Pathogen detection via inductively coupled plasma mass spectrometry analysis with nanoparticles

Infections caused by viruses and bacteria pose a significant threat to global public health, emphasizing the critical importance of timely and precise detection methods. Inductively coupled plasma mass spectrometry (ICP-MS), a contemporary approach for pathogen detection, offers distinct advantages such as high sensitivity, a wide linear range, and multi-index capabilities. This review elucidates the underexplored application of ICP-MS in conjunction with functional nanoparticles (NPs) for the identification of viruses and bacteria. The review commences with an elucidation of the underlying principles, procedures, target pathogens, and NP requirements for this innovative approach. Subsequently, a thorough analysis of the advantages and limitations associated with these techniques is provided. Furthermore, the review delves into a comprehensive examination of the challenges encountered when utilizing NPs and ICP-MS for pathogen detection, culminating in a forward-looking assessment of the potential pathways for advancement in this domain. Thus, this review contributes novel perspectives to the field of pathogen detection in biomedicine by showcasing the promising synergy of ICP-MS and NPs.

A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua

Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms.

Single-cell microliter-droplet screening system (MISS Cell): An integrated platform for automated high-throughput microbial monoclonal cultivation and picking

Solid plates have been used for microbial monoclonal isolation, cultivation, and colony picking since 1881. However, the process is labor- and resource-intensive for high-throughput requirements. Currently, several instruments have been integrated for automated and high-throughput picking, but complicated and expensive. To address these issues, we report a novel integrated platform, the single-cell microliter-droplet screening system (MISS Cell), for automated, high-throughput microbial monoclonal colony cultivation and picking. We verified the monoclonality of droplet cultures in the MISS Cell and characterized culture performance. Compared with solid plates, the MISS Cell generated a larger number of monoclonal colonies with higher initial growth rates using fewer resources. Finally, we established a workflow for automated high-throughput screening of Corynebacterium glutamicum using the MISS Cell and identified high glutamate-producing strains. The MISS Cell can serve as a universal platform to efficiently produce monoclonal colonies in high-throughput applications, overcoming the limitations of solid plates to promote rapid development in biotechnology.

A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non-pneumophila isolates from water by FT-IR spectroscopy

This study developed and validated a method, based on the coupling of Fourier-transform infrared spectroscopy (FT-IR) and machine learning, for the automated serotyping of Legionella pneumophila serogroup 1, Legionella pneumophila serogroups 2-15 as well as their successful discrimination from Legionella non-pneumophila. As Legionella presents significant intra- and inter-species heterogeneities, careful data validation strategies were applied to minimize late-stage performance variations of the method across a large microbial population. A total of 244 isolates were analyzed. In details, the method was validated with a multi-centric approach with isolates from Italian thermal and drinking water (n = 82) as well as with samples from German, Italian, French, and British collections (n = 162). Specifically, robustness of the method was verified over the time-span of 1 year with multiple operators and two different FT-IR instruments located in Italy and Germany. Moreover, different production procedures for the solid culture medium (in-house or commercial) and different culture conditions (with and without 2.5% CO₂) were tested. The method achieved an overall accuracy of 100, 98.5, and 93.9% on the Italian test set of Legionella, an independent batch of Legionella from multiple European culture collections, and an extra set of rare Legionella non-pneumophila, respectively.

Identifying Clinically Relevant Bacteria Directly from Culture and Clinical Samples with a Handheld Mass Spectrometry Probe

BACKGROUND

Rapid identification of bacteria is critical to prevent antimicrobial resistance and ensure positive patient outcomes. We have developed the MasSpec Pen, a handheld mass spectrometry-based device that enables rapid analysis of biological samples. Here, we evaluated the MasSpec Pen for identification of bacteria from culture and clinical samples.

METHODS

A total of 247 molecular profiles were obtained from 43 well-characterized strains of 8 bacteria species that are clinically relevant to osteoarticular infections, including Staphylococcus aureus, Group A and B Streptococcus, and Kingella kingae, using the MasSpec Pen coupled to a high-resolution mass spectrometer. The molecular profiles were used to generate statistical classifiers based on metabolites that were predictive of Gram stain category, genus, and species. Then, we directly analyzed samples from 4 patients, including surgical specimens and clinical isolates, and used the classifiers to predict the etiologic agent.

