Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry

Complete genome sequence of multi-drug-resistant Salmonella enterica subsp. enterica serovar Typhimurium strain Bnaya isolated from a dairy calf in Israel

This manuscript reports the complete genome sequence of a Salmonella enterica subsp. enterica serovar Typhimurium strain (designated "Bnaya"), isolated from a dead dairy calf with severe diarrhea in Israel. The isolate exhibited multi-drug resistance, which is highly unusual in bovine Salmonella spp. in Israel, prompting further investigation.

Rapid identification of Salmonella serovars Enteritidis and Typhimurium using whole cell matrix assisted laser desorption ionization - Time of flight mass spectrometry (MALDI-TOF MS) coupled with multivariate analysis and artificial intelligence

Salmonella is a common food-borne pathogen with Enteritidis and Typhimurium being among the most important serovars causing numerous outbreaks. A rapid method was investigated to identify these serovars using whole-cell MALDI-TOF MS coupled with multivariate analysis and artificial intelligence and 113 Salmonella strains, including 38 Enteritidis (SE), 38 Typhimurium (ST) and 37 strains from 32 other Salmonella serovars (SG). Datasets of ions (presence/absence) with high discriminative power were created using newly developed criteria and subject to multivariate analyses and eight artificial intelligence (AI) tools. Principal Component Analysis based on 55 or 88 selected ions separated SE, ST and SG without overlap on the first three principal components. Datasets were partitioned using five partitioning methods with 70% of samples for AI model training and 30% for validation. Of the eight AI models evaluated, high performance (HP) SVM and HP Neural were the top performers, identified three serovar groups 97% correctly on average (range 82%-100%) according to the validation results. Selection of serovar specific ions facilitated differentiation of serotypes using unsupervised model PCA and improved the accuracy of classification using AI significantly (p < 0.01). MALDI-TOF MS incorporated with advanced data processing and classification tools is a promising method to allow rapid identification of Salmonella serovars of concern in routine diagnostic laboratories.

A Bacteriophage Cocktail Reduces Five Relevant Salmonella Serotypes at Low Multiplicities of Infection and Low Temperatures

Salmonella are important pathogenic bacteria and, following Campylobacter, they are the second most common cause of bacterial foodborne infections worldwide. To reduce the presence of bacteria along the food chain, the application of bacteriophages (phages) may be a promising tool. In this study, the lytic properties of six phages against five relevant Salmonella serotypes (S. Enteritidis, S. Typhimurium, S. Infantis, S. Paratyphi B and S. Indiana) were analyzed. Three phages were able to lyse all five serotypes. We determined the lytic potential of each phage on indicator strains in vitro at room temperature (RT) and at 37 °C using low multiplicities of infection (MOIs). Most phages reduced their host more efficiently at RT than at 37 °C, even at the lowest MOI of 0.001. Following this, the lytic activity of a cocktail comprising five phages (MOI = 0.1) was examined with each of the five serotypes and a mix of them at RT, 15, 12, 10, 8 and 6 °C. All cultures of single serotypes as well as the mixture of strains were significantly reduced at temperatures as low as 8 °C. For single serotypes, reductions of up to 5 log10 units and up to 2.3 log10 units were determined after 6 h (RT) and 40 h (8 °C), respectively. The mixture of strains was reduced by 1.7 log10 units at 8 °C. The data clearly suggest that these phages are suitable candidates for biocontrol of various Salmonella serotypes under food manufacturing conditions.

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

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

16S rRNA gene sequencing and MALDI TOF mass spectroscopy identification of Leuconostoc mesenteroides isolated from Algerian raw camel milk

BACKGROUND

Eighty-three strains of Leuconostoc mesenteroides were isolated from Algerian raw camel milk. Based on morphological, biochemical, and physiological characters tests, strains were identified as Ln. mesenteroides subsp. mesenteroides. Seven strains had a remarkable antagonistic and probiotic characterization. The present study aims at identifying these strains by means of 16 s rRNA gene sequencing and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), extending phenotypic and genotypic studies done previously.

RESULTS

The phyloproteomic dendrograms of the studied strains based on MALDI-TOF MS provided the same identification with more intraspecific information from the 16S rRNA gene sequencing based on phylogenetic analysis. The latter were in agreement with the previous biochemical/physiological identification, the seven isolated strains were Ln. mesenteroides subsp. mesenteroides.

CONCLUSIONS

Remarkably, MALDI-TOF MS fingerprinting was found to be effective enough as 16S rRNA gene sequencing identification, allowing faster and more reliable analysis than biochemical/physiological methods.

Proteome-Based Serotyping of the Food-Borne Pathogens Salmonella Enterica by Label-Free Mass Spectrometry

Food-borne diseases caused by Salmonella enterica of 2500 serovars represent a serious public health problem worldwide. A quick identification for the pathogen serovars is critical for controlling food pollution and disease spreading. Here, we applied a mass spectrum-based proteomic profiling for identifying five epidemiologically important Salmonella enterica subsp. enterica serovars (Enteritidis, Typhimurium, London, Rissen and Derby) in China. By label-free analysis, the 53 most variable serovar-related peptides, which were almost all enzymes related to nucleoside phosphate and energy metabolism, were screened as potential peptide biomarkers, and based on which a C5.0 predicted model for Salmonella enterica serotyping with four predictor peptides was generated with the accuracy of 94.12%. In comparison to the classic gene patterns by PFGE analysis, the high-throughput proteomic fingerprints were also effective to determine the genotypic similarity among Salmonella enteric isolates according to each strain of proteome profiling, which is indicative of the potential breakout of food contamination. Generally, the proteomic dissection on Salmonella enteric serovars provides a novel insight and real-time monitoring of food-borne pathogens.

