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Journal of Clinical Microbiology Oct 2007We compared three novel methicillin-resistant Staphylococcus aureus (MRSA) genotyping methods with multilocus sequence typing (MLST) and spa typing to assess their... (Comparative Study)
Comparative Study
We compared three novel methicillin-resistant Staphylococcus aureus (MRSA) genotyping methods with multilocus sequence typing (MLST) and spa typing to assess their utility for routine strain typing. The new methods were femA and nuc sequence typing and toxin gene profiling (TGP), using a multiplex-PCR-based reverse line blot assay to detect 13 pyrogenic superantigen and exfoliative toxin genes. Forty-two well-characterized MRSA strains, representing 15 MLSTs or 9 clonal clusters (CCs), were genotyped by all methods. Twenty-two spa, nine femA, and seven nuc sequence types were identified. The femA sequence types correlated exactly with CCs; nuc sequences types were less discriminatory but generally correlated well with femA types and CCs. Ten isolates contained none of 13 toxin genes; TGPs of the remainder comprised 1 to 5 toxin genes. The combination of spa typing and TGPs identified 26 genotypes among the 42 strains studied. A combination of two or three rapid, inexpensive genotyping methods could potentially provide rapid MRSA strain typing as well as useful information about clonal origin and virulence.
Topics: Bacterial Typing Techniques; DNA, Bacterial; Humans; Methicillin Resistance; Polymorphism, Genetic; Sequence Analysis, DNA; Staphylococcus aureus
PubMed: 17715374
DOI: 10.1128/JCM.01082-07 -
Journal of Clinical Microbiology Apr 2012Propionibacterium acnes is a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris, in biofilm-associated infections of medical devices and... (Comparative Study)
Comparative Study
Propionibacterium acnes is a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris, in biofilm-associated infections of medical devices and endophthalmitis, and in infections of bone and dental root canals. Recent studies associate P. acnes with prostate cancer. As the species includes evolutionary lineages with distinct association with health and disease, there is a need for a high-resolution typing scheme. Recently, two multilocus sequence typing (MLST) schemes were reported, one based on nine and one based on seven housekeeping genes. In the present study, the two schemes were compared with reference to a phylogenetic tree based on 78 P. acnes genomes and their gene contents. Further support for a basically clonal population structure of P. acnes and a scenario of the global spread of epidemic clones of P. acnes was obtained. Compared to the Belfast scheme, the Aarhus MLST scheme (http://pacnes.mlst.net/), which is based on nine genes, offers significantly enhanced resolution and phylogenetic inferences more concordant with analyses based on a comprehensive sampling of the entire genomes, their gene contents, and their putative pathogenic potential.
Topics: Algorithms; Bacterial Typing Techniques; Genes, Bacterial; Genes, Essential; Humans; Models, Genetic; Multilocus Sequence Typing; Phenotype; Phylogeny; Propionibacterium acnes
PubMed: 22259216
DOI: 10.1128/JCM.r06129-11 -
Molecules (Basel, Switzerland) Apr 2020A universal method by considering different types of culture media can enable convenient classification of bacterial species. The study combined hyperspectral technology...
A universal method by considering different types of culture media can enable convenient classification of bacterial species. The study combined hyperspectral technology and versatile chemometric algorithms to achieve the rapid and non-destructive classification of three kinds of bacterial colonies (, and ) cultured on three kinds of agar media (Luria-Bertani agar (LA), plate count agar (PA) and tryptone soy agar (TSA)). Based on the extracted spectral data, partial least squares discriminant analysis (PLS-DA) and support vector machine (SVM) were employed to established classification models. The parameters of SVM models were optimized by comparing genetic algorithm (GA), particle swarm optimization (PSO) and grasshopper optimization algorithm (GOA). The best classification model was GOA-SVM, where the overall correct classification rates (OCCRs) for calibration and prediction of the full-wavelength GOA-SVM model were 99.45% and 98.82%, respectively, and the Kappa coefficient for prediction was 0.98. For further investigation, the CARS, SPA and GA wavelength selection methods were used to establish GOA-SVM simplified model, where CARS-GOA-SVM was optimal in model accuracy and stability with the corresponding OCCRs for calibration and prediction and the Kappa coefficients of 99.45%, 98.73% and 0.98, respectively. The above results demonstrated that it was feasible to classify bacterial colonies on different agar media and the unified model provided a continent and accurate way for bacterial classification.
