed. This review discusses the various uses of MALDI-TOF MS for the identification and susceptibility testing of positive blood cultures, the performance of these methods, and the outcomes involved with its implementation.

MALDI-TOF Mass Spectrometry Enables a Comprehensive and Fast Analysis of Dynamics and Qualities of Stress Responses of Lactobacillus paracasei subsp. paracasei F19

Lactic acid bacteria (LAB) are widely used as starter cultures in the manufacture of foods. Upon preparation, these cultures undergo various stresses resulting in losses of survival and fitness. In order to find conditions for the subsequent identification of proteomic biomarkers and their exploitation for preconditioning of strains, we subjected Lactobacillus (Lb.) paracasei subsp. paracasei TMW 1.1434 (F19) to different stress qualities (osmotic stress, oxidative stress, temperature stress, pH stress and starvation stress). We analysed the dynamics of its stress responses based on the expression of stress proteins using MALDI-TOF mass spectrometry (MS), which has so far been used for species identification. Exploiting the methodology of accumulating protein expression profiles by MALDI-TOF MS followed by the statistical evaluation with cluster analysis and discriminant analysis of principle components (DAPC), it was possible to monitor the expression of low molecular weight stress proteins, identify a specific time point when the expression of stress proteins reached its maximum, and statistically differentiate types of adaptive responses into groups. Above the specific result for F19 and its stress response, these results demonstrate the discriminatory power of MALDI-TOF MS to characterize even dynamics of stress responses of bacteria and enable a knowledge-based focus on the laborious identification of biomarkers and stress proteins. To our knowledge, the implementation of MALDI-TOF MS protein profiling for the fast and comprehensive analysis of various stress responses is new to the field of bacterial stress responses. Consequently, we generally propose MALDI-TOF MS as an easy and quick method to characterize responses of microbes to different environmental conditions, to focus efforts of more elaborate approaches on time points and dynamics of stress responses.

Development of a systematic feedback isolation approach for targeted strains from mixed culture systems

Elucidation of functions of bacteria in a mixed culture system (MCS) such as composting, activated sludge system is difficult, since the system is complicating with many unisolated bacteria. Here, we developed a systematic feedback isolation strategy for the isolation and rapid screening of multiple targeted strains from MCS. Six major strains (Corynebacterium sphenisci, Bacillus thermocloacae, Bacillus thermoamylovorans, Bacillus smithii, Bacillus humi, and Bacillus coagulans), which are detected by denaturing gradient gel electrophoresis (DGGE) analysis in our previous study on MCS for l-lactic acid production, were targeted for isolation. Based on information of suitable cultivation conditions (e.g., media, pH, temperature) from the literature, feedback isolation was performed to form 136 colonies. The following direct colony matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was optimised as the second screening to narrow down 20 candidate colonies from similar spectra patterns with six closest type strains. This step could distinguish bacteria at the species level with distance similarity scores ≥0.55 corresponding to 16S rRNA gene sequence similarity ≥98.2%, suggesting that this is an effective technique to minimize isolates close to targeted type strains. Analysis of 16S rRNA gene sequences indicated that two targeted strains and one strain related to the target had successfully been isolated, showing high similarities (99.5-100%) with the sequences from the DGGE bands, and that the other candidates were affiliated with three strains that were closely related to the target species. This study proposes a new method for systematic feedback isolation that may be useful for isolating targeted strains from MCS for further investigation.

Use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant

The study of bacterial communities throughout a drinking water treatment plant could provide a basic understanding of the effects of water processing that could then be used to improve the management of such plants. However, it is necessary to develop new analytical techniques that are sufficiently efficient, robust and fast for their effective and useful application in routine analysis. The aim of this study is therefore to assess the performance of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), as compared to the PhenePlate™ system, for routine analysis in a drinking water treatment plant. To this end we studied a total of 277 colonies isolated in different seasons and from different points throughout the water treatment process, including: raw water, sand filtration, ultrafiltration, reverse osmosis and chlorination. The colonies were analysed using MALDI-TOF MS by direct deposition of the cells on the plate. The colonies were also biochemically fingerprinted using the PhenePlate™ system, clustered according to their similarity and a representative strain was selected for 16S rRNA gene sequencing and API^® gallery-based identification. The use of MALDI-TOF MS was reliable compared to the PhenePlate™ system and has the advantage of being faster and relatively cheap. Bacteria typing by MALDI-TOF MS is therefore a promising method to replace conventional routine phenotypic methods for the identification of bacteria in drinking water laboratories, thanks to its robustness. The major limiting factor for MALDI-TOF MS is the lack of a suitable mass spectra database; although each laboratory can develop its own library. This methodology will provide a tracking tool for companies to use in risk management and the detection of possible failures in both the water treatment processes and the distribution network, as well as offering characterization of the intrinsic microbial populations.

