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Relevant bibliographies by topics / Bacterial typing techniques

Academic literature on the topic 'Bacterial typing techniques'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2024

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Journal articles on the topic "Bacterial typing techniques"

1

FARBER, J. M. "An Introduction to the Hows and Whys of Molecular Typing†." Journal of Food Protection 59, no. 10 (October 1, 1996): 1091–101. http://dx.doi.org/10.4315/0362-028x-59.10.1091.

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Until recently, the relatedness of bacterial isolates has been determined solely by testing for one or several phenotypic markers, using methods such as serotyping, phage typing, biotyping, antibiotic susceptibility testing, and bacteriocin typing. However, there are problems in the use of many of these phenotype-based methods. For example, phage and bacteriocin typing systems are not available for all bacterial species and serotyping can be labor-intensive and costly. In addition, phenotypic markers may not be stably expressed under certain environmental or culture conditions. In contrast, some of the newer molecular typing methods involving the analysis of DNA offer many advantages over traditional techniques. One of the more important advantages is that since DNA can always be extracted from bacteria, all bacteria should be typeable. Another is that the discriminatory power of DNA-based methods is greater than that of phenotypic procedures. This review focuses on the basics of molecular typing along with the advantages and disadvantages of several of the newer genotypic typing techniques. This includes methods such as plasmid typing, pulsed-field gel electrophoresis, ribotyping and its variations, and polymerase chain reaction-based methods such as random amplified polymorphic DNA analysis. Molecular typing of microorganisms has made great strides in the last decade, and many food microbiology laboratories have become more knowledgeable and better equipped to carry out these new molecular techniques. Molecular typing procedures can be broadly defined as methods used to differentiate bacteria, based on the composition of biological molecules such as proteins, fatty acids, carbohydrates, etc., or nucleic acids. The latter can also be more specifically defined as genotyping, and is the subject of this review.

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Zadoks, Ruth, Willem van Leeuwen, Herman Barkema, Otlis Sampimon, Henri Verbrugh, Ynte Hein Schukken, and Alex van Belkum. "Application of Pulsed-Field Gel Electrophoresis and Binary Typing as Tools in Veterinary Clinical Microbiology and Molecular Epidemiologic Analysis of Bovine and HumanStaphylococcus aureus Isolates." Journal of Clinical Microbiology 38, no. 5 (2000): 1931–39. http://dx.doi.org/10.1128/jcm.38.5.1931-1939.2000.

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Thirty-eight bovine mammary Staphylococcus aureusisolates from diverse clinical, temporal, and geographical origins were genotyped by pulsed-field gel electrophoresis (PFGE) afterSmaI digestion of prokaryotic DNA and by means of binary typing using 15 strain-specific DNA probes. Seven pulsed-field types and four subtypes were identified, as were 16 binary types. Concordant delineation of genetic relatedness was documented by both techniques, yet based on practical and epidemiological considerations, binary typing was the preferable method. Genotypes of bovine isolates were compared to 55 previously characterized human S. aureusisolates through cluster analysis of binary types. Genetic clusters containing strains of both human and bovine origin were found, but bacterial genotypes were predominantly associated with a single host species. Binary typing proved an excellent tool for comparison ofS. aureus strains, including methicillin-resistant S. aureus, derived from different host species and from different databases. For 28 bovine S. aureus isolates, detailed clinical observations in vivo were compared to strain typing results in vitro. Associations were found between distinct genotypes and severity of disease, suggesting strain-specific bacterial virulence. Circumstantial evidence furthermore supports strain-specific routes of bacterial dissemination. We conclude that PFGE and binary typing can be successfully applied for genetic analysis of S. aureusisolates from bovine mammary secretions. Binary typing in particular is a robust and simple method and promises to become a powerful tool for strain characterization, for resolution of clonal relationships of bacteria within and between host species, and for identification of sources and transmission routes of bovine S. aureus.

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Feng, Ye, Shengmei Zou, Hangfei Chen, Yunsong Yu, and Zhi Ruan. "BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking." Nucleic Acids Research 49, no. D1 (October 3, 2020): D644—D650. http://dx.doi.org/10.1093/nar/gkaa821.

