Application of MALDI-TOF MS for the Identification of Food Borne Bacteria

Monitoring and controlling bacteria in cleanrooms of pharmaceutical plant model: an in vitro study

This work aims to screen the major species of bacteria distributed in the filling area in one of the new pharmaceutical facilities in the 6th of October city in Egypt and their phylogenic relationship. One hundred percent of collected Gram-positive and Gram-negative isolates of bacteria were sensitive to Levofloxacin. There were five Gram-positive multidrug-resistant (MDR) bacterial isolates and one Gram-negative (MDR) bacterial isolate (three (from personnel), two (from surface), and one (from air)). The five Gram-positive MDR bacterial isolates were resistant to Tobramycin, Gentamicin, Piperacillin, Cefaclor, and Amikacin while the one Gram-negative MDR bacterial isolate was resistant to Ceftazidime, Cefotaxime, Tobramycin, Gentamicin, Piperacillin, Cefoperazone/Sulbactam, Ofloxacin, and Polymixin b. The existence of multidrug-resistant bacteria inside cleanrooms of pharmaceutical plants signifies a life-threatening danger on human through generating contaminated drugs and/or vaccines that undoubtedly harm the consumer's healthiness. The technique of 16SrRNA gene sequencing was used to identify multidrug-resistant bacterial isolates. All tested disinfectants were bactericidal except Dettol that was found to be a bacteriostatic agent and had an anti-biofilm effect. Clorox was the most potent disinfectant that had the least MIC and MBC of 0.0002% and 0.0004%, respectively. Ethanol and Klericide were excellent sanitizing agents. The strongest biofilm formed by Staphylococcus gallinarum strain MN1812 was disrupted by Clorox with a concentration of 0.000098%. Only Dettol with a concentration of 6.3% achieved the highest disruption for the biofilm of Staphylococcus gallinarum strain NM2009. Staphylococcus gallinarum strain MN1812 followed by Bacillus amyloliquefaciens showed the highest adhesion and invasion efficiencies to Caco-cells among the investigated bacterial strains. Klericide and Dettol mixture showed more anti adhesion and invasion effects against Staphylococcus gallinarum strain NM2009 and strain MN1812 and Pseudomonas putida compared to using Klericide alone. Ethanol and Klericide had the least contact time (30 s) against most of the tested bacteria.

Isolation, identification, and characterization of thermophilic lactic acid bacteria isolated from whey of Kars Kashar cheeses

Kars Kashar cheese is an artisanal pasta-filata type cheese and geographically marked in Eastern Anatolia of Turkey. The aims of this research were to determine for the first time thermophilic lactic acid bacteria (LAB) of Kars Kashar cheese and characterize the technological properties of obtained isolates. In our research, a number of 15 samples of whey were collected from the different villages in Kars. These samples were incubated at 45 °C and used as the source material for isolating thermophilic LAB. A total of 250 colonies were isolated from thermophilic whey, and 217 of them were determined to be presumptive LAB based on their Gram staining and catalase test. A total of 170 isolates were characterized by their phenotypic properties and identified using the MALDI-TOF mass spectrometry method. Phenotypic identification of isolates displayed that Enterococcus and Lactobacillus were the predominant microbiota. According to MALDI-TOF MS identification, 89 isolates were identified as Enterococcus (52.35%), 57 isolates as Lactobacillus (33.53%), 23 isolates as Streptococcus (13.53%), and one isolate as Lactococcus (0.59%). All thermophilic LAB isolates were successfully identified to the species level and it has been observed that MALDI-TOF MS can be successfully used for the identification of selected LAB. The acidification and proteolytic activities of the isolated thermophilic LAB were examined, and the isolates designated for use as starter cultures were also genotypically defined.

Line image sensor-based colony fingerprinting system for rapid pathogenic bacteria identification

The rapid identification of pathogenic bacteria is crucial across various industries, including food or beverage manufacturing. Bacterial microcolony image-based classification has emerged as a promising approach to expedite identification, automate inspections, and reduce costs. However, conventional imaging methods have significant practical limitations, namely low throughput caused by the limited imaging range and slow imaging speed. To address these challenges, we developed an imaging system based on a line image sensor for rapid and wide-field imaging compared to existing colony imaging methods. This system can image a standard Petri dish (92 mm in diameter) completely within 22 s, successfully acquiring bacterial microcolony images. This process yielded a set of discrimination parameters termed as colony fingerprints, which were employed for machine learning. We demonstrated the performance of our system by identifying Staphylococcus aureus in food products using a machine learning model trained on a colony fingerprint dataset of 15 species from 9 genera, including foodborne pathogens. While conventional mass spectrometry-based methods require 24 h of incubation, our colony fingerprinting approach achieved 96% accuracy in just 10 h of incubation. Line image sensor offer high imaging speeds and scalability, allowing for swift and straightforward microbiological testing, eliminating the need for specialized expertise and overcoming the limitations of conventional methods. This innovation marks a transformative shift in industrial applications.

The usefulness of the MALDI-TOF MS technique in the determination of dairy samples' microbial composition: comparison of the new EXS 2600 system with MALDI Biotyper platform

This study compared the EXS 2600 system with the MALDI Biotyper for identifying microorganisms in dairy samples. Of the 196 bacterial isolates from milk, whey, buttermilk, cream, and dairy wastewater, the species and genus consistent identification between two systems showed 74% and 99%, respectively. However, the level of species identification rate exhibited a difference, which was higher in Zybio than in Bruker-76.0% and 66.8%, respectively. Notably, the EXS 2600 system performed better with certain yeast species and H. alvei, while the Biotyper excelled with Pseudomonas bacteria. Unique microbial compositions were found in 85% of dairy samples, with whey and buttermilk having the highest diversity. This research highlights the EXS 2600's potential as a reliable dairy microbial identification tool and underscores the need for a more diverse and comprehensive spectral database, despite the database's focus on clinical applications (as announced).