RESULTS

High accuracies were achieved for all levels of classification with a mean accuracy of 93.3% considering training and validation sets. Several biomolecules were detected at varied abundances between classes, many of which were selected as predictive features in the classifiers including glycerophospholipids and quorum-sensing molecules. The classifiers also enabled correct identification of Gram stain type and genus of the etiologic agent from 3 surgical specimens and all classification levels for clinical specimen isolates.

CONCLUSIONS

The MasSpec Pen enables identification of several bacteria at different taxonomic levels in seconds from cultured samples and has potential for culture-independent identification of bacteria directly from clinical samples based on the detection of metabolic species.

Evaluating carbon-electrode dielectrophoresis under the ASSURED criteria

Extreme point-of-care refers to medical testing in unfavorable conditions characterized by a lack of primary resources or infrastructure. As witnessed in the recent past, considerable interest in developing devices and technologies exists for extreme point-of-care applications, for which the World Health Organization has introduced a set of encouraging and regulating guidelines. These are referred to as the ASSURED criteria, an acronym for Affordable (A), Sensitive (S), Specific (S), User friendly (U), Rapid and Robust (R), Equipment-free (E), and Delivered (D). However, the current extreme point of care devices may require an intermediate sample preparation step for performing complex biomedical analysis, including the diagnosis of rare-cell diseases and early-stage detection of sepsis. This article assesses the potential of carbon-electrode dielectrophoresis (CarbonDEP) for sample preparation competent in extreme point-of-care, following the ASSURED criteria. We first discuss the theory and utility of dielectrophoresis (DEP) and the advantages of using carbon microelectrodes for this purpose. We then critically review the literature relevant to the use of CarbonDEP for bioparticle manipulation under the scope of the ASSURED criteria. Lastly, we offer a perspective on the roadmap needed to strengthen the use of CarbonDEP in extreme point-of-care applications.

Application of MALDI-TOF MS for identification of environmental bacteria: A review

Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.

Bacterial classification and antibiotic susceptibility testing on an integrated microfluidic platform

With the prevalence of bacterial infections and increasing levels of antibiotic resistance comes the need for rapid and accurate methods for bacterial classification (BC) and antibiotic susceptibility testing (AST). Here we demonstrate the use of the fluid handling technique digital microfluidics (DMF) for automated and simultaneous BC and AST using growth metabolic markers. Custom instrumentation was developed for this application including an integrated heating module and a machine-learning-enabled low-cost colour camera for real-time absorbance and fluorescent sample monitoring on multipurpose devices. Antibiotic dilutions along with sample handling, mixing and incubation at 37 °C were all pre-programmed and processed automatically. By monitoring the metabolism of resazurin, resorufin beta-D-glucuronide and resorufin beta-D-galactopyranoside to resorufin, BC and AST were achieved in under 18 h. AST was validated in two uropathogenic E. coli strains with antibiotics ciprofloxacin and nitrofurantoin. BC was performed independently and simultaneously with ciprofloxacin AST for E. coli, K. pneumoniae, P. mirabilis and S. aureus. Finally, a proof-of-concept multiplexed system for breakpoint testing of two antibiotics, as well as E. coli and coliform classification was investigated with a multidrug-resistant E. coli strain. All bacteria were correctly identified, while AST and breakpoint test results were in essential and category agreement with reference methods. These results show the versatility and accuracy of this all-in-one microfluidic system for analysis of bacterial growth and phenotype.

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.

First preliminary study on identification of bacterial fish pathogens with Raman spectroscopy

Accurate and rapid determination of bacterial disease agents of fish is an important step for sustainable and efficient aquaculture production. In general, biochemical and molecular methods are used for pathogen detection but they are usually time-consuming and required qualified personnel. Recently spectroscopic methods are preferred in clinical and food microbiology and declared as a promising alternative method for pathogens diagnosis with many advantages. In this study, the significant spectra of three important bacterial fish pathogens (Lactococcus garvieae, Vibrio anguillarum and Yersinia ruckeri) were determined by Raman spectroscopy. The first data of the pathogens were obtained and the distinctive differences in polysaccharides, nucleic acids, fatty acids and amino acids were identified. This preliminary study aimed to be pioneer for further studies in aquaculture and veterinary microbiology toward developing an alternative method for routine identification.

Assessing direct analysis in real-time mass spectrometry for the identification and serotyping of Legionella pneumophila

AIMS

The efficacy of ambient mass spectrometry to identify and serotype Legionella pneumophila was assessed. To this aim, isolated waterborne colonies were submitted to a rapid extraction method and analysed by direct analysis in real-time mass spectrometry (DART-HRMS).