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Abstract An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic and multidrug-resistant bacteria has stimulated a pressing need for benchtop computational techniques to rapidly and accurately classify bacteria from genomic sequence data, and based on that, to trace the source of infection. BacWGSTdb (http://bacdb.org/BacWGSTdb) is a free publicly accessible database we have developed for bacterial whole-genome sequence typing and source tracking. This database incorporates extensive resources for bacterial genome sequencing data and the corresponding metadata, combined with specialized bioinformatics tools that enable the systematic characterization of the bacterial isolates recovered from infections. Here, we present BacWGSTdb 2.0, which encompasses several major updates, including (i) the integration of the core genome multi-locus sequence typing (cgMLST) approach, which is highly scalable and appropriate for typing isolates belonging to different lineages; (ii) the addition of a multiple genome analysis module that can process dozens of user uploaded sequences in a batch mode; (iii) a new source tracking module for comparing user uploaded plasmid sequences to those deposited in the public databases; (iv) the number of species encompassed in BacWGSTdb 2.0 has increased from 9 to 20, which represents bacterial pathogens of medical importance; (v) a newly designed, user-friendly interface and a set of visualization tools for providing a convenient platform for users are also included. Overall, the updated BacWGSTdb 2.0 bears great utility in continuing to provide users, including epidemiologists, clinicians and bench scientists, with a one-stop solution to bacterial genome sequence analysis.

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Almasian-Tehrani, Nasim, Masoud Alebouyeh, Shahnaz Armin, Neda Soleimani, Leila Azimi, and Roozbeh Shaker-Darabad. "Overview of typing techniques as molecular epidemiology tools for bacterial characterization." Cellular, Molecular and Biomedical Reports 1, no. 2 (December 1, 2021): 69–77. http://dx.doi.org/10.55705/cmbr.2021.143413.1016.

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Arturo Salazar, Nelson, Laura Patricia Uribe, and Dora Ines Ríos. "The molecular characterisation of bacteria associated with neonatal necrotising enterocolitis and sepsis which were isolated from hospitals in Bogotá, Colombia." ghalib quarterly journal 1, no. 1 (March 6, 2023): 1–8. http://dx.doi.org/10.58342/ajid/ghalibuni1.

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Background: The identification and molecular characterisation of bacteria associated with neonatal necrotising enterocolitis (NNE) and sepsis is very important in clarifying the role such bacteria play in the development of this disease. Methods: The present multicentre study was aimed at characterising bacteria isolated from haemocultures obtained from 20 neonates suffering NNE by using traditional and molecular methodologies (16 S rRNA subunit sequencing and multilocus sequence typing - MLST). Results: NNE incidence in hospitals in Bogotá was also estimated, finding rates similar to and higher than those reported in the literature (1 to 3 cases of NNE per 1,000 live-births). Staphylococcus epidermidis ST2, ST81, and ST126 sequence types were identified by using these two molecular techniques; the Escherichia coli ST394 sequence type was also identified. Species could not be identified for the Pantoea agglomerans isolate due to the high degree of intra-species identity. Interestingly, the bacterial isolates from the two neonates who died were classified in the same sequence type (i.e. S. epidermidis ST81), even though they came from different hospitals. Conclusion: Such molecular techniques allow characterising bacterial pathogen populations occurring in one or more hospitals in a particular city or determined geographical area and support taking more specific preventative measures directed against such particular clones. Key words: Necrotising enterocolitis (NNE), sepsis, molecular characterisation, multilocus sequence typing (MLST).

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Howell, S. A., and W. C. Noble. "Typing tools for the investigation of epidemic fungal infection." Epidemiology and Infection 105, no. 1 (August 1990): 1–9. http://dx.doi.org/10.1017/s0950268800047580.

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The epidemiology of bacterial infection is investigated by the use of identification procedures at a sub-species level by such techniques as serotyping, phage typing, various antigen recognition tests, plasmid profiling and DNA probes. Fungal epidemiology has tended to lag behind in the use of this technology, particularly with the filamentous fungi, though several techniques have been developed for yeasts and especially forCandida albicans. This review will briefly describe the application of these methods to outbreaks ofC. albicansinfection, describe the limited methods available for the investigation of filamentous fungal infection and indicate the necessity for increased research in this area.

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Dieckmann, Ralf, Jens Andre Hammerl, Hartmut Hahmann, Amal Wicke, Sylvia Kleta, Piotr Wojciech Dabrowski, Andreas Nitsche, Maren Stämmler, Sascha Al Dahouk, and Peter Lasch. "Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy." Faraday Discussions 187 (2016): 353–75. http://dx.doi.org/10.1039/c5fd00165j.