Differentiating between Enterococcusfaecium and Enterococcuslactis by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

Unlike Enterococcus faecium strains, some Enterococcus lactis strains are considered potential probiotic strains as they lack particular virulence and antibiotic resistance genes. However, these closely related species are difficult to distinguish via conventional taxonomic methods. Here, for the first time, we used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with BioTyper and in-house databases to distinguish between E. faecium and E. lactis. A total of 58 reference and isolated strains (89.2%) were correctly identified at the species level using MALDI-TOF MS with in-house databases. However, seven strains (10.8%) were not accurately differentiated as a single colony was identified as a different species with a similar score value. Specific mass peaks were identified by analyzing reference strains, and mass peaks at 10,122 ± 2 m/z, 3650 ± 1 m/z, and 7306 ± 1 m/z were unique to E. faecium and E. lactis reference strains, respectively. Mass peaks verified reproducibility in 60 isolates and showed 100% specificity, whereas 16S rRNA sequencing identified two different candidates for some isolates (E. faecium and E. lactis). Our specific mass peak method helped to differentiate two species, with high accuracy and high throughput, and provided a viable alternative to 16S rRNA sequencing.

Identification and Subtyping of Salmonella Isolates Using Matrix-Assisted Laser Desorption–Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF)

Subtyping of bacterial isolates of the same genus and species is an important tool in epidemiological investigations. A number of phenotypic and genotypic subtyping methods are available; however, most of these methods are labor-intensive and time-consuming and require considerable operator skill and a wealth of reagents. Matrix-Assisted Laser Desorption–Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF), an alternative to conventional subtyping methods, offers a rapid, reproducible method for bacterial identification with a high sensitivity and specificity and at minimal cost. The purpose of this study was to determine the feasibility of using MALDI-TOF to differentiate between six Salmonella serovars recovered from experimental microcosms inoculated with known strains of Salmonella. Following the establishment of a MALDI-TOF reference library for this project, the identity of 843 Salmonella isolates recovered from these microcosms was assessed using both MALDI-TOF and conventional methods (serotyping/PCR). All 843 isolates were identified as being Salmonella species. Overall, 803/843 (95%) of these isolates were identified similarly using the two different methods. Positive percent agreement at the serovar level ranged from 79 to 100%, and negative percent agreement for all serovars was greater than 98%. Cohen’s kappa ranged from 0.85 to 0.98 for the different serovars. This study demonstrates that MALDI-TOF is a viable alternative for the rapid identification and differentiation of Salmonella serovars.

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

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

Low occurrence of Salmonella spp. in wild birds from a Swiss rehabilitation centre

BACKGROUND

Salmonella are bacteria of the family Enterobacteriaceae with a wide host range. Infection in birds causes subclinical disease to mass mortality events. Wild birds may act as healthy carriers posing a hazard to livestock and humans. The present study investigated the occurrence of Salmonella in wild birds admitted to a rehabilitation centre in order to assess the exposure of the staff to this zoonotic pathogen.

METHODS

Faecal swabs of 552 avian patients (68 species) were collected over the course of 12 months. Each sample was propagated in enrichment broth and subsequently incubated on a RAPID'Salmonella plate. Salmonella isolates were serotyped, and antimicrobial susceptibility testing was performed.

RESULTS

Six Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and 1 S. Schleissheim were detected; all were pansusceptible to the antibiotics tested.

CONCLUSION

Despite the low positive rate in the tested population, the authors recommend applying protective equipment and hygiene measures when handling wild birds.

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.

Radiation-Inactivated S. gallinarum Vaccine Provides a High Protective Immune Response by Activating Both Humoral and Cellular Immunity

Salmonella enterica subsp. enterica serovar Gallinarum (SG) is a common pathogen in chickens, and causes an acute systemic disease that leads to high mortality. The live attenuated vaccine 9R is able to successfully protect chickens older than six weeks by activating a robust cell-mediated immune response, but its safety and efficacy in young chickens remains controversial. An inactivated SG vaccine is being used as an alternative, but because of its low cellular immune response, it cannot be used as a replacement for live attenuated 9R vaccine. In this study, we employed gamma irradiation instead of formalin as an inactivation method to increase the efficacy of the inactivated SG vaccine. Humoral, cellular, and protective immune responses were compared in both mouse and chicken models. The radiation-inactivated SG vaccine (r-SG) induced production of significantly higher levels of IgG2b and IgG3 antibodies than the formalin-inactivated vaccine (f-SG), and provided a homogeneous functional antibody response against group D, but not group B Salmonella. Moreover, we found that r-SG vaccination could provide a higher protective immune response than f-SG by inducing higher Th17 activation. These results indicate that r-SG can provide a protective immune response similar to the live attenuated 9R vaccine by activating a higher humoral immunity and a lower, but still protective, cellular immune response. Therefore, we expect that the radiation inactivation method might substitute for the 9R vaccine with little or no side effects in chickens younger than six weeks.

Phenotypic and Genetic Comparison of a Plant-Internalized and an Animal-Isolated Salmonella Choleraesuis Strain

Contamination of fresh produce with human pathogens poses an important risk for consumers, especially after raw consumption. Moreover, if microorganisms are internalized, no removal by means of further hygienic measures would be possible. Human pathogenic bacteria identified in these food items are mostly of human or animal origin and an adaptation to this new niche and particularly for internalization would be presumed. This study compares a plant-internalized and an animal-borne Salmonella enterica subsp. enterica serovar Choleraesuis aiming at the identification of adaptation of the plant-internalized strain to its original environment. For this purpose, a phenotypical characterization by means of growth curves under conditions resembling the indigenous environment from the plant-internalized strain and further analyses using Pulsed-field gel electrophoresis and Matrix-assisted laser desorption ionization time of flight spectrometry were assessed. Furthermore, comparative genomic analyses by means of single nucleotide polymorphisms and identification of present/absent genes were performed. Although some phenotypical and genetic differences could be found, no signs of a specific adaptation for colonization and internalization in plants could be clearly identified. This could suggest that any Salmonella strain could directly settle in this niche without any evolutionary process being necessary. Further comparative analysis including internalized strains would be necessary to assess this question. However, these kinds of strains are not easily available.