METHODS AND RESULTS

The DART-HRMS profiles, coupled with partial least squares discriminant analysis (PLS-DA), were first evaluated for their ability to differentiate Legionella spp. from other bacteria. The resultant classification model achieved an accuracy of 98.1% on validation. Capitalising on these encouraging results, DART-HRMS profiling was explored as an alternative approach for the identification of L. pneumophila sg. 1, L. pneumophila sg. 2-15 and L. non-pneumophila; therefore, a different PLS-DA classifier was built. When tested on a validation set, this second classifier reached an overall accuracy of 95.93%. It identified the harmful L. pneumophila sg. 1 with an impressive specificity (100%) and slightly lower sensitivity (91.7%), and similar performances were reached in the classification of L. pneumophila sg. 2-15 and L. non-pneumophila.

CONCLUSIONS

The results of this study show the DART-HMRS method has good accuracy, and it is an effective method for Legionella serogroup profiling.

SIGNIFICANCE AND IMPACT OF THE STUDY

These preliminary findings could open a new avenue for the rapid identification and quick epidemiologic tracing of L. pneumophila, with a consequent improvement to risk assessment.

Rapid and sensitive detection of Staphylococcus aureus and Klebsiella pneumonia based on bacitracin-modified Fe3O4@PDA magnetic beads combined with matrix-assisted laser desorption ionization-time of flight mass spectrometry

The highly effective detection of pathogens in complex biological samples is an attractive and critical topic of study. Bacitracin is a novel broad-spectrum antimicrobial peptide to enrich bacteria via interactions with the membrane surface of the different bacterial cells. In this study, for the first time, bacitracin was immobilized on the surface of Fe3O4@PDA magnetic nanoparticles for the enrichment of Staphylococcus aureus (G+) and Klebsiella pneumoniae (G-). Combined with matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a rapid and sensitive detection method for these two bacteria was developed. In this method, the detectable concentration of bacteria was decreased by 2-3 orders of magnitude in unenriched samples. The enrichment and identification can be completed in one hour. All these results demonstrated that the bacitracin-functionalized magnetic composite has potential for use in the large-scale enrichment and isolation of target pathogens from complex biological samples, opening a new avenue for the rapid and sensitive detection of pathogens.

Antimicrobial Resistance Gene Detection Methods for Bacteria in Animal-Based Foods: A Brief Review of Highlights and Advantages

Antimicrobial resistance is a major public health problem and is mainly due to the indiscriminate use of antimicrobials in human and veterinary medicine. The consumption of animal-based foods can contribute to the transfer of these genes between animal and human bacteria. Resistant and multi-resistant bacteria such as Salmonella spp. and Campylobacter spp. have been detected both in animal-based foods and in production environments such as farms, industries and slaughterhouses. This review aims to compile the techniques for detecting antimicrobial resistance using traditional and molecular methods, highlighting their advantages and disadvantages as well as the effectiveness and confidence of their results.

A Comprehensive Overview of Antibiotic Selection and the Factors Affecting It

In order to prescribe an antibiotic, a physician must go through a series of decision-making processes that involve both the drug and the host. In this review article, we outline exactly what those decision-making processes are and some of their limitations. Before a medication can be prescribed, a physician has to determine if the antibiotic works against the host pathogen. To do this, basic science techniques are employed including phenotypic methods such as broth dilution methods, Kirby-Bauer susceptibility testing, Epsilometer test (E-test), and genotypic methods such as the new and upcoming automated tests. After determining if a drug has potential to work, the physician must consider the drug’s mechanism of action in order to determine a dosing regimen. Some groups of drugs should be administered at high concentrations infrequently, others should be given more frequently in smaller doses, and others lie somewhere between this spectrum. Finally, external factors such as the patient's age, especially for pediatrics and geriatrics patients, need to be considered, as these groups have the highest health care burden but are among the most vulnerable when it comes to the side effects of drugs.