Bioterrorism and the Role of the Clinical Microbiology Laboratory

Regular review of the management of bioterrorism is essential for maintaining readiness for these sporadically occurring events. This review provides an overview of the history of biological disasters and bioterrorism. I also discuss the recent recategorization of tier 1 agents by the U.S. Department of Health and Human Services, the Laboratory Response Network (LRN), and specific training and readiness processes and programs, such as the College of American Pathologists (CAP) Laboratory Preparedness Exercise (LPX). LPX examined the management of cultivable bacterial vaccine and attenuated strains of tier 1 agents or close mimics. In the LPX program, participating laboratories showed improvement in the level of diagnosis required and referral of isolates to an appropriate reference laboratory. Agents which proved difficult to manage in sentinel laboratories included the more fastidious Gram-negative organisms, especially Francisella tularensis and Burkholderia spp. The recent Ebola hemorrhagic fever epidemic provided a check on LRN safety processes. Specific guidelines and recommendations for laboratory safety and risk assessment in the clinical microbiology are explored so that sentinel laboratories can better prepare for the next biological disaster.

Whole-cell-based identification of electrochemically active bacteria in microbial fuel cells by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

RATIONALE

Electrochemically active bacteria (EAB) that are capable of producing electricity from renewable biomass and organic wastes have been of particular interest in recent years. Methods for selective enrichment, accurate identification and easy acquisition of EAB fingerprints for phylogenetic characterization would facilitate utilization of these bioenergy-producing species in practical environmental engineering applications.

METHODS

Electricigens/exoelectrogens were selectively enriched from domestic wastewater in a microbial fuel cell (MFC). Whole EAB cell-derived mass spectra were obtained with simple agar incubation for 24 h and subsequent release of proteins by 25% formic acid (FA) and ultrasonication. Mass fingerprints of EAB were obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS) and species-specific analyses were completed by using the Spectral ARchive and Microbial Identification System (SARAMIS).

RESULTS

EAB could be discriminated by clustering of MALDI-TOF/TOF-MS results. Different species in mixtures originating from domestic sewage could be identified unambiguously at 99.90% confidence. Five species, namely Klebsiella oxytoca (K. oxytoca), Comamonas testosterone (C. testosterone), Pseudomonas putida (P. putida), Klebsiella pneumonia (K. pneumonia) and Raoultella ornithinolytica (R. ornithinolytica), that are known to be of clinical significance, were found to be enriched in MFCs and determined as high power-producing species. By using an agglomerative clustering algorithm to compute spectral similarity and diversity, a dendrogram was constructed to illustrate the phylogenetic relationships for EAB on the basis of mass spectral analyses.

CONCLUSIONS

An integrated method based on MFC-enrichment, agar-cultivation and MALDI-TOF/TOF-MS identification of whole-cell-extracted proteins has been proved to be a simple, rapid and reliable approach for rapid identification and routine inspection of EAB. Mixed phyla can be analyzed at species level to provide phylogenetic information on the highly efficient bacteria generating electricity from domestic wastewater.

