Identification of Adult Fasciola spp. Using Matrix-Assisted Laser/Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry

Application of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for Identification of Foodborne Pathogens: Current Developments and Future Trends

Foodborne pathogens have gained sustained public attention, exerted significant pressure on food manufacturers, and posed serious health risks to human. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been employed for quick and accurate identification of microorganisms in the prevention of foodborne epidemics in recent years. Herein, we first summarize the principle of MALDI and its workflow for foodborne pathogens. Subsequently, we review the recent progress and applications of MALDI-TOF MS in foodborne pathogen determination. Additionally, we outline the expanded utilization of MALDI-based techniques for the identification of closely related species. We also assess the current gaps and propose possible solutions to address the existing challenges. MALDI-TOF MS is a promising biotool for rapid and accurate identification of foodborne microbes at the species and genus level in food samples. Database expansion and direct quantification of spoilage microbes are two promising areas for future progress in MALDI-TOF MS applications.

Ornithodoros sonrai Soft Ticks and Associated Bacteria in Senegal

The soft ticks, Ornithodoros sonrai, are known as vectors of the tick-borne relapsing fever caused by Borrelia spp. and have also been reported to carry other micro-organisms. The objective of this study was to collect and to identify O. sonrai ticks and to investigate the micro-organisms associated with them. In 2019, an investigation of burrows within human dwellings was conducted in 17 villages in the Niakhar area and in 15 villages in the Sine-Saloum area in the Fatick region of Senegal. Ticks collected from the burrows were identified morphologically and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Micro-organism screening was performed by bacteria-specific qPCR and some identifications were made by standard PCR and gene sequencing. O. sonrai ticks were found in 100% (17/17) of the villages surveyed in the Niakhar area and in 66% (10/15) of the villages in the Sine-Saloum area. A total of 1275 soft tick specimens were collected from small mammal burrows. The ticks collected were morphologically identified as O. sonrai. About 20% (259/1275) of the specimens were also submitted to MALDI-TOF MS for identification. Among the resulting MS profiles, 87% (139/159) and 95% (95/100) were considered good quality specimens, preserved in alcohol and silica gel, respectively. All spectra of good quality were tested against our MALDI-TOF MS arthropod spectra database and identified as O. sonrai species, corroborating the morphological classification. The carriage of four micro-organisms was detected in the ticks with a high prevalence of Bartonella spp., Anaplasmataceae, and Borrelia spp. of 35, 28, and 26%, respectively, and low carriage of Coxiella burnetii (2%). This study highlights the level of tick infestation in domestic burrows, the inventory of pathogens associated with the O. sonrai tick, and the concern about the potential risk of tick involvement in the transmission of these pathogens in Senegal.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for differential identification of adult Schistosoma worms

BACKGROUND

Schistosomiasis is a major neglected tropical disease that affects up to 250 million individuals worldwide. The diagnosis of human schistosomiasis is mainly based on the microscopic detection of the parasite's eggs in the feces (i.e., for Schistosoma mansoni or Schistosoma japonicum) or urine (i.e., for Schistosoma haematobium) samples. However, these techniques have limited sensitivity, and microscopic expertise is waning outside endemic areas. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has become the gold standard diagnostic method for the identification of bacteria and fungi in many microbiological laboratories. Preliminary studies have recently shown promising results for parasite identification using this method. The aims of this study were to develop and validate a species-specific database for adult Schistosoma identification, and to evaluate the effects of different storage solutions (ethanol and RNAlater) on spectra profiles.

METHODS

Adult worms (males and females) of S. mansoni and S. japonicum were obtained from experimentally infected mice. Species identification was carried out morphologically and by cytochrome oxidase 1 gene sequencing. Reference protein spectra for the creation of an in-house MALDI-TOF MS database were generated, and the database evaluated using new samples. We employed unsupervised (principal component analysis) and supervised (support vector machine, k-nearest neighbor, Random Forest, and partial least squares discriminant analysis) machine learning algorithms for the identification and differentiation of the Schistosoma species.

RESULTS

All the spectra were correctly identified by internal validation. For external validation, 58 new Schistosoma samples were analyzed, of which 100% (58/58) were correctly identified to genus level (log score values ≥ 1.7) and 81% (47/58) were reliably identified to species level (log score values ≥ 2). The spectra profiles showed some differences depending on the storage solution used. All the machine learning algorithms classified the samples correctly.

CONCLUSIONS

MALDI-TOF MS can reliably distinguish adult S. mansoni from S. japonicum.