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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.

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NATSOS, G., N. K. MOUTTOTOU, S. AHMAD, Z. KAMRAN, A. IOANNIDIS, and K. C. KOUTOULIS. "The genus Campylobacter: detection and isolation methods, species identification & typing techniques." Journal of the Hellenic Veterinary Medical Society 70, no. 1 (April 24, 2019): 1327. http://dx.doi.org/10.12681/jhvms.20337.

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Campylobacter is well recognized as the leading cause of bacterial foodborne diarrheal disease worldwide; while, poultry has been identified as a significant cause of campylobacter infection in humans. The C. jejuni has been found to be the predominant species isolated from poultry samples and, yet, responsible for the majority of human campylobacteriosis. Campylobacter spp. are small, oxidase positive, microaerophilic, curved gram-negative rods exhibiting corkscrew motility and colonize the intestinal tract of most mammalian and avian species. From its very first description in late 19th century by Theodor Escherich until nowadays, a lot of research has been carried out providing a wealth of information regarding its microbiological properties. Since novel technologies constantly emerge, increasingly advanced methods for detection, identification and typing of Campylobacter spp. are becoming available. The aim of this article is to review the recent bibliography on Campylobacter focusing, especially, on its survival and growth characteristics, the laboratory methods used for its detection and isolation from clinical, animal, environmental, and food samples, the reported methods applied for its speciation, as well as the typing systems developed for subtyping of Campylobacter.

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Arturo Salazar, Nelson. "The molecular characterisation of bacteria associated with neonatal necrotising enterocolitis and sepsis which were isolated from hospitals in Bogotá, Colombia." Afghanistan Journal of Infectious Diseases 1, no. 2 (November 22, 2023): 11–23. http://dx.doi.org/10.60141/ajid/ghalibuni1.

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Background: The identification and molecular characterisation of bacteria associated with neonatal necrotising enterocolitis (NNE) and sepsis is very important in clarifying the role such bacteria play in the development of this disease. Methods: The present multicentre study was aimed at characterising bacteria isolated from haemocultures obtained from 20 neonates suffering NNE by using traditional and molecular methodologies (16 S rRNA subunit sequencing and multilocus sequence typing - MLST). Results: NNE incidence in hospitals in Bogotá was also estimated, finding rates similar to and higher than those reported in the literature (1 to 3 cases of NNE per 1,000 live-births). Staphylococcus epidermidis ST2, ST81, and ST126 sequence types were identified by using these two molecular techniques; the Escherichia coli ST394 sequence type was also identified. Species could not be identified for the Pantoea agglomerans isolate due to the high degree of intra-species identity. Interestingly, the bacterial isolates from the two neonates who died were classified in the same sequence type (i.e. S. epidermidis ST81), even though they came from different hospitals. Conclusion: Such molecular techniques allow characterising bacterial pathogen populations occurring in one or more hospitals in a particular city or determined geographical area and support taking more specific preventative measures directed against such particular clones.

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Agarkova, I. V., P. A. Lambrecht, A. K. Vidaver, and R. M. Harveson. "Genetic diversity among Curtobacterium flaccumfaciens pv. flaccumfaciens populations in the American High Plains." Canadian Journal of Microbiology 58, no. 6 (June 2012): 788–801. http://dx.doi.org/10.1139/w2012-052.

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Curtobacterium flaccumfaciens pv. flaccumfaciens is a Gram-positive bacterium and has reemerged as an incitant of bacterial wilt in common (dry, edible) beans in western Nebraska, eastern Colorado, and southeastern Wyoming. Curtobacterium flaccumfaciens pv. flaccumfaciens is diverse phenotypically and genotypically and is represented by several different pathogen color variants. The population structure of 67 strains collected between 1957 and 2009, including some isolated from alternate hosts, was determined with 3 molecular typing techniques: amplified fragment length polymorphism (AFLP), repetitive extragenic palindromic polymerase chain reaction (rep-PCR), and pulsed-field gel electrophoresis (PFGE). All 3 typing techniques showed a great degree of population heterogeneity, but they were not congruent in cluster analysis of the C. flaccumfaciens pv. flaccumfaciens populations. Cluster analysis of a composite data set (AFLP, PFGE, and rep-PCR) using averages from all experiments yielded 2 distinct groups: cluster A included strains with colonies of yellow, orange, and pink pigments, and cluster B had strains of only yellow pigment. Strains producing purple extracellular pigment were assigned to both clusters. Thus, C. flaccumfaciens pv. flaccumfaciens is diverse phenotypically and genotypically.