Utilization of Whole-Cell MALDI-TOF Mass Spectrometry to Differentiate Burkholderia pseudomallei Wild-Type and Constructed Mutants

Whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (whole-cell MALDI-TOF MS) has been widely adopted as a useful technology in the identification and typing of microorganisms. This study employed the whole-cell MALDI-TOF MS to identify and differentiate wild-type and mutants containing constructed single gene mutations of Burkholderia pseudomallei, a pathogenic bacterium causing melioidosis disease in both humans and animals. Candidate biomarkers for the B. pseudomallei mutants, including rpoS, ppk, and bpsI isolates, were determined. Taxon-specific and clinical isolate-specific biomarkers of B. pseudomallei were consistently found and conserved across all average mass spectra. Cluster analysis of MALDI spectra of all isolates exhibited separate distribution. A total of twelve potential mass peaks discriminating between wild-type and mutant isolates were identified using ClinProTools analysis. Two peaks (m/z 2721 and 2748 Da) were specific for the rpoS isolate, three (m/z 3150, 3378, and 7994 Da) for ppk, and seven (m/z 3420, 3520, 3587, 3688, 4623, 4708, and 5450 Da) for bpsI. Our findings demonstrated that the rapid, accurate, and reproducible mass profiling technology could have new implications in laboratory-based rapid differentiation of extensive libraries of genetically altered bacteria.

Direct Identification of Aerobic Bacteria by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry Is Accurate and Robust

BACKGROUND

Bacterial identification in the clinical laboratory can be laborious and expensive. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and cost-effective diagnostic tool for the identification of organisms routinely found in the microbiology laboratory. The objective of this study was to demonstrate that identification of aerobic Gram-positive and Gram-negative organisms could be performed accurately and efficiently by MALDI-TOF MS and the Bruker Biotyper system without the use of time-consuming extraction methodologies.

METHODS

Isolates previously recovered by routine culture and workup from clinical specimens were cultured to appropriate media, identified directly by MALDI-TOF MS, and compared to results from various biochemical identification methods.

RESULTS

Using the direct-smear method, 99.5% and 98.0% of aerobic Gram-negative and Gram-positive bacteria, respectively, were identified to the genus level. At a score of ≥1.9, 97.6% Gram-negative organisms and 94.6% Gram-positive organisms were correctly identified to the species level by direct-smear method. Only 1.1% of isolates required further reflex to direct-plate extraction. The direct-smear method proved to be robust, as various growth temperatures, media, culture age, and different operators had no notable impact on the bacterial identification rate.

CONCLUSION

The direct-smear method is an accurate and time-saving method for routine species-level bacterial identification.

Biomarker- and similarity coefficient-based approaches to bacterial mixture characterization using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)

MALDI-TOF MS profiling has been shown to be a rapid and reliable method to characterize pure cultures of bacteria. Currently, there is keen interest in using this technique to identify bacteria in mixtures. Promising results have been reported with two- or three-isolate model systems using biomarker-based approaches. In this work, we applied MALDI-TOF MS-based methods to a more complex model mixture containing six bacteria. We employed: 1) a biomarker-based approach that has previously been shown to be useful in identification of individual bacteria in pure cultures and simple mixtures and 2) a similarity coefficient-based approach that is routinely and nearly exclusively applied to identification of individual bacteria in pure cultures. Both strategies were developed and evaluated using blind-coded mixtures. With regard to the biomarker-based approach, results showed that most peaks in mixture spectra could be assigned to those found in spectra of each component bacterium; however, peaks shared by two isolates as well as peaks that could not be assigned to any individual component isolate were observed. For two-isolate blind-coded samples, bacteria were correctly identified using both similarity coefficient- and biomarker-based strategies, while for blind-coded samples containing more than two isolates, bacteria were more effectively identified using a biomarker-based strategy.

Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)

Current molecular methods to characterize microalgae are time-intensive and expensive. Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) may represent a rapid and economical alternative approach. The objectives of this study were to determine whether MALDI-TOF MS can be used to: 1) differentiate microalgae at the species and strain levels and 2) characterize simple microalgal mixtures. A common protein extraction sample preparation method was used to facilitate rapid mass spectrometry-based analysis of 31 microalgae. Each yielded spectra containing between 6 and 56 peaks in the m/z 2,000 to 20,000 range. The taxonomic resolution of this approach appeared higher than that of 18S rDNA sequence analysis. For example, two strains of Scenedesmus acutus differed only by two 18S rDNA nucleotides, but yielded distinct MALDI-TOF mass spectra. Mixtures of two and three microalgae yielded relatively complex spectra that contained peaks associated with members of each mixture. Interestingly, though, mixture-specific peaks were observed at m/z 11,048 and 11,230. Our results suggest that MALDI-TOF MS affords rapid characterization of individual microalgae and simple microalgal mixtures.