Phage-based assay for rapid detection of bacterial pathogens in blood by Raman spectroscopy

Sepsis is a systemic inflammatory response ensuing from presence and persistence of microorganisms in the bloodstream. The possibility to identify them at low concentrations may improve the problem of human health and therapeutic outcomes. So, sensitive and rapid diagnostic systems are essential to evaluate bacterial infections during the time, also reducing the cost. In this study, from random M13 phage display libraries, we selected phage clones that specifically bind surface of Staphyloccocus aureus, Pseudomonas aeruginosa and Escherichia coli. Then, commercial magnetic beads were functionalized with phage clones through covalent bond and used as capture and concentrating of pathogens from blood. We found that phage-magnetic beads complex represents a network which enables a cheap, high sensitive and specific detection of the bacteria involved in sepsis by micro-Raman spectroscopy. The enter process required 6 h and has the limit of detection of 10 Colony Forming Units on 7 ml of blood (CFU/7 ml).

Rapid identification of bovine mastitis pathogens by MALDI-TOF Mass Spectrometry

ABSTRACT: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been shown to be an alternative method for identification of bacteria via their protein profile spectra, being able to identify bacteria at the genus, species and even at subspecies level. With the aim of large-scale identification of pathogens causing mastitis by this platform, a total of 305 isolates of bacteria identified from cows with subclinical mastitis were analyzed by conventional microbiological culture (MC) as well as by MALDI-TOF MS coupled with Biotyper data processing. Approximately 89% of the identifications performed by MALDI-TOF MS were consistent with results obtained by MC. From the remaining isolates (11%), 6.3% of isolates were classified as misidentified (discordance for both genus and species level), and 4.7% showed identification agreement at the genus level but not at the species level, being classified as unidentified at species level. The disagreement results were mostly associated with identification of Streptococcus and Enterococcus species probably due to the narrow phenotypic similarity between these two genera. These disagreement results suggest that biochemical assays might be prone to identification errors and, MALDI-TOF MS therefore may be an alternative to overcome incorrect species-specific identification. Standard microbiological methods for bovine mastitis diagnosis are time consuming, laborious and prone to errors for some bacteria genera. In our study, we showed that MALDI-TOF MS coupled with Biotyper may be an alternative method for large-scale identification of bacteria isolated from milk samples compared to classical microbiological routine protocols.

Lipid and protein fingerprinting for Fusarium oxysporum f. sp. cubense strain-level classification

Banana is one of the most popular fruits in the world but has been substantially impaired by Panama disease in the last years. Fusarium oxysporum f. sp. cubense (Foc) is the causal agent and colonizes banana cultivars from many subgroups with different aggressiveness levels, often leading to plant death while compromising new crops in infested areas. This study has evaluated the ability of MALDI-MS protein and lipid fingerprinting to provide intraspecies classification of Foc isolates and to screen biomolecules related to host-pathogen relationship. The MS data, when inspected via partial least square discriminant analysis (PLS-DA), distinguished the isolates by aggressiveness as well as by specific location and host. Although both lipids and proteins show discriminating tendencies, these differences were more clearly perceived via the protein profiles. Considering that Cavendish cultivar is the more resistant option to endure Foc presence in the field, the lipids and proteins related to this subgroup might have an important role in pathogen adaptation. This study reports a new application of MALDI-MS for the analysis of a banana pathogen with intraspecies classification ability. Graphical abstract MALDI-MS classified Foc isolates by aggressiveness level on banana revealing the additional influence of location and host cultivar on the expression of lipids and proteins.

Molecular epidemiology of Streptococcus agalactiae isolated from mastitis in Brazilian dairy herds

Streptococcus agalactiae is one of the most common pathogens leading to mastitis in dairy herds worldwide; consequently, the pathogen causes major economic losses for affected farmers. In this study, multilocus sequence typing (MLST), genotypic capsular typing by multiplex polymerase chain reaction (PCR), and virulence gene detection were performed to address the molecular epidemiology of 59 bovine (mastitis) S. agalactiae isolates from 36 dairy farms located in the largest milk-producing mesoregions in Brazil (Minas Gerais, São Paulo, Paraná, and Pernambuco). We screened for the virulence genes bac, bca, bibA, cfb, hylB, fbsA, fbsB, PI-1, PI-2a, and PI-2b, which are associated with adhesion, invasion, tissue damage, and/or immune evasion. Furthermore, five capsular types were identified (Ia, Ib, II, III, and IV), and a few isolates were classified as non-typeable (NT). MLST revealed the following eight sequence types (STs): ST-61, ST-67, ST-103, ST-146, ST-226, ST-314, and ST-570, which were clustered in five clonal complexes (CC64, CC67, CC103, CC17, and CC314), and one singleton, ST-91. Among the virulence genes screened in this study, PI-2b, fbsB, cfb, and hylB appear to be the most important during mastitis development in cattle. Collectively, these results establish the molecular epidemiology of S. agalactiae isolated from cows in Brazilian herds. We believe that the data presented here provide a foundation for future research aimed at developing and implementing new preventative and treatment options for mastitis caused by S. agalactiae.

