Development and application of a multiple typing system for Clostridium difficile.

A combination of bacteriocin, bacteriophage, and plasmid typing techniques was used to differentiate strains of Clostridium difficile. A typing set of 20 bacteriocin-producing strains was established after 400 isolates of C. difficile were screened for the ability to produce bacteriocin. These strains were used to type a collection of 114 isolates of C. difficile. Forty-six (40%) of the 114 isolates were typeable, and 31 typing patterns were distinguishable. Plasmid typing of the same 114 isolates of C. difficile showed that 67 (59%) of the isolates carried up to four plasmids ranging from 7 to 60 kb in size, although most strains contained only one or two plasmids. Twenty different plasmid typing patterns were observed among the isolates. A combination of bacteriocin and plasmid typing provided 77% typeability. Fifteen (13%) of the 114 strains were typeable with five bacteriophages isolated in our laboratory, but the increase in typeability of strains over that obtainable by plasmid and bacteriocin typing was only 1.8%. Isolates that were nontypeable by bacteriocins, plasmids, or phages could be divided into two groups on the basis of positive or negative cytotoxin production. This further division of strains would increase the typeability potential by 7%; i.e., the ability to differentiate strains would rise from 77 to 84%, or perhaps 86%, if phage typing were included. We conclude that more than one of the techniques reported in this paper must be used to achieve an acceptable level of typeability of this species.     

Molecular characterization of the rpoB gene in Brucella species: new potential molecular markers for genotyping

The rpoB gene encoding the beta subunit of the DNA-dependent RNA polymerase was molecularly characterized by PCR amplification and DNA sequencing in 26 Brucella reference strains by using primers selected according to the B. melitensis 16 M rpoB published sequence. Comparison of the rpoB nucleotide sequence of all Brucella strains analysed revealed specific nucleotide variations associated with different Brucella species and biovars. 17 rpoB alleles were recognized and new Brucella typing is proposed. Our results suggest that the rpoB gene polymorphism can be used to identify all Brucella species and most of the biovars, offering an improvement over conventional typing methods.     

Development and application of a multiple typing system for Clostridium difficile

A combination of bacteriocin, bacteriophage, and plasmid typing techniques was used to differentiate strains of Clostridium difficile. A typing set of 20 bacteriocin-producing strains was established after 400 isolates of C. difficile were screened for the ability to produce bacteriocin. These strains were used to type a collection of 114 isolates of C. difficile. Forty-six (40%) of the 114 isolates were typeable, and 31 typing patterns were distinguishable. Plasmid typing of the same 114 isolates of C. difficile showed that 67 (59%) of the isolates carried up to four plasmids ranging from 7 to 60 kb in size, although most strains contained only one or two plasmids. Twenty different plasmid typing patterns were observed among the isolates. A combination of bacteriocin and plasmid typing provided 77% typeability. Fifteen (13%) of the 114 strains were typeable with five bacteriophages isolated in our laboratory, but the increase in typeability of strains over that obtainable by plasmid and bacteriocin typing was only 1.8%. Isolates that were nontypeable by bacteriocins, plasmids, or phages could be divided into two groups on the basis of positive or negative cytotoxin production. This further division of strains would increase the typeability potential by 7%; i.e., the ability to differentiate strains would rise from 77 to 84%, or perhaps 86%, if phage typing were included. We conclude that more than one of the techniques reported in this paper must be used to achieve an acceptable level of typeability of this species.     

Usefulness of Multiple-Locus VNTR Fingerprinting in detection of clonality of community- and hospital-acquired <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> isolates

Staphylococcus aureus has become a major source of hospital infections and the risk of colonisation and infection by community-acquired methicillin-resistant S. aureus (CA-MRSA) is increasingly higher. Because of the importance of S. aureus to public health, many molecular typing methods have been developed to determine its transmission routes and source of infection during epidemiological investigations. In this study we evaluated the usefulness of multiplex PCR based Multi-Locus VNTR Fingerprinting (MLVF) as the first step method for rapid differentiation of Croatian and Polish S. aureus isolates in hospital and community settings. This is a first report of the usefulness of MLVF in typing of hospital-acquired methicillin-sensitive S. aureus (HA-MSSA) and four CA-MRSA isolates. A total of 47 isolates of S. aureus recovered in Croatia in 2004 and in Poland in 2006 and 2007 were tested. The MLVF results were compared to those produced by other typing methods, such as Pulsed-Field Gel Electrophoresis (PFGE), Multi-Locus Sequence Typing (MLST) and spa typing. The MLVF analysis showed almost the same clonality results as the remaining typing methods although some differences were found. Epidemiological data about the relation among S. aureus isolates and the results produced by typing methods applied in the present study indicate that because of the advantages in ease and speed of Variable Number of Tandem Repeats (VNTR) procedure over PFGE, spa typing and MLST, MLVF can be used as a first screening method followed by additional typing.     

