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Current Issues in Molecular Biology Jul 2021Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification. It would be highly beneficial... (Review)
Review
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification. It would be highly beneficial to also be able to use the technology as a fast way to detect clinically relevant clones of bacterial species. However, studies to this aim have often had limited success. The methods used for data acquisition, processing and data interpretation are highly diverse amongst studies on MALDI-TOF MS sub-species typing. In addition to this, feasibility may depend on the bacterial species and strains investigated, making it difficult to determine what methods may or may not work. In our paper, we have reviewed recent research on MALDI-TOF MS typing of bacterial strains. Although we found a lot of variation amongst the methods used, there were approaches shared by multiple research groups. Multiple spectra of the same isolate were often combined before further analysis for strain distinction. Many groups used a protein extraction step to increase resolution in their MALDI-TOF MS results. Peaks at a high mass range were often excluded for data interpretation. Three groups have found ways to determine feasibility of MALDI-TOF MS typing for their set of strains at an early stage of their project.
Topics: Animals; Bacteria; Bacterial Proteins; Bacterial Typing Techniques; Humans; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 34294671
DOI: 10.3390/cimb43020054 -
European Journal of Clinical... Mar 2019The need to identify highly related bacterial strains is ancient in clinical, industrial, or environmental microbiology. Strategies based on different phenotypic and... (Review)
Review
The need to identify highly related bacterial strains is ancient in clinical, industrial, or environmental microbiology. Strategies based on different phenotypic and genotypic principles have been used since the early 1930s with variable outcomes and performances, accompanying the evolution of bacterial features' knowledge as well as technologies, instruments, and data analysis tools. Today, more than ever, the implementation of bacterial typing methods that combine a high reliability and accuracy with a rapid, low-cost, and user-friendly performance is highly desirable, especially for clinical microbiology. FT-IR developments for bacterial discrimination at the infra-species level settled on the identification of bacterial groups previously defined by phenotypic or genotypic typing methods. Therefore, this review provides a brief historical overview of main bacterial strain typing methods, and a comprehensive analysis of the fundamentals and applications of Fourier transform infrared spectroscopy, a phenotypic-based method with potential for routine strain typing. The different studies on FT-IR-based strain typing of diverse Gram-negative and Gram-positive bacterial species are discussed in light of genotypic, phenotypic, and biochemical aspects, in order to definitively give this methodology credit to be widely accepted by microbiologists. Importantly, the discriminatory biochemical fingerprints observed on FT-IR spectra have been consistently correlated with sugar-based coating structures that besides reflecting strain variation are also of high relevance for the specificity in pathogen-host interactions. Thus, FT-IR-based bacterial typing might not only be useful for quick and reliable strain typing but also to help understanding the diversity, evolution, and host adaptation factors of key bacterial pathogens or subpopulations.
Topics: Bacteria; Bacterial Typing Techniques; Genotype; Polysaccharides, Bacterial; Serogroup; Species Specificity; Spectroscopy, Fourier Transform Infrared
PubMed: 30483997
DOI: 10.1007/s10096-018-3431-3 -
Clinica Chimica Acta; International... Oct 2017Biochemical methods such as metabolite testing and serotyping are traditionally used in clinical microbiology laboratories to identify and categorize microorganisms. Due... (Review)
Review
Biochemical methods such as metabolite testing and serotyping are traditionally used in clinical microbiology laboratories to identify and categorize microorganisms. Due to the large variety of bacteria, identifying representative metabolites is tedious, while raising high-quality antisera or antibodies unique to specific biomarkers used in serotyping is very challenging, sometimes even impossible. Although serotyping is a certified approach for differentiating bacteria such as E. coli and Salmonella at the subspecies level, the method is tedious, laborious, and not practical during an infectious disease outbreak. Mass spectrometry (MS) platforms, especially matrix assisted laser desorption and ionization-time of flight mass spectrometry (MALDI-TOF-MS), have recently become popular in the field of bacterial identification due to their fast speed and low cost. In the past few years, we have used liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based approaches to solve various problems hindering serotyping and have overcome some insufficiencies of the MALDI-TOF-MS platform. The current article aims to review the characteristics, advantages, and disadvantages of MS-based platforms over traditional approaches in bacterial identification and categorization.