The use of molecular methods for the detection and identification of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen in many hospitals and long-term care facilities as well as in the community. To limit the spread of MRSA, early detection and proper treatment are essential. Because conventional culture as gold standard is time consuming, new techniques such as PCR-based and hybridization assays have emerged for the rapid detection of MRSA. This review will focus on the currently available molecular-based assays and on their utility and performance for detection of S. aureus, of its virulence factors and of the markers for acquired resistance.

Validation of nanodiamond-extracted CFP-10 antigen as a biomarker in clinical isolates of Mycobacterium tuberculosis complex in broth culture media

With detonation nanodiamonds (DNDs) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), we previously identified early secreted cell filtrate protein 10 (CFP-10) as a candidate Mycobacterium tuberculosis complex (MTC) biomarker. The performance of the CFP-10 biomarker was initially evaluated in relatively small mycobacterial samples (n = 42 samples) in our previous study. In this study, we conducted DND MALDI-TOF MS experiments to investigate the specificity and sensitivity of the MTC biomarker with 312 MTC and 52 nontuberculous mycobacteria (NTM) clinical samples. The frequency and intensity of the acquired CFP-10 mass-to-charge (m/z) peaks were checked with a program to validate that the singly and doubly charged CFP-10 antigen can be treated as a MTC biomarker. We confirmed that by detecting the singly charged species of CFP-10 antigen, the sensitivity and the specificity of MTC samples could reach 97.4% and 100% and no CFP-10 biomarker could be found in NTM samples. This indicates with CFP-10 biomarker it is easy to distinguish MTC from NTM. Besides, the observed intensity ratio of singly and doubly charged species of CFP-10 antigen was 3.3 ± 2.6 and the CFP-10 antigen could maintain good signal intensity for a week. Our results suggest that, with the DND MALDI-TOF mass spectrometry approach, CFP-10 antigen can be used as an early diagnosis biomarker in clinical practice.

Updates on quick identification of acetic acid bacteria with a focus on the 16S-23S rRNA gene internal transcribed spacer and the analysis of cell proteins by MALDI-TOF mass spectrometry

Acetic acid bacteria have attracted much attention over the past few years, due mainly to their metabolic traits that are of interest to the biotechnology industry. In addition, it turns out that their ecological habitats are almost unlimited since they have been found as symbionts in different insects and also as emerging opportunistic human pathogens. Very surprising is the finding that they colonize niches considered anaerobic, disproving the generalized statement that they are strict aerobes. Since they have taken on different biological roles in our environment, more and more people are charged with the task of identifying them. However, this turns out to be not always easy, especially if we are using phenotypic approaches for identification. A substantial step forward in making the identification of acetic acid bacteria easier was made possible using molecular biological methods, which have been extensively tested since 2000. However, some molecular methods require expensive machines and experienced staff, and moreover the level of their discrimination varies. All these factors must be considered when selecting the most appropriate approach for identifying acetic acid bacteria. With this objective in mind, this review article discusses the benefits and drawbacks of molecular biological methods for identification of acetic acid bacteria, with a focus on the 16S-23S rRNA gene ITS regions and the recently described alternative method for identification of acetic acid bacteria, MALDI-TOF MS.

Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus

Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the “sanguinis group.” As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the “mitis group.” On the basis of the findings, we propose a novel group, named “sinensis group,” to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy.

Emerging mass spectrometry techniques for the direct analysis of microbial colonies

One of the emerging areas in microbiology is detecting specialized metabolites produced by microbial colonies and communities with mass spectrometry. In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies. Mass spectrometry techniques such as imaging mass spectrometry and real-time mass spectrometry allow two and three-dimensional visualization of the distribution of metabolites, often with minimal sample pretreatment. The speed in which molecules are captured using these methods requires the development of new molecular visualization tools such as molecular networking. Together, these tools are beginning to provide unprecedented insight into the chemical world that microbes experience.