Dibutyl phthalate degradation by Paenarthrobacter ureafaciens PB10 through downstream product myristic acid and its bioremediation potential in contaminated soil

Dibutyl phthalate (DBP) is a widely used plasticizer to make plastic flexible and long-lasting. It is easily accessible in a broad spectrum of environments as a result of the rising level of plastic pollution. This compound is considered a top-priority toxicant and persistent organic pollutant by international environmental agencies for its endocrine disruptive and carcinogenic propensities. To mitigate the DBP in the soil, one DBP-degrading bacterial strain was isolated from a plastic-polluted landfill and identified as Paenarthrobacter ureafaciens PB10 by 16S rRNA gene sequence-based homology. The strain was found to develop a distinct transparent halo zone around grown colonies on an agar plate supplemented with DBP. The addition of yeast extract (100 mg/L) as a nutrient source accelerated cell biomass production and DBP degradation rate; however, the presence of glucose suppressed DBP degradation by the PB10 strain without affecting its ability to proliferate. The strain PB10 was efficient in eliminating DBP under various pH conditions (5.0-8.0). Maximum cell growth and degradation of 99.49% at 300 mg/L DBP were achieved in 72 h at the optimized mineral salt medium (MS) conditions of pH 7.0 and 32 °C. Despite that, when the concentration of DBP rose to 3000 mg/L, the DBP depletion rate was measured at 79.34% in 72 h. Some novel intermediate metabolites, like myristic acid, hexadecanoic acid, stearic acid, and the methyl derivative of 4-hydroxyphenyl acetate, along with monobutyl phthalate and phthalic acid, were detected in the downstream degradation process of DBP through GC-MS profiling. Furthermore, in synchronization with native soil microbes, this PB10 strain successfully removed a notable amount of DBP (up to 54.11%) from contaminated soil under microcosm study after 10 d. Thus, PB10 has effective DBP removal ability and is considered a potential candidate for bioremediation in DBP-contaminated sites.

Recent Advances in the Detection of Food Toxins Using Mass Spectrometry

Edibles are the only source of nutrients and energy for humans. However, ingredients of edibles have undergone many physicochemical changes during preparation and storage. Aging, hydrolysis, oxidation, and rancidity are some of the major changes that not only change the native flavor, texture, and taste of food but also destroy the nutritive value and jeopardize public health. The major reasons for the production of harmful metabolites, chemicals, and toxins are poor processing, inappropriate storage, and microbial spoilage, which are lethal to consumers. In addition, the emergence of new pollutants has intensified the need for advanced and rapid food analysis techniques to detect such toxins. The issue with the detection of toxins in food samples is the nonvolatile nature and absence of detectable chromophores; hence, normal conventional techniques need additional derivatization. Mass spectrometry (MS) offers high sensitivity, selectivity, and capability to handle complex mixtures, making it an ideal analytical technique for the identification and quantification of food toxins. Recent technological advancements, such as high-resolution MS and tandem mass spectrometry (MS/MS), have significantly improved sensitivity, enabling the detection of food toxins at ultralow levels. Moreover, the emergence of ambient ionization techniques has facilitated rapid in situ analysis of samples with lower time and resources. Despite numerous advantages, the widespread adoption of MS in routine food safety monitoring faces certain challenges such as instrument cost, complexity, data analysis, and standardization of methods. Nevertheless, the continuous advancements in MS-technology and its integration with complementary techniques hold promising prospects for revolutionizing food safety monitoring. This review discusses the application of MS in detecting various food toxins including mycotoxins, marine biotoxins, and plant-derived toxins. It also explores the implementation of untargeted approaches, such as metabolomics and proteomics, for the discovery of novel and emerging food toxins, enhancing our understanding of potential hazards in the food supply chain.

Unveiling the potential of proteomics in addressing food and feed safety challenges

The food and feed sector in Europe is rapidly evolving to address contemporary challenges, striving for fairer, safer, greener and more sustainable food systems. This includes the exploration of new protein sources for human consumption and animal feed such as protein derived from insects, algae or novel plant-derived proteins, and the re-evaluation of existing sources like processed animal protein (PAP). To generate reliable data on the diverse array of emerging protein sources for future food and feed safety assessments, a growing demand for the development and implementation of advanced analytical techniques exists. New approach methodologies (NAMs) including, mass spectrometry (MS)-based proteomics methods have been emerging as valuable techniques which potentially can be implemented in regulatory laboratory settings to complement conventional approaches in this realm. These MS-driven strategies have already proven their utility in diverse applications, including the detection of prohibited substances in feed, identification of allergens, differentiation of fish species in complex mixtures for fraud detection and the verification of novel foods and alternative protein sources. This EU-FORA programme was focused on three core objectives namely: (i) the training of the fellow in utilising MS-based proteomics for food and feed safety analyses, (ii) the involvement of the fellow in the development of standardised operating procedures (SOP) for targeted and non-targeted proteomic MS-based workflows for species and tissues specific PAP identification in a national reference laboratory (NRL) and (iii) the transfer and implementation of MS-based approaches and standardised protocols for PAP analysis at the fellow's home institution. Altogether, this programme facilitates the broadening and diversification of use of MS-based proteomic methodologies for reinforcing their significance within the domains of food and feed safety research and regulatory science applications.

Peptide barcode of multidrug-resistant strains of Neisseria gonorrhoeae isolated from patients in Thailand

The emergence of multidrug-resistant strains of Neisseria gonorrhoeae constitutes a serious threat to public health. The present study aimed to investigate peptidome-based biomarkers of multidrug-resistant N. gonorrhoeae, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography tandem mass spectrometry (LC-MS). The peptide barcode database of multidrug resistant N. gonorrhoeae was generated from the whole-cell peptides of 93 N. gonorrhoeae isolated from patients in Thailand. The dendrogram of 93 independent isolates of antibiotic-resistant N. gonorrhoeae revealed five distinct clusters including azithromycin resistance group (AZ), ciprofloxacin resistance group (C), ciprofloxacin and penicillin resistance group (CP), ciprofloxacin and tetracycline resistance group (CT), ciprofloxacin, penicillin and tetracycline resistance group (CPT). The peptidomes of all clusters were comparatively analyzed using a high-performance liquid chromatography-mass spectrometry method (LC-MS). Nine peptides derived from 9 proteins were highly expressed in AZ (p value < 0.05). These peptides also played a crucial role in numerous pathways and showed a strong relationship with the antibiotic resistances. In conclusion, this study showed a rapid screening of antibiotic-resistant N. gonorrhoeae using MALDI-TOF MS. Additionally, potential specific peptidome-based biomarker candidates for AZ, C, CP, CT and CPT-resistant N. gonorrhoeae were identified.