Five-locus HLA typing of hematopoietic stem cell donor volunteers using PCR sequence specific primers

We have developed a strategy for five-locus human leukocyte antigen (HLA) typing of hematopoeitic stem cell (HSC) donors using the polymerase chain reaction with sequence-specific primers (PCR-SSP). The PCR-SSP method is robust, reproducible, and accurate. New PCR-SSP mixtures can be added as required and all reactions are carried out under the same conditions, which can easily be applied to the typing of other loci, e.g., ABO blood groups. Initially, 127 PCR-SSP reactions were used to detect simultaneously HLA-A, -B, -C, -DRB1/3/4/5, and DQB1 alleles, differentiated generally to the level of the first two digits of the allele name, essentially equivalent to the serological split specificity. Approximately 40% of subjects were tested against a further 29 HLA-A, -B SSP mixtures to exclude rare alleles and unambiguously assign a two-digit HLA allele family. This gave an overall typing resolution equivalent to or greater than the split specificity level and covered all HLA-A, -B, -C, -DRBland DQB1 alleles listed in the WHO's Nomenclature for Factors of the HLA System, 2000. The Welsh Bone Marrow Donor Registry has used this strategy to HLA type over 35,000 HSC donors over 9 years. Comprehensive and accurate five-locus HLA typing allows confident and rapid identification of potential matched HSC donors for patients requiring stem cell transplantation generally without the need for typing additional loci. This allows resources to be focused directly on allele level typing of DRB1 and other loci. This strategy decreases overall donor work-up time, which is a major benefit to patients.     

Comparison of Capsular Typing of Staphylococcus aureus with Bacteriophage Typing: A Study in Gulbarga, India

Staphylococcus aureus (S. aureus) is important both as a nosocomial and community acquired pathogen causing various degrees of infections. Typing S. aureus has been a question that is still being addressed. Bacteriophage typing is still used as a golden standard for typing though molecular methods are investigated. In developing countries where neither molecular typing nor the bacteriophage typing methods can be routinely used, the recently developed capsular typing method can be considered as screening method. We compared capsular typing with bacteriophage typing of the strains isolated in Gulbarga, India. We observed that the typeability of capsular typing was significantly higher (96%) among the phage typed strains, and the predominant capsular type in the region was type-8. The data so generated can be used to group S. aureus based on capsules both as a screening prior to bacteriophage typing, and to identify capsular candidate for developing prophylactic and therapeutic alternatives.     

Harmonization of the multiple-locus variable-number tandem repeat analysis method between Denmark and Norway for typing Salmonella Typhimurium isolates and closer examination of the VNTR loci

AIMS: Harmonization and evaluation of the multiple-locus variable-number tandem repeat analysis (MLVA) method for sub-typing Salmonella enterica ssp. enterica serovar Typhimurium (Salm. Typhimurium) in Denmark and Norway, and analysis of the typing data. METHODS AND RESULTS: The Salm. Typhimurium MLVA (STMLVA) method, which uses length polymorphisms in five tandem-repeated DNA loci to differentiate isolates, was harmonized between Denmark and Norway, using a common set of 14 isolates. The MLVA assay that is routinely used at the Norwegian Institute of Public Health was set up at the Statens Serums Institute. Both the institutes used an ABI-310 Genetic Analyzer for capillary separation of PCR products, and the same internal size standard. Running the same set of 14 test isolates in both countries and comparing the results showed an excellent typing match at all loci in all isolates. Subsequently, 461 isolates were genotyped in Norway and 454 isolates were genotyped in Denmark. The STMLVA assay displayed a large number of allelic profiles that were distinct for each country as well as shared profiles. Differences in variable number of tandem repeats allele frequencies and absence of amplification products were observed between Denmark and Norway. CONCLUSIONS: The MLVA method was set up in two different laboratories and produced completely matching typing data that could be shared rapidly by e-mail for comparison. Notably, differences in allele frequencies and absence of amplification were noted between the countries. SIGNIFICANCE AND IMPACT OF THE STUDY: The STMLVA method was shown to be easily implemented and to produce typing data, which were shared over the Internet. This enables increased speed of typing and comparison of data between countries, when compared with earlier typing methods. Information embedded in the allele frequencies might give clues to the origin and source of isolates.     