Topics: Algorithms; Bacterial Typing Techniques; Colony Count, Microbial; Hyperspectral Imaging; Machine Learning; Models, Theoretical; Support Vector Machine
PubMed: 32295273
DOI: 10.3390/molecules25081797 -
Epidemiology and Infection Dec 2019Homology surveillance of carbapenem-resistant Klebsiella pneumoniae (CRKP) is critical to monitor and prevent outbreaks of nosocomial infections. In the present study, a... (Comparative Study)
Comparative Study
Homology surveillance of carbapenem-resistant Klebsiella pneumoniae (CRKP) is critical to monitor and prevent outbreaks of nosocomial infections. In the present study, a matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF MS)-based method was evaluated as a rapid tool for typing CRKP in comparison with pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST). Drug-resistant phenotypes and genotypes of 44 CRKP isolates were detected by microdilution broth method and polymerase chain reaction, and typed by PFGE, MLST and MALDI-TOF MS. Simpson's Index of Diversity was used to evaluate taxonomic diversity, Adjusted Rand Index (ARI) for congruence between the typing methods and Wallace coefficients (W) for the ability of either method to predict each other. Forty-four CRKP isolates of 15 sequence types (STs) produced either NDM-1 (n = 16), NDM-5 (n = 9) or KPC-2 (n = 19) carbapenemases. PFGE differentiated these isolates into 16 distinct types, and two deoxyribonucleic acid profiles were assigned to ST337 and ST11, respectively. MALDI-TOF MS failed to clearly delineate between clusters on dendrograms based on principal components analysis and main spectrum profile. The chosen parameters resulted in a maximum ARI of 0.310 (95% CI 0.088-0.531) between MALDI-TOF MS typing and the PFGE reference, indicating a low ability of the former to correctly identify related isolates. Likewise, the maximum W coefficient of 0.367 (95% CI 0.203-0.532) showed that MALDI-TOF MS had a lower predictive power than PFGE. We conclude that MALDI-TOF MS lacks the discriminatory power necessary for clone assignment of CRKP isolates and consequently cannot be considered as a rapid and creditable method for this purpose.
Topics: Bacterial Typing Techniques; Carbapenem-Resistant Enterobacteriaceae; China; Clone Cells; DNA, Bacterial; Electrophoresis, Gel, Pulsed-Field; Genotype; Klebsiella pneumoniae; Microbial Sensitivity Tests; Multilocus Sequence Typing; Phenotype; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 31845635
DOI: 10.1017/S0950268819002097 -
BMC Bioinformatics Jun 2018Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and...
BACKGROUND
Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by targeting housekeeping genes that provide resolution down to the family, genera, and sometimes species level. Unfortunately, this level of resolution is not sufficient in many applications where strain-level identification of bacteria is required (biodefense, forensics, clinical diagnostics, and outbreak investigations). Adding more genomic targets will increase the resolution, but the challenge is identifying the appropriate targets. VaST was developed to address this challenge by finding the minimum number of targets that, in combination, achieve maximum strain-level resolution for any strain complex. The final combination of target regions identified by the algorithm produce a unique haplotype for each strain which can be used as a fingerprint for identifying unknown samples in a TAS assay. VaST ensures that the targets have conserved primer regions so that the targets can be amplified in all of the known strains and it also favors the inclusion of targets with basal variants which makes the set more robust when identifying previously unseen strains.
RESULTS
We analyzed VaST's performance using a number of different pathogenic species that are relevant to human disease outbreaks and biodefense. The number of targets required to achieve full resolution ranged from 20 to 88% fewer sites than what would be required in the worst case and most of the resolution is achieved within the first 20 targets. We computationally and experimentally validated one of the VaST panels and found that the targets led to accurate phylogenetic placement of strains, even when the strains were not a part of the original panel design.
CONCLUSIONS
VaST is an open source software that, when provided a set of variant sites, can find the minimum number of sites that will provide maximum resolution of a strain complex, and it has many different run-time options that can accommodate a wide range of applications. VaST can be an effective tool in the design of strain identification panels that, when combined with TAS technologies, offer an efficient and inexpensive strain typing protocol.
Topics: Bacteria; Bacterial Typing Techniques; Genes, Bacterial; Genome, Bacterial; Genomics; Genotype; Humans; Multilocus Sequence Typing; Phylogeny; Polymorphism, Single Nucleotide
PubMed: 29890941
DOI: 10.1186/s12859-018-2225-z -
Clinical Microbiology and Infection :... Jun 2011Genotyping of Mycobacterium tuberculosis has been extensively used for investigating epidemics of multidrug-resistant strains of M. tuberculosis, in order to identify... (Review)
Review
Genotyping of Mycobacterium tuberculosis has been extensively used for investigating epidemics of multidrug-resistant strains of M. tuberculosis, in order to identify the factors involved in the transmission of such strains and determine effective control programmes to limit their expansion at both the individual and population levels. Here, we review the methods currently used to study the molecular epidemiology of multidrug-resistant M. tuberculosis strains, and the insights provided by these techniques regarding global trends and the transmission dynamics of multidrug-resistant tuberculosis at a world scale.
Topics: Antitubercular Agents; Bacterial Typing Techniques; Drug Resistance, Multiple, Bacterial; Genotype; Humans; Molecular Epidemiology; Molecular Typing; Mycobacterium tuberculosis; Tuberculosis, Multidrug-Resistant
PubMed: 21682800
DOI: 10.1111/j.1469-0691.2011.03577.x -
Poultry Science Mar 2017Poultry is recognized as the most important source of food-related transmission of Campylobacter jejuni to humans and campylobacteriosis is the most commonly reported...