Rapid Detection of Salmonella Enteritidis, Typhimurium, and Thompson by Specific Peak Analysis Using Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

Rapid detection of Salmonella serovars is important for the effective control and monitoring of food industries. In this study, we evaluate the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid detection of three serovars, Enteritidis, Typhimurium, and Thompson, that are epidemiologically important in Korea. All strains were identified at the genus level, with a mean score of 2.319 using the BioTyper database, and their protein patterns were confirmed to be similar by principal component analysis and main spectrum profile dendrograms. Specific peaks for the three serovars were identified by analyzing 65 reference strains representing 56 different serovars. Specific mass peaks at 3018 ± 1 and 6037 ± 1, 7184 ± 1, and 4925 ± 1 m/z were uniquely found in the reference strains of serovars Enteritidis, Typhimurium, and Thompson, respectively, and they showed that the three serovars can be differentiated from each other and 53 other serovars. We verified the reproducibility of these mass peaks in 132 isolates, and serovar classification was achieved with 100% accuracy when compared with conventional serotyping through antisera agglutination. Our method can rapidly detect a large number of strains; hence, it will be useful for the high-throughput screening of Salmonella serovars.

Prevalence, Risk Factors, and Antibiogram of Nontyphoidal Salmonella from Beef in Ambo and Holeta Towns, Oromia Region, Ethiopia

Background

Salmonella has been recognized as a major cause of food-borne illness associated with the consumption of food of animal origin. The present cross-sectional study was conducted from December 2017 to May 2018 in Ambo and Holeta towns to assess the prevalence, risk factors, and antimicrobial susceptibility patterns of nontyphoidal Salmonella isolates from raw beef samples from abattoirs, butchers, and restaurants in Ambo and Holeta towns, Oromia region, Ethiopia.

Methods

A total of 354 beef samples were collected from abattoirs, butchers, and restaurants. Salmonella isolation and identification were carried out using standard bacteriological methods recommended by the International Organization for Standardization. Antimicrobial susceptibility testing was performed using the disk diffusion method. Besides, a structured questionnaire was used to collect sociodemographic data and potential risk factors for contamination of meat. Chi-square tests and logistic regression were used for data analyses.

Results

Of the total 354 meat samples examined, 20 (5.7%, 95% confidence interval (CI): 3.5–8.6) were positive for Salmonella. Two serotypes belonging to S. typhimurium (11 isolates) and I:4,5,12: i:- (9 isolates) were identified. The Salmonella detection rate in abattoirs, butchers, and restaurants was 4.2% (5/118), 8.5% (10/118), and 4.2% (5/118), respectively. The antimicrobial susceptibility test showed that 40%, 30%, and 20% of the Salmonella isolates were resistant to azithromycin, amoxicillin, and ceftriaxone, respectively. The odds of Salmonella isolation when meat handlers are illiterate were 7.8 times higher than those when they are educated to the level of secondary and above (P=0.032). Similarly, the likelihood of Salmonella isolation was 6.3 and 7.6 times higher among workers of butcher and restaurants, respectively, who had no training (P=0.003) and no knowledge (P=0.010) on food safety and hygiene.

Conclusions

The study showed widespread multidrug-resistant Salmonella isolates in the study areas. Therefore, raw meat consumption and indiscriminate use of antimicrobial drugs should be discouraged. Provision of food safety education for meat handlers and further surveillance of antimicrobial-resistant isolates are suggested.

Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendorf and Orion var. 15+, 34. Int J Food Microbiol 2021;346:109167. [PMID: 33774575 DOI: 10.1016/j.ijfoodmicro.2021.109167]

Our previous study demonstrated that whole genome sequencing (WGS) data generated by Oxford Nanopore Technologies (ONT) can be used for rapid and accurate prediction of selected Salmonella serotypes. However, one limitation is that established methods for WGS-based serotype prediction, utilizing data from either ONT or Illumina, cannot differentiate certain serotypes and serotype variants with the same or closely related antigenic formulae. This study aimed to evaluate nanopore sequencing and additional data analysis for identification of Salmonella enterica Choleraesuis var. Kunzendorf and S. enterica Orion var. 15⁺, 34⁺, thus overcoming this limitation. Five workflows that combined different flow cells, library construction methods and basecaller models were evaluated and compared. The workflow that consisted of the R9 flow cell, rapid sequencing library construction kit and guppy basecaller with base modified model performed best for Single Nucleotide Polymorphism (SNP) analysis. With this workflow, 99.98% of matching identity between assembled genomes from ONT and that from Illumina was achieved. Less than five high-quality SNPs differed when comparing sequencing data between ONT and Illumina. SNP typing successfully identified Choleraesuis var. Kunzendorf. While prophage prediction further differentiated Orion var. 15⁺, 34⁺ from the other two Orion variants. Our study improves the readiness of ONT as a Salmonella subtyping and source tracking tool for food industry applications.

Exploring the value of MALDI-TOF MS for the detection of clonal outbreaks of Burkholderia contaminans

BACKGROUND

Molecular genetics has risen in both output and affordability to become the gold standard in diagnosis, however it is not yet available for most routine clinical microbiology due to cost and the level of skill it requires. Matrix assisted laser desorption/ionisation - time of flight mass spectrometry (MALDI-TOF MS) approaches may be useful in bridging the gap between low-resolution phenotypic methods and bulky genotypic methods in the goal of epidemiological source-typing of microbes. Burkholderia has been shown to be identifiable at the subspecies level using MALDI-TOF MS. There have not yet been studies assessing the ability of MALDI-TOF MS to source-type Burkholderia contaminans isolates into epidemiologically relevant outbreak clusters.

METHODS

55 well-characterised B. contaminans isolates were used to create a panel for analysis of MALDI-TOF MS biomarker peaks and their relation to outbreak strains, location, source, patient, diagnosis and isolate genetics. Unsupervised clustering was performed and classification models were generated using biostatistical analysis software.

RESULTS

B. contaminans spectra derived from MALDI-TOF MS were of sufficiently high resolution to identify 100% of isolates. Unsupervised clustering methods showed poor evidence of spectra clustering by all characteristics measured. Classification algorithms were discriminatory, with Genetic Algorithm models showing 100% recognition capability for all outbreaks, the pulsed-field gel electrophoresis (PFGE) typeability model, and 96.63% recognition for the location model. A consistent peak at m/z of approximately 6943 was identified in all non-typeable strains but in none of the typeable strains.