Measuring Ambiguity in HLA Typing Methods

In hematopoietic stem cell transplantation, donor selection is based primarily on matching donor and patient HLA genes. These genes are highly polymorphic and their typing can result in exact allele assignment at each gene (the resolution at which patients and donors are matched), but it can also result in a set of ambiguous assignments, depending on the typing methodology used. To facilitate rapid identification of matched donors, registries employ statistical algorithms to infer HLA alleles from ambiguous genotypes. Linkage disequilibrium information encapsulated in haplotype frequencies is used to facilitate prediction of the most likely haplotype assignment. An HLA typing with less ambiguity produces fewer high-probability haplotypes and a more reliable prediction. We estimated ambiguity for several HLA typing methods across four continental populations using an information theory-based measure, Shannon's entropy. We used allele and haplotype frequencies to calculate entropy for different sets of 1,000 subjects with simulated HLA typing. Using allele frequencies we calculated an average entropy in Caucasians of 1.65 for serology, 1.06 for allele family level, 0.49 for a 2002-era SSO kit, and 0.076 for single-pass SBT. When using haplotype frequencies in entropy calculations, we found average entropies of 0.72 for serology, 0.73 for allele family level, 0.05 for SSO, and 0.002 for single-pass SBT. Application of haplotype frequencies further reduces HLA typing ambiguity. We also estimated expected confirmatory typing mismatch rates for simulated subjects. In a hypothetical registry with all donors typed using the same method, the entropy values based on haplotype frequencies correspond to confirmatory typing mismatch rates of 1.31% for SSO versus only 0.08% for SBT. Intermediate-resolution single-pass SBT contains the least ambiguity of the methods we evaluated and therefore the most certainty in allele prediction. The presented measure objectively evaluates HLA typing methods and can help define acceptable HLA typing for donor recruitment.     

Conservation of components of the Escherichia coli export machinery in prokaryotes

Esterase electrophoretic typing was used to classify clinical isolates of Pseudomonas aeruginosa. One hundred and twenty-seven P. aeruginosa strains belonging to 16 serotypes (including 16 non-typeable strains) and isolated from diverse human infections in three hospitals, and the type strain ATCC 10 145, were tested. Four main kinds of esterase and 4 additional esterases were distinguished by their spectra of hydrolytic activity toward synthetic substrates and by their sensitivity or resistance to di-isopropyl fluorophosphate. The electrophoretic variations of these enzymes were used to define 42 zymotypes. Electrophoretic typing of esterase appeared to be more sensitive than serotyping and the results of the two methods did not correlate. When the two typing methods were used in parallel, 78 different combinations of serotype and zymotype were obtained.     

多位点测序分型技术在病原微生物分型鉴定中的应用

多位点测序分型(Multilocus sequence typing,MLST)技术是一种以核苷酸序列为基础的病原菌分型方法,它是高通量测序技术与成熟的群体遗传学相结合的产物。该方法简单易行,重复性强,可以通过国际互联网对某一致病菌株在全球范围内的传播分布情况进行追踪监控。目前,MLST技术已被广泛应用于原核病原菌及一些真核病原菌(如真菌)的分型鉴定中。主要对MLST技术的原理及其在一些常见病原菌分型鉴定中的应用进行了简要的阐述。     

The use of (GTG)5 oligonucleotide as an RAPD primer to type Campylobacter concisus

AIM: DNA fingerprinting using (GTG)(5) oligonucleotide as a primer in a random amplified polymorphic DNA (RAPD) assay was assessed by typing isolates of Campylobacter concisus strains, collected over a period of 8 years. METHODS AND RESULTS: RAPD analysis using the (GTG)(5) oligonucleotide as a primer was used to type 100 isolates of C. concisus comprising mostly isolates from children with diarrhoea. Using this method, 86% of the isolates were found to be genotypically diverse. Of these heterogeneous isolates, 25 of the strains were also shown to be genetically distinct in a previous study using pulsed field gel electrophoresis. The remaining isolates (14) could be classified into five profile groups based on the DNA fingerprinting patterns. The assay successfully identified epidemiologically linked strains from the unrelated genetically diverse pool of strains. CONCLUSIONS: Laboratory RADP typing using the (GTG)(5) primer proved to be useful in distinguishing related strains of C. concisus from a large pool of unrelated strains of this organism. SIGNIFICANCE AND IMPACT OF THE STUDY: RAPD typing using (GTG)(5) is a simple method that could be used to investigate the epidemiology of C. concisus. The results suggest that homologous lineages of C. concisus may exist within an otherwise heterogeneous species complex. However, these data need to be confirmed using a more robust typing method.     