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Dissertations / Theses on the topic "Bacterial typing techniques"

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Roberts, Jill Carolyne. "Characterization of Community-acquired Methicillin-resistant Staphylococcus aureus by Pulsed-field Gel Electrophoresis, Multilocus Sequence Typing, and Staphylococcal Protein A Sequencing: Establishing a Strain Typing Database." [Tampa, Fla] : University of South Florida, 2006. http://purl.fcla.edu/usf/dc/et/SFE0001489.

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Davis, Carisa Renee. "Pandemic Vibrio parahaemolyticus: Defining Strains Using Molecular Typing and a Growth Advantage at Lower Temperatures." [Tampa, Fla] : University of South Florida, 2008. http://purl.fcla.edu/usf/dc/et/SFE0002531.

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Box, Matthew. "Multiple-locus variable-number tandem-repeat analysis (MLVA) for clonal characterization of methicillin resistant Staphylococcus aureus strains." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2006. https://www.mhsl.uab.edu/dt/2008r/box.pdf.

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Petersson, Ramona. "Molecular epidemiology of tuberculosis." Stockholm : Umeå universitet, 2009. http://diss.kib.ki.se/2009/978-91-7409-456-5/.

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Cheng, Allen Cheuk-Seng, and allencheng@ozemail com au. "MELIOIDOSIS: EPIDEMIOLOGY, PATHOPHYSIOLOGY AND MANAGEMENT." Flinders University. Medicine, 2005. http://catalogue.flinders.edu.au./local/adt/public/adt-SFU20051121.141305.

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In under a century, melioidosis, the infection due to Burkholderia pseudomallei, has emerged from Whitmores series of glanders-like infections amongst the morphia addicts in Burma to a major cause of mortality in northeastern Thailand and northern Australia. Also endemic in other parts of south-east Asia, melioidosis may have varied presentations ranging from severe, overwhelming infection to chronic, low grade disease. Observational evidence had suggested that granulocyte colony stimulating factor (G-CSF), a naturally occurring substance produced by the body in response to infection, may have been useful in reducing the high mortality associated with the more severe forms of this infection. Other observations linked the occurrence of this disease to various environmental factors, such as contamination of drinking water and the annual rainfall. This thesis explores and attempts to quantify these associations. There are three parts to this thesis. In the first part, I reviewed the epidemiology and management of patients with melioidosis. The use of G-CSF and meropenem was associated with a fall in mortality, although other factors may have at least partially contributed to this effect. In the second part, I progressed towards a clinical trial of G-CSF. There was no other evidence supporting the use of G-CSF in severe sepsis and ethical issues precluded a trial in Darwin. There was not evidence from laboratory models of G-CSF action in melioidosis to support the use of G-CSF in patients, although there remained some doubt regarding the applicability of such models to human disease. I examined clinical methods to identify patients at high risk of death from melioidosis. A simple scoring system based on clinical and laboratory parameters was developed and externally validated. However, clinical definitions of severe sepsis appeared to be better predictors of mortality. A clinical trial based on clinical definitions was commenced in Thailand. In the final part, I explored the question of whether different strains or B. pseudomallei or different environmental conditions caused different patterns of infection. There was no evidence that strain types of this bacterium determine the pattern or severity of disease, but weather conditions appeared to influence the distribution of disease in northern Australia.

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Ip, Ka-fai, and 葉嘉輝. "Molecular epidemiological study of mycobacterium tuberculosis using IS6110-RFLP and MIRU typing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B45010092.

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Kruczkiewicz, Peter. "A comparative genomic framework for the in silico design and assessment of molecular typing methods using whole-genome sequence data with application to Listeria monocytogenes." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, c2013, 2013. http://hdl.handle.net/10133/3391.