CONCLUSIONS

MALDI-TOF MS successfully discriminates B. contaminans isolates into clonal, epidemiological clusters, and can recognise isolates non-typeable by PFGE. Further work should investigate this capability, and include peptide studies and genomic sequencing to identify individual proteins or genes responsible for this non-typeablity, particularly at the peak weight identified.

Review of the impact of MALDI-TOF MS in public health and hospital hygiene, 2018

Introduction

MALDI-TOF MS represents a new technological era for microbiology laboratories. Improved sample processing and expanded databases have facilitated rapid and direct identification of microorganisms from some clinical samples. Automated analysis of protein spectra from different microbial populations is emerging as a potential tool for epidemiological studies and is expected to impact public health.

Aim

To demonstrate how implementation of MALDI-TOF MS has changed the way microorganisms are identified, how its applications keep increasing and its impact on public health and hospital hygiene.

Methods

A review of the available literature in PubMED, published between 2009 and 2018, was carried out.

Results

Of 9,709 articles retrieved, 108 were included in the review. They show that rapid identification of a growing number of microorganisms using MALDI-TOF MS has allowed for optimisation of patient management through prompt initiation of directed antimicrobial treatment. The diagnosis of Gram-negative bacteraemia directly from blood culture pellets has positively impacted antibiotic streamlining, length of hospital stay and costs per patient. The flexibility of MALDI-TOF MS has encouraged new forms of use, such as detecting antibiotic resistance mechanisms (e.g. carbapenemases), which provides valuable information in a reduced turnaround time. MALDI-TOF MS has also been successfully applied to bacterial typing.

Conclusions

MALDI-TOF MS is a powerful method for protein analysis. The increase in speed of pathogen detection enables improvement of antimicrobial therapy, infection prevention and control measures leading to positive impact on public health. For antibiotic susceptibility testing and bacterial typing, it represents a rapid alternative to time-consuming conventional techniques.

Improved MALDI-MS method for the highly sensitive and reproducible detection of biomarker peaks for the proteotyping of Salmonella serotypes

The rapid identification and classification of pathogenic microorganisms, including Salmonella enterica, is important for the surveillance and prevention of foodborne diseases. Matrix-assisted laser desorption\ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been shown to be an effective tool for the rapid identification of microorganisms. In a previous report, a mass database consisting of 12 biomarker proteins, S8, L15, L17, L21, L25, S7, superoxide dismutase (SodA), peptidylprolyl cis-trans isomerase C, Gns, YibT, YaiA, and YciF, was introduced for the serotyping of S. enterica via MALDI-MS (Applied Microbiology and Biotechnology, 2017, 101, 8557-8569). However, the reproducibility of peak detection of biomarkers such as SodA at m\z 23 000 was poor. We report here an optimized MALDI-MS method for detecting these biomarkers with high sensitivity and reproducibility. The issue was solved by controlling the bacterial concentration at 1 × 10 to 1 × 10² MFU (3 × 10⁶ to 3 × 10⁷ CFU\μL, as calculated from the MFU), using the colony suspension supernatant obtained by centrifugation, and using matrix additives such as methylenediphosphonic acid and N-decyl-β-D-maltopyranoside. We propose that the method including the above steps is one of the best for detecting biomarkers with high sensitivity and reproducibility.

Bacteriophages as Potential Tools for Detection and Control of Salmonella spp. in Food Systems

The global problem of antibiotic resistance in bacteria is quickly developing in most antibiotics used in hospitals and livestock. Recently, the infections with multi-drug resistant (MDR) bacteria become a major cause of death worldwide. Current antibiotics are not very effective in treating MDR Salmonella infections, which have become a public health threat. Therefore, novel approaches are needed to rapidly detect and effectively control antibiotic-resistant pathogens. Bacteriophages (phages) have seen renewed attention for satisfying those requirements due to their host-specific properties. Therefore, this review aims to discuss the possibility of using phages as a detection tool for recognizing bacterial cell surface receptors and an alternative approach for controlling antibiotic-resistant pathogens in food systems.

Pulsed-field gel electrophoresis (PFGE): A review of the "gold standard" for bacteria typing and current alternatives

Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for bacteria typing. The method involves enzyme restriction of bacteria DNA, separation of the restricted DNA bands using a pulsed-field electrophoresis chamber, followed by clonal assignment of bacteria based on PFGE banding patterns. Various PFGE protocols have been developed for typing different bacteria, leading it to be one of the most widely used methods for phylogenetic studies, food safety surveillance, infection control and outbreak investigations. On the other hand, as PFGE is lengthy and labourious, several PCR-based typing methods can be used as alternatives for research purposes. Recently, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole genome sequencing (WGS) have also been proposed for bacteria typing. In fact, as WGS provides more information, such as antimicrobial resistance and virulence of the tested bacteria in comparison to PFGE, more and more laboratories are currently transitioning from PFGE to WGS for bacteria typing. Nevertheless, PFGE will remain an affordable and relevant technique for small laboratories and hospitals in years to come.

Parallel evolution leading to impaired biofilm formation in invasive Salmonella strains

Pathogenic Salmonella strains that cause gastroenteritis are able to colonize and replicate within the intestines of multiple host species. In general, these strains have retained an ability to form the rdar morphotype, a resistant biofilm physiology hypothesized to be important for Salmonella transmission. In contrast, Salmonella strains that are host-adapted or even host-restricted like Salmonella enterica serovar Typhi, tend to cause systemic infections and have lost the ability to form the rdar morphotype. Here, we investigated the rdar morphotype and CsgD-regulated biofilm formation in two non-typhoidal Salmonella (NTS) strains that caused invasive disease in Malawian children, S. Typhimurium D23580 and S. Enteritidis D7795, and compared them to a panel of NTS strains associated with gastroenteritis, as well as S. Typhi strains. Sequence comparisons combined with luciferase reporter technology identified key SNPs in the promoter region of csgD that either shut off biofilm formation completely (D7795) or reduced transcription of this key biofilm regulator (D23580). Phylogenetic analysis showed that these SNPs are conserved throughout the African clades of invasive isolates, dating as far back as 80 years ago. S. Typhi isolates were negative for the rdar morphotype due to truncation of eight amino acids from the C-terminus of CsgD. We present new evidence in support of parallel evolution between lineages of nontyphoidal Salmonella associated with invasive disease in Africa and the archetypal host-restricted invasive serovar; S. Typhi. We hypothesize that the African invasive isolates are becoming human-adapted and 'niche specialized' with less reliance on environmental survival, as compared to gastroenteritis-causing isolates.

