Application of MALDI Biotyper System for Rapid Identification of Bacteria Isolated from a Fresh Produce Market

El-Nemr, Israa; Mushtaha, Mohanad; Sundararaju, Sathyavathi; Fontejon, Charmaine; Suleiman, Mohammed; Tang, Patrick; Goktepe, Ipek; Hasan, Mohammad Rubayet

doi:10.1007/s00284-018-01624-1

Cited by 14 publications

(7 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similarly, Böhme et al compared the efficacy of MALDI-TOF MS (Voyager STR-DE, Applied Biosystems) and 16S rRNA gene sequencing and pointed out that MALDI-TOF MS identified 76% of 50 seafood-borne bacterial strains isolated from commercial seafood products at species level while 16S rRNA gene sequencing only identified the species of 50% of the strains [ 51 ]. Our outcomes are also consistent with the study of El-Nemr et al in which MALDI-TOF MS identified more bacteria isolated from a market area (e.g., vegetables, soil, air, and hand palms of fresh produce handlers) at species level (41%) than 16S rRNA gene sequencing (28%) did [ 21 ]. In another study, Pandey et al identified psychrotolerant bacteria isolated from high-altitude soil with only 4.92% of the isolates identified similarly by MALDI-TOF MS and 16S rRNA gene sequencing [ 19 ], whereas in our case 73.81% of the isolates were identified identical.…”

Section: Discussionsupporting

confidence: 92%

“…Our results and the findings of several other authors reassure the potential of MALDI-TOF MS (Bruker Biotyper) to act as an alternative to 16S rRNA gene sequencing or in the future even replace it in environmental microbiology screening [ 17 , 18 , 19 , 20 , 21 , 50 , 51 ]. Still, to identify and thoroughly characterize the bigger, uncultivable part of the microbial community of irrigation water, culture-independent methods such as amplicon sequence analysis of 16S rRNA genes are necessary.…”

Section: Discussionsupporting

confidence: 80%

“…Uchida-Fuji et al showed the potential of MALDI-TOF MS (Bruker Biotyper) in environmental microbiology as the authors were able to identify 86.2% of 3724 isolates at species level [ 17 ]. In addition, MALDI-TOF MS (Bruker Biotyper) and 16S rRNA gene sequencing identification techniques have been compared in various environments such as environmental mining samples, high-altitude soil samples, soil samples, and fresh vegetables [ 18 , 19 , 20 , 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

et al. 2023

View full text Add to dashboard Cite

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

show abstract

Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2023

View full text Add to dashboard Cite

show abstract

“…Confirmatory qPCR for S. agalactiae were performed as described previously 29 . Bacterial 16S rRNA PCR was performed as described previously 30 .…”

Section: Specimensmentioning

confidence: 99%

A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting

Hasan

Sundararaju

Tang

et al. 2020

Sci Rep

Self Cite

View full text Add to dashboard Cite

The etiology of central nervous system (CNS) infections such as meningitis and encephalitis remains unknown in a large proportion of cases partly because the diversity of pathogens that may cause CNS infections greatly outnumber available test methods. We developed a metagenomic next generation sequencing (mNGS)-based approach for broad-range detection of pathogens associated with CNS infections suitable for application in the acute care hospital setting. The analytical sensitivity of mNGS performed on an Illumina MiSeq was assessed using simulated cerebrospinal fluid (CSF) specimens (n = 9). mNGS data were then used as a training dataset to optimize a bioinformatics workflow based on the IDseq pipeline. For clinical validation, residual CSF specimens (n = 74) from patients with suspected CNS infections previously tested by culture and/or PCR, were analyzed by mNGS. In simulated specimens, the NGS reads aligned to pathogen genomes in IDseq were correlated to qPCR CT values for the respective pathogens (R = 0.96; p < 0.0001), and the results were highly specific for the spiked pathogens. In clinical samples, the diagnostic accuracy, sensitivity and specificity of the mNGS with reference to conventional methods were 100%, 95% and 96%, respectively. The clinical application of mNGS holds promise to benefit patients with CNS infections of unknown etiology.

show abstract

“…The technique is tremendously useful for the identification of different microbial strains and their associated metabolites using either whole cells or cell extracts. The main disadvantage of MALDI‐ToF‐MS is that the technique is unable to identify new species as the detection and identification processes are conducted using existing spectral databases of the peptide mass fingerprints of strains (El‐Nemr et al, 2019; Pinu, 2016). MALDI‐ToF‐MS determines a unique proteomic fingerprint of an organism and matches characteristic patterns with an extensive reference library to determine the organism's identity (Madsen et al, 2015; Zervas et al, 2019).…”

Section: Analytical Methods For Microbial Pathogen Identification In ...mentioning

confidence: 99%

Disease diagnostic strategies and emerging analytical metabolomics techniques for waterborne microbial pathogens in vegetable crops—A critical review

et al. 2023

View full text Add to dashboard Cite

A significant number of people around the world suffer from illnesses that are related to the consumption of unsafe vegetable crops. Early identification of waterborne microbial pathogens affecting vegetable crops can be an important step towards the control of disease. Microbial pathogens secrete extracellular metabolic volatiles or molecular biomarkers that affect the yield and quality of vegetable crops. These secreted compounds can be investigated using several applied analytical techniques, such as metabolomics, proteomics and other ‘omics’ tools. Currently, it is possible to use these approaches to characterize a broad range of specialized metabolites present in vegetable crops affected by waterborne and soilborne microbial pathogens. Such approaches may be used to determine molecular biomarkers, which can subsequently be exploited for the diagnosis of microbial pathogens that affect vegetable crops. Molecular biomarkers are involved in complex pathogenic biological processes involving mechanisms of pathogenesis and could be of great interest in the field of metabolomics. This review investigates disease diagnostic strategies and emerging analytical metabolomics techniques for waterborne microbial pathogens in vegetable crops. These will be vital in building comprehensive and more reliable data regarding the nature of secreted proteins and other specialized metabolites in vegetable crops and will lead to an increased understanding of the interactions between the host and pathogenic oomycetes, fungi, bacteria and viruses.

show abstract

Application of MALDI Biotyper System for Rapid Identification of Bacteria Isolated from a Fresh Produce Market

Cited by 14 publications

References 28 publications

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

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

A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting

Disease diagnostic strategies and emerging analytical metabolomics techniques for waterborne microbial pathogens in vegetable crops—A critical review

Contact Info

Product

Resources

About