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Although increased genome sequencing e orts have increased our understanding of genomic variability within many bacterial species, there has been limited application of this knowledge towards assessing current molecular typing methods and developing novel molecular typing methods. This thesis reports a novel in silico comparative genomic framework where the performance of typing methods is assessed on the basis of the discriminatory power of the method as well as the concordance of the method with a whole-genome phylogeny. Using this framework, we designed a comparative genomic ngerprinting (CGF) assay for Listeria monocytogenes through optimized molecular marker selection. In silico validation and assessment of the CGF assay against two other molecular typing methods for L. monocytogenes (multilocus sequence typing (MLST) and multiple virulence locus sequence typing (MVLST)) revealed that the CGF assay had better performance than these typing methods. Hence, optimized molecular marker selection can be used to produce highly discriminatory assays with high concordance to whole-genome phylogenies. The framework described in this thesis can be used to assess current molecular typing methods against whole-genome phylogenies and design the next generation of high-performance molecular typing methods from whole-genome sequence data.
xiii, 100 leaves : ill. ; 29 cm

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Brandt, Kátia Galeão. "Análise molecular da microbiota fecal de recém-nascidos saudáveis." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/5/5141/tde-24032009-164452/.

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Objetivo: Analisar através de metodologia molecular a microbiota fecal de recém-nascidos (RN) saudáveis, em aleitamento materno exclusivo. Materiais e métodos: Amostras fecais de dez RN foram avaliadas no 2º, 7º e 30º dias de vida (DV), através de sequenciamento do 16S rDNA bacteriano. Real-time PCR para bifidobacterias foi empregado nas amostras de 30 dias. Resultados: A diversidade bacteriana fecal aumentou do 2º para o 30º DV. E. coli predominou no 2º e 7º DV, e Clostridium no 30º DV. Usando real-time PCR, bifidobacterias foram identificadas em todas as amostras de 30 dias. Conclusão: Enterobacterias predominaram na primeira semana de vida. Aos 30 DV observou-se uma maior diversidade bacteriana, com predomínio de Clostridium.. A técnica inicial não permitiu identificar bifidobacterias.
Purpose: To evaluate by molecular methodology the fecal microbiota of healthy newborns, exclusively breastfed. Materials and methods: Fecal samples from ten neonates were analyzed on 2nd, 7th and 30th day of life, using 16S rDNA sequencing and real-time PCR for bifidobacteria. Results: The fecal bacteria diversity increased from the second to the 30th day of life. E. coli was predominant in the fecal samples from the 2nd and 7th day of life, and Clostridium.in the samples of the 30th day. Using real-time PCR bifidobacteria were identified in all 30th day samples. Conclusion: Enterobacteria were predominant in the first week of life. On 30th day of life a greater bacterial diversity was observed with predominance of Clostridium. The initial technique didnt allow the identification of bifidobacteria.

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Moussaoui, Louardi. "Applications de la spectrométrie de masse type MALDI-TOF à la bactériologie et à la distinction de variants génétiques." Phd thesis, Université de Strasbourg, 2012. http://tel.archives-ouvertes.fr/tel-00872251.

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L'objectif de mon travail fut de valider et d'optimiser la spectrométrie de masse de type MALDI-TOF pour l'identification et la classification d'un ensemble de bactéries pathogènes ou opportunistes chez l'homme, en enrichissant une base de données et en testant la robustesse de la méthode, afin d'obtenir une méthode rapide fixe et fiable d'acquisition de résultats. Les différents résultats obtenus ont permis la validation de la technique comme outil d'identification bactérienne fiable en routine. Elle permet désormais de caractériser les mélanges de deux bactéries voir même la différentiation d'espèces très proches comme les Shigella spp et E. coli. Nous avons montré que la technique sera encore améliorée par un outil supplémentaire de comparaison des souches pour une veille épidémiologique "en temps réel", sans investissement supplémentaire, en permettant plusieurs types d'économie. Elle apporte un gain réel dans la prise en charge du patient et le choix éclairé des antibiotiques testés pour l'antibiogramme. La technique peut aussi constituer un outil alternatif de sérotypage.

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Friedland, Hillel David. "Evaluation of the random amplified polymorphic DNA technique for the epidemiological investigation of streptococcus pneumoniae outbreaks." Thesis, 1994. https://hdl.handle.net/10539/24704.

