MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and Surface Water

PURPOSE OF REVIEW

Mounting evidence indicates that habitats such as wastewater and environmental waters are pathways for the spread of antibiotic-resistant bacteria (ARB) and mobile antibiotic resistance genes (ARGs). We identified antibiotic-resistant members of the genera Acinetobacter, Aeromonas, and Pseudomonas as key opportunistic pathogens that grow or persist in built (e.g., wastewater) or natural aquatic environments. Effective methods for monitoring these ARB in the environment are needed to understand their influence on dissemination of ARB and ARGs, but standard methods have not been developed. This systematic review considers peer-reviewed papers where the ARB above were cultured from wastewater or surface water, focusing on the accuracy of current methodologies.

RECENT FINDINGS

Recent studies suggest that many clinically important ARGs were originally acquired from environmental microorganisms. Acinetobacter, Aeromonas, and Pseudomonas species are of interest because their ability to persist and grow in the environment provides opportunities to engage in horizontal gene transfer with other environmental bacteria. Pathogenic strains of these organisms resistant to multiple, clinically relevant drug classes have been identified as an urgent threat. However, culture methods for these bacteria were generally developed for clinical samples and are not well-vetted for environmental samples. The search criteria yielded 60 peer-reviewed articles over the past 20 years, which reported a wide variety of methods for isolation, confirmation, and antibiotic resistance assays. Based on a systematic comparison of the reported methods, we suggest a path forward for standardizing methodologies for monitoring antibiotic resistant strains of these bacteria in water environments.

Quality and Microbiological Safety of Poultry Meat Marinated with the Use of Apple and Lemon Juice

The aim of the study was to evaluate the use of apple juice for the marinating of poultry meat and its effect on the technological as well as sensory characteristics and microbiological safety of the raw product after heat treatment. Broiler chicken breast muscles were marinated for 12 h in apple juice (n = 30), a mixture of apple and lemon juice (n = 30) and compared with those in lemon juice (n = 30). The control group (n = 30) consisted of unmarinated breast muscles. Following the evaluation of the technological parameters (pH, L*, a*, b* colour, cutting force, cooking losses) quantitative and qualitative microbiological evaluations were performed on the raw and roasted products. The microbiological parameters were determined as total Mesophilic aerobic microorganisms, Enterobacteriaceae family, and Pseudomonas count. The bacterial identification was performed using a matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The marinating resulted in lower pH value, but increased tenderness of raw and roasted products. Marinating chicken meat in both apple and lemon juices, including their mixtures and in the control sample, resulted in increased yellow saturation (b*). The highest flavour desirability and overall desirability were obtained in products marinated using a mixture of apple and lemon juice, while the most desirable aroma was obtained from products marinated with apple juice. A significant antimicrobial effect was observed in marinated meat products compared to unmarinated, irrespective of the type of marinade used. The lowest microbial reduction was observed in the roasted products. Apple juice can be used as a meat marinade because it promotes interesting sensory properties and improves the microbiological stability of poultry meat while maintaining the product's good technological characteristics. It makes a good combination with the addition of lemon juice.

Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals

Most bacteria live in dense, spatially structured communities such as biofilms. The high density allows cells to alter the local microenvironment, whereas the limited mobility can cause species to become spatially organized. Together, these factors can spatially organize metabolic processes within microbial communities so that cells in different locations perform different metabolic reactions. The overall metabolic activity of a community depends both on how metabolic reactions are arranged in space and on how they are coupled, i.e., how cells in different regions exchange metabolites. Here, we review mechanisms that lead to the spatial organization of metabolic processes in microbial systems. We discuss factors that determine the length scales over which metabolic activities are arranged in space and highlight how the spatial organization of metabolic processes affects the ecology and evolution of microbial communities. Finally, we define key open questions that we believe should be the main focus of future research.

Usefulness of Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry in the Characterization of Leishmania Strains Causing Tegumentary Leishmaniasis in Bolivia versus hsp70 Gene Sequencing

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a proteomic technique with proven efficiency in the identification of microorganisms, such as bacteria, fungi, and parasites. The present study aimed to evaluate the usefulness of MALDI-TOF MS for the characterization of Leishmania species circulating in Bolivia using hsp70 gene sequencing as a reference technique. 55 Leishmania strains that were isolated from patients with tegumentary leishmaniasis were analyzed. MALDI-TOF MS identified two species of the L. braziliensis complex (L. braziliensis, n = 26; L. braziliensis outlier, n = 18), one species of the L. guyanensis complex (L. guyanensis, n = 1), one species of the L. lainsoni complex (L. lainsoni, n = 2), and two species of the L. mexicana complex (L. amazonensis, n = 5; and L. garnhami, n = 3). All of the strains were correctly identified at the subgenus, genus, and complex level, but 10 of them (18%) were misidentified as other species within the same complex by the hsp70 gene sequencing, with 7 of these corresponding to possible hybrids. Thus, one L. braziliensis corresponded to L. peruviana, two L. braziliensis corresponded to L. braziliensis/L. peruviana possible hybrids, two L. amazonensis corresponded to L. mexicana, and three L. garnhami and two L. amazonensis corresponded to L. mexicana/L. amazonensis possible hybrids. Accordingly, MALDI-TOF MS could be used as an alternative to molecular techniques for the identification of Leishmania spp., as it is low cost, simple to apply, and able to quickly produce results. In Bolivia, its application would allow for the improvement of the management of patient follow-ups, the updating of the epidemiological data of the Leishmania species, and a contribution to the control of tegumentary leishmaniasis. IMPORTANCE The objective of the study was to evaluate the usefulness of MALDI-TOF MS for the characterization of Leishmania species circulating in Bolivia, in comparison with the sequencing of the hsp70 gene. In our study, all of the isolates could be identified, and no misidentifications were observed at the complex level. Although the equipment implies a high initial investment in our context, MALDI-TOF MS can be used in different areas of microbiology and significantly reduces the cost of testing. Once the parasite culture is obtained, the technique quickly yields information by accessing a free database that is available online. This would allow for the improvement of the management of patients and follow-ups, the updating of the epidemiological data of the species, and a contribution to the control of tegumentary leishmaniasis in Bolivia. Likewise, it can be used to determine a specific treatment to be given, according to the causal species of Leishmania, when there are protocols in this regard in the area.

