Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists

A rare urinary tract infection of multidrug-resistant Chryseobacterium urinae sp. nov. isolated from a diabetic, non-catheterized patient

Chryseobacterium demonstrates a diverse environmental presence and a significant pathogenic potential across various ecosystems. This clinical case showcases a rare instance of bacterial infection in a 75-year-old male with untreated diabetes and recurrent urinary tract infections (UTIs). The patient presented symptoms of abdominal pain, burning urination, fever, and an elevated eosinophil count. A subsequent urine culture identified a Chryseobacterium-related bacterium as the causative agent, exhibiting sensitivity to piperacillin/tazobactam, trimethoprim/sulfamethoxazole, and nitrofurantoin, which led to successful treatment using oral nitrofurantoin. Analysis of the 16S rRNA gene sequence of APV-1T revealed a close relationship of 98.2% similarity to Chryseobacterium gambrini strain 5-1St1aT (AM232810). Furthermore, comparative genome analysis, incorporating Average Nucleotide Identity (ANI), Digital DNA-DNA Hybridization (dDDH) values, and comprehensive phylogenetic assessments utilizing 16S rRNA gene sequences, core genes, and amino acid sequences of core proteins, highlighted the unique phylogenetic positioning of APV-1T within the Chryseobacterium genus. Distinct carbon utilization and assimilation patterns, along with major fatty acid content, set APV-1T apart from C. gambrini strain 5-1St1aT. These findings, encompassing phenotypic, genotypic, and chemotaxonomic characteristics, strongly support the proposal of a novel species named Chryseobacterium urinae sp. nov., with APV-1T designated as the type strain (= MCC 50690 = JCM 36476). Despite its successful treatment, the strain displayed resistance to multiple antibiotics. Genomic analysis further unveiled core-conserved genes, strain-specific clusters, and genes associated with antibiotic resistance and virulence. This report underscores the vital importance of elucidating susceptibility patterns of rare pathogens like Chryseobacterium, particularly in immunocompromised individuals. It advocates for further analyses to understand the functional significance of identified genes and their implications in treatment and pathogenesis.

Identification of environmental Actinobacteria in buildings by means of chemotaxonomy, 16S rRNA sequencing, and MALDI-TOF MS

Actinobacteria are abundant in soil and other environmental ecosystems and are also an important part of the human microbiota. Hence, they can also be detected in indoor environments and on building materials, where actinobacterial proliferation on damp materials can indicate moisture damage. The aim of this study was to evaluate the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of 28 environmental strains of Actinobacteria isolated from building materials and indoor and outdoor air samples, mainly collected in the context of moisture damage investigations in buildings in Finland. The 16S rRNA gene sequencing and chemotaxonomic analyses were performed, and results were compared with the MALDI-TOF MS Biotyper identification. Using 16S rRNA gene sequencing, all isolates were identified on the species or genus level and were representatives of Streptomyces, Nocardia, and Pseudonocardia genera. Based on MALDI-TOF MS analysis, initially, 11 isolates were identified as Streptomyces spp. and 1 as Nocardia carnea with a high identification score. After an upgrade in the MALDI-TOF MS in-house database and re-evaluation of mass spectra, 13 additional isolates were identified as Nocardia, Pseudonocardia, and Streptomyces. MALDI-TOF MS has the potential in environmental strain identification; however, the standard database needs to be considerably enriched by environmental Actinobacteria representatives.

IMPORTANCE

The manuscript addresses the challenges in identifying environmental bacteria using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) Biotyper-based protein profiling. The matter of the studies-actinobacterial strains-has been isolated mostly from building materials that originated from a confirmed moisture-damaged situation. Polyphasic taxonomy, 16S RNA gene sequencing, and MALDI-TOF mass spectrometry were applied for identification purposes. In this experimental paper, a few important facts are highlighted. First, Actinobacteria are abundant in the natural as well as built environment, and their identification on the species and genus levels is difficult and time-consuming. Second, MALDI-TOF MS is an effective tool for identifying bacterial environmental strains, and in parallel, continuous enrichment of the proteomics mass spectral databases is necessary for proper identification. Third, the chemical approach aids in the taxonomical inquiry of Actinobacteria environmental strains.

MALDI-TOF as a powerful tool for identifying and differentiating closely related microorganisms: the strange case of three reference strains of Paenibacillus polymyxa

Accurate identification and typing of microbes are crucial steps in gaining an awareness of the biological heterogeneity and reliability of microbial material within any proprietary or public collection. Paenibacillus polymyxa is a bacterial species of great agricultural and industrial importance due to its plant growth-promoting activities and production of several relevant secondary metabolites. In recent years, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an alternative rapid tool for identifying, typing, and differentiating closely related strains. In this study, we investigated the diversity of three P. polymyxa strains. The mass spectra of ATCC 842T, DSM 292, and DSM 365 were obtained, analysed, and compared to select discriminant peaks using ClinProTools software and generate classification models. MALDI-TOF MS analysis showed inconsistent results in identifying DSM 292 and DSM 365 as belonging to P. polimixa species, and comparative analysis of mass spectra revealed the presence of highly discriminatory biomarkers among the three strains. 16S rRNA sequencing and Average Nucleotide Identity (ANI) confirmed the discrepancies found in the proteomic analysis. The case study presented here suggests the enormous potential of the proteomic-based approach, combined with statistical tools, to predict and explore differences between closely related strains in large microbial datasets.

Genome sequence-based identification of Enterobacter strains and description of Enterobacter pasteurii sp. nov

IMPORTANCE

Accurate taxonomy is essential for microbial biological resource centers, since the microbial resources are often used to support new discoveries and subsequent research. Here, we used genome sequence data, alongside matrix-assisted laser desorption/ionization time-of-flight mass spectrometer biotyper-based protein profiling, to accurately identify six Enterobacter cloacae complex strains. This approach effectively identified distinct species within the E. cloacae complex, including Enterobacter asburiae, "Enterobacter xiangfangensis," and Enterobacter quasihormaechei. Moreover, the study revealed the existence of a novel species within the Enterobacter genus, for which we proposed the name Enterobacter pasteurii sp. nov. In summary, this study demonstrates the significance of adopting a genome sequence-driven taxonomy approach for the precise identification of bacterial strains in a biological resource center and expands our understanding of the E. cloacae complex.

Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina

The aim of this study was to compare the performance of two MALDI-TOF MS systems in the identification of clinically relevant strict anaerobic bacteria. The 16S rRNA gene sequencing was the gold standard method when discrepancies or inconsistencies were observed between platforms. A total of 333 isolates were recovered from clinical samples of different centers in Buenos Aires City between 2016 and 2021. The isolates were identified in duplicate using two MALDI-TOF MS systems, BD Bruker Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMèrieux, Marcy-l'Etoile, France). Using the Vitek MS system, the identification of anaerobic isolates yielded the following percentages: 65.5% (n: 218) at the species or species-complex level, 71.2% (n: 237) at the genus level, 29.4% (n: 98) with no identification and 5.1% (n: 17) with misidentification. Using the Bruker Biotyper system, the identification rates were as follows: 85.3% (n: 284) at the species or species-complex level, 89.7% (n: 299) at the genus level, 14.1% (n: 47) with no identification and 0.6% (n: 2) with misidentification. Differences in the performance of both methods were statistically significant (p-values <0.0001). In conclusion, MALDI-TOF MS systems speed up microbial identification and are particularly effective for slow-growing microorganisms, such as anaerobic bacteria, which are difficult to identify by traditional methods. In this study, the Bruker system showed greater accuracy than the Vitek system. In order to be truly effective, it is essential to update the databases of both systems by increasing the number of each main spectrum profile within the platforms.