Identification of Salmonella Taxon-Specific Peptide Markers to the Serovar Level by Mass Spectrometry

We present an LC-MS/MS pipeline to identify taxon-specific tryptic peptide markers for the identification of Salmonella at the genus, species, subspecies, and serovar levels of specificity. Salmonella enterica subsp. enterica serovars Typhimurium and its four closest relatives, Saintpaul, Heidelberg, Paratyphi B, and Muenchen, were evaluated. A decision-tree approach was used to identify peptides common to the five Salmonella proteomes for evaluation as genus-, species-, and subspecies-specific markers. Peptides identified for two or fewer Salmonella strains were evaluated as potential serovar markers. Currently, there are approximately 140 000 assembled bacterial genomes publicly available, more than 8500 of which are for Salmonella. Consequently, the specificity of each candidate peptide marker was confirmed across all publicly available protein sequences in the NCBI nonredundant (nr) database. The performance of a subset of candidate taxon-specific peptide markers was evaluated in a targeted mass-spectrometry method. The presented workflow offers a marked improvement in specificity over existing MALDI-TOF-based bacterial identification platforms for the identification of closely related Salmonella serovars.

Isolation, identification and biodiversity of antiscalant degrading seawater bacteria using MALDI-TOF-MS and multivariate analysis

Seawater reverse osmosis (SWRO) is a commonly used desalination technique owing to its lesser environmental and economic impacts as compared to thermal desalination techniques. Antiscalants are used in SWRO to reduce membrane scaling caused by the supersaturation of salts present in feed water. However, to remain effective in reducing membrane scaling, antiscalants should be highly stable and resistant to biological degradation by seawater microorganisms. In this research, several bacteria from Qatar's seawater were isolated and screened for their ability to use antiscalants as a carbon and energy source. The biodiversity of antiscalant degrading seawater bacteria was demonstrated through combining the techniques of MALDI-TOF MS and principle component analysis. It was found that the bacteria isolated from Qatar's seawater such as H. aquamarina, H. elongata, P. fragi, P. stutzeri and others can degrade antiscalants and use them as a carbon and energy source. It was observed that the growth rates varied based on the type of antiscalant and the bacteria used. Among the tested strains, H. aquamarina, which is also known for its potential to cause biofouling, demonstrated the highest growth rates in antiscalants media. Thus, it was concluded that there is wide variety of bacteria in Qatar's seawater that can biodegrade the antiscalants; reducing their efficiency to combat membrane scaling. Since, these antiscalants will be used as a source of carbon and energy, microbial growth will increase resulting in enhanced membrane biofouling in SWRO.

Salmonella Serotyping Using Whole Genome Sequencing

Until recently, traditional serology and the Kauffmann White Scheme (KWS) have been the gold standard for Salmonella serotyping. Whole Genome Sequencing (WGS) has now emerged as an alternative in this field. Serotype information remains a cornerstone in food safety and public health activities to reduce the burden of salmonellosis. At the same time, recent advances in WGS have improved the ability to perform advanced pathogen characterization while improving trace back investigations to determine the source of foodborne illness during outbreaks. Serovar prediction based on WGS can be performed using in silico data analysis tools. Three such tools have been developed: (a). Salmonella in silico Typing Resource (SISTR), (b). SeqSero, and (c). in silico 7-gene MLST ST (Multilocus Sequence Typing Sub-Typing) which was generated using the SISTR platform. Public health officials around the world are diligently working to validate these tools for replacing traditional surveillance methods to provide a more powerful approach for molecular epidemiology in support of public health investigations. In this study, we report a retrospective analysis of our laboratory inventory of 1,041 Salmonella isolates collected between 1999 and 2017. These isolates are of public health significance since they all came from either food, feed or environmental swabs. They were all serotyped by both traditional serology and WGS using an in silico SeqSero tool for serovar prediction. Both predicted identical Salmonella serotypes in 899 isolates (86.4% of the 1,041 Salmonella isolates). SeqSero assignments differed from traditional serological testing in 80 isolates (7.7%) and no serotype prediction was ascertained from 62 isolates (5.9%). This retrospective study is an excellent example of using WGS and SeqSero as a data analysis tool to predict Salmonella serotypes that can provide numerous advantages including molecular and genetic details regarding the characteristics of the Salmonella isolates compared to traditional KWS serotyping. In conclusion, it is evident that using WGS and in silico tools for Salmonella serotyping might someday replace traditional serotyping.

MALDI-TOF mass spectrometry-based serotyping of V. parahaemolyticus isolated from the Zhejiang province of China

BACKGROUND

Vibrio parahaemolyticus is as an important food-borne pathogen circulating in China. Since 1996, the core serotype has become O3:K6, which has specific genetic markers. This serotype causes the majority of outbreaks worldwide. Until now, nearly 21 serotypes were considered as serovariants of O3:K6. Among these, O4:K68, O1:K25 and O1:KUT have caused pandemic outbreaks. O4:K8, a serovariant of O3:K6, has become the second most dominant serotype circulating in China after O3:K6. In this study, we report the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze and characterize 146 V. parahaemolyticus isolates belonging to 23 serotypes.

RESULTS

Upon mass spectral analysis, isolates belonging to O4:K8 formed a distinct group among the five main pandemic groups (O3:K6, O4:K8, O4:K68, O1:K25 and O1:KUT). Two major protein peaks (m/z 4383 and 4397) were significantly different between serotype O4:K8 and the four other pandemic strains. Both of these peaks were present in 32 out of 36 O4:K8 isolates, but were absent in 105 out of 110 non-O4:K8 isolates. These peaks were also absent in all 74 pandemic serotypes (O3:K6, O4:K68, O1:K25 and O1:KUT).