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A dissertation submitted to the Faculty of Medicine, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Medicine.
The emergence of strains of S. pneumoniae resistant to penicillin and to other antibiotics, and the spread of that resistance over the world, have become major concerns and increase the need for epidemiological surveillance. The following typing methods have been used to detect strain variability in pneumococci: Serotyping, antibiotic susceptibility profiles, multilocus enzyme electrophoresis (MLEE), penicillin-binding protein (PBP) profiles, pulse-field gel electrophoresis (pFGE), and ribotyping. Serotyping, antibiograms, and MLEE only detect phenotypic variability. PBP gene profiles, PFGE, and ribotyping detect genotypic differences but these techniques are labour intensive and time consuming. Random amplified polymorphic DNA (RAPD) is a new technique that bas proved useful for typing bacteria, fungi, and parasites, but has not been. studied using pneumococci. Unlike conventional polymerase chain reaction (peR), RAPD utilizes single, short primers, usually 10 oligonucleotides in length. As the primer is short and low astringency annealing temperatures are used, there will be many complimentary sites scattered randomly throughout a bacterium's genome, When such sites occur a few hundred base pairs away from each other and on opposite DNA strands, the enclosed region can be amplified by peR This results in numerous discrete target fragments which can be separated by agarose-gel electrophoresis and ethidium bromide staining. RAPD requires no sequence information and it scans the whole genome rather than relying on hypervariability within one specific gene. The aims of this study were: to determine strain variability using RAPD, to determine the reproducibility ofRAPD, and to demonstrate intercontinental spread of a multiresistant pneumococcal strain. The following strains were evaluated: a) 10 strains from a day-care centre (DCC), the index case being a 3 year old girl 'with otitis media. An aunt from Spain had recently been staying with the family. The other strains were isolated from class mates and siblings of the index case.; b) 18 clinical isolates from Seoul, Korea; and c) 11 epidemiologically unrelated isolates from South Africa, including the reference strain, R6. Two DNA extraction methods were used. The first involving lysis with sodmm-dodecyl-sulphaze and proteinase K. Proteins were removed with phenol-chloroform, and the DNA precipitated with ethanol. The second method involved incubating the cells at 95 0C for 15 microlitres, followed by centrifugation. 2 microlitres of the supernatant was then used for each PCR reaction, Three primers were evaluated. After 01uimisation of the RAPDreaction for pneumococci, the final peR mixtures per 50 ul was: primer (4 plY1), template (0.5 ng), nuc1eotides (300 pMeach), magnesium (4 mM~, and Taq polymerase (2 U). 35 cycles were used with an annealing temperature of 35'C. Both DNA extraction methods: gave reproducible results but were not comparable to each other. All 10 strains from the DCC gave the same banding pattern as the Spanish done for all 3 primers. 7 of the Korean strains gave the same banding pattern as the Spanish clone using the first two primers, however one strain showed an additional band using the third primer. Of the remaining 22 strains, 21 different banding patterns were obtained. This study has shown that RAPD is a simple and rapid technique that can distinguish strain variation among pneumococci. The reproducibility is excellent within the same laboratory. Finally using RAPD. this study identified a Spanish multiresistant 23F clone in South Africa and Korea.
Andrew Chakane 2018

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Books on the topic "Bacterial typing techniques"

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Dostal, Stefan. Concise guide to mycobacteria and their molecular differentiation. Würzburg, Germany: Ridom Press, 2003.

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A, Cockayne, ed. Molecular methods for microbial identification and typing. London: Chapman & Hall, 1993.

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H, Persing David, ed. PCR protocols for emerging infectious diseases: A supplement to Diagnostic Molecular Microbiology : principles and applications. Washington, D.C: ASM Press, 1996.

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Towner, K. J., and A. Cockayne. Molecular Methods for Microbial Identification and Typing. Springer London, Limited, 2013.

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Rivas, Lucia, Glen E. Mellor, Kari Gobius, and Narelle Fegan. Detection and Typing Strategies for Pathogenic Escherichia Coli. Springer London, Limited, 2015.

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Rivas, Lucia, Glen E. Mellor, Kari Gobius, and Narelle Fegan. Detection and Typing Strategies for Pathogenic Escherichia coli. Springer, 2015.

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Pcr Protocols for Emerging Infectious Diseases A Supplement to Diagnostic Molecular Microbiology: Principles and Applications. ASM Press, 1996.

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Book chapters on the topic "Bacterial typing techniques"

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Boldis, V., E. Spitalska, and R. Toman. "Molecular Typing of Coxiella burnetii: A Review of Available Methods with Major Focus on PCR-Based Techniques." In Molecular Typing in Bacterial Infections, 457–69. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-185-1_26.