A comprehensive review of microbial contamination in the indoor environment: sources, sampling, health risks, and mitigation strategies

The quality of the indoor environment significantly impacts human health and productivity, especially given the amount of time individuals spend indoors globally. While chemical pollutants have been a focus of indoor air quality research, microbial contaminants also have a significant bearing on indoor air quality. This review provides a comprehensive overview of microbial contamination in built environments, covering sources, sampling strategies, and analysis methods. Microbial contamination has various origins, including human occupants, pets, and the outdoor environment. Sampling strategies for indoor microbial contamination include air, surface, and dust sampling, and various analysis methods are used to assess microbial diversity and complexity in indoor environments. The review also discusses the health risks associated with microbial contaminants, including bacteria, fungi, and viruses, and their products in indoor air, highlighting the need for evidence-based studies that can relate to specific health conditions. The importance of indoor air quality is emphasized from the perspective of the COVID-19 pandemic. A section of the review highlights the knowledge gap related to microbiological burden in indoor environments in developing countries, using India as a representative example. Finally, potential mitigation strategies to improve microbiological indoor air quality are briefly reviewed.

Salt tolerant Pseudomonas taiwanensis PWR-1 in combination with a reduced dose of mineral fertilizers improves the nutritional and antioxidant properties of wheatgrass grown in saline soil

Salt-tolerant plant growth promoting rhizobacteria (ST-PGPR) are known to ameliorate salt stress in plants by various mechanisms. The current study aims to investigate the role of an ST-PGPR strain Pseudomonas taiwanensis PWR-1 applied along with a reduced dose of mineral fertilizers (N, P, and K) in the improvement of the antioxidant and nutritional properties of wheatgrass (Triticum aestivum L.) grown in saline soil. Application of P. taiwanensis PWR-1 along with 50% of the recommended dose of mineral fertilizers resulted in a significant improvement of growth parameters including shoot length (22.79%), root length (20.38%), fresh weight (13.15%), dry weight (92.34%), vigor index (13.36%), and relative water content (48.24%). The combined application of PWR-1 and mineral fertilizers increased the production of osmoprotectants (proline, total soluble sugars, glycine betaine), antioxidants (SOD, POD, APX, CAT, PPO, and reduced glutathione), and free radical scavengers (DPPH and H2O2) in wheatgrass. Furthermore, the concentration of micronutrients (Zn and Fe), macronutrients (N, and P), and vitamins (B1 and E) also increased in the above treatment. Oxidative stress markers (malondialdehyde and electrolyte leakage) and Na+ accumulation were significantly reduced whilst K+ content increased in the shoot, which helped in maintaining the K+/Na+ ratio in wheatgrass under saline conditions. The results indicated that the application of ST-PGPR could not only reduce the dosage of mineral fertilizers but might be useful for improving the nutritional and antioxidant properties of medicinal crops such as wheatgrass under salt-stress conditions. Implementing this approach could result in the reduction of chemical usage, while also facilitating enhanced uptake of micronutrients in crops, particularly in regions affected by salinity.

Galvanic Displacement Reaction Enabled Specific and Sensitive Detection of Bacteria with a Digital Photocorrosion GaAs/AlGaAs Biosensor

The conjugation of ionic gold with bacterial antibodies makes it possible to induce a specific interaction between targeted bacteria and the surface of a GaAs/AlGaAs biochip. The process of immobilization is based on a galvanic displacement reaction (GDR) involving electron transfer between GaAs and Au3+ ions that leads to the formation of a Au-Ga alloy anchoring bacteria to the biochip surface. The GDR-based immobilization of Escherichia coli on biochips comprising a stack of GaAs/AlGaAs nanolayers (dGaAs = 12 nm, dAlGaAs = 10 nm) was confirmed by X-ray photoelectron spectroscopy and atomic force microscopy-based infrared experiments. We report the successful application of this approach for highly sensitive detection of E. coli with a digital photocorrosion (DIP) biosensor. The photoluminescence (PL) monitored DIP of GaAs/AlGaAs nanolayers results in the formation of a PL intensity maximum whose temporal appearance depends on the electric charge transfer between bacteria and the biochip. The formation of a robust bacteria-biochip interface achieved with the GDR process allowed us to observe the role of bacteria on the temporal position of a PL intensity maximum related to the etching of two pairs of GaAs/AlGaAs nanolayers extending up to 24 nm below the biochip surface. We demonstrate the attractive detection of E. coli at 250 CFU/mL, and we discuss the potential of this approach for designing a family of biosensors addressing the quasi-continuous monitoring of a water environment for the presence of pathogenic bacteria.

A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables

MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.

Resolution of inter/intraspecies variation in Weissella group requires multigene analysis and functional characterization

Weissella confusa and Weissella cibaria strains isolated from the human- gut are considered as potential probiotics, but remain under-explored owing to their ambiguous taxonomic assignment. The present study assesses the taxonomic resolution of 11 strains belonging to W. confusa and W. cibaria species and highlights the inter- and intraspecies variations using an array of phenetic and molecular methods. Remarkable genomic variability among the strains was observed by phylogenetic analysis using concatenated housekeeping genes (pheS, gyrB, and dnaA) along with 16S rRNA gene sequence, suggesting intraspecies variations; which is also supported by the phenetic data. Analysis showed that 16S rRNA gene sequence alone could not resolve the variation, and among the tested marker genes, signals from pheS gene provide better taxonomic resolution. The biochemical and antibiotic susceptibility tests also showed considerable variations among the isolates. Additionally, 'quick' identification using mass spectroscopy-based matrix-assisted laser desorption/ionization-time of flight mass spectra was accurate up to genus only, and not species level, for the Weissella group. The study highlights need for inclusion of functional, phenetic, and multigene phylogenetic analysis in addition to 16S rRNA gene-based identification for the Weissella group, to provide better resolution in taxonomic assignments, which is often a prerequisite for the selection of potential strains with biotechnological applications.

Comparative genomic analyses of the clinically-derived Winkia strain NY0527: the reassignment of W. neuii subsp. neuii and W. neuii subsp. antitratus into two separate species and insights into their virulence characteristics

Background

Winkia neuii, previously known as Actinomyces neuii, is increasingly recognized as a causative agent of various human infections, while its taxonomy and genomic insights are still understudied.

Methods

A Winkia strain NY0527 was isolated from the hip abscess of a patient, and its antibiotic susceptibility was assessed. The genome was hybrid assembled from long-reads and short-reads sequencing. Whole-genome-based analyses on taxa assignment, strain diversity, and pathogenesis were conducted.

Results

The strain was found to be highly susceptible to beta-lactam antibiotics, but resistant to erythromycin, clindamycin, and amikacin. The complete genome sequences of this strain were assembled and found to consist of a circular chromosome and a circular plasmid. Sequence alignment to the NCBI-nt database revealed that the plasmid had high sequence identity (>90%) to four Corynebacterium plasmids, with 40-50% query sequence coverage. Furthermore, the plasmid was discovered to possibly originate from the sequence recombination events of two Corynebacterium plasmid families. Phylogenomic tree and genomic average nucleotide identity analyses indicated that many Winkia sp. strains were still erroneously assigned as Actinomyces sp. strains, and the documented subspecies within W. neuii should be reclassified as two separate species (i.e., W. neuii and W. anitratus). The core genome of each species carried a chromosome-coded beta-lactamase expression repressor gene, which may account for their broadly observed susceptibility to beta-lactam antibiotics in clinical settings. Additionally, an ermX gene that expresses fluoroquinolone resistance was shared by some W. neuii and W. anitratus strains, possibly acquired by IS6 transposase-directed gene transfer events. In contrast, tetracycline resistance genes were exclusively carried by W. neuii strains. In particular, W. neuii was found to be more pathogenic than W. anitratus by encoding more virulence factors (i.e., 35-38 in W. neuii vs 27-31 in W. anitratus). Moreover, both species encoded two core pathogenic virulence factors, namely hemolysin and sialidase, which may facilitate their infections by expressing poreformation, adhesion, and immunoglobulin deglycosylation activities.