Direct, label-free, selective, and sensitive microbial detection using a bacteriorhodopsin-based photoelectric immunosensor

A photoelectric immunosensor using purple membranes (PM) as the transducer, which contains photoactive bacteriorhodopsin, is here first demonstrated for direct and label-free microbial detection. Biotinylated polyclonal antibodies against Escherichia coli were immobilized on a PM-coated electrode through further surface biotinylation and bridging avidin or NeutrAvidin. The photocurrent generated by the antibody-coated sensor was reduced after incubation with E. coli K-12 cultures, with the reduction level increased with the culture populations. The immunosensor prepared via NeutrAvidin exhibited much better selectivity than the one prepared via avidin, recognizing almost none of the tested Gram-positive bacteria. Cultures with populations ranging from 1 to 10⁷CFU/10mL were detected in a single step without any preprocessing. Both AFM and Raman analysis confirmed the layer-by-layer fabrication of the antibody-coated substrates as well as the binding of microorganisms. By investigating the effect of illumination orientation and simulating the photocurrent responses with an equivalent circuit model containing a chemical capacitance, we suggest that the photocurrent reduction was primarily caused by the light-shielding effect of the captured bacteria. Using the current fabrication technique, versatile bacteriorhodopsin-based photoelectric immunosensors can be readily prepared to detect a wide variety of biological cells.

Fabrication challenges and perspectives on the use of carbon-electrode dielectrophoresis in sample preparation

The focus of this review is to assess the current status of three-dimensional (3D) carbon-electrode dielectrophoresis (carbonDEP) and identify the challenges currently preventing it from its use in high-throughput applications such as sample preparation for diagnostics. The use of 3D electrodes over more traditional planar ones is emphasised here as a way to increase the throughput of DEP devices. Glass-like carbon electrodes are derived through the carbonisation of photoresist structures made using photolithography. These biocompatible carbon electrodes are not ideal electrical conductors but are more electrochemically stable than noble metals such as gold and platinum. They are also significantly less expensive than common electrode materials, both in terms of material cost and fabrication process. CarbonDEP has been demonstrated for the manipulation of microorganisms and biomolecules. This review is divided in three main sections: (i) carbonDEP fabrication process; (ii) applications using 3D carbonDEP; and (iii) challenges and perspectives on the use of carbonDEP for high-throughput applications.

Rapid discrimination of bacteria using a miniature mass spectrometer

Bacteria colonies were analyzed using paper spray ionization coupled with a portable mass spectrometer. The spectra were averaged and processed using multivariate analysis to discriminate between different species of bacteria based on their unique phospholipid profiles. Full scan mass spectra and product ion MS/MS data were compared to those recorded using a benchtop linear ion trap mass spectrometer.

Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS

Identification of bacteria in aquatic and environmental applications, for monitoring purposes and research, for health assessments and therapy considerations of farmed and free-living aquatic organisms, still relies on conventional phenotypic and biochemical protocols. Although molecular techniques based on DNA amplification and sequencing are finding ways into diagnostic laboratories, they are time-consuming, costly and difficult in the case of multiplex assays. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate proteomic method reliable for identification of unknown bacteria to the genus and species level. Upon extension of databases, it will certainly find its position in environmental sciences. The paper presents an overview of the principle of the method, its effectiveness in comparison with conventional and molecular identification procedures, and applicability on environmental and aquatic isolates, discussing its advantages and shortcomings, as well as possible future implementations.

Sensitive detection of Listeria monocytogenes based on highly efficient enrichment with vancomycin-conjugated brush-like magnetic nano-platforms