Identification of Pathogenic and Opportunistic Yeasts in Pigeon Excreta by MALDI-TOF Mass Spectrometry and Their Prevalence in Chon Buri Province, Thailand

Pigeon excreta can cause environmental and public health issues, particularly in urban and public areas. They are reservoirs of several human pathogens including fungi, bacteria, and viruses. Epidemiological data of pathogenic and opportunistic yeasts in pigeon droppings in Chon Buri, one of the most reputable tourist cities of Thailand, are scarce. The present study aimed to identify yeasts in pigeon droppings by MALDI-TOF mass spectrometry, and to study their prevalence in Chon Buri, Thailand. A total of 200 pigeon fecal samples were collected randomly from all 11 districts of Chon Buri. A sum of 393 yeast-like colonies were isolated on Sabourand's dextrose agar and CHROMagar media. These isolates were further confirmed for their species by MALDI-TOF MS. Twenty-four yeast species belonging to 11 different genera were identified in pigeon fecal samples. Candida spp., predominantly C. krusei (14.32%), were the most prevalent yeast species. Other yeast species, including C. glabrata (12.73%), C. metapsilosis (11.93%), Lodderomyces elongisporus (10.87%), C. tropicalis (7.16%), C. albicans (5.83%), and Cryptococcus neoformans (4.77%) were identified. This study provides valuable epidemiological data and diversity of yeasts in pigeon droppings in Chon Buri, Thailand, and also supports the use of MALDI-TOF MS for yeast identification and epidemiological surveillance.

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.

Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean

Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1-C6 females) of three co-occurring Calanus species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic Calanus species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods.

Characteristics of Environmental Klebsiella pneumoniae and Klebsiella oxytoca Bacteriophages and Their Therapeutic Applications

In recent years, multidrug-resistant (MDR) strains of Klebsiella pneumoniae have spread globally, being responsible for the occurrence and severity of nosocomial infections. The NDM-1-kp, VIM-1 carbapenemase-producing isolates as well as extended-spectrum beta lactamase-producing (ESBL) isolates along with Klebsiella oxytoca strains have become emerging pathogens. Due to the growing problem of antibiotic resistance, bacteriophage therapy may be a potential alternative to combat such multidrug-resistant Klebsiella strains. Here, we present the results of a long-term study on the isolation and biology of bacteriophages active against K. pneumoniae, as well as K. oxytoca strains. We evaluated biological properties, morphology, host specificity, lytic spectrum and sensitivity of these phages to chemical agents along with their life cycle parameters such as adsorption, latent period, and burst size. Phages designated by us, vB_KpnM-52N (Kpn52N) and VB_KpnM-53N (Kpn53N), demonstrated relatively broad lytic spectra among tested Klebsiella strains, high burst size, adsorption rates and stability, which makes them promising candidates for therapeutic purposes. We also examined selected Klebsiella phages from our historical collection. Notably, one phage isolated nearly 60 years ago was successfully used in purulent cerebrospinal meningitis in a new-born and has maintained lytic activity to this day. Genomic sequences of selected phages were determined and analyzed. The phages of the sequenced genomes belong to the Slopekvirus and Jiaodavirus genus, a group of phages related to T4 at the family level. They share several features of T4 making them suitable for antibacterial therapies: the obligatorily lytic lifestyle, a lack of homologs of known virulence or antibiotic resistance genes, and a battery of enzymes degrading host DNA at infection.

Screening the Efficacy of a Microbial Consortium of Bacteria and Fungi Isolated from Different Environmental Samples for the Degradation of LDPE/TPS Films

In this study, a screening of the efficacy of a microbial consortium of bacteria and fungi isolated from activated sludge, river sediment, and compost for the degradation of LDPE/TPS was performed. According to the morphological and biochemical characterization, eight bacteria, Bacillus sonorensis, Bacillus subtilis, Lysinibacillus massiliensis, Bacillus licheniformis, Bacillus indicus, Bacillus megaterium, Bacillus cereus, and Pseudomonas alcaligenes, five molds, Aspergillus sp. 1, Aspergillus sp. 2, Trichoderma sp., Rhizopus sp., Penicillium sp., and Alternaria sp., and a yeast, Candida parapsilosis, were identified. The first experiment E1 was inoculated with microorganisms isolated from activated sludge and river sediment, and E2 with microorganisms isolated from compost. In both experiments, different types of polymeric materials, low density polyethylene (E1-1 and E2-1), thermoplastic starch (E1-2 and E2-2), low density polyethylene + thermoplastic starch (E1-3 and E2-3), low density polyethylene + thermoplastic starch + styrene-ethylene-styrene (E1-4 and E2-4) were added. The obtained results, weight loss, SEM, and FTIR analysis showed that the microorganisms in both experiments were able to degrade polymeric materials. The mixed culture of microorganisms in experiments E1-2 and E2-2 completely degraded TPS (thermoplastic starch). The percent weight losses of LDPE, LDPE+20% TPS, and LDPE+20% TPS+SEBS in experiment E1 were 3.3184%, 14.1152%, and 16.0062% and in experiment E2 were 3.9625%, 20.4520% and 21.9277%, respectively. SEM microscopy shows that the samples with a LDPE matrix exhibited moderate surface degradation and negligible oxidative degradation under the given conditions. FTIR/ATR data demonstrate that degradation was more intense in E2 than in E1.

Qualification of Human Liver Microsomes for Antibacterial Activity Screening of Drug Metabolites

Microsomes are commonly used to perform in vitro drug metabolism, predominantly to form phase I drug metabolites. Pooled microsomes from multiple donors can contain microorganisms from underlying microbial diseases. Exposure to microbes can also occur during extraction if aseptic processing is compromised. Although microbial presence does not affect the metabolic activity of microsomes, presence of unwanted microorganisms can cause interference if the downstream application of microsomal drug metabolites is screening for antibacterial activity. In this work, traditional biochemical tests and advanced proteomics-based identification techniques were used to identify two gram-negative bacteria in pooled human liver microsomes. Several decontamination procedures were assessed to eradicate these two bacteria from the microsomes without affecting its metabolic capacity, and organic extraction was found to be the most convenient and efficient approach to decontaminate microsomes and screen drug metabolites for antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA).

Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water

In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world's rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.

Analyses and Localization of Phosphatidylcholine and Phosphatidylserine in Murine Ocular Tissue Using Imaging Mass Spectrometry

Imaging mass spectrometry (IMS) allows for spatial visualization of proteins, lipids, and metabolite distributions in a tissue. Identifying these compounds through mass spectrometry, combined with mapping the compound distribution in the sample in a targeted or untargeted approach, renders IMS a powerful tool for lipidomics. IMS analysis for lipid species such as phosphatidylcholine and phosphatidylserine allows researchers to pinpoint areas of lipid deficiencies or accumulations associated with ocular disorders such as age-related macular degeneration and diabetic retinopathy. Here, we describe an end-to-end IMS approach from sample preparation to data analysis for phosphatidylcholine and phosphatidylserine analysis.