Determination of Pathogens by Electrophoretic and Spectrometric Techniques

In modern medical diagnostics, where analytical chemistry plays a key role, fast and accurate identification of pathogens is becoming increasingly important. Infectious diseases pose a growing threat to public health due to population growth, international air travel, bacterial resistance to antibiotics, and other factors. For instance, the detection of SARS-CoV-2 in patient samples is a key tool to monitor the spread of the disease. While there are several techniques for identifying pathogens by their genetic code, most of these methods are too expensive or slow to effectively analyze clinical and environmental samples that may contain hundreds or even thousands of different microbes. Standard approaches (e.g., culture media and biochemical assays) are known to be very time- and labor-intensive. The purpose of this review paper is to highlight the problems associated with the analysis and identification of pathogens that cause many serious infections. Special attention was paid to the description of mechanisms and the explanation of the phenomena and processes occurring on the surface of pathogens as biocolloids (charge distribution). This review also highlights the importance of electromigration techniques and demonstrates their potential for pathogen pre-separation and fractionation and demonstrates the use of spectrometric methods, such as MALDI-TOF MS, for their detection and identification.

Multi-point scanning confocal Raman spectroscopy for accurate identification of microorganisms at the single-cell level

Raman spectroscopy has been widely used for microbial analysis due to its exceptional qualities as a rapid, simple, non-invasive, reproducible, and real-time monitoring tool. The Raman spectrum of a cell is a superposition of the spectral information of all biochemical components in the laser focus. In the case where the microbial size is larger than the laser spot size, the Raman spectrum measured from a single-point within a cell cannot capture all biochemical information due to the spatial heterogeneity of microorganisms. In this work, we have proposed a method for the accurate identification of microorganisms using multi-point scanning confocal Raman spectroscopy. Through an image recognition algorithm and the control of a high-precision motorized stage, Raman spectra can be integrated at one time to measure the multi-point biochemical information of microorganisms. This solves the problem that the measured single microbial cells are of different sizes, and the laser spot of the confocal Raman system is not easy to change. Here, the single-cell Raman spectra of three Escherichia coli and seven Lactobacillus species were measured separately. The commonly used supervised classification method, support vector machine (SVM), was applied to compare the data based on the single-point spectra and multi-point scanning spectra. Multi-point spectra showed superior performance in terms of their accuracy and recall rates compared with single-point spectra. The results show that multi-point scanning confocal Raman spectra can be used for more accurate species classification at different taxonomic levels, which is of great importance in species identification.

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.

Occurrence of Campylobacter in Faeces, Livers and Carcasses of Wild Boars Hunted in Tuscany (Italy) and Evaluation of MALDI-TOF MS for the Identification of Campylobacter Species

A total of 193 wild boars hunted in Tuscany, an Italian region with a high presence of wild ungulates, were examined to assess the occurrence of Campylobacter species in faeces, bile, liver and carcasses, with the aim of clarifying their contribution to human infection through the food chain. Campylobacter spp. were found in 44.56% of the animals, 42.62% of the faecal samples, 18.18% of the carcass samples, 4.81% of the liver tissues and 1.97% of the bile samples. The Campylobacter species genotypically identified were C. coli, C. lanienae, C. jejuni and C. hyointestinalis. The prevalent species transpired to be C. coli and C. lanienae, which were isolated from all the matrices; C. jejuni was present in faeces and liver, while C. hyointestinalis only in faeces. Identification was carried out by matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) on 66 out of 100 isolates identified genotypically, and the technique yielded unsatisfactory results in the case of C. lanienae, which is responsible for sporadic human disease cases. The level of Campylobacter spp. contamination of meat and liver underlines the need to provide appropriate food safety information to hunters and consumers.

Integration of Non-targeted Proteomics Mass Spectrometry with Machine Learning for Screening Cooked Beef Adulterated Samples

The degradation of ingredients in heat-processed meat products makes their authentication challenging. In this study, protein profiles of raw beef, chicken, duck, pork, and binary simulated adulterated beef samples (chicken-beef, duck-beef, and pork-beef) and their heat-processed samples were obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Heat-stable characteristic proteins were found by screening the overlapping characteristic protein ion peaks of the raw and corresponding heat-processed samples, which were discovered by partial least-squares discriminant analysis. Based on the 36 heat-stable characteristic proteins, qualitative classification for the raw and heat-processed meats was achieved by extreme gradient boosting. Moreover, quantitative analysis via partial least squares regression was applied to determine the adulteration ratio of the simulated adulterated beef samples. The validity of the approach was confirmed by a blind test with the mean accuracy of 97.4%. The limit of detection and limit of quantification of this method were determined to be 5 and 8%, respectively, showing its practical aspect for the beef authentication.

Identification of yeasts in fermented foods and beverages using MALDI-TOF MS

Yeasts are an important group of microorganisms and contribute to the fermentation of a broad range of foods and beverages spontaneously or as a starter culture. Rapid and reliable microbial species identification is essential to evaluate biodiversity in fermented foods and beverages. Nowadays, high-throughput omics technologies and bioinformatics tools produce large-scale molecular-level data in many fields. These omics technologies generate data at different expression levels and are used to identify microorganisms. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful analytical technique in proteomic technology. It is a tool used to analyze the peptides or proteins of microorganisms for identification. MALDI-TOF MS has been used for the taxonomic identification of microorganisms as a fast, high-throughput, and cost-effective method. This review briefly discussed the application of MALDI-TOF MS in identifying yeasts in fermented foods and beverages.