Pathogens pose a significant threat to public health worldwide. Despite many technological advances in the rapid diagnosis of pathogens, sensitive pathogen detection remains challenging because target pathogenic bacteria usually exist in complex samples at very low concentrations. Here, the construction of multivalent brush-like magnetic nanoprobes and their application for the efficient enriching of pathogens are demonstrated. Brush-like magnetic nanoprobes were constructed by modification with poly-L-lysine (PLL) onto amino-modified magnetic beads, followed by coupling of PEG (amine-PEG₅₀₀₀-COOH) to the amine sites of PLL. Subsequently, vancomycin (Van), a small-molecule antibiotic with affinity to the terminal peptide (D-alanyl-D-alanine) on the cell wall of Gram-positive bacteria, was conjugated to the carboxyl of the PEG. The use of multivalent brush-like magnetic nanoprobes (Van-PEG-PLL-MNPs) results in a high enrichment efficiency (>94%) and satisfactory purity for Listeria monocytogenes (employed as a model) within 20min, even at bacterial concentrations of only 10²cfumL^-1. Integrated with the enrichment of the Van-PEG-PLL-MNP nano-platform and electrochemiluminescence (ECL) detection, Listeria monocytogenes can be rapidly and accurately detected at levels as low as 10cfumL^-1. The approach described herein holds great potential for realizing rapid and sensitive pathogen detection in clinical samples.

Early release of 1-pyrroline by Pseudomonas aeruginosa cultures discovered using ambient corona discharge ionization mass spectrometry

1-Pyrroline detected by ambient mass spectrometry is suggested as a potential volatile biomarker for early identification of Pseudomonas aeruginosa infections.

In Situ Analysis of Bacterial Lipopeptide Antibiotics by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a technique developed in the late 1990s enabling the two-dimensional mapping of a broad variety of biomolecules present at the surface of a sample. In many applications including pharmaceutical studies or biomarker discovery, the distribution of proteins, lipids or drugs, and metabolites may be visualized within tissue sections. More recently, MALDI MSI has become increasingly applied in microbiology where the versatility of the technique is perfectly suited to monitor the metabolic dynamics of bacterial colonies. The work described here is focused on the application of MALDI MSI to map secondary metabolites produced by Bacilli, especially lipopeptides, produced by bacterial cells during their interaction with their environment (bacteria, fungi, plant roots, etc.). This chapter addresses the advantages and challenges that the implementation of MALDI MSI to microbiological samples entails, including detailed protocols on sample preparation (from both microbiologist and mass spectrometrist points of view), matrix deposition, and data acquisition and interpretation. Lipopeptide images recorded from confrontation plates are also presented.

Thin Layer Chromatography-Autography-High Resolution Mass Spectrometry Analysis: Accelerating the Identification of Acetylcholinesterase Inhibitors

INTRODUCTION

The prevailing treatment for Alzheimer's disease is the use of acetylcholinesterase (AChE) inhibitors. Natural extracts are the principal source of AChE's inhibitors. However, their chemical complexity demands for simple, selective and rapid assays.

OBJECTIVE

To develop a strategy for identification of AChE inhibitors present in mixtures employing high resolution mass spectrometry (HRMS) and thin layer chromatography (TLC)-biological staining.

METHODOLOGY

The strategy uses an autographic assay based on the α-naphthyl acetate - fast blue B system for the detection of AChE activity. The immobilisation of AChE in agar allowed the extraction of the compounds for analysis by HRMS. Three TLC experiments employing different solvent systems were used in parallel and the mass spectra of the compounds extracted from the inhibition halos, were compared. The analysis was performed under MatLab environment.

RESULTS

The strategy was used to detect the presence of physostigmine in an extract of Brassica rapa L. spiked with the inhibitor. Similarly, caffeine was straightforwardly spotted as responsible for the inhibitory properties of an extract of Ilex paraguariensis Saint-Hilaire. Comparison of the HRMS profiles lead to the facile identification of the [M+H](+) and [M+Na](+) of the compounds responsible for the inhibition.

CONCLUSION

The proposed methodology, coupling TLC-AChE autography-HRMS, illustrates the feasibility of assigning molecular formulas of active compounds present in complex mixtures directly from autography. The new AChE agar-immobilised assay presented a more homogenous colour and a better definition than direct spraying methods, reducing the cost of the assay and improving its sensitivity.

Antibacterial Discovery and Development: From Gene to Product and Back

Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement.