Poultry is recognized as the most important source of food-related transmission of Campylobacter jejuni to humans and campylobacteriosis is the most commonly reported zoonotic bacterial disease in the European Union. It has been documented that C. jejuni is genetically diverse and analyses of bacterial isolates usually show a large strain variety. Therefore, molecular typing of strains represents an important tool to study the genetic diversity of isolates and to trace individual strains that cause human infections. The aim of the study was characterization of genetic population structure and antimicrobial resistance (AMR) of C. jejuni isolated from Polish chickens. C. jejuni from chicken ceca and the corresponding carcasses (72 and 61 strains, respectively), originating from 128 flocks in Poland during February 2011 and May 2013, were used in the study. The isolates were tested for their population structure and genetic diversity using a multilocus sequence typing (MLST) scheme with connection to their antimicrobial resistance. The molecular analysis of 133 C. jejuni generated 39 different sequence types (ST); 3 of them were defined for the first time. Additionally, 16 STs were represented by single isolates. The most common STs observed were 6411 (16.5% isolates) and 257 (15.0% strains). The first mentioned ST was resistant to 3 different classes of antibiotics, i.e., quinolones, tetracyclines, and aminoglycosides. Overall, 125 (94.4%) of C. jejuni isolates demonstrated antimicrobial resistance and the most frequent AMR profile observed was ciprofloxacin, nalidixic acid, tetracycline (47.4% strains). Likewise, the clonal complexes CC 257 and CC 353 were defined as the predominant molecular groups covering altogether 37 C. jejuni strains. No associations between CCs and the origin of the samples as well as the place of isolation were found. This study highlights that the C. jejuni population from chickens in Poland was diverse and showed a weak clonal structure.
Topics: Animals; Anti-Bacterial Agents; Bacterial Typing Techniques; Campylobacter Infections; Campylobacter jejuni; Chickens; Drug Resistance, Bacterial; Genetic Variation; Multilocus Sequence Typing; Poland; Poultry Diseases; Prevalence
PubMed: 27702925
DOI: 10.3382/ps/pew343 -
Applied and Environmental Microbiology Nov 2011For more than 80 years, subtyping of Salmonella enterica has been routinely performed by serotyping, a method in which surface antigens are identified based on... (Review)
Review
For more than 80 years, subtyping of Salmonella enterica has been routinely performed by serotyping, a method in which surface antigens are identified based on agglutination reactions with specific antibodies. The serotyping scheme, which is continuously updated as new serovars are discovered, has generated over time a data set of the utmost significance, allowing long-term epidemiological surveillance of Salmonella in the food chain and in public health control. Conceptually, serotyping provides no information regarding the phyletic relationships inside the different Salmonella enterica subspecies. In epidemiological investigations, identification and tracking of salmonellosis outbreaks require the use of methods that can fingerprint the causative strains at a taxonomic level far more specific than the one achieved by serotyping. During the last 2 decades, alternative methods that could successfully identify the serovar of a given strain by probing its DNA have emerged, and molecular biology-based methods have been made available to address phylogeny and fingerprinting issues. At the same time, accredited diagnostics have become increasingly generalized, imposing stringent methodological requirements in terms of traceability and measurability. In these new contexts, the hand-crafted character of classical serotyping is being challenged, although it is widely accepted that classification into serovars should be maintained. This review summarizes and discusses modern typing methods, with a particular focus on those having potential as alternatives for classical serotyping or for subtyping Salmonella strains at a deeper level.
Topics: Animals; Bacterial Typing Techniques; Epidemiologic Methods; Humans; Salmonella Infections; Salmonella Infections, Animal; Salmonella enterica
PubMed: 21856826
DOI: 10.1128/AEM.05527-11 -
Biocontrol Science 2022Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was approved for medical use in 2011 and is currently used as a rapid,...
Examination of Conditions for External Quality Control in Identification of Microorganisms using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was approved for medical use in 2011 and is currently used as a rapid, accurate and lowcost technique for bacterial identification. External quality control for medical analysis is monitored using tests of the Japanese Association of Medical Technologists and Prefectural Association of Clinical Laboratory Technologists and through user surveys of reagent and equipment manufacturers. However, external quality control of bacterial typing using MS is not performed. Therefore, we examined procedures for evaluating quality control of bacterial typing using an identification reliability index at 38 facilities.
Topics: Bacterial Typing Techniques; Lasers; Quality Control; Reproducibility of Results; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 36216570
DOI: 10.4265/bio.27.179 -
Clinical Microbiology Reviews Jul 2001Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary... (Review)
Review
Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiological research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made.
Topics: Bacteria; Bacterial Infections; Bacterial Typing Techniques; Classification; Evolution, Molecular; Genome, Bacterial; Humans; Molecular Epidemiology
PubMed: 11432813
DOI: 10.1128/CMR.14.3.547-560.2001