Conclusion

This study highlights the underappreciated taxonomic diversity of Winkia spp. and provides populational genomic insights into their antibiotic susceptibility and pathogenesis for the first time, which could be helpful in the clinical diagnosis and treatment of Winkia spp. infections.

Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens

16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S rRNA gene sequencing from direct clinical specimens on antimicrobial management. Adult inpatients whose attending physician requested 16S rRNA gene sequencing and corresponding bacterial culture from a direct clinical specimen between January and December 2021 in a university hospital were prospectively included in this study. A total of 434 specimens from 374 patients were requested. Of these, 253 (58.3%) specimens were collected from patients whose final diagnosis indicated a bacterial infection, whereas 181 (41.7%) specimens were from nonbacterial infections. Using the final diagnosis as a "gold standard," the sensitivity and specificity of 16S rRNA gene sequencing were 38.3% and 93.9%, respectively. Among the bacterial infection cases, the proportion of 16S rRNA gene sequencing-positive and culture-positive cases was 32.4%, and the proportion of sequencing-positive and culture-negative cases was 5.9%. The impact on antimicrobial management was evident in 10 (2.3%) specimens, which all resulted in the continuation of antibiotics. The impact on antimicrobial management was highest in skin and soft tissue infections, followed by bone and joint infections. In this study, the long turnaround time of 16S rRNA gene sequencing of clinical specimens was a limiting factor. In conclusion, the overall diagnostic yield of 16S rRNA gene sequencing in bacterial infection cases was fair, being useful in selected cases. Restrictions on test requests may improve test utilization in this setting. IMPORTANCE 16S rRNA gene sequencing has been increasingly used in clinical practice. Using the final diagnosis as a gold standard, the sensitivity of 16S rRNA gene sequencing was fair. In the setting with no 16S rRNA gene sequencing test ordering restrictions, only small percentages of the test results had an impact on antimicrobial management. Restrictions on test requests should be developed to maximize the benefit of the test.

Label-free designed nanomaterials enrichment and separation techniques for phosphoproteomics based on mass spectrometry

The surface chemical characteristics of nanomaterials have a substantial impact on the affinity probe used to enrich proteins and peptides for MALDI-MS analysis of a real human sample. Detecting phosphoproteins involved in signalling is always difficult, even with recent developments in mass spectrometry, because protein phosphorylation is often temporary from complicated mixtures. This review summarizes current research on the successful enrichment of various intriguing glycoproteins and glycol peptides using surface affinity materials with distinctive qualities such as low cost, excellent structural stability, diversity, and multifunction. As a consequence, this review will provide a quick overview of the scholars from various backgrounds who are working in this intriguing interdisciplinary field. Label-free cancer biomarkers and other diseases will benefit from future challenges.

MALDI-TOF MS database expansion for identification of Bacillus and related genera isolated from a pharmaceutical facility

Bacillus and related genera are among the main bacterial groups isolated from pharmaceutical production areas. The identification of Bacillus species and related genera by classical methods is particularly difficult, due to similarities between closely related species. The Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is one of the most promising techniques for chemotaxonomic characterization of microorganisms, being an alternative to genotypic methods. This study aimed to identify Bacillus strains and related genera isolated from immunobiological production areas by phylogenetic analysis of housekeeping genes and expand the database associated with MALDI-TOF MS to improve their identification. In a previous study, 97 aerobic endospore-forming bacteria isolated from a pharmaceutical facility were analyzed by MALDI-TOF MS and 16S rRNA gene full-length sequencing. All strains were identified as Bacillus and related genera by the latest methodology. Among the 97 strains, 22 were unidentified and 2 strains were misidentified by MALDI-TOF MS. In the present study, these 24 strains were subjected to 16S rRNA gene phylogenetic analysis. Strains not identified at species level by this methodology were submitted to rpoB gene phylogenetic analysis. After identifying the strains, 19 of the 24 strains were incubated for 24, 48, and 72 h on Tryptic Soy Agar and Sheep Blood Agar and subjected to analysis by MALDI-TOF MS. A SuperSpectrum for each strain was created and entered into the equipment database. Finally, the 24 strains were again submitted to proteomic analysis by MALDI-TOF MS, and, at this time, all were correctly identified. The genotypic identification of in-house isolated strains and the introduction of these spectra in MALDI-TOF MS, in order to obtain a customized database, proved to be an extremely effective tool in the identification of Bacillus and related genera from pharmaceutical industry origin.

How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings

Healthcare settings have been utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) since 2010. MALDI-TOF MS has various benefits over the conventional method of biochemical identification, including ease of use, speed, accuracy, and low cost. This approach can solve many of the obstacles to identifying bacteria, fungi and viruses. As technology advanced, more and more databases kept track of spectra, allowing species with similar morphological, genotypic, and biochemical traits to be identified. Using MALDI-TOF MS for identification has become more accurate and quicker due to advances in sample preparation and database enrichment. Rapid sample detection and colony identification using MALDI-TOF MS have produced promising results. A key application of MALDI-TOF MS is quickly identifying highly virulent and drug-resistant diseases. Here, we present a review of the scientific literature assessing the effectiveness of MALDI-TOF MS for locating clinically relevant pathogenic bacteria, fungi, and viruses. MALDI-TOF MS is a useful strategy for locating clinical pathogens, however, it also has some drawbacks. A small number of spectra in the database and inherent similarities among organisms can make it difficult to distinguish between different species, which can result in misidentifications. The majority of the time additional testing may correct these problems, which happen very seldom. In conclusion, infectious illness diagnosis and clinical care are being revolutionized by the use of MALDI-TOF MS in the clinical microbiology laboratory.

Cultivable microbial diversity in speleothems using MALDI-TOF spectrometry and DNA sequencing from Krem Soitan, Krem Lawbah, Krem Mawpun, Khasi Hills, Meghalaya, India

The microbial diversity in the Indian caves is inadequately characterized. This study reports on the culturable microbial communities in caves from the Indian sub-continent. This study aims to expand the current understanding of bacterial diversity in the speleothems and wall deposits from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. A culture-dependent approach was employed for elucidating the community structure in the caves using MALDI-TOF spectrometry and 16S rRNA gene sequencing. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. High microbial enumerations were observed on dilute nutrient agar (5.3 × 103 to 8.8 × 105) followed by M9 minimal medium (4 × 104 to 1.7 × 105) and R2A medium (1.0 × 104 to 5.7 × 105). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. A total 91% of the bacterial diversity was dominated by Proteobacteria (61%) and Actinobacteria (30%). In addition, bacterial phyla include Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%) were found in the samples. At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.