Topics: Bacteria; Bacterial Typing Techniques; Mass Spectrometry
PubMed: 28866114
DOI: 10.1016/j.cca.2017.08.035 -
The Veterinary Quarterly Dec 1993The ability to subtype bacteria by typing methods provides the bacteriologist with a powerful means to identify relationships between bacteria. This knowledge is used to... (Review)
Review
The ability to subtype bacteria by typing methods provides the bacteriologist with a powerful means to identify relationships between bacteria. This knowledge is used to identify routes of disease transmission among livestock and from livestock to humans. In the present paper, the principles of bacterial typing and the most commonly applied typing methods for use in veterinary public health are discussed in the context of their application in the investigation of salmonella epidemiology. Typing methods are now routinely used in most investigations on this subject and have provided insight into routes of transmission, reservoirs of infection and mechanisms of persistent infection. Under the EC order on zoonotic diseases, extended surveillance on the presence of zoonotic bacteria in livestock must be expected. To receive the maximum benefits of this surveillance, selected typing methods must be applied to all isolates of e.g. salmonella. At present, serotyping, and phage typing where applicable, are the most obvious choices for continuous surveillance of this organism. Random amplification of polymorphic DNA (PCR based typing) may have the potential for allocating strains into relevant groups quicker and without the requirement for additional manpower, and this method may be preferred in future.
Topics: Animals; Animals, Domestic; Bacterial Typing Techniques; Electrophoresis, Polyacrylamide Gel; Epidemiologic Methods; European Union; Genotype; Phenotype; Polymerase Chain Reaction; Salmonella; Salmonella Infections, Animal
PubMed: 8122347
DOI: 10.1080/01652176.1993.9694390 -
Klinicka Mikrobiologie a Infekcni... Dec 2022Whole-genome sequencing (WGS) is a modern method that allows deep understanding of studied organisms and is currently gaining importance in molecular microbiology. Data... (Review)
Review
Whole-genome sequencing (WGS) is a modern method that allows deep understanding of studied organisms and is currently gaining importance in molecular microbiology. Data obtained by whole-genome sequencing can be used for a number of different analyses, specifically in bacterial epidemiology. The authors provide an overview of the methods that are used for bacterial typing, description of their principles with subsequent possibilities for evaluation of the obtained data and applications in hospital research.
Topics: Humans; Bacteria; Bacterial Typing Techniques; Multilocus Sequence Typing; Whole Genome Sequencing
PubMed: 37586043
DOI: No ID Found -
Talanta Feb 2020Accurate and effective identification and typing of microorganisms is important in epidemiological surveillance. Fourier transform infrared (FTIR) spectroscopy is a... (Review)
Review
Accurate and effective identification and typing of microorganisms is important in epidemiological surveillance. Fourier transform infrared (FTIR) spectroscopy is a promising bacterial typing method based on extracting the infrared spectrum signal-related biochemical features of intact microbiological cells. Unfortunately, the FTIR signals of bacteria are disturbed by many factors, especially the unavoidable absorbance of HO, and many studies have focused only on the internal biochemical information. In this study, the interference from water was analyzed and verified by experimental data. The infrared absorbance of HO overlapped with the protein (1200-1800 cm) and lipid regions (2800-3700 cm), but had little impact on the polysaccharide and nucleic acid region (900-1200 cm). The elimination of the protein and lipid region markedly decreased the interference of HO and increased the typing accuracy. The results indicate that the polysaccharide and nucleic acid region (900-1200 cm) is the only credible region for bacterial typing, and typing based on this region not only reduces the size of the data analysis, but results in more reliable typing results.
Topics: Bacteria; Bacterial Typing Techniques; Fourier Analysis; Humans; Nucleic Acids; Polysaccharides, Bacterial; Spectroscopy, Fourier Transform Infrared; Water
PubMed: 31816678
DOI: 10.1016/j.talanta.2019.120347 -
Polish Journal of Veterinary Sciences Mar 2018Staphylococci are very common human and animal pathogens. A variety of staphylococcal virulence determinates leads to vast range of infections. One of them is mastitis... (Review)
Review
Staphylococci are very common human and animal pathogens. A variety of staphylococcal virulence determinates leads to vast range of infections. One of them is mastitis which is a common disease of the mammary glands. The incidence of this disease is widespread all over the world and depends on bacterial virulence and on prevention programs. The influence of mastitis on human health is not globally evaluated, however, in veterinary fields loses in milk production caused by bovine mastitis are a constant economic problem. One of the most important parts of the mastitis control programs is accurate diagnosis of the inflammation and characterization of the etiological factors which leads to reduction of mastitis spread. Recent reports show that staphylococci are common bacterial etiological factors of mastitis, and this paper is an overview of the diagnostic typing methods used for characterization of staphylococcal isolates. A number of different techniques available to applicate is described. Phenotypic methods to identify and to differentiate isolates or discriminate virulence factors are still in use, however, some advanced genetic methods offering higher discriminatory power are reported as more accurate. In fact, nowadays the most powerful tool on that field is next generation sequencing (NGS) of the whole genome, but its high cost and requirement of special laboratory equipment makes it hard to use for routine diagnostics. That is why standard PCR techniques-based methods, and the sequencing of particular genes, are mostly used for typing bacterial isolates. Most of these techniques are characterized by a high discriminatory power, big epidemiological concordance, and repeatable results. The presented report describes the techniques used most frequent in mastitis diagnostics related to staphylococci typing and shows their advantages and disadvantages.