中国人常见HLA—DPB1不明确杂合子SSP分型解决方案

目的：人类染色体是二倍体,这使得以测序方法研究多态性区域时会遇到不明确杂合子,这个问题在HLA-DPB1的分型上尤为突出。试图寻找一个来解决HLA-DPB1分型中不明确杂合子比例高给分型带来的困难的方案。方法：对946例样品进行HLA-DPB1分型,其中不明确杂合子有353例,共30种,占总例数的37％。建立了一套SSP分型方法,设计上游引物6条,下游引物15条,每一个样品同时用两对特异性引物进行扩增,两对引物分别代表两种不同的杂合模式。再从30种不明确杂合子类型中各挑2个样品进行克隆测序,结果与SSP分型结果比较。结果：SSP分型方法采用同一套扩增体系与两套循环反应条件,只需一次PCR扩增,就可以方便快捷地实现不明确杂合子的分辨,其结果与克隆测序结果相符。结论：与以往的克隆测序、SSCP方法相比,本研究中SSP分型方法具有高效率、高通量、省时省力的特点。     

Major histocompatibility complex class II polymorphisms in Macaca mulatta: factors influencing comprehensive genotyping of Macaca mulatta (Mamu)-DQA1 alleles by PCR-RFLP in archival samples.

In the last 5 years, HLA class II genotyping methods have been adapted for genotyping of class II loci in rhesus macaques. Since previously published typing protocols were used on samples that were collected and stored under ideal conditions, it was of interest to determine if these methods were adequate for genotyping a large collection of archival samples from which DNA had been isolated and stored under various conditions. Established macaque DQA1 typing protocols were modified to optimize the typing procedure and enhance the ability to successfully genotype DNA from samples that were of poor quality and/or quantity. Long-term storage of whole-blood buffy coats or stored DNA extracted from whole-blood buffy coats did not affect typing success; however, amplification and typing of DNA extracted from archival samples of plasma were difficult and resulted in a low success rate. This suggests that amplification and DQA1-genotyping of archival samples is possible with a modified protocol, but is influenced by the age and source of the sample, and to a lesser extent, the method used to extract DNA from sample substrates.     

Multipoint linkage map of the human pseudoautosomal region,based on single-sperm typing: do double crossovers occur during male meiosis?

Sperm typing was used to measure recombination fractions among pseudoautosomal markers and the beginning of the X/Y-specific sequences located at the pseudoautosomal boundary. These experiments included primer-extension preamplification and PCR followed by allele typing using gel electrophoresis. A newly developed data-analysis program allowed the construction of the first multipoint-linkage sperm-typing map, using results obtained on seven loci from three individuals. The large sample size not only confirmed the increased recombination activity of the pseudoautosomal region but allowed an estimate of interference of recombination to be made. The coefficient of coincidence was calculated to be .26 over a physical distance of only approximately 1,800 kb. The observation of a few sperm presumably resulting from double recombination argues that more than one crossover event can occur in this region during male meiosis.     

Potential of three-Way randomly amplified polymorphic DNA analysis as a typing method for twelve Salmonella serotypes.

The potential of a three-way randomly amplified polymorphic DNA (RAPD) procedure (RAPD typing) for typing Salmonella enterica strains assigned to 12 serotypes was analyzed. The series of organisms used included 235 strains (326 isolates) collected mainly from clinical samples in the Principality of Asturias and 9 reference strains. RAPD typing was performed directly with broth cultures of bacteria by using three selected primers and optimized PCR conditions. The profiles obtained with the three primers were used to define RAPD types and to evaluate the procedure as a typing method at the species and serotype levels. The typeability was 100%; the reproducibility and in vitro stability could be considered good. The concordance of RAPD typing methods with serotyping methods was 100%, but some profiles obtained with two of the three primers were obtained with strains assigned to different serotypes. The discrimination index (DI) within the series of organisms was 0.94, and the DI within serotypes Typhimurium, Enteritidis, and Virchow were 0.72, 0.52, and 0.66, respectively. Within these serotypes the most common RAPD types were differentiated into phage types and vice versa; combining the types identified by the two procedures (RAPD typing and phage typing) resulted in further discrimination (DI, 0. 96, 0.74, and 0.87, respectively). The efficiency, rapidity, and flexibility of the RAPD typing method support the conclusion that it can be used as a tool for identifying Salmonella organisms and as a typing method that is complementary to serotyping and phage typing methods.     