New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia

Since early studies, the history of prokaryotes taxonomy has dealt with many changes driven by the development of new and more robust technologies. As a result, the number of new taxa descriptions is exponentially increasing, while an increasing number of others has been subject of reclassification, demanding from the taxonomists more effort to maintain an organized hierarchical system. However, expectations are that the taxonomy of prokaryotes will acquire a more stable status with the genomic era. Other analyses may continue to be necessary to determine microbial features, but the use of genomic data might be sufficient to provide reliable taxa delineation, helping taxonomy to reach the goal of correct classification and identification. Here we describe the evolution of prokaryotes' taxonomy until the genomic era, emphasizing bacteria and taking as an example the history of rhizobia taxonomy. This example was chosen because of the importance of the symbiotic nitrogen fixation of legumes with rhizobia to the nitrogen input to both natural ecosystems and agricultural crops. This case study reports the technological advances and the methodologies used to classify and identify bacterial species and indicates the actual rules required for an accurate description of new taxa.

Discrimination of Euglena gracilis strains Z and bacillaris by MALDI-TOF MS

AIMS

Euglena gracilis is used as model organism for various microbiological, molecular biological and biotechnological studies. Its most studied wild type strains are Z and bacillaris, but their discrimination by standard molecular methods is difficult. Therefore, we decided to test the suitability of MALDI-TOF MS (matrix assisted laser desorption/ionization - time of flight mass spectrometry) for identification of E. gracilis and for discrimination of these two strains possessing functional chloroplasts. MALDI-TOF MS profiling was also tested for two white (non-photosynthetic) stable E. gracilis mutant strains W_gm ZOflL and W₁₀ BSmL.

METHODS AND RESULTS

We have successfully obtained main spectrum profiles (MSPs) of E. gracilis strains Z, SAG 1224-5/25 and bacillaris, SAG 1224-5/15 using protein extraction procedure. Subsequent MALDI-TOF MS profiling of a number of tested samples and the comparison of the obtained protein profiles with our in-house database including MSPs of both strains has revealed that these two strains can be easily distinguished by MALDI-TOF MS based on score values over two in most cases. This method has also confirmed the ancestry of white mutant strains W_gm ZOflL and W₁₀ BSmL, originally derived from strains Z and bacillaris, respectively.

CONCLUSIONS

MALDI-TOF MS is suitable, accurate and rapid method for discrimination of E. gracilis strains.

SIGNIFICANCE AND IMPACT OF STUDY

These results can have broad practical implications for laboratories cultivating various strains of euglenids, and they can be applied for their discrimination by MALDI-TOF MS.

Classification of Environmental Strains from Order to Genus Levels Using Lipid and Protein MALDI-ToF Fingerprintings and Chemotaxonomic Network Analysis

During the last two decades, MALDI-ToF mass spectrometry has become an efficient and widely-used tool for identifying clinical isolates. However, its use for classification and identification of environmental microorganisms remains limited by the lack of reference spectra in current databases. In addition, the interpretation of the classical dendrogram-based data representation is more difficult when the quantity of taxa or chemotaxa is larger, which implies problems of reproducibility between users. Here, we propose a workflow including a concurrent standardized protein and lipid extraction protocol as well as an analysis methodology using the reliable spectra comparison algorithm available in MetGem software. We first validated our method by comparing protein fingerprints of highly pathogenic bacteria from the Robert Koch Institute (RKI) open database and then implemented protein fingerprints of environmental isolates from French Guiana. We then applied our workflow for the classification of a set of protein and lipid fingerprints from environmental microorganisms and compared our results to classical genetic identifications using 16S and ITS region sequencing for bacteria and fungi, respectively. We demonstrated that our protocol allowed general classification at the order and genus level for bacteria whereas only the Botryosphaeriales order can be finely classified for fungi.

In vitro Sequestration of Molecular and Mass Spectra Characterized Metallophilic Cadmium Tolerant Bacteria for Sustainable Agriculture

Due to industrialization, the contamination of toxic metals in soils is currently one of the major concerns to scientists worldwide. The presence of high concentrations of heavy metals including cadmium in the environment is mainly attributed to human activities. Being a highly toxic metal, cadmium can enter plant cell transporters usually used for the uptake of essential cations, such as iron, calcium, and zinc. This study deals with the appraisement of response and tolerance shown by various bacteria in varied cadmium concentrations (100-1,000 ppm). The optical density (OD) of the isolates was measured to determine the minimum inhibitory concentration (MIC) of cadmium. Isolated bacteria have been identified using 16S rRNA gene sequence and Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Among the 72 isolates, 07 (Bacillus pumilus, Enterobacter kobei, Klebsiella pneumonia, Pseudomonas mandelii, Pseudomonas putida, Pseudomonas avellanae, and Staphylococcus equorum), isolates had efficacy for cadmium tolerance and showed sequestration potential at varying MIC. Furthermore, K. pneumonia was observed to have the highest (900 ppm) tolerance for cadmium and the lowest (600 ppm) was shown by E. kobei. Besides, K. pneumonia showed the highest (75.2%) sequestration potential while the least (52.4%) potential was observed for P. putida. These cadmium tolerant species can be implemented in contaminated environments for detoxification and elimination of cadmium from these agricultural fields. Graphical Abstract.

Characterization of Allergic Polymerized Impurities in Cephalosporins by MALDI-TOF MS/MS Spectrometry

Background:

Characterization of allergic polymerized impurities in cephalosporins is significant to ensure the safety and quality of the products.

Objective:

To develop a MALDI-TOF MS/MS method to characterize the structures of polymerized impurities in cefuroxime axetil drug substance and cefetamet pivoxil drug substance.

Methods:

Calibrant references were TOF mix, including Angiotensin 2, Angiotensin 1, Glu-1-fibrino, N-Acetyl renin, ACTH 1-17, ACTH 18-39 and ACTH 7-38. Matrix was DHB at a concentration of 10 mg•mL-1. Acetone and water were used as solvent to dissolve cefuroxime axetil and cefetamet pivoxil hydrochloride drug substances, respectively. The prepared solutions were mixed with DHB, volatilized to dry, and subjected to MALDI-TOF MS/MS analysis, respectively. MS data was obtained in the linear mode with a power of 80, and MS2 data was obtained in the reflection mode with a power of 120. Molecular weights of polymerized impurities in cefuroxime axetil and cefetamet pivoxil were obtained based on the MS data. Their fragmentation patterns and structural assignments were studied based on the MS2 data.

Results:

Eight polymerized impurities in cefuroxime axetil drug substance and cefetamet pivoxil hydrochloride drug substance made in China were characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS/MS), among which impurity Ⅰ-Ⅴ were in cefuroxime axetil and impurities Ⅵ-Ⅷ were in cefetamet pivoxil. Based on the experimental results, the polymerization mechanism of polymerized impurities in cephalosporins was discussed.

Conclusion:

MALDI-TOF MS/MS was proved to be simple, quick and sensitive for the analysis of polymerized impurities in cephalosporins.

Application of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for the Rapid Identification of Yeast Species From Polar Regions

Protein profiling based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has proved to be a powerful tool for yeast identification. However, it is rarely used in the identification of yeast isolates from polar regions, which may be due to the limited data available for the differentiation of polar yeast species. The present study constructed a supplementary database of MALDI-TOF MS, including 33 yeast species from the Arctic and Antarctica. These yeast species were used to assess the accuracy and practicality of MALDI-TOF MS-based identification compared to the ribosomal DNA [internal transcribed spacer (ITS) and large subunit (LSU) gene regions] sequencing identification. Their dendrogram based on main spectra profiles (MSPs) in the supplementary database was somewhat consistent with their phylogenetic tree. The accuracy of MALDI-TOF MS identification was also compared by the ethanol-formic acid extraction method and the on-plate extraction method. In addition, peptide markers of some yeast species (e.g., Glaciozyma, Phenoliferia, Mrakia, and Vishniacozyma) were identified. It is concluded that the MALDI-TOF MS method can differentiate some closely related yeast species from polar regions, thus is suitable for the identification of polar yeasts.

Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges

Microbial drug discovery programs rely heavily on accessing bacterial diversity from the environment to acquire new specialized metabolite (SM) lead compounds for the therapeutic pipeline. Therefore, knowledge of how commonly culturable bacterial taxa are distributed in nature, in addition to the degree of variation of SM production within those taxa, is critical to informing these front-end discovery efforts and making the overall sample collection and bacterial library creation process more efficient. In the current study, we employed MALDI-TOF mass spectrometry and the bioinformatics pipeline IDBac to analyze diversity within phylotype groupings and SM profiles of hundreds of bacterial isolates from two Eunapius fragilis freshwater sponges, collected 1.5 km apart. We demonstrated that within two sponge samples of the same species, the culturable bacterial populations contained significant overlap in approximate genus-level phylotypes but mostly nonoverlapping populations of isolates when grouped lower than the level of genus. Further, correlations between bacterial phylotype and SM production varied at the species level and below, suggesting SM distribution within bacterial taxa must be analyzed on a case-by-case basis. Our results suggest that two E. fragilis freshwater sponges collected in similar environments can exhibit large culturable diversity on a species-level scale, thus researchers should scrutinize the isolates with analyses that take both phylogeny and SM production into account to optimize the chemical space entering into a downstream bacterial library.

Overcoming Multidrug Resistance of Antibiotics via Nanodelivery Systems

Antibiotic resistance has become a threat to microbial therapies nowadays. The conventional approaches possess several limitations to combat microbial infections. Therefore, to overcome such complications, novel drug delivery systems have gained pharmaceutical scientists’ interest. Significant findings have validated the effectiveness of novel drug delivery systems such as polymeric nanoparticles, liposomes, metallic nanoparticles, dendrimers, and lipid-based nanoparticles against severe microbial infections and combating antimicrobial resistance. This review article comprises the specific mechanism of antibiotic resistance development in bacteria. In addition, the manuscript incorporated the advanced nanotechnological approaches with their mechanisms, including interaction with the bacterial cell wall, inhibition of biofilm formations, activation of innate and adaptive host immune response, generation of reactive oxygen species, and induction of intracellular effect to fight against antibiotic resistance. A section of this article demonstrated the findings related to the development of delivery systems. Lastly, the role of microfluidics in fighting antimicrobial resistance has been discussed. Overall, this review article is an amalgamation of various strategies to study the role of novel approaches and their mechanism to fight against the resistance developed to the antimicrobial therapies.

A breath of fresh air in microbiome science: shallow shotgun metagenomics for a reliable disentangling of microbial ecosystems

Next-generation sequencing technologies allow accomplishing massive DNA sequencing, uncovering the microbial composition of many different ecological niches. However, the various strategies developed to profile microbiomes make it challenging to retrieve a reliable classification that is able to compare metagenomic data of different studies. Many limitations have been overcome thanks to shotgun sequencing, allowing a reliable taxonomic classification of microbial communities at the species level. Since numerous bioinformatic tools and databases have been implemented, the sequencing methodology is only the first of many choices to make for classifying metagenomic data. Here, we discuss the importance of choosing a reliable methodology to achieve consistent information in uncovering microbiomes.

Evaluation of VITEK® 2 and MALDI-TOF/MS automated methodologies in the identification of atypical Listeria spp. isolated from food in different regions of Brazil

Listeria monocytogenes is a pathogen responsible for listeriosis, a foodborne disease with high mortality rates (20-30%). It mainly affects the elderly, pregnant women, and immunocompromised people. Although not pathogenic, the isolation and identification of Listeria innocua are critical since they can indicate L. monocytogenes' presence as they are closely related and widely distributed in the environment and food processing plants. The objective of this study was to evaluate the effectiveness of the automated methods VITEK® 2 and MALDI-TOF/MS in identifying 94 strains of the genus Listeria with atypical identification profile. The resulting identification by Polymerase Chain Reaction (PCR), using specific primers for the most common species of Listeria, was considered the correct identification and presented a total of 31 strains identified as Listeria innocua (LI), 54 as L. monocytogenes (LM), 8 as Listeria welshimeri (LW) and 1 as Listeria grayi (LG). The VITEK® 2 automated system correctly identified, on average, 79% of the LI strains, 16% of the LM strains, and 88.0% of the LW strains. In the analysis by MALDI-TOF/MS, on average, 73% of LM strains were correctly identified, few LW strains were correctly identified, and all LI strains were incorrectly identified. Both VITEK® 2 and MALDI-TOF/MS correctly identified the LG strain in both analyzes. The results demonstrate that automated methodologies could not discriminate atypical strains of the Listeria genus and point to the need for the use of complementary tests, such as PCR and chromogenic media, for the correct identification of these strains.

Phylogenetic diversity and plant growth-promoting activities of rhizobia nodulating fenugreek (Trigonella foenum-graecum Linn.) cultivated in different agroclimatic regions of India

Fenugreek (Trigonella foenum-graecum Linn.), is an extensively cultivated legume crop used as a herb, spice, and traditional medicine in India. The symbiotic efficiency and plant growth-promoting potential of fenugreek rhizobia depend on the symbiont strain and environmental factors. We isolated 176 root-nodulating bacteria from fenugreek cultivated in different agroclimatic regions of India. MALDI-TOF MS-based identification and phylogenetic analyses based on 16S rRNA and five housekeeping genes classified the fenugreek-rhizobia as Ensifer (Sinorhizobium) meliloti. However, the strains represent separate sub-lineages of E. meliloti, distinct from all reported sub-lineages across the globe. We also observed the spatial distribution of fenugreek rhizobia, as the three sub-lineages of E. meliloti recorded during this study were specific to their respective agroclimatic regions. According to the symbiotic gene (nodC and nifH) phylogenies, all three sub-lineages of E. meliloti harboured symbiotic genes similar to symbiovar meliloti; as with the housekeeping genes, these also revealed a spatial distribution for different clades of sv. meliloti. The strains could nodulate fenugreek plants and they showed plant growth-promoting potential. Significant differences were found in the plant growth parameters in response to inoculation with the various strains, suggesting strain-level differences. This study demonstrates that fenugreek rhizobia in India are diverse and spatially distributed in different agro-climatic regions.

Bacteremia caused by Enterobacter asburiae misidentified biochemically as Cronobacter sakazakii and accurately identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a case report

Background

Biochemical analyses of causative bacteria do not always result in clear identification, and new technologies aimed at improving diagnostic accuracy continue to be developed. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is a rapid and accurate technique for bacterial identification. Misidentification of Cronobacter sakazakii is related to clinical and industrial problems. Here, we encountered a case of rare bacteremia in which the causative organism Enterobacter asburiae was biochemically misidentified as C. sakazakii before being correctly identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Case presentation

An 87-year-old Asian man with no diabetes or active disease developed bacteremia and was admitted to our hospital. While the route of infection could not be determined despite various examinations, the clinical course was good following antibiotic therapy. Biochemical analyses identified the causative organism as C. sakazakii, but colonies on the blood agar medium showed a grayish coloration, differing from the yellowish coloration of typical Cronobacter colonies. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was therefore performed, identifying the bacterium as E. asburiae on three independent analyses. This result was confirmed by multilocus sequence analysis using five housekeeping genes.