Laboratory Diagnostic Methods and Antibiotic Resistance Patterns of Staphylococcus aureus and Escherichia coli Strains: An Evolving Human Health Challenge

Raw ground meat is known as a transmission vehicle for biological agents that may be harmful to human health. The objective of the present study was to assess microbiological quality of the ground meats. A total of 280 samples of local and imported chilled meats were randomly collected from retail shops in Buraydah City, Saudi Arabia. The meat samples were microbiologically analyzed using standard methods, peptide mass fingerprinting (PMF) technique, MicroScan Walkaway System (MicroScan) and qPCR System. The imported meat was more bacterially contaminated than local meat, with variable contamination degrees of Staphylococcus aureus (40.33%), Escherichia coli (36.13%), Hafnia alvei (7.56%), Pseudomonas spp. (6.72%), Salmonella spp. (5.88%) and Aeromonas spp. (3.36%). PMF verified all the isolated bacteria by 100%, compared to 75-95% achieved by MicroScan. The gene encoding flagellin (fliC) was recognized in 67.44% of E. coli strains, while the thermonuclease (nuc) and methicillin resistance (mecA) genes were detected in 100% S. aureus and 39.6% of methicillin-resistant S. aureus (MRSA) strains, respectively. The S. aureus and E. coli strains were highly resistant to multiple antibiotics (e.g., ampicillin, amoxicillin-clavulanic acid and cephalothin). For identifying various foodborne pathogens, PMF has been recognized as a powerful and precise analytical method. In light of the increasing use of PMF to detect multidrug-resistant bacteria, this study emphasizes the need for improved ways of treating and preventing pathogens, as well as setting up monitoring systems to guarantee hygiene and safety in meat production.

Whole-Genome Sequence Comparisons of Listeria monocytogenes Isolated from Meat and Fish Reveal High Inter- and Intra-Sample Diversity

Interpretation of whole-genome sequencing (WGS) data for foodborne outbreak investigations is complex, as the genetic diversity within processing plants and transmission events need to be considered. In this study, we analyzed 92 food-associated Listeria monocytogenes isolates by WGS-based methods. We aimed to examine the genetic diversity within meat and fish production chains and to assess the applicability of suggested thresholds for clustering of potentially related isolates. Therefore, meat-associated isolates originating from the same samples or processing plants as well as fish-associated isolates were analyzed as distinct sets. In silico serogrouping, multilocus sequence typing (MLST), core genome MLST (cgMLST), and pangenome analysis were combined with screenings for prophages and genetic traits. Isolates of the same subtypes (cgMLST types (CTs) or MLST sequence types (STs)) were additionally compared by SNP calling. This revealed the occurrence of more than one CT within all three investigated plants and within two samples. Analysis of the fish set resulted in predominant assignment of isolates from pangasius catfish and salmon to ST2 and ST121, respectively, potentially indicating persistence within the respective production chains. The approach not only allowed the detection of distinct subtypes but also the determination of differences between closely related isolates, which need to be considered when interpreting WGS data for surveillance.

Proteomics as a promising biomarker in food authentication, quality and safety: A review

Adulteration and mislabeling have become a very common global malpractice in food industry. Especially foods of animal origin are prepared from plant sources and intentionally mislabeled. This type of mislabeling is an important concern in food safety as the replaced ingredients may cause a food allergy or toxicity to vulnerable consumers. Moreover, foodborne pathogens also pose a major threat to food safety. There is a dire need to develop strong analytical tools to deal with related issues. In this context, proteomics stands out as a promising tool used to report the aforementioned issues. The development in the field of omics has inimitable advantages in enabling the understanding of various biological fields especially in the discipline of food science. In this review, current applications and the role of proteomics in food authenticity, safety, and quality and food traceability are highlighted comprehensively. Additionally, the other components of proteomics have also been comprehensively described. Furthermore, this review will be helpful in the provision of new intuition into the use of proteomics in food analysis. Moreover, the pathogens in food can also be identified based on differences in their protein profiling. Conclusively, proteomics, an indicator of food properties, its origin, the processes applied to food, and its composition are also the limelight of this article.

Synergistic antibacterial activity of tetrandrine combined with colistin against MCR-mediated colistin-resistant Salmonella

It has been recognized that colistin resistance is a growing problem that seriously impairs the clinical efficacy of colistin against bacterial infections. One strategy that has been proven to have therapeutic effect is to overcome the widespread emergence of antibiotic-resistant pathogens by combining existing antibiotics with promising non-antibiotic agents. In this work, antibiotic susceptibility testing, checkerboard assays and time-kill curves were used to investigate the antibacterial activity of the individual drugs and the potential synergistic activity of the combination. The molecular mechanisms of tetrandrine in combination with colistin were analyzed using fluorometric assay and Real-time PCR. To predict possible interactions between tetrandrine and MCR-1, molecular docking assay was taken. Finally, we evaluated the in vivo efficacy of tetrandrine in combination with colistin against MCR-positive Salmonella. Overall, the combination of tetrandrine and colistin showed significant synergistic activity. In-depth mechanistic analysis showed that the combination of tetrandrine with colistin enhances the membrane-damaging ability of colistin, undermines the functions of proton motive force (PMF) and efflux pumps in MCR-positive bacteria. The results of molecular docking and RT-PCR analyses showed that tetrandrine not only affects the expression of mcr-1 but is also an effective MCR-1 inhibitor. Compared with colistin monotherapy, the combination of tetrandrine with colistin significantly reduced the bacterial load in vivo. Our findings demonstrated that tetrandrine serves as a potential colistin adjuvant against MCR-positive Salmonella.