Current Landscape of Methods to Evaluate Antimicrobial Activity of Natural Extracts

Natural extracts have been and continue to be used to treat a wide range of medical conditions, from infectious diseases to cancer, based on their convenience and therapeutic potential. Natural products derived from microbes, plants, and animals offer a broad variety of molecules and chemical compounds. Natural products are not only one of the most important sources for innovative drug development for animal and human health, but they are also an inspiration for synthetic biology and chemistry scientists towards the discovery of new bioactive compounds and pharmaceuticals. This is particularly relevant in the current context, where antimicrobial resistance has risen as a global health problem. Thus, efforts are being directed toward studying natural compounds' chemical composition and bioactive potential to generate drugs with better efficacy and lower toxicity than existing molecules. Currently, a wide range of methodologies are used to analyze the in vitro activity of natural extracts to determine their suitability as antimicrobial agents. Despite traditional technologies being the most employed, technological advances have contributed to the implementation of methods able to circumvent issues related to analysis capacity, time, sensitivity, and reproducibility. This review produces an updated analysis of the conventional and current methods to evaluate the antimicrobial activity of natural compounds.

The Association of the Oral Microbiota with the Effects of Acid Stress Induced by an Increase of Brain Lactate in Schizophrenia Patients

The altered cerebral energy metabolism central to schizophrenia can be linked to lactate accumulation. Lactic acid is produced by gastrointestinal bacteria, among others, and readily crosses the blood-brain barrier, leading to the brain acidity. This study aimed to examine the association of the oral microbiota with the effects of acid stress induced by an increase of brain lactate in schizophrenia patients. The study included patients with a diagnosis of acute polyphasic psychotic disorder meeting criteria for schizophrenia at 3-month follow-up. Results: Individuals with a significantly higher total score on the Positive and Negative Syndrome Scale had statistically significantly lower lactate concentrations compared to those with a lower total score and higher brain lactate. We observed a positive correlation between Actinomyces and lactate levels in the anterior cingulate cap and a negative correlation between bacteria associated with lactate metabolism and some clinical assessment scales. Conclusions: Shifts in the oral microbiota in favour of lactate-utilising bacterial genera may represent a compensatory mechanism in response to increased lactate production in the brain. Assessment of neuronal function mediated by ALA-LAC-dependent NMDA regulatory mechanisms may, thus, support new therapies for schizophrenia, for which acidosis has become a differentiating feature of individuals with schizophrenia endophenotypes.

Clinical and Laboratory Diagnosis of Legionella Pneumonia

Legionella pneumonia is a relatively rare but extremely progressive pulmonary infection with high mortality. Traditional cultural isolation remains the gold standard for the diagnosis of Legionella pneumonia. However, its harsh culture conditions, long turnaround time, and suboptimal sensitivity do not meet the clinical need for rapid and accurate diagnosis, especially for critically ill patients. So far, pathogenic detection techniques including serological assays, urinary antigen tests, and mass spectrometry, as well as nucleic acid amplification technique, have been developed, and each has its own advantages and limitations. This review summarizes the clinical characteristics and imaging findings of Legionella pneumonia, then discusses the advances, advantages, and limitations of the various pathogenetic detection techniques used for Legionella pneumonia diagnosis. The aim is to provide rapid and accurate guiding options for early identification and diagnosis of Legionella pneumonia in clinical practice, further easing healthcare burden.

Impact of Helicobacter pylori virulence markers on clinical outcomes in adult populations

BACKGROUND

In recent years, associations between specific virulence markers of Helicobacter pylori (H. pylori) and gastrointestinal disorders have been suggested.

AIM

To investigate the presence of virulence factors including vacuolating cytotoxin A genotypes (s1m1, s1m2, s2m1, and s2m2), cytotoxin-associated gene A (CagA), and urease activity in H. pylori strains isolated from Arab and Jewish populations in northern Israel and to assess associations between these factors and patients’ demographics and clinical outcomes.

METHODS

Patients (n = 108) who underwent gastroscopy at the Baruch Padeh Medical Center, Poriya due to symptomatic gastroduodenal pathologies as part of H. pylori diagnosis were enrolled in the study. Gastric biopsy specimens were collected from the antrum of the stomach. Clinical condition was assessed by clinical pathology tests. Bacteria were isolated on modified BD Helicobacter Agar (BD Diagnostics, Sparks, MD, United States). Bacterial DNA was extracted, and PCR was performed to detect CagA and vacuolating cytotoxin A genes. Urease activity was assessed using a rapid urease test.

RESULTS

A significant correlation was found between disease severity and patient ethnicity (P = 0.002). A significant correlation was found between CagA presence and the s1m1 genotype (P = 0.02), which is considered the most virulent genotype. Further, a higher level of urease activity was associated with isolates originating from the Jewish population. Moreover, higher urease activity levels were measured among CagA-/s1m1 and CagA-/s2m2 isolates.

CONCLUSION

Our study highlights the importance of incorporating molecular methods for detection of virulence markers of H. pylori in order to tailor optimal treatments for each patient. Further investigation should be performed regarding associations between H. pylori virulence factors and ethnicity.

Mapping of audiometric analysis with microbiological findings in patients with chronic suppurative otitis media (CSOM): a neglected clinical manifestation

Otitis media (OM) is an umbrella term for a number of conditions associated with middle ear inflammation. Chronic suppurative otitis media (CSOM), a type of OM, is characterized by long-term middle ear infection with perforated ear drum and otorrhea. The most common outcome associated with it is acquired hearing impairment in infected individuals which ultimately affects their cognitive and scholastic developments. Clinically, CSOM is thought to be a sequel of re-occurring episodes of Acute otitis media (AOM). Pseudomonas aeruginosa and Staphylococcus aureus are found to be the predominant pathogenic isolates in these patients. However, with the emergence of antibiotic resistance amongst these pathogens, the adequate evaluation and treatment of this condition has become more problematic. The disease has also been recognized as one of the neglected tropical clinical manifestations with high prevalence in school-age children, especially in poor or underprivileged countries. Moreover, untreated cases have further worsened the situation by contributing to various life-threatening complications. Thus, effective treatment and surgical strategies, as well as strengthening of hearing care algorithms along with the discovery of novel animal models for advanced clinical research, can jointly help to fight this disease. In this regard, mapping of the audiological analysis with microbiological findings in CSOM patients may help elucidate the frequency that favors growth of specific pathogens. Knowledge about this potential correlation can then support timely detection of the infection, which is perceived as one of the emerging approaches for its management. In addition to these strategies, creating a true sense of awareness among people can also help mitigate this pathological condition by facilitating early identification, prevention, and treatment. This review discusses the incidence, pathogenesis, investigations, complications, and available treatment modalities associated with CSOM.