Conclusions

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry may reduce misidentification of bacteria as C. sakazakii and improve the reporting rate of E. asburiae. This technique should be considered when biochemical bacterial misidentification is suspected.

A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology

The objective of this study was to construct a novel strategy for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants using multiplex PCR-mass spectrometry minisequencing technique (mPCR-MS minisequencing). Using the nucleic acid sequence of a SARS-CoV-2 nonvariant and a synthetic SARS-CoV-2 variant-carrying plasmid, a matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) method based on the single-base mass probe extension of multiplex PCR amplification products was established to detect 9 mutation types in 7 mutated sites (HV6970del, N501Y, K417N, P681H, D614G, E484K, L452R, E484Q, and P681R) in the receptor-binding domain of the spike protein of SARS-CoV-2 variants. Twenty-one respiratory tract pathogens (9 bacteria and 12 respiratory viruses) and nucleic acid samples from non-COVID-19 patients were selected for specific validation. Twenty samples from COVID-19 patients were used to verify the accuracy of this method. The 9 mutation types could be detected simultaneously by triple PCR amplification coupled with MALDI-TOF MS. SARS-CoV-2 and six variants, B.1.1.7 (Alpha), B.1.351 (Beta), B.1.429 (Epsilon), B.1.526 (Iota), P.1 (Gamma) and B.1.617.2 (Delta), could be identified. The detection limit for all 9 sites was 1.5 × 10³ copies. The specificity of this method was 100%, and the accuracy of real-time PCR cycle threshold (C_T) values less than 27 among positive samples was 100%. This method is open and extensible, and can be used in a high-throughput manner, easily allowing the addition of new mutation sites as needed to identify and track new SARS-CoV-2 variants as they emerge. mPCR-MS minisequencing provides a new detection option with practical application value for SARS-CoV-2 and its variant infection.

IMPORTANCE The emergence of SARS-CoV-2 variants is the key factor in the second wave of the COVID-19 pandemic. An all-in-one SARS-CoV-2 variant identification method based on a multiplex PCR-mass spectrometry minisequencing system was developed in this study. Six SARS-CoV-2 variants (Alpha, Beta, Epsilon, Iota, Gamma, and Delta) can be identified simultaneously. This method can not only achieve the multisite simultaneous detection that cannot be realized by PCR coupled with first-generation sequencing technology and quantitative PCR (qPCR) technology but also avoid the shortcomings of time-consuming, high-cost, and high technical requirements of whole-genome sequencing technology. As a simple screening assay for monitoring the emergence and spread of SARS-CoV-2 and variants, mPCR-MS minisequencing is expected to play an important role in the detection and monitoring of SARS-CoV-2 infection as a supplementary technology.

Prolonged carriage of ESBL-producing enterobacterales and potential cross-transmission among residents in geriatric long-term care facilities

Previous studies indicated residents in geriatric long-term care facilities (LTCFs) had much higher prevalence of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) carriage than the general population. Most ESBL-E carriers are asymptomatic. The study tested the hypothesis that residents with ESBL-E carriage may accumulate inside geriatric LTCFs through potential cross-transmission after exposure to residents with prolonged ESBL-E carriage. 260 residents from four Japanese LTCFs underwent ESBL-E testing of fecal specimens and were divided into two cohorts: Cohort 1,75 patients with ≥ 2 months residence at study onset; Cohort 2, 185 patients with < 2 months residence at study onset or new admission during the study period. Three analyses were performed: (1) ESBL-E carriage statuses in Cohort 1 and Cohort 2; (2) changes in ESBL-E carriage statuses 3-12 months after the first testing and ≥ 12 months after the second testing; and (3) lengths of positive ESBL-E carriage statuses. Compared with the residents in Cohort 1, a significantly larger proportion of residents in Cohort 2 were positive for ESBL-E carriage (28.0% in Cohort 1 vs 40.0% in Cohort 2). In the subsequent testing results, 18.3% of residents who were negative in the first testing showed positive conversion to ESBL-E carriage in the second testing, while no patients who were negative in the second testing showed positive conversion in the third testing. The maximum length of ESBL-E carriage was 17 months. The findings indicated that some residents acquired ESBL-E through potential cross-transmission inside the LTCFs after short-term residence. However, no residents showed positive conversion after long-term residence, which indicates that residents with ESBL-E carriage may not accumulate inside LTCFs. Practical infection control and prevention measures could improve the ESBL-E prevalence in geriatric LTCFs.

Historical, current, and emerging tools for identification and serotyping of Shigella

The Shigella genus includes serious foodborne disease etiologic agents, with 4 species and 54 serotypes. Identification at species and serotype levels is a crucial task in microbiological laboratories. Nevertheless, the genetic similarity between Shigella spp. and Escherichia coli challenges the correct identification and serotyping of Shigella spp., with subsequent negative repercussions on surveillance, epidemiological investigations, and selection of appropriate treatments. For this purpose, multiple techniques have been developed historically ranging from phenotype-based methods and single or multilocus molecular techniques to whole-genome sequencing (WGS). To facilitate the selection of the most relevant method, we herein provide a global overview of historical and emerging identification and serotyping techniques with a particular focus on the WGS-based approaches. This review highlights the excellent discriminatory power of WGS to more accurately elucidate the epidemiology of Shigella spp., disclose novel promising genomic targets for surveillance methods, and validate previous well-established methods.

Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database

According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDI-TOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water.

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.

Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor

A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA-DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).

Lipidomic Profiling of Algae with Microarray MALDI-MS toward Ecotoxicological Monitoring of Herbicide Exposure

Misuse of agrochemicals has a long-lasting negative impact on aquatic systems. Mismanagement of herbicides in agri-food sectors is often linked to a simultaneous decline in the health of downstream waterways. However, monitoring the herbicide levels in these areas is a laborious task, and modern analytical approaches, such as solid-phase extraction-liquid chromatography-mass spectrometry (SPE-LC-MS) and enzyme-linked immunosorbent assay, are low-throughput and require significant sample preparation. We report here the use of microchip technology in combination with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) for the assessment of the ecotoxicological effect of agrochemicals on aquatic species at the single-cell level. This approach quantifies the fluctuations in lipid content in sentinel organisms and targets the microalga, Chlamydomonas reinhardtii (C. reinhardtii), as the model system. Specifically, we investigated the cytotoxicity of three herbicides (atrazine, clomazone, and norflurazon) on C. reinhardtii by analyzing the lipid component variation upon assorted herbicide exposure. Lipidomic profiling reveals a significantly altered lipid content at >EC₅₀ in atrazine-exposed cells. The response for norflurazon showed similar trends but diminished in magnitude, while the result for clomazone was near muted. At lower herbicide concentrations, digalactosyldiacylglycerols showed a rapid decrease in abundance, while several other lipids displayed a moderate increase. The microchip-based MALDI technique demonstrates the ability to achieve lipidomic profiling of aquatic species exposed to different stressors, proving effective for high-throughput screening and single-cell analysis in ecotoxicity studies.