CONCLUSION

Our results highlight the threat of O4:K8 forming a distinct group, which differs significantly from pandemic serotypes on the proteomic level. The use of MALDI-TOF MS has not been reported before in a study of this nature. Mass spectrum peaks at m/z 4383 and 4397 may be specific for O4:K8. However, we cannot conclude that MALDI-TOF MS can be used to serotype V. parahaemolyticus.

Development of a Custom MALDI-TOF MS Database for Species-Level Identification of Bacterial Isolates Collected From Spacecraft and Associated Surfaces

Since the 1970s, the Planetary Protection Group at the Jet Propulsion Laboratory (JPL) has maintained an archive of spacecraft-associated bacterial isolates. Identification of these isolates was routinely performed by sequencing the 16S rRNA gene. Although this technique is an industry standard, it is time consuming and has poor resolving power for some closely related taxa. Matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry is widely used in clinical diagnostics and is a promising method to substitute standard 16S rRNA sequencing. However, manufacturer-provided databases lack the bacterial diversity found in spacecraft-assembly cleanrooms. This study reports the development of the first custom database of MALDI-TOF MS profiles of bacterial isolates obtained from spacecraft and associated cleanroom environments. With the use of this in-house database, 454 bacterial isolates were successfully identified in concurrence with their 16S rRNA sequence-based classifications. Additionally, MALDI-TOF MS resolved strain-level variations, identified potential novel species and distinguished between members of taxonomic groups, which is not possible using conventional 16S rRNA sequencing. MALDI-TOF MS has proved to be an accurate, high-throughput approach for real-time identification of bacterial isolates during the spacecraft assembly process.

Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy

Microbiological monitoring of consumer products and the efficiency of early warning systems and outbreak investigations depend on the rapid identification and strain characterisation of pathogens posing risks to the health and safety of consumers. This study evaluates the potential of three rapid analytical techniques for identification and subtyping of bacterial isolates obtained from a liquid hand soap product, which has been recalled and reported through the EU RAPEX system due to its severe bacterial contamination. Ten isolates recovered from two bottles of the product were identified as Klebsiella oxytoca and subtyped using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI TOF MS), near-infrared Fourier transform (NIR FT) Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy. Comparison of the classification results obtained by these phenotype-based techniques with outcomes of the DNA-based methods pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis of whole-genome sequencing (WGS) data revealed a high level of concordance. In conclusion, a set of analytical techniques might be useful for rapid, reliable and cost-effective microbial typing to ensure safe consumer products and allow source tracking.

Molecular Tools To Study Preharvest Food Safety Challenges

Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.

MALDI-TOF-MS with PLS Modeling Enables Strain Typing of the Bacterial Plant Pathogen Xanthomonas axonopodis

Matrix-assisted desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) is a fast and effective tool for microbial species identification. However, current approaches are limited to species-level identification even when genetic differences are known. Here, we present a novel workflow that applies the statistical method of partial least squares discriminant analysis (PLS-DA) to MALDI-TOF-MS protein fingerprint data of Xanthomonas axonopodis, an important bacterial plant pathogen of fruit and vegetable crops. Mass spectra of 32 X. axonopodis strains were used to create a mass spectral library and PLS-DA was employed to model the closely related strains. A robust workflow was designed to optimize the PLS-DA model by assessing the model performance over a range of signal-to-noise ratios (s/n) and mass filter (MF) thresholds. The optimized parameters were observed to be s/n = 3 and MF = 0.7. The model correctly classified 83% of spectra withheld from the model as a test set. A new decision rule was developed, termed the rolled-up Maximum Decision Rule (ruMDR), and this method improved identification rates to 92%. These results demonstrate that MALDI-TOF-MS protein fingerprints of bacterial isolates can be utilized to enable identification at the strain level. Furthermore, the open-source framework of this workflow allows for broad implementation across various instrument platforms as well as integration with alternative modeling and classification algorithms. Graphical abstract ᅟ.

Isolation, differentiation and biodiversity of ureolytic bacteria of Qatari soil and their potential in microbially induced calcite precipitation (MICP) for soil stabilization

Biomineralization plays a key role in modifying the geological properties of soil, thereby stabilizing it against wind erosion, especially in areas characterized by harsh weather and harsh soil (calcareous and arid); i.e. Arabic Gulf region. Among soil microorganisms, ureolytic bacteria are capable of modifying soil characteristics and thus, inducing biomineralization. This research investigated the occurrence and diversity of ureolytic bacteria in Qatari soils, specifically to study their acquired potential to adapt to harsh conditions exhibiting ureolytic activity. Soil samples were collected from various locations in Qatar and were used to isolate the indigenous ureolytic bacteria. It was noticed that most of the ureolytic bacteria in Qatari soil belong to the genus Bacillus mainly Bacillus cereus. Identification and differentiation of 18 ureolytic isolates were performed using MALDI-TOF MS techniques while ribotyping (16S rRNA) molecular technique was used mainly for 6 selected strains. This study not only shows the diversity of species of ureolytic bacteria in Qatari soil but also shows the diversity in their protein profiles, which confirms that bacteria have adapted well to the harsh environment. In addition, the strains were evaluated based on a newly modified screening method in this work; i.e. production of arbitrary urease activity (AUA). Thus, the strains showing the highest AUA, exhibited the highest capability to produce urease enzymes induced by urea. Analysis of calcium carbonate precipitation utilizing SEM-EDX showed that the ureolytic bacteria also play a significant role in the precipitation of minerals such as CaCO₃, in the presence of urea in soil. Therefore, this research showed a high occurrence of indigenous Bacillus bacteria in Qatari soil that can perform biomineralization and thus can be helpful, if properly stimulated, in enhancing soil stabilization, and for other local applications as well, since they are adapted to these soil and weather conditions.

Biomineralization plays a key role in modifying the geological properties of soil, thereby stabilizing it against wind erosion, especially in areas characterized by harsh weather and harsh soil (calcareous and arid); i.e. Arabic Gulf region.