Proteomics-based screening and antibiotic resistance assessment of clinical and sub-clinical Brucella species: An evolution of brucellosis infection control

Brucellae are intracellular sneaky bacteria and they can elude the host's defensive mechanisms, resulting in therapeutic failure. Therefore, the goal of this investigation was to rapid identification of Brucella species collected from animals and humans in Saudi Arabia, as well as to evaluate their resistance to antibiotics. On selective media, 364 animal samples as well as 70 human blood samples were cultured. Serological and biochemical approaches were initially used to identify a total of 25 probable cultured isolates. The proteomics of Brucella species were identified using the MALDI Biotyper (MBT) system, which was subsequently verified using real-time polymerase chain reaction (real-time PCR) and microfluidic electrophoresis assays. Both Brucella melitensis (B. melitensis) and Brucella abortus (B. abortus) were tested for antimicrobial susceptibility using Kirby Bauer method and the E-test. In total, 25 samples were positive for Brucella and included 11 B. melitensis and 14 B. abortus isolates. Twenty-two out of 25 (88%) and 24/25 (96%) of Brucella strains were recognized through the Vitek 2 Compact system. While MBT was magnificently identified 100% of the strains at the species level with a score value more than or equal to 2.00. Trimethoprim-sulfamethoxazole, rifampin, ampicillin-sulbactam, and ampicillin resistance in B. melitensis was 36.36%, 31.82%, 27.27%, and 22.70%, respectively. Rifampin, trimethoprim-sulfamethoxazole, ampicillin, and ampicillin-sulbactam resistance was found in 35.71%, 32.14%, 32.14%, and 28.57% of B. abortus isolates, correspondingly. MBT confirmed by microfluidic electrophoresis is a successful approach for identifying Brucella species at the species level. The resistance of B. melitensis and B. abortus to various antibiotics should be investigated in future studies.

Aus der § 64 LFGB-Arbeitsgruppe MALDI-TOF: Leitlinien für die Validierung von Spezies-Identifizierungen mittels MALDI-TOF-MS

Matrix-assisted laser-desorption/ionization-time-of-flight-mass-spectrometry (MALDI-TOF-MS) is widely used to identify microorganisms. Recently, new applications such as identification of the animal species from meat, milk or fish are emerging. Standards for the validation of species identifications are still missing. Now, the § 64-LFGB working-group “MALDI-TOF”, established at the Federal Office of Consumer Protection and Food Safety, has compiled a guideline for the validation of species identifications. This guideline is intended for single laboratories as well as for lab networks and shows practical ways for validation of qualitative MALDI-TOF-MS methods. The special opportunities of the technology, in particular the use of extended reference databases and of collections of well-documented individual spectra for validation, have been taken into account in the guideline presented.

Technological and Sensory Quality and Microbiological Safety of RIR Chicken Breast Meat Marinated with Fermented Milk Products

Simple Summary

The use of meat from hens after the end of the laying period is limited due to their inferior sensory properties compared to the meat of young slaughter birds, mainly due to the age of the hens. Therefore, we are looking for effective methods of softening the meat of laying hens after the end of the annual laying use. One way to reduce the hardness of hen meat after the laying period is to marinate it with fermented milk products. The aim of the research was to evaluate the effect of marinating with buttermilk and sour milk on the quality of Rhode Island Red (RIR) hen meat after the first year of laying use. In the conducted research, it was found that marinating hen meat after the first year of laying with fermented milk products has a beneficial effect on the characteristics of raw and roasted meat. Roasted hen meat was characterised by a brighter colour, lower hardness, and better microbiological quality, and had greater overall acceptability. The obtained results allow us to conclude that marinating hen meat with fermented milk products creates new opportunities and prospects for the culinary use of the meat of RIR hens after one year of laying use.

Abstract

The aim of the study was to determine the effect of marinating with fermented milk products (buttermilk and sour milk) on the physical characteristics, microbiological quality, and sensory acceptability of Rhode Island Red (RIR) hen meat after the first year of laying use. The hen breast meat was marinated with fermented dairy products, buttermilk and sour milk, by the immersion method for 12 h at 4 °C. The assessed features included the quality of raw and roasted marinated and non-marinated meat in terms of physical characteristics (marinade absorption, water absorption, pH, L*, a*, b* colour, shear strength, texture profile analysis (TPA) test), microbiological parameters, and sensory characteristics. Bacteria were identified by the mass spectrometry method (MALDI-TOF MS Biotyper). Marinating meat with fermented dairy products lightened the colour, decreased the value of shear force, reduced hardness and chewiness, and limited the growth of aerobic bacteria and Pseudomonas spp. Additionally, after heat treatment, the number of identified aerobic bacteria families in the marinated in buttermilk and marinated in sour milk groups was smaller than in the non-marinated muscle group. The sensory evaluation showed a beneficial effect of marinating with buttermilk and sour milk on the tenderness, juiciness, and colour of roasted meat.

Combating Childhood Infections in LMICs: evaluating the contribution of Big Data Big data, biomarkers and proteomics: informing childhood diarrhoeal disease management in Low- and Middle-Income Countries

Despite efforts to reduce the global burden of childhood diarrhoea, 50% of all cases globally occur in children under five years in Low–Income and Middle- Income Countries (LMICs) and knowledge gaps remain regarding the aetiological diagnosis, introduction of diarrhoeal vaccines, and the role of environmental enteric dysfunction and severe acute malnutrition. Biomarkers may assist in understanding disease processes, from diagnostics, to management of childhood diarrhoea and the sequelae to vaccine development. Proteomics has the potential to assist in the identification of new biomarkers to understand the processes in the development of childhood diarrhoea and to aid in developing new vaccines. Centralised repositories that enable mining of large data sets to better characterise risk factors, the proteome of both the patient and the different diarrhoeal pathogens, and the environment, could inform patient management and vaccine development, providing a systems biological approach to address the burden of childhood diarrhoea in LMICs.