Construction of Fe3O4/Vancomycin/PEG Magnetic Nanocarrier for Highly Efficient Pathogen Enrichment and Gene Sensing

Infectious diseases, especially pathogenic bacterial infections, pose a growing threat to public health worldwide. As pathogenic bacteria usually exist in complex experimental matrixes at very low concentrations, developing a technology for rapid and biocompatible sample enrichment is essential for sensitive diagnosis. In this study, an Fe3O4/Vancomycin/PEG magnetic nanocarrier was constructed for efficient sample enrichment and in situ nucleic acid preparation of pathogenic bacteria for subsequent gene sensing. We attached Vancomycin, a well-known broad-spectrum antibiotic, to the surface of Fe3O4 nanoparticles as a universal molecular probe to target bacterial cells. Polyethylene glycol (PEG) was introduced to enhance the nanocarrier's water solubility and biocompatibility. Results show that the proposed nanocarrier achieved a 90% capture efficiency even if at a Listeria monocytogenes concentration of 1×10(2) cfu/mL. Contributing to the good water solubility achieved by the employment of modified PEG, highly efficient enrichment (enrichment factor 10 times higher than PEG-free nanocarrier) can be completed in 30 min. Moreover, PEG would also develop the nanoparticles' biocompatibility by passivating the positively charged unreacted amines on the magnetic nanoparticles, thus helping to release the negatively charged bacterial genome from the nanocarrier/bacteria complexes when an in situ nucleic acids extraction step was executed. The outstanding bacterial capture capability and biocompatibility of this nanocarrier enabled the implementation of a highly sensitive gene-sensing strategy of pathogens. By employing an electrochemiluminescence-based gene-sensing assay, L. monocytogenes can be rapidly detected with a limit of detection of 10 cfu/mL, which shows great potential for clinical applications.

Scale-up of removal process using a remediating-bacterium isolated from marine coastal sediment

Nowadays, a wide variety of pollutants are discharged to different water sources and become water contaminants.

Evaluation of imprint DESI-MS substrates for the analysis of fungal metabolites

Optimized in situ screening, characterization and imaging of fungal metabolites by imprint DESI-MS.

Pyrimidine-based functional fluorescent organic nanoparticle probe for detection of Pseudomonas aeruginosa

Organic nanoparticles are developed for the sensing of Pseudomonas aeruginosa.

Cationic benzylidene cyclopentanone photosensitizers for selective photodynamic inactivation of bacteria over mammalian cells

Cationic modified benzylidene cyclopentanone photosensitizers selectively photo-inactivate bacterial cells over mammalian cells.

Rapid recognition of bacteremia in humans using atmospheric pressure chemical ionization mass spectrometry of volatiles emitted by blood cultures

Human bacteremia is rapidly diagnosed by direct atmospheric pressure chemical ionization mass spectrometry analysis of blood culture volatiles.

Identification of Corynebacterium spp. isolated from bovine intramammary infections by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Corynebacterium species (spp.) are among the most frequently isolated pathogens associated with subclinical mastitis in dairy cows. However, simple, fast, and reliable methods for the identification of species of the genus Corynebacterium are not currently available. This study aimed to evaluate the usefulness of matrix-assisted laser desorption ionization/mass spectrometry (MALDI-TOF MS) for identifying Corynebacterium spp. isolated from the mammary glands of dairy cows. Corynebacterium spp. were isolated from milk samples via microbiological culture (n=180) and were analyzed by MALDI-TOF MS and 16S rRNA gene sequencing. Using MALDI-TOF MS methodology, 161 Corynebacterium spp. isolates (89.4%) were correctly identified at the species level, whereas 12 isolates (6.7%) were identified at the genus level. Most isolates that were identified at the species level with 16 S rRNA gene sequencing were identified as Corynebacterium bovis (n=156; 86.7%) were also identified as C. bovis with MALDI-TOF MS. Five Corynebacterium spp. isolates (2.8%) were not correctly identified at the species level with MALDI-TOF MS and 2 isolates (1.1%) were considered unidentified because despite having MALDI-TOF MS scores >2, only the genus level was correctly identified. Therefore, MALDI-TOF MS could serve as an alternative method for species-level diagnoses of bovine intramammary infections caused by Corynebacterium spp.

Identification of coagulase-negative staphylococci from bovine intramammary infection by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Coagulase-negative staphylococci (CoNS) are among the main pathogens causing bovine intramammary infection (IMI) in many countries. However, one of the limitations related to the specific diagnosis of CoNS is the lack of an accurate, rapid, and convenient method that can differentiate the bacterial species comprising this group. The aim of this study was to evaluate the ability of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to accurately identify CoNS species in dairy cow IMI. In addition, the study aimed to determine the frequency of CoNS species causing bovine IMI. A total of 108 bacterial isolates were diagnosed as CoNS by microbiological cultures from two milk samples collected from 21 dairy herds; the first sample was collected at the cow level (i.e., 1,242 composite samples from all quarters), while the second sample was collected at the mammary quarter level (i.e., 1,140 mammary samples collected from 285 cows). After CoNS isolation was confirmed by microbiological culture for both samples, all CoNS isolates (n=108) were genotypically differentiated by PCR restriction fragment length polymorphism (RFLP) analysis of a partial groEL gene sequence and subjected to the MALDI-TOF MS identification procedure. MALDI-TOF MS correctly identified 103 (95.4%) of the CoNS isolates identified by PCR-RFLP at the species level. Eleven CoNS species isolated from bovine IMI were identified by PCR-RFLP, and the most prevalent species was Staphylococcus chromogenes (n=80; 74.1%). In conclusion, MALDI-TOF MS may be a reliable alternative method for differentiating CoNS species causing bovine IMI.