Evaluation of Two Different Preparation Protocols for MALDI-TOF MS Nontuberculous Mycobacteria Identification from Liquid and Solid Media

Nontuberculous mycobacteria (NTM) identification is essential for establishing the relevance of the isolate and for appropriate antimicrobial therapy. Traditionally, NTM identification is performed by using Line Probe Assays (LPA), a costly and time-consuming technique requiring trained personnel. MALDI-TOF MS is a promising tool for NTM identification, and its use is rapidly growing. We evaluated the newly introduced MBT Mycobacteria kit (MBT) and the MycoEx preparation protocol (Bruker Daltonics, Germany) for NTM MALDI-TOF MS identification using LPA results as a reference. Fifty NTM grown on 7H11 agar and MGIT broth were analyzed with both protocols using the Bruker Microflex^® LT MALDI-TOF MS (Bruker Daltonics) instrument. MBT and MycoEx provided identification results in 97.0% and 95.0% of the cases, respectively. With both protocols, 100% of the provided results agreed with LPA with no registered mismatch. MBT achieved an elevated number of highly probable identifications (88.0% vs. 83.0%) and a higher reproducibility rate of correct results (86.6% vs. 75.8%) in comparison to MycoEx. This study provides results about MBT performance for liquid and solid media, underlining the strengths and weakness under different conditions. Our results suggest that MALDI-TOF MS could provide a great advantage for timely and cost-saving NTM identification with potential implications for patient outcome.

Visualisation of Host-Pathogen Communication

The core of biomedical science is the use of laboratory techniques to support the diagnosis and treatment of disease in clinical settings. Despite tremendous advancement in our understanding of medicine in recent years, we are still far from having a complete understanding of human physiology in homeostasis, let alone the pathology of disease states. Indeed medical advances over the last two hundred years would not have been possible without the invention of and continuous development of visualisation techniques available to research scientists and clinicians. As we have all learned from the recent COVID pandemic, despite advances in modern medicine we still have much to learn regarding infection biology. Indeed antimicrobial resistant (AMR) bacteria are a global threat to human health, meaning research into bacterial pathogenesis is vital. In this chapter, we will briefly describe the nature of microbes and host immune responses before delving into some of the visualisation techniques utilised in the field of biomedical research with a focus on host-pathogen interactions. We will give a brief overview of commonly used techniques from gold standard staining methods, in situ hybridisation, microscopy, western blotting, microbial characterisation, to cutting-edge image flow cytometry and mass spectrometry. Specifically, we will focus on techniques utilised to visualise interactions between the host, our own bodies, and invading organisms including bacteria. We will touch on in vitro and ex vivo modelling methodology with examples utilised to delineate pathogenicity in disease. A better understanding of bacterial biology, immunology and how these fields interact (host-pathogen communications) in biomedical research is integral to developing novel therapeutic approaches which circumvent the need for antibiotics, an important issue as we enter a post-antibiotic era.

Cutaneous tuberculosis-ambiguous transmission, bacterial diversity with biofilm formation in humoral abnormality: case report illustration

Background

Cutaneous tuberculosis (CTB) and its paucibacillary forms are rare and difficult to diagnose, especially in immunocompromised patients with significant comorbidity. The aim of the study was to introduce the modern concept of the microbiome and diagnostic chain into clinical practice (patient-centered care) with the presentation of an atypical form of cutaneous tuberculosis with necrotizing non-healing ulcers leading to polymicrobial infection.

Methods

The study material included samples from sputum, broncho-alveolar lavage and skin ulcer, taken from a patient developing cutaneous tuberculosis. The microbiological investigation was performed, and identification of the isolates was carried out using genotyping and the matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Results

The immunocompromised patient with humoral abnormality (plasma cell dyscrasia) and severe paraproteinemia developed multiorgan tuberculosis. Although cutaneous manifestation preceded systemic and pulmonary symptoms (approximately half a year), the mycobacterial genotyping confirmed the same MTB strain existence in skin ulcers and the respiratory system. Therefore, the infectious chain: transmission, the portal of entry, and bacterial spreading in vivo, were unclear. Microbial diversity found in wound microbiota (among others Gordonia bronchialis, Corynebacterium tuberculostearicum, Staphylococcus haemolyticus, and Pseudomonas oryzihabitans) was associated with the spread of a skin lesion. The in vitro biofilm-forming capacity of strains isolated from the wound may represent the potential virulence of these strains. Thus, the role of polymicrobial biofilm may be crucial in ulcer formation and CTB manifestation.

Conclusions

Severe wound healing as a unique biofilm-forming niche should be tested for Mycobacterium (on species and strain levels) and coexisting microorganisms using a wide range of microbiological techniques. In immunodeficient patients with non-typical CTB presentation, the chain of transmission and MTB spread is still an open issue for further research.

Molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital environment

This study aimed to investigate sites for colonization and molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital. Bacterial specimens from surface and liquid samples (n = 165) located in five rooms were collected three times every 2 months, and antimicrobial susceptibility was subsequently determined by minimum inhibitory concentrations. The genomes of resistant strains were further analyzed using whole-genome sequencing. Among 19 P. aeruginosa isolates (11.5%, 19/165), sinks were the most frequent colonization site (53.3%), followed by rubber tubes (44.4%), and anesthesia-breathing circuit (33.3%). The highest resistance to gentamicin (47.4%), followed by piperacillin/tazobactam (36.8%), levofloxacin (36.8%), and ciprofloxacin (36.8%), was observed from 19 P. aeruginosa isolates, of which 10 were resistant strains. Of these 10 antimicrobial-resistant isolates, five were multidrug-resistant isolates, including carbapenem. From the multilocus sequence typing (MLST) analysis, five sequence types (STs), including a high-risk clone of human ST235 (n = 3), and ST244 (n = 3), ST606 (n = 2), ST485 (n = 1), and ST3405 (n = 1) were identified in resistant strains. Multiresistant genes were identified consistent with STs, except ST235. The MLST approach and single nucleotide polymorphism analysis revealed a link between resistant strains from ward rooms and those from examination, wound care, and operating rooms. The improvement of routine cleaning, especially of sink environments, and the continued monitoring of antimicrobial resistance of P. aeruginosa in veterinary hospitals are necessary to prevent the spread of resistant clones and ensure infection control.