An exploratory MALDI-TOF MS library based on SARAMIS superspectra for rapid identification of Aspergillus section Nigri

Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is a broadly used technique for identification and typing of microorganisms. However, its application to filamentous fungi has been delayed. The objective of this study was to establish a data library for rapid identification of the genus Aspergillus sect. Nigri using MALDI-TOF MS. With respect to sample preparation, we compared the utility of using mature mycelia, including conidial structures, to accumulate a wider range of proteins versus the conventional method relying on young hyphae. Mass spectral datasets obtained for 61 strains of 17 species were subjected to cluster analysis and compared with a phylogenetic tree based on calmodulin gene sequences. Specific and frequent mass spectral peaks corresponding to each phylogenetic group were selected (superspectra for the SARAMIS system). Fifteen superspectra representing nine species were ultimately created. The percentage of correct identification for 217 spectra was improved from 36.41% to 86.64% using the revised library. Additionally, 2.76% of the spectra were assigned to candidates that comprised several related species, including the correct species.

MALDI-TOF MS as a method for rapid identification of Phytophthora de Bary, 1876

The number of described species of the oomycete genus Phytophthora is growing rapidly, highlighting the need for low-cost, rapid tools for species identification. Here, a collection of 24 Phytophthora species (42 samples) from natural as well as anthropogenic habitats were genetically identified using the internal transcribed spacer (ITS) and cytochrome c oxidase subunit I (COI) regions. Because genetic identification is time consuming, we have created a complementary method based on by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Both methods were compared and hypothesis that the MALDI-TOF MS method can be a fast and reliable method for the identification of oomycetes was confirmed. Over 3500 mass spectra were acquired, manually reviewed for quality control, and consolidated into a single reference library using the Bruker MALDI Biotyper platform. Finally, a database containing 144 main spectra (MSPs) was created and published in repository. The method presented in this study will facilitate the use of MALDI-TOF MS as a complement to existing approaches for fast, reliable identification of Phytophthora isolates.

Virgibacillus doumboii sp. nov., a halophilic bacterium isolated from the stool of a healthy child in Mali

A moderately halophilic and strictly aerobic bacterium was isolated from a human stool as part of a study on the diagnosis of childhood malnutrition in Mali. Strain Marseille-Q1616T is a Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative bacterium. It has a genome size of 3.91 Mbp with 39.79% G+C content, which contains 3954 protein-coding genes including genes encoding phosphomycin resistance and Listeria monocytogenes, 16 rRNA genes and 64 tRNA genes. Strain Marseille-Q1616T exhibited a 96.3% 16S rRNA gene sequence similarity and shared an OrthoANI value of 70.64% (the highest observed) with Virgibacillus kekensis, the phylogenetically closest validly published species. Based on phenotypic and phylogenetic evidence and genomic average nucleotide identity values, we suggest the creation of a new species within the Virgibacillus genus, named Virgibacillus doumboii sp. nov., type strain Marseille-Q1616T (= CSURQ1616).

Human tear fluid analysis for clinical applications: progress and prospects

Introduction: Human blood and saliva are increasingly under investigation for the detection of biomarkers for early diagnosis of non-communicable (e.g.cancers) and communicable diseases like COVID-19. Exploring the potential application of human tears, an easily accessible body fluid, for the diagnosis of various diseases is the need of the hour.Areas covered: This review deals with a comprehensive account of applications of tear analysis using different techniques, their comparison and overall progress achieved till now. The techniques used for tear fluid analysis are HPLC/UPLC/SDS-PAGE, CE, etc., together with ELISA, Mass Spectrometry, etc. But, with advances in instrumentation and data processing methods, it has become easy to couple the various separation methods with highly sensitive optical techniques for the analysis of body fluids.Expert opinion: Tear analysis can provide valuable information about the health condition of the eyes since it contains several molecular constituents, and their relative concentrations may alter under abnormal conditions. Tear analysis has the advantage that it is totally non-invasive. This study recommends tear fluid as a reliable clinical sample to be probed by highly sensitive optical techniques to diagnose different health conditions, with special emphasis on eye diseases.

Cholesterol Reduction and Vitamin B12 Production Study on Enterococcus faecium and Lactobacillus pentosus Isolated from Yoghurt

The present study was aimed to test cholesterol reduction and vitamin B12 production abilities of the isolated lactic acid bacteria (LAB). Three LAB isolates, namely, Enterococcus faecium (EF), Enterococcus faecium (Chole1), and Lactobacillus pentosus (7MP), having probiotic potential, were isolated from yoghurt. These isolates were screened for bile salt hydrolase (BSH) activity, cholesterol reduction property in MRS broth, and the production of vitamin B12. The present study revealed that the isolate 7MP possesses the highest potential of (48%) cholesterol reduction compared to the other isolates. The isolates EF and Chole1 produced a good amount of (1 ng/mL) vitamin B12. These isolates were identified by 16S rRNA gene sequencing and confirmed by MALD_TOF analysis. Thus, the use of these LAB isolates for yoghurt-making can offer the value addition of lowering cholesterol and vitamin B12 fortification in fermented food.

Biodegradation of azo dye-containing wastewater by activated sludge: a critical review

The effluent from the textile industry is a complex mixture of recalcitrant molecules that can harm the environment and human health. Biological treatments are usually applied for this wastewater, particularly activated sludge, due to its high efficiency, and low implementation and operation costs. However, the activated sludge microbiome is rarely well-known. In general, activated sludges are composed of Acidobacteria, Bacillus, Clostridium, Pseudomonas, Proteobacteria, and Streptococcus, in which Bacillus and Pseudomonas are highlighted for bacterial dye degradation. Consequently, the process is not carried out under optimum conditions (treatment yield). Therefore, this review aims to contextualize the potential environmental impacts of azo dye-containing wastewater from the textile industry, including toxicity, activated sludge microbiome identification, in particular using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a novel, rapid and accurate strategy for the identification of activated sludge microbiome (potential to enhance treatment yield).

A multisite SNP genotyping and macrolide susceptibility gene method for Mycoplasma pneumoniae based on MALDI-TOF MS

In this study, a multisite SNP genotyping and macrolide (ML) susceptibility gene test method for Mycoplasma pneumoniae (M. pneumoniae) was developed based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The detection limit of this method for nucleic acids was 10² -10³ copies/reaction. Six SNP site-based genotyping and 3 ML susceptibility sites could be detected simultaneously based on multiplex PCR and mass probe. Using the method constructed in this study, 141 Chinese clinical isolates were divided into 8 SNP types. All the SNP test results for the ML susceptibility gene were in line with those of the 23S rRNA sequencing results. With this method, the multisite SNP genotyping and ML susceptibility determination of M. pneumoniae can be completed simultaneously in one test, which greatly reduces the workload and cost, improves the genotyping ability of M. pneumoniae and deserves clinical application.

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An all-in-one genotyping and macrolide resistance testing method for M. pneumoniae

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Multisite SNP detection technology was used for genotyping and resistance testing

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The cost of M. pneumoniae genotyping and macrolide resistance detection was reduced

Network Analysis Based on Unique Spectral Features Enables an Efficient Selection of Genomically Diverse Operational Isolation Units

Culturomics-based bacterial diversity studies benefit from the implementation of MALDI-TOF MS to remove genomically redundant isolates from isolate collections. We previously introduced SPeDE, a novel tool designed to dereplicate spectral datasets at an infraspecific level into operational isolation units (OIUs) based on unique spectral features. However, biological and technical variation may result in methodology-induced differences in MALDI-TOF mass spectra and hence provoke the detection of genomically redundant OIUs. In the present study, we used three datasets to analyze to which extent hierarchical clustering and network analysis allowed to eliminate redundant OIUs obtained through biological and technical sample variation and to describe the diversity within a set of spectra obtained from 134 unknown soil isolates. Overall, network analysis based on unique spectral features in MALDI-TOF mass spectra enabled a superior selection of genomically diverse OIUs compared to hierarchical clustering analysis and provided a better understanding of the inter-OIU relationships.