Improvements on colony morphology identification towards bacterial profiling

Colony morphology may be an indicator of phenotypic variation, this being an important adaptive process adopted by bacteria to overcome environmental stressors. Furthermore, alterations in colony traits may reflect increased virulence and antimicrobial resistance. Despite the potential relevance of using colony morphological traits, the influence of experimental conditions on colony morphogenesis has been scarcely studied in detail. This study aims to clearly and systematically demonstrate the impact of some variables, such as colony growth time, plate colony density, culture medium, planktonic or biofilm mode of growth and strain genetic background, on bacterial colony morphology features using two Pseudomonas aeruginosa strains. Results, based on 5-replicate experiments, demonstrated that all variables influenced colony morphogenesis and 18 different morphotypes were identified, showing different sizes, forms, colours, textures and margins. Colony growth time and composition of the medium were the variables that caused the highest impact on colony differentiation both derived from planktonic and biofilm cultures. Colony morphology characterization before 45 h of incubation was considered inadequate and TSA, a non-selective medium, provided more colony diversity in contrast to P. aeruginosa selective media. In conclusion, data obtained emphasized the need to perform comparisons between colony morphologies in equivalent experimental conditions to avoid misinterpretation of microbial diagnostics and biomedical studies. Since colony morphotyping showed to be a reliable method to evaluate phenotypic switching and also to infer about bacterial diversity in biofilms, these unambiguous comparisons between morphotypes may offer a quite valuable input to clinical diagnosis, aiding the decision-making towards the selection of the most suitable antibiotic and supportive treatments.

Optimal single-embryo mass spectrometry fingerprinting

In pre-implantation embryos, lipids play key roles in determining viability, cryopreservation and implantation properties, but often their analysis is analytically challenging because of the few picograms of analytes present in each of them. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) allows obtaining individual phospholipid profiles of these microscopic organisms. This technique is sensitive enough to enable analysis of individual intact embryos and monitoring the changes in membrane lipid composition in the early stages of development serving as screening method for studies of biology and biotechnologies of reproduction. This article introduces an improved, more comprehensive MALDI-MS lipid fingerprinting approach that considerably increases the lipid information obtained from a single embryo. Using bovine embryos as a biological model, we have also tested optimal sample storage and handling conditions before the MALDI-MS analysis. Improved information at the molecular level is provided by the use of a binary matrix that enables phosphatidylcholines, sphingomyelins, phosphatidylserines, phosphatidylinositols and phosphoethanolamines to be detected via MALDI(±)-MS in both the positive and negative ion modes. An optimal MALDI-MS protocol for lipidomic monitoring of a single intact embryo is therefore reported with potential applications in human and animal reproduction, cell development and stem cell research.

Microorganisms in cryopreserved semen and culture media used in the in vitro production (IVP) of bovine embryos identified by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS)

Commercial cattle breeders produce their own herd offspring for the dairy and beef market using artificial insemination. The procedure involves sanitary risks associated with the collection and commercialization of the germplasm, and the in vitro production and transfer of the bovine embryos must be monitored by strict health surveillance. To avoid the spreading of infectious diseases, one must rely on using controlled and monitored germplasm, media, and reagents that are guaranteed free of pathogens. In this article, we investigated the use of a new mass spectrometric approach for fast and accurate identification of bacteria and fungi in bovine semen and in culture media employed in the embryo in vitro production process. The microorganisms isolated from samples obtained in a commercial bovine embryo IVP setting were identified in a few minutes by their conserved peptide/protein profile, obtained applying matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS), matched against a commercial database. The successful microorganisms MS identification has been confirmed by DNA amplification and sequencing. Therefore, the MS technique seems to offer a powerful tool for rapid and accurate microorganism identification in semen and culture media samples.