Multifocal Serpiginoid Choroiditis Due to Mycobacterium Mageritense following Laparoscopic Hysterectomy in an Immunocompetent Host

PURPOSE

To report nontubercular choroiditis, caused by Mycobacterium mageritense isolated using MALDI-TOF MS, following laparoscopic hysterectomy in an immunocompetent patient.

CASE REPORT

A 42-year-old female presented with gradual, painless diminution of vision in the right eye for six weeks. She had undergone laparoscopic hysterectomy two months back. BCVA was 2/60 OD. Clinical presentation and imaging all pointed to a diagnosis of serpiginous-like choroiditis. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) had led to isolation of Mycobacterium mageritense. Patient was treated with systemic antibiotics. At 3 months follow up, BCVA improved to 6/60; fundus showed healed choroiditis and chorioretinal thinning.

CONCLUSION

Atypical mycobacterial infections associated with laparoscopic surgeries can rarely lead to debilitating systemic bacteremia resulting in profound visual impairment. The importance of timely diagnosis using specific and sophisticated methods such as MALDI-TOF MS as well as maintaining aseptic precautions perioperatively during major surgeries cannot be overemphasized.

Analyses and Localization of Serotonin and L-DOPA in Ocular Tissues by Imaging Mass Spectrometry

Imaging mass spectrometry (IMS) allows for visualization of the spatial distribution of proteins, lipids, and other metabolites in a targeted or untargeted approach. The identification of compounds through mass spectrometry combined with the mapping of compound distribution in the sample establishes IMS as a powerful tool for metabolomics. IMS analysis for serotonin will allow researchers to pinpoint areas of deficiencies or accumulations associated with ocular disorders such as serotonin selective reuptake inhibitor optic neuropathy. Furthermore, L-DOPA has shown great promise as a therapeutic approach for disorders such as age-related macular degeneration, and IMS allows for localization, and relative magnitudes, of L-DOPA in the eye. We describe here an end-to-end approach of IMS from sample preparation to data analysis for serotonin and L-DOPA analysis.

MRSA carriage among healthcare workers in a Vietnamese intensive care unit: a prospective cohort study

Background:

Little is known about the magnitude and patterns of methicillin-resistant Staphylococcus aureus (MRSA) carriage among intensive care unit (ICU) healthcare workers (HCWs), especially in lower-middle-income countries like Vietnam.

Materials and methods:

A prospective cohort study was conducted on HCWs working in the adult ICU of the Hospital for Tropical Diseases in Vietnam between October 28 and December 20, 2019. These HCWs included physicians, nurses, and nursing assistants who were responsible for all essential medical activities and basic patient care. A questionnaire was used to collect participants’ information, including age, sex, profession, ICU working time, and underlying diseases. Hand and nasal swabs were collected weekly for 8 consecutive weeks for MRSA screening. Staphylococcal isolates were checked for catalase and coagulase and, for methicillin resistance using cefoxitin disk diffusion, then rechecked on the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Results:

Among 55 HCWs, 16 (29.1%) carried MRSA in their noses or hands. MRSA intermittent hand carriage was documented in 2 (3.6%) HCWs. Among 53 HCWs undertaking nasal swabs, 13 (24.5%) were MRSA persistent and 3 (5.6%) were intermittent carriers. The MRSA carriage rate was highest among nursing assistants (50%, 4/8). More HCWs with underlying diseases were found to be MRSA carriers (31.8%, 7/22) compared with those without comorbidities (27.3%, 9/33).

Conclusion:

MRSA carriage among HCWs is not rare. The findings highlight an urgent need to review and update the local infection prevention and control measures to prevent MRSA transmission from HCWs to patients.

Lethal action of Licarin A derivatives in Leishmania (L.) infantum: Imbalance of calcium and bioenergetic metabolism

Natural metabolites present an extraordinary chemo-diversity and have been used as the inspiration for new drugs. Considering the need for new treatments against the neglected parasitic disease leishmaniasis, three semi-synthetic derivatives of natural neolignane licarin A were prepared: O-acetyl (1a), O-allyl (1b), and 5-allyl (1c). Using an ex vivo assay, compounds 1a, 1b, and 1c showed activity against the intracellular amastigotes of Leishmania (L.) infantum, with IC₅₀ values of 9, 13, and 10 μM, respectively. Despite no induction of hemolytic activity, only compound 1b resulted in mammalian cytotoxicity (CC₅₀ = 64 μM). The most potent compounds (1a and 1c) resulted in selectivity indexes >18. The mechanism of action of compound 1c was evaluated by fluorescent/luminescent based techniques and MALDI-TOF/MS. After a short incubation period, increased levels of the cytosolic calcium were observed in the parasites, with alkalinization of the acidocalcisomes. Compound 1c also induced mitochondrial hyperpolarization, resulting in decreased levels of ATP without altering the reactive oxygen species (ROS). Neither plasma membrane damages nor DNA fragmentation were observed after the treatment, but a reduction in the cellular proliferation was detected. Using MALDI-TOF/MS, mass spectral alterations of promastigote proteins were observed when compared to untreated and miltefosine-treated groups. This chemically modified neolignan induced lethal alterations of the bioenergetic and protein metabolism of Leishmania. Future PKPD and animal efficacy studies are needed to optimize this promising natural-derived compound.

What's New in Cryptococcus gattii: From Bench to Bedside and Beyond

Cryptococcus species are a major cause of life-threatening infections in immunocompromised and immunocompetent hosts. While most disease is caused by Cryptococcus neoformans, Cryptococcus gattii, a genotypically and phenotypically distinct species, is responsible for 11-33% of global cases of cryptococcosis. Despite best treatment, C. gattii infections are associated with early mortality rates of 10-25%. The World Health Organization's recently released Fungal Priority Pathogen List classified C. gattii as a medium-priority pathogen due to the lack of effective therapies and robust clinical and epidemiological data. This narrative review summarizes the latest research on the taxonomy, epidemiology, pathogenesis, laboratory testing, and management of C. gattii infections.