Novel Strategy for Rapidly and Safely Distinguishing Bacillus anthracis and Bacillus cereus by Use of Peptide Mass Fingerprints Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

The objective of this study was to construct a rapid, high-throughput, and biosafety-compatible screening method for Bacillus anthracis and Bacillus cereus based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS coupled to ClinProTools was used to discover MALDI-TOF MS biomarker peaks and generate a classification model based on a genetic algorithm (GA) to differentiate between different Bacillus anthracis and Bacillus cereus isolates. Thirty Bacillus anthracis and 19 Bacillus cereus strains were used to construct and analyze the model, and 40 Bacillus strains were used for validation. For the GA screening model, the cross-validation values, which reflect the ability of the model to handle variability among the test spectra, and the recognition capability values, which reflect the model's ability to correctly identify its component spectra, were all 100%. This model contained 10 biomarker peaks (m/z 3,339.9, 3,396.3, 3,682.4, 5,476.7, 6,610.6, 6,680.1, 7,365.3, 7,792.4, 9,475.8, and 10,934.1) used to correctly identify 28 Bacillus anthracis and 12 Bacillus cereus isolates from 40 Bacillus isolates, with a sensitivity and specificity of 100%. With the obvious advantages of being rapid, highly accurate, and highly sensitive and having a low cost and high throughput, MALDI-TOF MS ClinProTools is a powerful and reliable tool for screening Bacillus anthracis and Bacillus cereus strains.

Pseudomonas entomophila PE3 and its exopolysaccharides as biostimulants for enhancing growth, yield and tolerance responses of sunflower under saline conditions

Evaluation of plant growth promoting bacteria and the associated metabolites under saline conditions can be a potential eco-friendly remediation and productivity enhancement strategy. Salt-tolerant Pseudomonas entomophila PE3 was isolated from saline soil and screened for plant growth promoting (PGP) traits. The isolate produced indole acetic acid (IAA), gibberellic acid (GA), exopolysaccharides (EPS) and siderophore along with the potential to solubilize potassium (K), zinc (Zn) and phosphorus (P). Maximum stimulation of PGP attributes was recorded at 2% NaCl concentration. To determine the role of EPS, their composition was analyzed (at different salt concentrations) and comparison was done to determine the changes upon exposure to salinity. EPS was found to be rich in carbohydrates, proteins and phenolic compounds. The extracted EPS were also found to possess salt-tolerance properties including antioxidant, hydroxyl scavenging activity, reducing power, emulsification and flocculation potential, and Na⁺ accumulation ability. Interestingly, the salt tolerance properties of EPS were enhanced upon exposure to salinity (2% NaCl). Finally, EPS based bioformulation of isolate PE3 was checked through field assay in saline soil. With promising results on growth promotion and improved salinity tolerance attributes of inoculated sunflower plants, the bioformulation of PE3 amended with EPS can be a breakthrough for remediation of saline-agroecosystems.

Rhizobium indicum sp. nov., isolated from root nodules of pea (Pisum sativum) cultivated in the Indian trans-Himalayas

Three strains of rhizobia isolated from effective root nodules of pea (Pisum sativum L.) collected from the Indian trans-Himalayas were characterized using 16S rRNA, atpD and recA genes. Phylogeny of the 16S rRNA genes revealed that the newly isolated strains were members of the genus Rhizobium with ≥99.9% sequence similarity to the members within the "Rhizobium leguminosarum" group. Phylogenetic analyses based on the concatenated sequences of atpD and recA gene, and 92 core genes extracted from the genome sequences indicated that strains JKLM 12A2T and JKLM 13E are grouped as a separate clade closely related to R. laguerreae FB206T. In contrast, the strain JKLM 19E was placed with "R. hidalgonense" FH14T. Whole-genome average nucleotide identity (ANI) values were 97.6% within strains JKLM 12A2T and JKLM 13E, and less than 94% with closely related species. The digital DNA-DNA hybridization (dDDH) values were 81.45 within the two strains and less than 54.8% to closely related species. The major cellular fatty acids were C18:1w7c in summed feature 8, C14:0 3OH/C16:1 iso I in summed feature 2, and C18:0. The DNA G+C content of JKLM 12A2T and JKLM 13E was 60.8mol%. The data on genomic, chemotaxonomic, and phenotypic characteristics indicates that the strains JKLM 12A2T and JKLM 13E represent a novel species, Rhizobium indicum sp. nov. The type strain is JKLM 12A2T (= MCC 3961T=KACC 21380T=JCM 33658T). However, the strain JKLM 19E represents a member of "R. hidalgonense" and the symbiovar viciae.

Mechanisms of halotolerant plant growth promoting Alcaligenes sp. involved in salt tolerance and enhancement of the growth of rice under salinity stress

In the present study halotolerant bacteria were isolated from saline soil (EC ~ 11.9). Based on salt tolerance and plant growth promoting characteristics isolate AF7 was selected for further study. It was identified as Alcaligenes sp. on the basis of protein profiling and 16S rRNA sequence homology. Interestingly, AF7 showed diverse PGP characters at different salinity levels. While phosphate solubilization activity was expressed up to 300 mM NaCl, siderophore production was shown up to 700 mM, zinc solubilization up to 1000 mM and indole acetic acid (IAA), gibberellic acid (GA) and exopolysaccharides (EPS) production were depicted till 1400 mM. Correlative and regression analysis suggested positive relation between IAA, GA, EPS, siderophore production and zinc solubilization capability of AF7 and salinity up to 300 mM NaCl. EPS was found to be the most significant response and there was 263% increment in presence of 300 mM NaCl when compared to non-saline control. Analysis also showed that while growth promoting attributes were significant up to a threshold salinity level, further increasing the stress deviates the mechanism towards survival involving proline, antioxidant and hydroxyl scavenging activities. Combination of halotolerant AF7 and EPS showed more than twofold increase in the vegetative growth parameters of rice at ~ 170 mM NaCl (EC 9 dS/m). The study shows the mechanisms/metabolites of the plant growth promoting bacterium (PGPB) AF7 prominently involved during the salinity stress. Study also proves that novel bioformulations can be developed by integrative use of EPS and salt tolerant-PGPB which can be effective for saline soils.

MALDI-TOF-MS and 16S rRNA characterization of lead tolerant metallophile bacteria isolated from saffron soils of Kashmir for their sequestration potential

Toxic metal contamination in soils due industrialization is nowadays a concern to the scientists worldwide. The current study deals with the evaluation of response and tolerance by isolated metallophilic bacteria in different lead concentrations (100 ppm to 1000 ppm). By taking optical densities of the isolates, the minimum inhibitory concentration (MIC) of Pb²⁺ were determined.16S rRNA and MALDI-TOF MS were used for the identification of the bacteria. Total of 37 isolates were observed, among them 04 (Staphylococcus equorum, Staphylococcus warneri, Bacillus safensis and Bacillus thuringiensis), isolated were detected having efficacy of Pb²⁺tolerance and sequestration at varying MIC. Furthermore, B. thuringiensis was observed to have highest (900 ppm) tolerance for lead and lowest (500 ppm) for Staphylococcus warneri. Moreover, the highest (65.3%) sequestration potential has been observed for B. thuringiensis and least (52.8%) for S. warneri. The tolerance and sequestration potential properties of these isolated species can be utilised to exterminate heavy metals and reduce their toxicity from the contaminated environment.