A simplified multiplex PCR-based typing method for common Salmonella enterica serovars supported by online server-based detection system

Background & objectives:

A rapid and simple alternative method is needed to replace the laborious, time-consuming Salmonella serotyping. The objective of the present study was to improve and simplify a previously reported multiplex polymerase chain reaction (PCR)-based method and to create an online server to enable rapid determination of serovars.

Methods:

A method of multiplex PCR-based genome typing (MPGT) was standardized using 59 Salmonella isolates of 31 serovars. Several previously reported primers were modified to obtain a more accurate performance. The screen was separated into four different multiplex reactions distinguishable on standard electrophoresis. A blind study was subsequently performed with 81 isolates of 10 serovars most prevalent in India. Whole genome information from 440 Salmonella isolates was used to confirm the usefulness of this method and concurrence of in silico predictions and PCR results were investigated. A public server (http://www.mpgt-salmonella.res.in) was established for data storage and determination of closest previously observed Salmonella isolates based on obtained MPGT patterns.

Results:

The 16 target genes amplified showed variability in their presence in strains from different serotypes. Hence, identical amplification patterns suggested genetic relatedness of strains and usually identical serological behaviour. The observed absence/presence patterns of genes were converted to an MPGT code. Altogether, 83 different codes were predicted in silico based on the whole genome information of 440 strains. Results confirmed that major serovars usually displayed unique MPGT codes.

Interpretation & conclusions:

The multiplex PCR assay resulted in specific binary codes for isolates from each of the 31 Salmonella serovars tested. The online server allowed the user to compare obtained PCR results with stored previous patterns. Simplicity, speed and cost-effectiveness make this tool useful for quick outbreak management.

Application of proteotyping Strain Solution™ ver. 2 software and theoretically calculated mass database in MALDI-TOF MS typing of Salmonella serotype

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based microbial identification is a popular analytical method. Strain Solution proteotyping software available for MALDI-TOF MS has great potential for the precise and detailed discrimination of microorganisms at serotype- or strain-level, beyond the conventional mass fingerprinting approaches. Here, we constructed a theoretically calculated mass database of Salmonella enterica subspecies enterica consisting of 12 biomarker proteins: ribosomal proteins S8, L15, L17, L21, L25, and S7, Mn-cofactor-containing superoxide dismutase (SodA), peptidyl-prolyl cis-trans isomerase C (PPIase C), and protein Gns, and uncharacterized proteins YibT, YaiA, and YciF, that can allow serotyping of Salmonella. Strain Solution ver. 2 software with the novel database constructed in this study demonstrated that 109 strains (94%), including the major outbreak-associated serotypes, Enteritidis, Typhimurium, and Infantis, could be correctly identified from others by colony-directed MALDI-TOF MS using 116 strains belonging to 23 kinds of typed and untyped serotypes of S. enterica from culture collections, patients, and foods. We conclude that Strain Solution ver. 2 software integrated with the accurate mass database will be useful for the bacterial proteotyping by MALDI-TOF MS-based microbial classification in the clinical and food safety fields.

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis

Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.

Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry as a reliable proteomic method for characterization of Escherichia coli and Salmonella isolates

Aim:

Identification of pathogenic clinical bacterial isolates is mainly dependent on phenotypic and genotypic characteristics of the microorganisms. These conventional methods are costive, time-consuming, and need special skills and training. An alternative, mass spectral (proteomics) analysis method for identification of clinical bacterial isolates has been recognized as a rapid, reliable, and economical method for identification. This study was aimed to evaluate and compare the performance, sensitivity and reliability of traditional bacteriology, phenotypic methods and matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (MALDI-TOF MS) in the identification of clinical Escherichia coli and Salmonella isolates recovered from chickens.

Materials and Methods:

A total of 110 samples (cloacal, liver, spleen, and/or gall bladder) were collected from apparently healthy and diseased chickens showing clinical signs as white chalky diarrhea, pasty vent, and decrease egg production as well as freshly dead chickens which showing postmortem lesions as enlarged liver with congestion and enlarged gall bladder from different poultry farms.

Results:

Depending on colonial characteristics and morphological characteristics, E. coli and Salmonella isolates were recovered and detected in only 42 and 35 samples, respectively. Biochemical identification using API 20E identification system revealed that the suspected E. coli isolates were 33 out of 42 of colonial and morphological identified E. coli isolates where Salmonella isolates were represented by 26 out of 35 of colonial and morphological identified Salmonella isolates. Serological identification of isolates revealed that the most predominant E. coli serotypes were O1 and O78 while the most predominant Salmonella serotype of Salmonella was Salmonella Pullorum. All E. coli and Salmonella isolates were examined using MALDI-TOF MS. In agreement with traditional identification, MADI-TOF MS identified all clinical bacterial samples with valid scores as E. coli and Salmonella isolates except two E. coli isolates recovered from apparently healthy and diseased birds, respectively, with recovery rate of 93.9% and 2 Salmonella isolates recovered from apparently healthy and dead birds, respectively, with recovery rate of 92.3%.

Conclusion:

Our study demonstrated that Bruker MALDI-TOF MS Biotyper is a reliable rapid and economic tool for the identification of Gram-negative bacteria especially E. coli and Salmonella which could be used as an alternative diagnostic tool for routine identification and differentiation of clinical isolates in the bacteriological laboratory. MALDI-TOF MS need more validation and verification and more study on the performance of direct colony and extraction methods to detect the most sensitive one and also need using more samples to detect sensitivity, reliability, and performance of this type of bacterial identification.