Potential of Three-Way Randomly Amplified Polymorphic DNA Analysis as a Typing Method for Twelve Salmonella Serotypes

The potential of a three-way randomly amplified polymorphic DNA (RAPD) procedure (RAPD typing) for typing Salmonella enterica strains assigned to 12 serotypes was analyzed. The series of organisms used included 235 strains (326 isolates) collected mainly from clinical samples in the Principality of Asturias and 9 reference strains. RAPD typing was performed directly with broth cultures of bacteria by using three selected primers and optimized PCR conditions. The profiles obtained with the three primers were used to define RAPD types and to evaluate the procedure as a typing method at the species and serotype levels. The typeability was 100%; the reproducibility and in vitro stability could be considered good. The concordance of RAPD typing methods with serotyping methods was 100%, but some profiles obtained with two of the three primers were obtained with strains assigned to different serotypes. The discrimination index (DI) within the series of organisms was 0.94, and the DI within serotypes Typhimurium, Enteritidis, and Virchow were 0.72, 0.52, and 0.66, respectively. Within these serotypes the most common RAPD types were differentiated into phage types and vice versa; combining the types identified by the two procedures (RAPD typing and phage typing) resulted in further discrimination (DI, 0.96, 0.74, and 0.87, respectively). The efficiency, rapidity, and flexibility of the RAPD typing method support the conclusion that it can be used as a tool for identifying Salmonella organisms and as a typing method that is complementary to serotyping and phage typing methods.     

Identification of microorganisms by FTIR spectroscopy: perspectives and limitations of the method

Fourier transform infrared (FTIR) spectroscopy was introduced in 1991 as a technique to identify and classify microbes. Since then, it has gained growing interest and has undergone a remarkable evolution. Highly sophisticated spectrometers have been developed, enabling a high sample throughput. Today, the generation of high-quality data in a short time and the application of the technique for rapid and reliable identification of microbes to the species level are well documented. What makes FTIR spectroscopy even more attractive is the fact that spectral information can also be exploited for strain typing purposes, which is particularly important for epidemiological analyses and some technological applications. Accordingly, in recent years, FTIR spectroscopy has been increasingly used for typing and classifying microorganisms below the species level. The intention of this review is to give an overview over current knowledge and strategies of using FTIR spectroscopy for species identification and to describe different approaches for strain typing.     

Short tandem repeat typing technologies used in human identity testing

Short tandem repeat (STR) typing methods are widely used today for human identity testing applications including forensic DNA analysis. Following multiplex PCR amplification, DNA samples containing the length-variant STR alleles are typically separated by capillary electrophoresis and genotyped by comparison to an allelic ladder supplied with a commercial kit. This article offers a brief perspective on the technologies and issues involved in STR typing.     

Evaluation of randomly amplified polymorphic DNA and pulsed field gel electrophoresis techniques for molecular typing of Dermatophilus congolensis

This study aimed to evaluate molecular typing methods useful for standardization of strains in experimental work on dermatophilosis. Fifty Dermatophilus congolensis isolates, collected from sheep, cattle, horse and a deer, were analyzed by randomly amplified polymorphic DNA (RAPD) method using twenty-one different primers, and the results were compared with those obtained by typing with a pulsed field gel electrophoresis (PFGE) method using the restriction digest enzyme Sse8387I. The typeability, reproducibility and discriminatory power of RAPD and Sse8387I-PFGE typing were calculated. Both typing methods were highly reproducible. Of the two techniques, Sse8387I-PFGE was the least discriminating (Dice Index (DI), 0.663) and could not distinguish between epidemiologically related isolates, whereas RAPD showed an excellent discriminatory power (DI, 0.7694-0.9722). Overall, the degree of correlation between RAPD and PFGE typing was significantly high (r, 0.8822). We conclude that the DNA profiles generated by either RAPD or PFGE can be used to differentiate epidemiologically unrelated isolates. The results of this study strongly suggest that at least two independent primers are used for RAPD typing in order to improve its discriminatory power, and that PFGE is used for confirmation of RAPD results.     

Metabolic heterogeneity of muscle fibers classified by myosin ATPase.

Muscle fibers are commonly classified histochemically into three types by the staining intensity for myosin ATPase combined with those for metabolic enzymes. Preincubation at pH 4.6 gives rise to three staining intensities of myosin ATPase which are also used for fiber typing. The two classification systems were compared by computer analysis of the individual staining profiles of over 2,500 fibers, and found not to be equivalent. The analysis showed metabolic heterogeneity among the fiber groups distinguished according to their differences in myosin ATPase.