Recent Advances and Potential Future Applications of MALDI-TOF Mass Spectrometry for Identification of Helminths

Helminth infections caused by nematodes, trematodes, and cestodes are major neglected tropical diseases and of great medical and veterinary relevance. At present, diagnosis of helminthic diseases is mainly based on microscopic observation of different parasite stages, but microscopy is associated with limited diagnostic accuracy. Against this background, recent studies described matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry as a potential, innovative tool for helminth identification and differentiation. MALDI-TOF mass spectrometry is based on the analysis of spectra profiles generated from protein extracts of a given pathogen. It requires an available spectra database containing reference spectra, also called main spectra profiles (MSPs), which are generated from well characterized specimens. At present, however, there are no commercially available databases for helminth identification using this approach. In this narrative review, we summarize recent developments and published studies between January 2019 and September 2022 that report on the use of MALDI-TOF mass spectrometry for helminths. Current challenges and future research needs are identified and briefly discussed.

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.

Development and validation of main spectral profile for rapid identification of Yersinia ruckeri isolated from Atlantic salmon using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows rapid and reliable identification of microorganisms. The accuracy of bacterial identification using MALDI-TOF MS depends on main spectral profiles (MSPs) provided in a quality-assured commercial reference library, which requires ongoing improvement. This study aimed to develop and validate an in-house MALDI-TOF MS MSP to rapidly identify Yersinia ruckeri isolated from Atlantic salmon (Salmo salar). The novel MSP was prepared using an isolate of Y. ruckeri recovered from Atlantic salmon and confirmed by 16S rRNA gene sequencing. Subsequently, a validation set which comprises 29 isolates of Y. ruckeri were examined from three fishes: Atlantic salmon (Salmo salar) (n = 26), American eel (Anguilla rostrata) (n = 1), and Atlantic cod (Gadus morhua) (n = 2). These isolates were randomly selected from the Atlantic Veterinary College, Aquatic Diagnostic Services Bacteriology Laboratory's culture collection to validate the novel MSP. Analytical sensitivity of MALDI-TOF MS using the novel MSP to identify the validation set was 86.2%. Repeatability was assessed by acquiring spectra from 30 different spots of a randomly-selected isolate of Y. ruckeri, and analyzed spectra from each spot were compared against the novel MSP. The coefficient of variation was 3.3%. The novel MSP clustered with Bruker MSPs (n = 3) of Y. ruckeri in the reference library and did not falsely identify any closely related bacteria to Y. ruckeri. This study reports the development of a novel MSP of high analytical sensitivity and specificity for rapid identification of Y. ruckeri using MALDI-TOF MS.

The Use of MALDI-TOF MS as a Diagnostic Tool for Adult Trichuris Species

Trichuriasis is considered a neglected tropical disease, being the second most common helminthiasis in humans. Detection of Trichuris in routine diagnosis is usually done by microscopic detection of eggs in fecal samples. Other molecular analyses are more reliable and could be used, but these analyses are not routinely available in clinical microbiology laboratories. The use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is increasing since the last decades due to its recent evidence as a potential role for reliable identification of microorganisms and a few nematodes. But, for parasites detection, normalized protocols and the acquisition and introduction of new species to the database are required. We carried out a preliminary study confirming the usefulness of MALDI-TOF MS for the rapid and reliable identification of Trichuris suis used as control and the creation of an internal database. To create main spectra profiles (MSPs), the different parts of five whipworms (esophagus and intestine) were used, developing different tests to verify the repeatability and reproducibility of the spectra. Thus, to validate the new internal database, 20 whipworms, separating the esophagus and intestine, were used, of which 100% were accurately identified as T. suis, but could not distinguish between both parts of the worm. Log score values ranged between 1.84 and 2.36, meaning a high-quality identification. The results confirmed that MALDI-TOF MS was able to identify Trichuris species. Additionally, a MALDI-TOF MS profile of T. suis proteome was carried out to develop the first internal database of spectra for the diagnosis of trichuriasis and other Trichuris spp.