Examining the Link between Biofilm Formation and the Ability of Pathogenic Salmonella Strains to Colonize Multiple Host Species

Salmonella are important pathogens worldwide and a predominant number of human infections are zoonotic in nature. The ability of strains to form biofilms, which is a multicellular behavior characterized by the aggregation of cells, is predicted to be a conserved strategy for increased persistence and survival. It may also contribute to the increasing number of infections caused by ingestion of contaminated fruits and vegetables. There is a correlation between biofilm formation and the ability of strains to colonize and replicate within the intestines of multiple host species. These strains predominantly cause localized gastroenteritis infections in humans. In contrast, there are salmonellae that cause systemic, disseminated infections in a select few host species; these “invasive” strains have a narrowed host range, and most are unable to form biofilms. This includes host-restricted Salmonella serovar Typhi, which are only able to infect humans, and atypical gastroenteritis strains associated with the opportunistic infection of immunocompromised patients. From the perspective of transmission, biofilm formation is advantageous for ensuring pathogen survival in the environment. However, from an infection point of view, biofilm formation may be an anti-virulence trait. We do not know if the capacity to form biofilms prevents a strain from accessing the systemic compartments within the host or if loss of the biofilm phenotype reflects a change in a strain’s interaction with the host. In this review, we examine the connections between biofilm formation, Salmonella disease states, degrees of host adaptation, and how this might relate to different transmission patterns. A better understanding of the dynamic lifecycle of Salmonella will allow us to reduce the burden of livestock and human infections caused by these important pathogens.

Head-to-head comparison of Microflex LT and Vitek MS systems for routine identification of microorganisms by MALDI-TOF mass spectrometry in Chile

Background

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a new and revolutionary identification method for microorganisms and has recently been introduced into clinical microbiology in many industrialized countries in Europe and North America.

Objectives

Our study aimed to compare the performance and practicality of two commercial MALDI-TOF MS platforms in a head-to head manner at a routine laboratory in Chile.

Methods

During a five-month period in 2012–13, the diagnostic efficiency (correct identification rate) and agreement between Microflex LT (Bruker Daltonics) and Vitek MS (bioMérieux) was compared in a parallel manner to conventional identification including genotypic analysis for difficult-to-identify strains. The study included 804 microbial isolates: 252 Enterobacteriaceae, 126 non-fermenters, 36 other gram-negative rods, 279 gram-positive cocci, 32 gram-positive rods, 32 anaerobes, and 47 yeasts. Other relevant factors of the two devices such as user friendliness and connectivity were also evaluated and compared.

Results

Both systems correctly identified the vast majority (98%) of the isolates to the genus level. Vitek MS reached higher rates of identification to species and species complex level than Microflex LT (81% vs. 85% and 87% vs. 93%, respectively), which was mainly based on the higher performance among coagulase negative staphylococci and Candida isolates. The evaluation of user friendliness and other technical aspects showed only marginal differences, which slightly favored Vitek MS, mainly due to its ready-to-use supplies, easier connectivity and workflow integration, and availability of local technical support.

Conclusions

Both MALDI-TOF MS systems permitted fast and accurate identification of most microbial strains and showed a high level of user-friendliness. The observed differences were marginal and slightly favored Vitek MS, mainly due to practicality and connectivity issues within our setting.

MALDI-TOF mass spectrometry provides high accuracy in identification of Salmonella at species level but is limited to type or subtype Salmonella serovars

Salmonella can cause global foodborne illnesses in humans and many animals. The current diagnostic gold standard used for detecting Salmonella infection is microbiological culture followed by serological confirmation tests. However, these methods are complicated and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis offers some advantages in rapid identification, for example, simple and fast sample preparation, fast and automated measurement, and robust and reliable identification up to genus and species levels, possibly even to the strain level. In this study, we established a reference database for species identification using whole-cell MALDI-TOF MS; the database consisted of 12 obtained main spectra of the Salmonella culture collection strains belonged to seven serotypes. Eighty-two clinical isolates of Salmonella were identified using established database, and partial 16S rDNA gene sequencing and serological method were used as comparison. We found that MALDI-TOF mass spectrometry provided high accuracy in identification of Salmonella at species level but was limited to type or subtype Salmonella serovars. We also tried to find serovar-specific biomarkers and failed. Our study demonstrated that (a) MALDI-TOF MS was suitable for identification of Salmonella at species level with high accuracy and (b) that MALDI-TOF MS method presented in this study was not useful for serovar assignment of Salmonella currently, because of its low matching with serological method and (c) MALDI-TOF MS method presented in this study was not suitable to subtype S. typhimurium because of its low discriminatory ability.

Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives

INTRODUCTION

Advancements in microbial identification occur increasingly faster as more laboratories explore, refine and extend the use of mass spectrometry in the field of microbiology. Areas covered: This review covers the latest knowledge found in the literature for quick identification of various classes of bacterial pathogens known to cause human infection by the use of MALDI-TOF MS technology. Except for identification of bacterial strains, more researchers try to 'battle time' in favor of the patient. These novel approaches to identify bacteria directly from clinical samples and even determine antibiotic resistance are extensively revised and discussed. Expert commentary: Mass spectrometry is the future of bacterial identification and creates a new era in modern microbiology. Its incorporation in routine practice seems to be not too far, providing a valuable alternative, especially in terms of time, to conventional techniques. If the technology further advances, quick bacterial identification and probable identification of common antibiotic resistance might guide patient decision-making regarding bacterial infectious diseases in the near future.

Current developments to use linear MALDI-TOF spectra for the identification and typing of bacteria and the characterization of other cells/organisms related to infectious diseases

Within the past few years identification of bacteria by MALDI-TOF MS has become a standard technique in bacteriological laboratories for good reasons. MALDI-TOF MS identification is rapid, robust, automatable, and the per-sample costs are low. Yet, the spectra are very informative and the reliable identification of bacterial species is usually possible. Recently, new MS-based approaches for the identification of bacteria are emerging that are based on the detailed analysis of the bacterial proteome by high-resolution MS. These "proteotyping" approaches are highly discriminative and outperform MALDI-TOF MS-based identification in terms of specificity, but require a laborious proteomic workflow and far more expertise and sophisticated instrumentation than identification on basis of MALDI-TOF MS spectra, which can be obtained with relative simple and uncostly linear MALDI-TOF mass spectrometers. Thus MALDI-TOF MS identification of bacteria remains an attractive option for routine diagnostics. Additionally, MALDI-TOF MS identification protocols have been extended and improved in many respects making linear MALDI-TOF MS a versatile tool that can be useful beyond the identification of a bacterial species, e.g. for the characterization of leucocytes and arthropod vectors of infectious diseases. This review focuses on such improvements and extensions of the typical MALDI-TOF MS workflow in the field of infectious diseases.