Screening of Antimicrobial and Adhesive Activity of Lactobacilli Isolated from the National Food Products from Different Districts of the Karaganda Region (Kazakhstan)

BACKGROUND: It is a national priority to look for new probiotic bacteria with highly active biological properties to create a new generation of probiotics, ferments, therapeutic, and prophylactic fermented milk products, taking into account ethnocultural and regional characteristics. AIM: The aim of the study is to assess probiotic properties of strains of lactobacilli (antimicrobial and adhesive), which are isolated from national lactic acid products from different districts of the Karaganda region (Kazakhstan). MATERIALS AND METHODS: There were modern microbiological methods applied during the experiment. To determine the morpho-cultural properties, the following methods were used: Gram staining, a catalase test, serial dilutions. The Matrix Supported Laser Desorption/Ionization Flight Time Mass Spectrometry was used for identification, and the deferred-antagonism method was used to determine the antimicrobial activity. The buccal epithelial cells were used for the cell object as a test system to determine the adhesive activity. RESULTS: In this experiment, 26 lactobacillus isolates were isolated from 68 samples of national lactic acid products produced in a traditional homemade way in different districts of the Karaganda region (Kazakhstan). As a result of the studies carried out on the cultural and morphological characteristics and identification by the mass spectrometer, the following lactobacilli were obtained: Lactobacillus acidophilus (two strains), Lactobacillus delbrueckii subsp. bulgaricum (two strains), Lactobacillus rhamnosus (seven strains), Lactobacillus plantarum (two strains), Lactobacillus paracasei (11 strains), and Lactobacillus fermentum (two strains). Twenty-six isolates of lactobacilli were tested for antimicrobial activity, 13 isolates of which showed an inhibitory effect, but the degree of antagonism varied among lactobacillus isolates. In general, the inhibitory activity of lactobacillus isolates was shown against the Gram-negative indicator microorganisms Salmonella typhimurium NCTC 12023, Escherichia coli NCTC 12923. The antibacterial activity was shown against the Staphylococcus aureus NCTC 12973 indicator microorganism in nine isolates of lactobacilli. Only six isolates of lactobacilli showed antifungal activity against the test strain of Candida albicans NCPF 3179. Out of 13 isolates of lactobacilli, nine isolates of medium and high activity competed for binding to buccal epithelial cells. CONCLUSION: The obtained isolates from traditional dairy products are considered to be promising candidates and competitive isolates with some probiotic potential. This study calls for further researches to be made in this area.

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

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

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

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

Assessment of technological characteristics and microbiological quality of marinated turkey meat with the use of dairy products and lemon juice

Objective

The aim of this study was to evaluate the effect of marinating turkey meat with buttermilk and acid whey on the technological traits and microbiological quality of the product.

Methods

Slices of turkey meat muscles were marinated for 12 hours in buttermilk (n = 30), acid whey (n = 30) and comparatively, in lemon juice (n = 30). The control group (n = 30) consisted of unmarinated slices of turkey breast muscles. Physical parameters (pH, water holding capacity, colour L*a*b*, shear force, weight loss) were assessed and quantitative and qualitative microbiological evaluation of raw and roasted products was performed. The microbiological parameters were determined as the total viable counts of mesophilic aerobic bacteria, of the Enterobacteriaceae family, and Pseudomonas spp. Bacterial identification was performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Results

Marinating turkey meat in buttermilk and whey compared to marinating in lemon juice and the control sample resulted in a higher (p<0.05) degree of yellow color saturation (b*) and a reduction (p<0.05) in the number of mesophilic aerobic bacteria, Pseudomonas spp. and Enterobacteriaceae family as well as the number of identified mesophilic aerobic bacteria in both raw and roasted samples. The lowest (p<0.05) shear force values were found in products marinated in whey.

Conclusion

The use of buttermilk and acid whey as a marinade for meat increases the microbiological safety of the product compared to marinating in lemon juice, while maintaining good technological features of the product.

Streptococcus suis serotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Streptococcus suis, particularly S. suis serotype 2 (SS2), is an important zoonotic pathogen causing meningitis in humans worldwide. Although the proper classification of the causative and pathogenic serotype is salutary for the clinical diagnosis, cross-reactions leading to the indistinguishability of serotypes by the current serotyping methods are significant limitations. In the present study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of extracted peptides was developed to improve the classification of serotype of S. suis. The peptide mass fingerprint (PMFs) database of S. suis was generated from the whole-cell peptides of 32 reference strains of S. suis isolates obtained from pigs. Thirty-two human S. suis isolates from clinical cases in Thailand were used to validate this alternative serotyping method in direct comparison to the multiplex (m)PCR approach. All reference strains, representing 32 serotypes of S. suis, exhibited their individual PMFs patterns, thus allowing differentiation from one another. Highly pathogenic SS2 and SS14 were clearly differentiated from the otherwise serologically closely related SS1/2 and SS1, respectively. The developed MALDI-TOF-MS serotyping method correctly classified the serotype in 68.8% (22/32) of the same serotype isolates generated from the PMFs database; while the validity for the clinical human isolates was 62.5% (20/32). The agreement between the MALDI-TOF-MS and mPCR serotyping was moderate with a Kappa score of 0.522, considering that mPCR could correctly serotype up to 75%. The present study demonstrated that PMFs from the developed MALDI-TOF-MS-based method could successfully discriminate the previously indistinguishable highly pathogenic SS2 and SS14 from SS1/2 and SS1, respectively. Moreover, this serotyping method distinguished pathogenic SS6, and so is an alternative approach of choice to rapidly and reliably serotype clinically pathogenic S. suis isolates.

Biodiversity of Lactobacillus helveticus isolates from dairy and cereal fermentations reveals habitat-adapted biotypes

For the present study, we collected 22 Lactobacillus helveticus strains from different dairy (n = 10) and cereal (n  = 12) fermentations to investigate their biodiversity and to uncover habitat-specific traits. Biodiversity was assessed by comparison of genetic fingerprints, low-molecular-weight subproteomes, metabolic and enzymatic activities, growth characteristics and acidification kinetics in food matrices. A clear distinction between the dairy and cereal strains was observed in almost all examined features suggesting that the different habitats are domiciled by different L. helveticus biotypes that are adapted to the specific environmental conditions. Analysis of the low-molecular-weight subproteome divided the cereal isolates into two clusters, while the dairy isolates formed a separate homogeneous cluster. Differences regarding carbohydrate utilization were observed for lactose, galactose, sucrose and cellobiose as well as for plant-derived glucosides. Enzymatic differences were observed mainly for ß-galactosidase and ß-glucosidase activities. Further, growth temperature was optimal in the range from 33 to 37°C for the cereal strains, whereas the dairy strains showed optimal growth at 40°C. Taken together, adaptation of the various biotypes results in a growth benefit in the particular environment. Acidification and growth tests using either sterile skim milk or a wheat flour extract confirmed these results. Differentiation of these biotypes and their physiological characteristics enables knowledge-based starter culture development for cereal versus dairy products within one species.