Morphological, Molecular and MALDI-TOF MS Identification of Bedbugs and Associated Wolbachia Species in Rural Senegal

Bed bugs are known to carry several microorganisms. The purpose of this study was to assess the prevalence of bed bug infestation in two rural areas of Senegal and determine the species present in the population. A screening was conducted to detect some arthropod associated pathogenic bacteria in bed bugs and to evaluate the prevalence of endosymbiont carriage. One survey took place in 17 villages in Niakhar and two surveys in Dielmo and Ndiop and surroundings area in the same 20 villages. Bed bugs collected were identified morphologically and by MALDI-TOF MS tools. Microorganisms screening was performed by qPCR and confirmed by sequencing. During the survey in the Niakhar region, only one household 1/255 (0.4%) in the village of Ngayokhem was found infested by bed bugs. In a monitoring survey of the surroundings of Dielmo and Ndiop area, high prevalence was found during the two rounds of surveys in 65/314 (21%) in 16/20 villages (January-March) and 93/351 (26%) in 19/20 villages (December). All bed bugs were morphologically identified as the species Cimex hemipterus, of which 285/1,637 (17%) were randomly selected for MALDI-TOF MS analysis and bacteria screening. Among the Bacteria tested only Wolbachia (Alphaproteobacteria, Rickettsiales, Rickettsiaceae) DNA was found in 248/276 (90%) of the bedbugs. We briefly describe a high level of non-generalized bed bug infestation in rural Senegal and the diversity of Wolbachia strains carried by C. hemipterus. This study opens perspectives for raising household awareness of bed bug infestations and possibilities for appropriate control.

A Comparative Study of Fasciola Parasite Infection Rates in Local and Imported Sheep in Jeddah, Saudi Arabia

Fasciola hepatica and Fasciola gigantica are two trematodes (liver flukes) that cause water- and food-borne disease Fasciolosis. Many animals are involved in the life cycle of the Fasciola spp., such as sheep, cattle, and camels, and humans are the definitive host. This work investigated the prevalence of Fasciola among imported and local slaughtered sheep and the relation between infection rate and seasons of the year. A total of 720,290 local and imported sheep (251,701 and 468,489, respectively) were slaughtered in a Jeddah slaughterhouse (Western region of Saudi Arabia) over the periods of 2017-2018, 2018-2019, and 2019-2020. In the three years of inspection, the infection rate at slaughter was higher among imported than local sheep. In 2017-2018, both local and imported sheep had the highest level of infection in the spring and the lowest in the winter. However, in 2018-2019, the highest rate of infection for both was documented in the summer and the lowest in the winter. Lastly, in 2019-2020, the highest rate of infection for local sheep was observed in the summer of 2020 and the lowest rate of infection was observed in the spring of 2020. Among imported sheep, the highest rate of infection was in the summer and the lowest was in winter for both 2019 and 2020. To control this disease, there is the need to apply for successful integrated programs and practice adaptive management techniques.

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

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

Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study

There is a need for active molecular surveillance of human and veterinary Campylobacter infections. However, sequencing of all isolates is associated with high costs and a considerable workload. Thus, there is a need for a straightforward complementary tool to prioritize isolates to sequence. In this study, we proposed to investigate the ability of MALDI-TOF MS to pre-screen C. jejuni genetic diversity in comparison to MLST and cgMLST. A panel of 126 isolates, with 10 clonal complexes (CC), 21 sequence types (ST) and 42 different complex types (CT) determined by the SeqSphere+ cgMLST, were analysed by a MALDI Biotyper, resulting into one average spectra per isolate. Concordance and discriminating ability were evaluated based on protein profiles and different cut-offs. A random forest algorithm was trained to predict STs. With a 94% similarity cut-off, an AWC of 1.000, 0.933 and 0.851 was obtained for MLST_CC, MLST_ST and cgMLST profile, respectively. The random forest classifier showed a sensitivity and specificity up to 97.5% to predict four different STs. Protein profiles allowed to predict C. jejuni CCs, STs and CTs at 100%, 93% and 85%, respectively. Machine learning and MALDI-TOF MS could be a fast and inexpensive complementary tool to give an early signal of recurrent C. jejuni on a routine basis.

Evaluating Different Storage Media for Identification of Taenia saginata Proglottids Using MALDI-TOF Mass Spectrometry