Petri-plate, bacteria, and laser optical scattering sensor

Classical microbiology has paved the path forward for the development of modern biotechnology and microbial biosensing platforms. Microbial culturing and isolation using the Petri plate revolutionized the field of microbiology. In 1887, Julius Richard Petri invented possibly the most important tool in microbiology, the Petri plate, which continues to have a profound impact not only on reliably isolating, identifying, and studying microorganisms but also manipulating a microbe to study gene expression, virulence properties, antibiotic resistance, and production of drugs, enzymes, and foods. Before the recent advances in gene sequencing, microbial identification for diagnosis relied upon the hierarchal testing of a pure culture isolate. Direct detection and identification of isolated bacterial colonies on a Petri plate with a sensing device has the potential for revolutionizing further development in microbiology including gene sequencing, pathogenicity study, antibiotic susceptibility testing , and for characterizing industrially beneficial traits. An optical scattering sensor designated BARDOT (bacterial rapid detection using optical scattering technology) that uses a red-diode laser, developed at the beginning of the 21^st century at Purdue University, some 220 years after the Petri-plate discovery can identify and study bacteria directly on the plate as a diagnostic tool akin to Raman scattering and hyperspectral imaging systems for application in clinical and food microbiology laboratories.

Clinical Microbial Identification of Severe Oral Infections by MALDI-TOF Mass Spectrometry in Stockholm County: an 11-Year (2010 to 2020) Epidemiological Investigation

Growing evidence suggests that oral infections can modify the course of systemic diseases. To date, epidemiological data on microbial oral infections are scarce. Here, we performed a comprehensive analysis of the trend and microbial diversity in oral infection specimens referred for clinical microbiology analysis from 2010 to 2020. The microbes were isolated by culture and were identified via matrix-assisted laser desorption ionization-time of flight mass spectrometry technology (MALDI-TOF MS) throughout the study period. A total of 1,014 referred samples from dental clinics in Stockholm County with dentoalveolar abscesses and jaw osteomyelitis being the main reason were identified. Overall, the microbial composition was dominated by Firmicutes (51%), followed by Bacteroidetes (19%), Proteobacteria (12%), and Actinobacteria (5%). At the genus level, Streptococcus spp. (36%), Prevotella spp. (18%), and Staphylococcus spp. (11%) were among the most frequently reported. Interestingly, a strong increase in trend was noted for Streptococcus anginosus, Streptococcus mitis, Streptococcus sanguinis, Eikenella corrodens, Actinomyces spp., Aggregatibacter aphrophilus, Staphylococcus epidermidis, and Granulicatella adiacens during the study time (R = 0.66 to 0.89, P < 0.05), and a minor increase was noted for Enterococcus faecalis and Klebsiella spp., whereas steady levels were noted for most of the others. The present study shows the diversity of bacteria that have been involved in dental infections during the last decade in the capital of Sweden, as well as the emerging oral microbiota trend, with clear clinical implications on the oral-systemic link. IMPORTANCE Oral diseases and associated microbes are a risk factor for systemic diseases and can change the courses of these diseases. To date, epidemiological data on microbial oral infections are scarce, and longitudinal reports are lacking. We present for the first time the microbial composition of severe oral bacterial infections determined via the MALDI-TOF mass spectrometry technique in a comprehensive study between 2010 and 2020 (11 years) in Stockholm County. The trend and microbial diversity of oral infections were analyzed on referred clinical microbiological samples and were processed by standardized protocols. Trend increase was noted for Streptococcus anginosus, Streptococcus mitis, Streptococcus sanguinis, Eikenella corrodens, Actinomyces spp., Aggregatibacter aphrophilus, Staphylococcus epidermidis, Granulicatella adiacens, Enterococcus faecalis, and Klebsiella spp. Our results provide new insights into the diversity and trend of oral microbiota that were involved in serious oral infections over the past decade in the capital of Sweden and may influence the oral-systemic link.

Multiplex high-resolution melting assay for simultaneous detection of five key bacterial pathogens in urinary tract infections: A pilot study

The diagnosis of urinary tract infections (UTIs) is usually based on the results of urine culture, but it is time-consuming, labor-intensive and has a low sensitivity. The aim of this study was to develop multiplex high-resolution melting assay (MHRM) for the simultaneous detection of five common bacterial pathogens (Escherichia coli, Klebsiella pneumoniae, Staphylococcus saprophyticus, Enterococcus faecalis, and group B streptococci (GBS)) directly from urine samples. A total of 287 urine specimens were evaluated by HRM assay and the results were compared with the conventional culture method. Five different melt curves generated and differentiated five bacterial pathogens. The detection limit of the MHRM assay was 1.5 × 10³ CFU/ml for E. coli and K. pneumoniae and 1.5 × 10² CFU/ml for S. saprophyticus, E. faecalis and GBS. Compared to culture, the specificity of the MHRM assay ranged from 99.3 to 100%, and sensitivity 100% for all test pathogens. The MHRM assay developed in the current study might be functional tool for the diagnosis of UTIs and has the potential for direct detection of the organism in the clinical samples. Additionally, it creates results in less than 5 h, helping clinicians to start treatment with appropriate antimicrobial agents. This method could be a useful supplement to urine culture.

Epidemiology and antimicrobial resistance of staphylococci other than Staphylococcus aureus from domestic animals and livestock in Africa: a systematic review

Introduction

Staphylococci other than Staphylococcus aureus (SOSA) in animals are becoming more pathogenic and antibiotic resistant and can potentially disseminate to humans. However, there is little synthesized information regarding SOSA from animals in Africa. This systematic review provides a comprehensive overview of the epidemiology and antimicrobial resistance of SOSA in companion animals (pets) and livestock in Africa.

Method

This systematic review (PROSPERO-CRD42021252303) was conducted according to the PRISMA guidelines, and 75 eligible studies from 13 countries were identified until August 2022. Three electronic databases (Pubmed, Scopus and Web of Science) were employed.

Results

The frequently isolated SOSA were S. epidermidis, S. intermedius, S. pseudintermedius, S. xylosus, S. chromogenes, S. hyicus, M. sciuri, S. hominis, and S. haemolyticus. Thirty (40%) studies performed antibiotic susceptibility testing (AST). Penicillin (58%) and tetracycline (28%) resistance were most common across all SOSA with high rates of resistance to aminoglycosides, fluoroquinolones, and macrolides in some species. Resistance to last-resort antibiotics such as linezolid and fusidic acid were also reported. Limited data on strain typing and molecular resistance mechanisms precluded analysis of the clonal diversity of SOSA on the continent.

Conclusion

The findings of this review indicate that research on livestock-associated SOSA in Africa is lacking in some regions such as Central and Western Africa, furthermore, research on companion animals and more advanced methods for identification and strain typing of SOSA need to be encouraged.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier: CRD42021252303.