Topics: Animals; Bacterial Typing Techniques; Female; Mastitis; Staphylococcal Infections; Staphylococcus
PubMed: 29624017
DOI: 10.24425/119041 -
Journal of Clinical Microbiology Aug 2005A multilocus sequence typing (MLST) scheme was developed for Klebsiella pneumoniae. Sequences of seven housekeeping genes were obtained for 67 K. pneumoniae strains,...
A multilocus sequence typing (MLST) scheme was developed for Klebsiella pneumoniae. Sequences of seven housekeeping genes were obtained for 67 K. pneumoniae strains, including 19 ceftazidime- and ciprofloxacin-resistant isolates. Forty distinct allelic profiles were identified. MLST data were validated against ribotyping and showed high (96%) discriminatory power. The MLST approach provides unambiguous data useful for the epidemiology of K. pneumoniae isolates.
Topics: Bacterial Typing Techniques; Base Sequence; Cross Infection; Drug Resistance, Bacterial; Humans; Klebsiella pneumoniae; Microbial Sensitivity Tests; Molecular Sequence Data; Ribotyping; Sequence Analysis, DNA
PubMed: 16081970
DOI: 10.1128/JCM.43.8.4178-4182.2005 -
Current Protocols in Microbiology Nov 2009In 1884, Hans Christian Gram, a Danish doctor, developed a differential staining technique that is still the cornerstone of bacterial identification and taxonomic...
In 1884, Hans Christian Gram, a Danish doctor, developed a differential staining technique that is still the cornerstone of bacterial identification and taxonomic division. This multistep, sequential staining protocol separates bacteria into four groups based on cell morphology and cell wall structure: Gram-positive cocci, Gram-negative cocci, Gram-positive rods, and Gram-negative rods. The Gram stain is useful for assessing bacterial contamination of tissue culture samples or for examining the Gram stain status and morphological features of bacteria isolated from mixed or isolated bacterial cultures.
Topics: Bacteria; Bacterial Typing Techniques; Coloring Agents; Staining and Labeling
PubMed: 19885931
DOI: 10.1002/9780471729259.mca03cs15 -
International Journal of Biological... May 2022Bacterial FT-IR signals are extremely specific and highly reproducible, making FT-IR an efficient tool for bacterial typing at the subspecies level. The polysaccharide...
Bacterial FT-IR signals are extremely specific and highly reproducible, making FT-IR an efficient tool for bacterial typing at the subspecies level. The polysaccharide and nucleic acid FT-IR regions (1200-900 cm) are recommended as a precise and reproducible pattern for bacterial typing. However, proteins are the major macromolecules present in bacteria, and the FT-IR spectral region of proteins (1800-1300 cm) is conceivably an important factor in bacterial typing. In this study, we investigated the influence of water on bacterial protein amide bands by comparing spectra obtained with and without FT-IR system dehydration. Eight Escherichia coli, ten Klebsiella pneumoniae, and eleven Staphylococcus aureus strains were typed by FT-IR under different conditions in a blinded experimental setup. Hierarchical clustering analysis (HCA) showed that, when protein signals were included (1800-900 cm), the typing accuracies for select E. coli, K. pn and S. aureus strains without system dehydration were 50%, 30% and 18.2%, respectively. However, the accuracies greatly improved to 100%, 90% and 90.9% when the FT-IR system was dehydrated. These results indicate that the FT-IR signals of protein amide bands are beneficial for bacterial typing.
Topics: Amides; Bacteria; Bacterial Typing Techniques; Dehydration; Escherichia coli; Humans; Spectroscopy, Fourier Transform Infrared; Staphylococcus aureus
PubMed: 35245578
DOI: 10.1016/j.ijbiomac.2022.02.161