Taenia saginata is a helminth that can cause taeniasis in humans and cysticercosis in cattle. A species-specific diagnosis and differentiation from related species (e.g., Taenia solium) is crucial for individual patient management and disease control programs. Diagnostic stool microscopy is limited by low sensitivity and does not allow discrimination between T. saginata and T. solium. Molecular diagnostic approaches are not routinely available outside research laboratories. Recently, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) was proposed as a potentially suitable technique for species-specific helminth diagnosis. However, standardized protocols and commercial databases for parasite identification are currently unavailable, and pre-analytical factors have not yet been assessed. The purpose of this study was to employ MALDI-TOF MS for the identification of T. saginata proglottids obtained from a human patient, and to assess the effects of different sample storage media on the technique’s diagnostic accuracy. We generated T. saginata-specific main spectral profiles and added them to an in-house database for MALDI-TOF MS-based diagnosis of different helminths. Based on protein spectra, T. saginata proglottids could be successfully differentiated from other helminths, as well as bacteria and fungi. Additionally, we analyzed T. saginata proglottids stored in (i) LC–MS grade water; (ii) 0.45% sodium chloride; (iii) 70% ethanol; and (iv) 37% formalin after 2, 4, 6, 8, 12, and 24 weeks of storage. MALDI-TOF MS correctly identified 97.2–99.7% of samples stored in water, sodium chloride, and ethanol, with log-score values ≥2.5, thus indicating reliable species identification. In contrast, no protein spectra were obtained for samples stored in formalin. We conclude that MALDI-TOF-MS can be successfully employed for the identification of T. saginata, and that water, sodium chloride, and ethanol are equally effective storage solutions for prolonged periods of at least 24 weeks.

Development of a Novel Method for Identification of Alaria alata Mesocercariae by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Alaria (A.) alata mesocercariae (AM) have increasingly appeared as incidental findings during the mandatory inspection of wild boars for Trichinella in many European countries. An Alaria spp.-specific PCR is available for the identification of AM; however, it is time- and cost-intensive. Therefore, we propose a rapid and cost-efficient MALDI-TOF assay for the identification of AM in wild boar meat that can be applied in routine diagnostics. In this study, a fast and methodologically simple protocol for the protein extraction of AM from different host species in different countries was established, and an AM-specific reference spectra database was created as part of the ongoing development of an existing Trichinella spp. database. A formic acid protein extraction was performed after pooling 10 AM from the same host individual. In total, 61 main spectra profiles (MSPs) from different host individuals were stored in an AM-specific MSP library. The cluster analysis of these 61 MSPs indicated a possible variation within the A. alata species with a tentative association with the geographical origin of the host, but not the host species. This MALDI-TOF assay allows for a fast verification of the AM isolates, which is the next step in the development of a universal database for the identification of several parasites isolated from meat.

Update on Coagulase-Negative Staphylococci-What the Clinician Should Know

Coagulase-negative staphylococci (CoNS) are among the most frequently recovered bacteria in routine clinical care. Their incidence has steadily increased over the past decades in parallel to the advancement in medicine, especially in regard to the utilization of foreign body devices. Many new species have been described within the past years, while clinical information to most of those species is still sparse. In addition, interspecies differences that render some species more virulent than others have to be taken into account. The distinct populations in which CoNS infections play a prominent role are preterm neonates, patients with implanted medical devices, immunodeficient patients, and those with other relevant comorbidities. Due to the property of CoNS to colonize the human skin, contamination of blood cultures or other samples occurs frequently. Hence, the main diagnostic hurdle is to correctly identify the cases in which CoNS are causative agents rather than contaminants. However, neither phenotypic nor genetic tools have been able to provide a satisfying solution to this problem. Another dilemma of CoNS in clinical practice pertains to their extensive antimicrobial resistance profile, especially in healthcare settings. Therefore, true infections caused by CoNS most often necessitate the use of second-line antimicrobial drugs.

Trematode Proteomics: Recent Advances and Future Directions

Trematodes cause disease in millions of people worldwide, but the absence of commercial vaccines has led to an over-reliance on a handful of monotherapies to control infections. Since drug-resistant fluke populations are emerging, a deeper understanding of parasite biology and host interactions is required to identify new drug targets and immunogenic vaccine candidates. Mass spectrometry-based proteomics represents a key tool to that end. Recent studies have capitalised on the wider availability of annotated helminth genomes to achieve greater coverage of trematode proteomes and discover new aspects of the host-parasite relationship. This review focusses on these latest advances. These include how the protein components of fluke extracellular vesicles have given insight into their biogenesis and cellular interactions. In addition, how the integration of transcriptome/proteome datasets has revealed that the expression and secretion of selected families of liver fluke virulence factors and immunomodulators are regulated in accordance with parasite development and migration within the mammalian host. Furthermore, we discuss the use of immunoproteomics as a tool to identify vaccine candidates associated with protective antibody responses. Finally, we highlight how established and emerging technologies, such as laser microdissection and single-cell proteomics, could be exploited to resolve the protein profiles of discrete trematode tissues or cell types which, in combination with functional tools, could pinpoint optimal targets for fluke control.