Characterization of pTS14, an IncF2:A1:B1 Plasmid Carrying tet(M) in a Salmonella enterica Isolate

The objective of this study was to explore the genetic and biological features of the tet(M)-harboring plasmid pTS14 in Salmonella enterica strain S14 isolated from a chicken fecal sample. Plasmid pTS14 was identified by conjugation, S1-pulsed-field gel electrophoresis (PFGE), Southern hybridization, and plasmid sequencing. The biological characteristics of pTS14 were assessed via stability, growth kinetics, and starvation survival experiments. Strain S14, belonging to ST3007, harbored a 119-kb tet(M)-bearing IncF2:A1:B1 conjugative plasmid pTS14. The plasmid pTS14 contained a novel transposon Tn6709 with the genetic structure IS26-tnpA1-tnpA2-Δorf13-LP-tet(M)-tnpX-ΔtnpR-IS26, and the resistance genes tet(B), tet(D), strAB, sul2, and bla_TEM–1b. In addition, pTS14 was found to be highly stable in the recipient strain E. coli J53. The transconjugant TS14 exhibited a higher survival ratio than E. coli J53 under permanent starvation-induced stress. The tet(M)-bearing IncF2 epidemic plasmid lineage may accelerate the dissemination of tet(M) and other genes by coselection, which could constitute a potentially serious threat to clinical treatment regimens.

Reliable differentiation of a non-toxigenic tox gene-bearing Corynebacterium ulcerans variant frequently isolated from game animals using MALDI-TOF MS

Corynebacterium (C.) ulcerans is a zoonotic member of the C. diphtheriae group and is known to cause abscesses in humans and several animal species. Toxigenic strains, expressing the tox gene encoding diphtheria toxin, are also able to cause diphtheria in humans. In recent years, a non-toxigenic but tox gene-bearing (NTTB) variant of C. ulcerans has been identified that was frequently isolated from clinically healthy as well as from diseased wildlife animals, especially wild boars (Sus scrofa scrofa) in Germany and Austria. The described clinical cases showed similar signs of disease and the isolated corynebacteria displayed common genetic features as well as similar spectroscopic characteristics, therefore being assigned to a so called wild boar cluster (WBC). This study describes the establishment and validation of a method using MALDI-TOF mass spectrometry for a reliable differentiation between various members of the C. diphtheriae group at species level as well as a reliable sub-level identification of C. ulcerans isolates of the WBC variant. For this study 93 C. ulcerans isolates from wildlife animals, 41 C. ulcerans isolates from other animals and humans, and 53 isolates from further representatives of the C. diphtheriae group, as well as 26 non-diphtheriae group Corynebacteria collected via the MALDI user platform from seven MALDI users were used. By assigning 86 C. ulcerans isolates to the WBC the extensive geographical distribution of this previously less noticed variant in two Central European countries could be shown.

Utility of MALDI-TOF MS as a new tool for Streptococcus pneumoniae serotyping

Nowadays, more than 95 different Streptococcus pneumoniae serotypes are known, being less than one third responsible for the majority of severe pneumococcal infections. After the introduction of conjugate vaccines, a change in the epidemiology of the serotypes causing invasive pneumococcal disease has been observed making the surveillance of circulating serotypes especially relevant. Some recent studies have used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology to identify the most frequent pneumococcal serotypes that cause invasive disease. The objectives of this study were to evaluate the efficacy of previously described discriminatory peaks determined by MALDI-TOF MS for the identification of serotypes 6B, 19F, 19A and 35B using reference and clinical isolates and to try to identify other discriminatory peaks for serotypes 11A, 19F and 19A using transformed pneumococcal strains. Most of the proposed peaks defined in the literature for the identification of serotypes 6B, 19F, 19A, 35B were not found in the spectra of the 10 reference isolates nor in those of the 60 clinical isolates tested corresponding to these four serotypes. The analysis and comparison of the mass spectra of genetically modified pneumococci (transformed strains) did not allow the establishment of new discriminatory peaks for serotypes 11A, 19F, and 19A. MALDI-TOF MS in the usual range of 2,000 to 20,000 m/z did not prove to be a valid technique for direct S. pneumoniae serotyping.

Impact of a Pilot-Scale Plasma-Assisted Washing Process on the Culturable Microbial Community Dynamics Related to Fresh-Cut Endive Lettuce

Cold plasma is described as a promising technique for the treatment of fresh food. In particular, the application of plasma-treated water gained interest in fresh-cut produce processing. This study aimed to evaluate the effectiveness of plasma-treated water (PTW) to decontaminate lettuce during washing on a pilot-scale level with special interest in the dynamics of the culturable microbial community in a first approach. PTW was used in pilot-scale washing at different processing steps, and the total viable count (TVC) of endive lettuce was determined after treatment and after storage (seven days, 2 °C). Microflora representatives were identified using MALDI-ToF MS. The highest reduction of TVC (1.8 log units) was achieved using PTW for washing whole lettuce before cutting. The microbial community structure showed high variations in the composition along the processing chain and during storage with a decrease in diversity after washing with PTW. PTW reduced the microbial load of endive lettuce; however, this was not clearly detectable at the end of storage, similar to other sanitizers used in comparable studies. To assure the safety of fresh products, detailed knowledge about the microbial load and the composition of the microbial community close to the end of shelf life is of high interest for optimized process design.