Application of Microfluidics for Bacterial Identification

Bacterial infections continue to pose serious public health challenges. Though anti-bacterial therapeutics are effective remedies for treating these infections, the emergence of antibiotic resistance has imposed new challenges to treatment. Often, there is a delay in prescribing antibiotics at initial symptom presentation as it can be challenging to clinically differentiate bacterial infections from other organisms (e.g., viruses) causing infection. Moreover, bacterial infections can arise from food, water, or other sources. These challenges have demonstrated the need for rapid identification of bacteria in liquids, food, clinical spaces, and other environments. Conventional methods of bacterial identification rely on culture-based approaches which require long processing times and higher pathogen concentration thresholds. In the past few years, microfluidic devices paired with various bacterial identification methods have garnered attention for addressing the limitations of conventional methods and demonstrating feasibility for rapid bacterial identification with lower biomass thresholds. However, such culture-free methods often require integration of multiple steps from sample preparation to measurement. Research interest in using microfluidic methods for bacterial identification is growing; therefore, this review article is a summary of current advancements in this field with a focus on comparing the efficacy of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and emerging spectroscopic methods.

MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology

Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.

Characterization of virulence and antimicrobial resistance genes of Aeromonas media strain SD/21-15 from marine sediments in comparison with other Aeromonas spp

Aeromonas media is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen associated with diarrhea in humans and skin ulceration in fish. In this study, we used whole genome sequencing to profile all antimicrobial resistance (AMR) and virulence genes found in A. media strain SD/21-15 isolated from marine sediments in Denmark. To gain a better understanding of virulence and AMR genes found in several A. media strains, we included 24 whole genomes retrieved from the public databanks whose isolates originate from different host species and environmental samples from Asia, Europe, and North America. We also compared the virulence genes of strain SD/21-15 with A. hydrophila, A. veronii, and A. salmonicida reference strains. We detected Msh pili, tap IV pili, and lateral flagella genes responsible for expression of motility and adherence proteins in all isolates. We also found hylA, hylIII, and TSH hemolysin genes in all isolates responsible for virulence in all isolates while the aerA gene was not detected in all A. media isolates but was present in A. hydrophila, A. veronii, and A. salmonicida reference strains. In addition, we detected LuxS and mshA-Q responsible for quorum sensing and biofilm formation as well as the ferric uptake regulator (Fur), heme and siderophore genes responsible for iron acquisition in all A. media isolates. As for the secretory systems, we found all genes that form the T2SS in all isolates while only the vgrG1, vrgG3, hcp, and ats genes that form parts of the T6SS were detected in some isolates. Presence of bla MOX-9 and bla OXA-427 β-lactamases as well as crp and mcr genes in all isolates is suggestive that these genes were intrinsically encoded in the genomes of all A. media isolates. Finally, the presence of various transposases, integrases, recombinases, virulence, and AMR genes in the plasmids examined in this study is suggestive that A. media has the potential to transfer virulence and AMR genes to other bacteria. Overall, we anticipate these data will pave way for further studies on virulence mechanisms and the role of A. media in the spread of AMR genes.

Aeromonas species isolated from aquatic organisms, insects, chicken, and humans in India show similar antimicrobial resistance profiles

Aeromonas species are Gram-negative bacteria that infect various living organisms and are ubiquitously found in different aquatic environments. In this study, we used whole genome sequencing (WGS) to identify and compare the antimicrobial resistance (AMR) genes, integrons, transposases and plasmids found in Aeromonas hydrophila, Aeromonas caviae and Aeromonas veronii isolated from Indian major carp (Catla catla), Indian carp (Labeo rohita), catfish (Clarias batrachus) and Nile tilapia (Oreochromis niloticus) sampled in India. To gain a wider comparison, we included 11 whole genome sequences of Aeromonas spp. from different host species in India deposited in the National Center for Biotechnology Information (NCBI). Our findings show that all 15 Aeromonas sequences examined had multiple AMR genes of which the Ambler classes B, C and D β-lactamase genes were the most dominant. The high similarity of AMR genes in the Aeromonas sequences obtained from different host species point to interspecies transmission of AMR genes. Our findings also show that all Aeromonas sequences examined encoded several multidrug efflux-pump proteins. As for genes linked to mobile genetic elements (MBE), only the class I integrase was detected from two fish isolates, while all transposases detected belonged to the insertion sequence (IS) family. Only seven of the 15 Aeromonas sequences examined had plasmids and none of the plasmids encoded AMR genes. In summary, our findings show that Aeromonas spp. isolated from different host species in India carry multiple AMR genes. Thus, we advocate that the control of AMR caused by Aeromonas spp. in India should be based on a One Health approach.

Towards the standardization of Enterococcus culture methods for waterborne antibiotic resistance monitoring: A critical review of trends across studies

Antibiotic resistance is a major 21^st century One Health (humans, animals, environment) challenge whose spread limits options to treat bacterial infections. There is growing interest in monitoring water environments, including surface water and wastewater, which have been identified as key recipients, pathways, and sources of antibiotic resistant bacteria (ARB). Aquatic environments also facilitate the transmission and amplification of ARB. Enterococcus spp. often carry clinically-important antibiotic resistance genes and are of interest as environmental monitoring targets. Enterococcus spp. are Gram-positive bacteria that are typically of fecal origin; however, they are also found in relevant environmental niches, with various species and strains that are opportunistic human pathogens. Although the value of environmental monitoring of antibiotic-resistant Enterococcus has been recognized by both national and international organizations, lack of procedural standardization has hindered generation of comparable data needed to implement integrated surveillance programs. Here we provide a comprehensive methodological review to assess the techniques used for the culturing and characterization of antibiotic-resistant Enterococcus across water matrices for the purpose of environmental monitoring. We analyzed 117 peer-reviewed articles from 33 countries across six continents. The goal of this review is to provide a critical analysis of (i) the various methods applied globally for isolation, confirmation, and speciation of Enterococcus isolates, (ii) the different methods for profiling antibiotic resistance among enterococci, and (iii) the current prevalence of resistance to clinically-relevant antibiotics among Enterococcus spp. isolated from various environments. Finally, we provide advice regarding a path forward for standardizing culturing of Enterococcus spp. for the purpose of antibiotic resistance monitoring in wastewater and wastewater-influenced waters within a global surveillance framework.

Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review

The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.