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Terletskiy, Valery, Valentina Tyshchenko, Oksana Novikova, and Lidiya Shinkarenko. "Application of the Double Digests Selective Label Typing Technique for Bacteria Genotyping." In Fundamental and Applied Scientific Research in the Development of Agriculture in the Far East (AFE-2021), 964–72. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-91405-9_109.

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Brown, Eric W. "Molecular differentiation of bacterial strains." In Molecular Epidemiology, 29–66. Oxford University PressOxford, 2007. http://dx.doi.org/10.1093/oso/9780199638116.003.0002.

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Abstract Understanding the epidemiological principles that govern bacterial populations has become paramount in the fields of medical, environmental, and agricultural microbiology (1). The introduction of bacterial strains which exhibit more aggressive and deadly pathological phenotypes, development of multi-drug antibiotic resistance, and acquisition of novel modes of transmission between host organisms has placed a renewed pressure on researchers to be able to identify and monitor the origins and dissemination of destructive genetic variants (strains) within a species. It has become apparent that the best approaches to characterizing individual strains are founded in the practical application of molecular biology. Molecular genetic techniques such as polymerase chain reaction (PCR), nucleic acid fingerprinting, and DNA sequence analysis of the bacterial chromo-some have allowed for remarkable advances in bacterial identification as in many other areas of microbiology (2). Whether the need for molecular typing involves the tracking of nosocomial (hospital-borne) outbreaks, identifying the reservoirs of food-borne infections, or the discrimination of plant pathogenic strains in the field, the isolation of a specific genotype in conjunction with a specific bacteria often allows for a larger understanding of the epidemiological principles that govern the evolution and spread of many bacterial diseases.

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Spickett, Gavin P. "Immunochemistry." In Oxford Handbook of Clinical Immunology and Allergy, 433–72. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199603244.003.0017.

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Techniques α‎₁-acid glycoprotein α‎₁-antichymotrypsin α‎₁-antitrypsin (α‎₁-AT) α‎₁-antitrypsin (α‎₁-AT) genotype (PI typing) α‎₂-macroglobulin Acute-phase proteins (CRP, ESR, SAA) Amyloid proteins Avian precipitins Bacterial and viral antibodies (specific antibodies; functional antibodies)...

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Ramdev, Poornima Devi C., Divya K. Shankar, and B. Renuka. "CRISPR-Cas for Genome Editing - Molecular Scissors for Combating Pathogens." In Genome Editing in Bacteria (Part 2), 68–105. BENTHAM SCIENCE PUBLISHERS, 2024. http://dx.doi.org/10.2174/9789815223798124010005.

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Clustered Regularly Interspaced Short Palindromic Repeats, abbreviated as CRISPR, is a genome-editing technology that permits the creation of precise knock-out mutants by aiding the modification of gene sequences devoid of the steps involving the insertion of foreign DNA into pathogenic microorganisms. The microorganisms are ubiquitous in nature and harbor in the complex ecosystem of the human being. Cas (acronym for CRISPR-associated) genes are present in many microbial genomes. The variable nature of the microbial genome has been utilized as an integral typing tool in epidemiologic, diagnostic, and evolutionary analyses of the prokaryotic species. The past decade has seen an accumulating growth in the development of gene-editing tools utilizing the CRISPR-Cas system, which essentially is a part of the prokaryotic immune system. The development of these unique gene-editing techniques has empowered researchers to alter and investigate organisms with ease and efficiency as never before. This editing tool can efficiently be programmed and delivered into the bacterial populations to explicitly eliminate members of a targeted micro biome. Manipulation of the gene expression and regulation of the synthesis of metabolites and proteins can be achieved by utilizing an engineered CRISPR-Cas system. Put together, these tools present with the exhilarating opportunity to explore the complex interaction between the individual species of the microbiome and the host organism and thereby reveal novel avenues for the generation of drugs to selectively target the microbiome. CRISPR-Cas technology has been employed to cope with antibiotic resistance in intracellular and extracellular pathogens. The widespread use of antibiotics and the escalation of multidrug-resistant (MDR) bacteria boost the prospect of a post-antibiotic era, which emphasizes the need for novel strategies to target MDR pathogens. The development of permissive synthetic biology techniques offers favorable solutions to carry through safe and efficient antibacterial therapies.

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Poxton, I. R. "Immunochemical methods." In Anaerobic Microbiology, 101–20. Oxford University PressOxford, 1991. http://dx.doi.org/10.1093/oso/9780199632046.003.0006.