The role of arsenic resistant Bacillus aryabhattai MCC3374 in promotion of rice seedlings growth and alleviation of arsenic phytotoxicity

The biological agents have been utilized as an affordable alternative to conventional costly metal remediation technologies for last few years. The present investigation introduces arsenic (As) resistant plant growth promoting rhizobacteria (PGPR) isolated from the As-contaminated agricultural field of West Bengal, India that alleviates arsenic-induced toxicity and exhibited many plant growth promoting traits (PGP). The isolated strain designated as AS6 has identified as Bacillus aryabhattai based on phenotypic characteristics, physio-biochemical tests, MALDI-TOFMS bio-typing, FAME analysis and 16S rDNA sequence homology. The strain found to exhibit five times more resistance to arsenate than arsenite with minimum inhibitory concentrations (MIC) being 100 mM and 20 mM respectively. The result showed that accumulation of As was evidenced by SEM- EDAX, TEM-EDAX studies. The intracellular accumulation of arsenic was also confirmed as in bacterial biomass by AAS, FTIR, XRD and XRF analyses. The increased rate of As (V) reduction by this strain found to be exploited for the remediation of arsenic in the contaminated agricultural field. The strain also found to exhibit important PGP traits viz., ACC deaminase activity (2022 nmol α-ketobutyrate/mg protein/h), IAA production (166 μg/ml), N₂ fixation (0.32 μgN fixed/h/mg proteins) and siderophore production (72%) etc. Positive influenced of AS6 strain on rice seedlings growth promotion under As stress was observed considering the several morphological, biochemical parameters including antioxidants activities as compared with an uninoculated set. Thus this strain might be exploited for stress amelioration and plant growth enhancement of rice cultivar under arsenic spiked agricultural soil.

The Lactobacillus casei Group: History and Health Related Applications

The Lactobacillus casei group (LCG), composed of the closely related Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are some of the most widely researched and applied probiotic species of lactobacilli. The three species have been extensively studied, classified and reclassified due to their health promoting properties. Differentiation is often difficult by conventional phenotypic and genotypic methods and therefore new methods are being continually developed to distinguish the three closely related species. The group remain of interest as probiotics, and their use is widespread in industry. Much research has focused in recent years on their application for health promotion in treatment or prevention of a number of diseases and disorders. The LCG have the potential to be used prophylactically or therapeutically in diseases associated with a disturbance to the gut microbiota. The group have been extensively researched with regard to stress responses, which are crucial for their survival and therefore application as probiotics.

Identification and Classification for the Lactobacillus casei Group

Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.

Bioaccumulation of cadmium by Enterobacter sp. and enhancement of rice seedling growth under cadmium stress

Bacteria-mediated plant growth promotion and bioremediation of heavy metal containing soil is a widely accepted eco-friendly method. The present study is aimed to screen out cadmium resistant bacterial strain from metal contaminated rice rhizosphere and evaluate its effects on the growth of rice seedlings under cadmium stress. Among four different isolates (designated as S1, S2, S3 and S5), the S2 isolate was screened on the basis of different PGP traits and multi heavy metal resistance (minimum inhibitory concentration for cadmium, lead and arsenic were 3500, 2500 and 1050 µg/ml respectively). The selected S2 strain has ability to produce ACC deaminase (236.11 ng α-keto-butyrate/mg protein/h), IAA (726 µg/ml), solubilize phosphate (73.56 ppm) and fix nitrogen (4.4 µg of nitrogen fixed/h/mg protein). The selected strain was identified as Enterobacter sp. on the basis of phenotypic characterization, MALDI-TOF MS analysis of ribosomal proteins, FAME analysis and 16 S rDNA sequence homology. The high cadmium removal efficiency (> 95%) of this strain from the growth medium was measured by Atomic Absorption Spectrophotometer and it was due to intracellular cadmium accumulation evidenced by SEM-EDX-TEM-EDX study. SEM analysis also revealed no distortion of surface morphology of this strain even grown in the presence of high cadmium concentration (3000 µg/ml). Inoculation of this strain with rice seedlings significantly enhanced various morphological, biochemical characters of seedling growth compared with un-inoculated seedlings under Cd stress. The strain also exhibited alleviation of cadmium-induced oxidative stress, reduction of stress ethylene and decreased the accumulation of cadmium in seedlings as well that conferred cadmium tolerance to the plant. Thus the S2 strain could be considered as a potent heavy metal resistant PGPR applicable in heavy metal contaminated agricultural soil for bioremediation and plant growth promotion as well.

MAIN FINDING

A cadmium resistant plant growth promoting Enterobacter sp. was isolated that accumulated cadmium evidenced by SEM-TEM-EDX study. It reduced Cd uptake and enhanced growth in rice seedlings.

Screening of microbial communities associated with endive lettuce during postharvest processing on industrial scale

In this study, the composition of the microbial community on endive lettuce (Cichorium endivia) was evaluated during different postharvest processing steps. Microbial community structure was characterized by culture-dependent and culture-independent methods. Endive lettuce was sampled exemplarily at four different stages of processing (raw material, cut endive lettuce, washed endive lettuce, and spin-dried (ready to pack) endive lettuce) and analysed by plate count analysis using non-selective and selective agar plates with subsequent identification of bacteria colonies by matrix-assisted laser desorption/ionization time-of light mass spectrometry (MALDI-TOF MS). Additionally, terminal-restriction fragment length polymorphism (TRFLP) analysis and 16S rRNA gene nucleotide sequence analysis were conducted.

The results revealed structural differences in the lettuce microbiomes during the different processing steps. The most predominant bacteria on endive lettuce were detected by almost all methods. Bacterial species belonging to the families Pseudomonadaceae, Enterobacteriaceae, Xanthomonadaceae, and Moraxellaceae were detected in most of the examined samples including some unexpected potentially human pathogenic bacteria, especially those with the potential to build resistance to antibiotics (e.g., Stenotrophomonas maltophilia (0.9 % in cut sample, 0.4 % in spin-dried sample), Acinetobacter sp. (0.6 % in raw material, 0.9 % in cut sample, 0.9 % in washed sample, 0.4 % in spin-dried sample), Morganella morganii (0.2 % in cut sample, 3 % in washed sample)) revealing the potential health risk for consumers.

However, more seldom occurring bacterial species were detected in varying range by the different methods. In conclusion, the applied methods allow the determination of the microbiome's structure and its dynamic changes during postharvest processing in detail. Such a combined approach enables the implementation of tailored control strategies including hygienic design, innovative decontamination techniques, and appropriate storage conditions for improved product safety.