Use of MALDI-TOF MS to Discriminate between Aflatoxin B1-Producing and Non-Producing Strains of Aspergillus flavus

Aflatoxin B₁ (AFB₁) is one of the most toxic mycotoxins. One of the producers of AFB₁ is Aspergillus flavus. Therefore, its rapid identification plays a key role in various sectors of the food and feed industry. MALDI-TOF mass spectrometry is one of the fastest and most accurate methods today. Therefore, the aim of this research was to develop the rapid identification of producing and non-producing strains of A. flavus based on the entire mass spectrum. To accomplish the main goal a different confirmatory MALDI-TOF MS and TLC procedures such as direct AFB₁ identification by scraping from TLC plates, A. flavus mycelium, nutrient media around A. flavus growth, and finally direct AFB₁ identification from infected wheat and barley grains had to be conducted. In this experiment, MALDI-TOF mass spectrometry with various modifications was the main supporting technology. All confirmatory methods confirmed the presence of AFB₁ in the samples of aflatoxin-producing strains of A. flavus and vice versa; AFB₁ was not detected in the case of non-producing strains. Entire mass spectra (from 2 to 20 kDa) of aflatoxin-producing and non-producing A. flavus strains were collected, statistically analyzed and clustered. An in-depth analysis of the obtained entire mass spectra showed differences between AFB₁-producing and non-producing strains of A. flavus. Statistical and cluster analysis divided AFB₁-producing and non-producing strains of A. flavus into two monasteries. The results indicate that it is possible to distinguish between AFB₁ producers and non-producers by comparing the entire mass spectra using MALDI-TOF MS. Finally, we demonstrated that if there are established local AFB₁-producing and non-producing strains of A. flavus, the entire mass spectrum database identification of aflatoxigenic A. flavus strains can be even faster and cheaper, without the need to identify the toxin itself.

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.

Biomolecular Profiling by MALDI-TOF Mass Spectrometry in Food and Beverage Analyses

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has frequently been applied to the analysis of biomolecules. Its strength resides not only in compound identification but particularly in acquiring molecular profiles providing a high discriminating power. The main advantages include its speed, simplicity, versatility, minimum sample preparation needs, and a relatively high tolerance to salts. Other benefits are represented by the possibility of automation, high throughput, sensitivity, accuracy, and good reproducibility, allowing quantitative studies. This review deals with the prominent use of MALDI-TOF MS profiling in food and beverage analysis ranging from the simple detection of sample constituents to quantifications of marker compounds, quality control, and assessment of product authenticity. This review summarizes relevant discoveries that have been obtained with milk and milk products, edible oils, wine, beer, flour, meat, honey, and other alimentary products. Marker molecules are specified: proteins and peptides for milk, cheeses, flour, meat, wine and beer; triacylglycerols and phospholipids for oils; and low-molecular-weight metabolites for wine, beer and chocolate. Special attention is paid to sample preparation techniques and the combination of spectral profiling and statistical evaluation methods, which is powerful for the differentiation of samples and the sensitive detection of frauds and adulterations.

Bacterial polysaccharides-A big source for prebiotics and therapeutics

Bacterial polysaccharides are unique due to their higher purity, hydrophilic nature, and a finer three-dimensional fibrous structure. Primarily, these polymers provide protection, support, and energy to the microorganism, however, more recently several auxiliary properties of these biopolymers have been unmasked. Microbial polysaccharides have shown therapeutic abilities against various illnesses, augmented the healing abilities of the herbal and Western medicines, improved overall health of the host, and have exerted positive impact on the growth of gut dwelling beneficial bacteria. Specifically, the review is discussing the mechanism through which bacterial polysaccharides exert anti-inflammatory, antioxidant, anti-cancer, and anti-microbial properties. In addition, they are holding promising application in the 3D printing. The review is also discussing a perspective about the metagenome-based screening of polysaccharides, their integration with other cutting-edge tools, and synthetic microbiome base intervention of polysaccharides as a strategy for prebiotic intervention. This review has collected interesting information about the bacterial polysaccharides from Google Scholar, PubMed, Scopus, and Web of Science databases. Up to our knowledge, this is the first of its kind review article that is summarizing therapeutic, prebiotics, and commercial application of bacterial polysaccharides.

A Review on Data Fusion of Multidimensional Medical and Biomedical Data

Data fusion aims to provide a more accurate description of a sample than any one source of data alone. At the same time, data fusion minimizes the uncertainty of the results by combining data from multiple sources. Both aim to improve the characterization of samples and might improve clinical diagnosis and prognosis. In this paper, we present an overview of the advances achieved over the last decades in data fusion approaches in the context of the medical and biomedical fields. We collected approaches for interpreting multiple sources of data in different combinations: image to image, image to biomarker, spectra to image, spectra to spectra, spectra to biomarker, and others. We found that the most prevalent combination is the image-to-image fusion and that most data fusion approaches were applied together with deep learning or machine learning methods.

Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in veterinary medicine: Recent advances (2019-present)

Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a valuable laboratory tool for rapid diagnostics, research, and exploration in veterinary medicine. While instrument acquisition costs are high for the technology, cost per sample is very low, the method requires minimal sample preparation, and analysis is easily conducted by end-users requiring minimal training. Matrix-assisted laser desorption ionization-time-of-flight MS has found widespread application for the rapid identification of microorganisms, diagnosis of dermatophytes and parasites, protein/lipid profiling, molecular diagnostics, and the technique demonstrates significant promise for 2D chemical mapping of tissue sections collected postmortem. In this review, an overview of the MALDI-TOF technique will be reported and manuscripts outlining current uses of the technology for veterinary science since 2019 will be summarized. The article concludes by discussing gaps in knowledge and areas of future growth.

Proteomic evaluation of nanotoxicity in aquatic organisms: A review

The alteration of organisms protein functions by engineered nanoparticles (ENPs) is dependent on the complex interplay between their inherent physicochemical properties (e.g., size, surface coating, shape) and environmental conditions (e.g., pH, organic matter). To date, there is increasing interest on the use of 'omics' approaches, such as proteomics, genomics, and others, to study ENPs-biomolecules interactions in aquatic organisms. However, although proteomics has recently been applied to investigate effects of ENPs and associated mechanisms in aquatic organisms, its use remain limited. Herein, proteomics techniques widely applied to investigate ENPs-protein interactions in aquatic organisms are reviewed. Data demonstrates that 2DE and mass spectrometry and/or their combination, thereof, are the most suitable techniques to elucidate ENPs-protein interactions. Furthermore, current status on ENPs and protein interactions, and possible mechanisms of nanotoxicity with emphasis on those that exert influence at protein expression levels, and key influencing factors on ENPs-proteins interactions are outlined. Most reported studies were done using synthetic media and essay protocols and had wide variability (not standardized); this may consequently limit data application in actual environmental systems. Therefore, there is a need for studies using realistic environmental concentrations of ENPs, and actual environmental matrixes (e.g., surface water) to aid better model development of ENPs-proteins interactions in aquatic systems.