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Abstract As in any branch of modern bacteriology, immunological techniques are used for a vast and increasing number of applications. The applications in the past were mainly in medical microbiology, especially in the diagnosis of disease, in epidemiological typing, and in the fundamental investigation of pathogenic mechanisms. In the future this trend is likely to continue, but the exploitation of immunological methods for the detection and quantitation of any bacterial component or product is likely to increase. In anaerobic bacteriology, however, it is by no means an area of great activity. Many workers have been disillusioned by the complexity of the subject, and it is true to say that much of the past work has been greatly compromised by a lack of appreciation of the complexity of the antigenic composition of anaerobes. They are no more complex than aerobes but, especially for the Bacteroides spp., there are no traditional serotyping schemes available as there were for theenterobacteria, and attempts at extrapolating from enterobacterial serology have been largely unsuccessful. Apart from certain clostridial infections there is little evidence of a one organism/one disease relationship and again this has confused the unwary.

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Qin, Qin, Yun Liu, Yuxiang Wan, and Haifeng Qin. "Identification of Microorganisms by Mass Spectrometry in Clinical Microbiology Laboratories." In Detection and Analysis of Microorganisms by Mass Spectrometry, 263–76. Royal Society of Chemistry, 2023. http://dx.doi.org/10.1039/bk9781837670338-00263.

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MALDI-TOF MS is a rapid microbial diagnosis method developed based on MS technology, which has been widely used in clinical microbiology laboratories around the world, due to its accurate and efficient performance in microbial identification. This chapter introduces the specific applications of MALDI-TOF MS in clinical laboratories, including strain identification, antibiotic resistance mechanism tests, bacterial strain typing, and virulence marker detection. Besides, the current situation and development trends of this technique are analyzed and its application prospects are discussed.

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Ogunremi, Dele, Ruimin Gao, Rosemarie Slowey, Shu Chen, Olga Andrievskaia, Sadjia Bekal, Lawrence Goodridge, and Roger C. Levesque. "Tracking Salmonella Enteritidis in the Genomics Era: Clade Definition Using a SNP-PCR Assay and Implications for Population Structure." In Salmonella spp. - A Global Challenge. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.98309.

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Salmonella enterica serovar Enteritidis (or Salmonella Enteritidis, SE) is one of the oldest members of the genus Salmonella, based on the date of first description and has only gained prominence as a significant bacterial contaminant of food over the last three or four decades. Currently, SE is the most common Salmonella serovar causing foodborne illnesses. Control measures to alleviate human infections require that food isolates be characterized and this was until recently carried out using Pulsed-Field Gel Electrophoresis (PFGE) and phage typing as the main laboratory subtyping tools for use in demonstrating relatedness of isolates recovered from infected humans and the food source. The results provided by these analytical tools were presented with easy-to-understand and comprehensible nomenclature, however, the techniques were inherently poorly discriminatory, which is attributable to the clonality of SE. The tools have now given way to whole genome sequencing which provides a full and comprehensive genetic attributes of an organism and a very attractive and superior tool for defining an isolate and for inferring genetic relatedness among isolates. A comparative phylogenomic analysis of isolates of choice provides both a visual appreciation of relatedness as well as quantifiable estimates of genetic distance. Despite the considerable information provided by whole genome analysis and development of a phylogenetic tree, the approach does not lend itself to generating a useful nomenclature-based description of SE subtypes. To this end, a highly discriminatory, cost-effective, high throughput, validated single nucleotide based genotypic polymerase chain reaction assay (SNP-PCR) was developed focussing on 60 polymorphic loci. The procedure was used to identify 25 circulating clades of SE, the largest number so far described for this organism. The new subtyping test, which exploited whole genome sequencing data, displays the attributes of an ideal subtyping test: high discrimination, low cost, rapid, highly reproducible and epidemiological concordance. The procedure is useful for identifying the subtype designation of an isolate, for defining the population structure of the organism as well as for surveillance and outbreak detection.

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"Molecular Techniques for Detecting, Quantifying, and Subspecies Typing of Foodborne Pathogenic Bacteria." In Rapid Detection and Characterization of Foodborne Pathogens by Molecular Techniques, 1–31. CRC Press, 2009. http://dx.doi.org/10.1201/9781420092431.ch1.

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