Typing

About: Typing is a research topic. Over the lifetime, 5010 publications have been published within this topic receiving 146539 citations.

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.

Abstract: Clostridium difficile, recently renamed Clostridioides difficile, is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C. difficile Initially, we determined the breadth of the C. difficile population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with C. difficile clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping (n = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole C. difficile population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange.

Typing of Listeria spp. by random amplified polymorphic DNA (RAPD) analysis.

Abstract: Random amplified polymorphic DNA (RAPD) analysis, a variation of the polymerase chain reaction (PCR) in which a single primer is used, was evaluated for use as a simple and reliable method with which to type Listeria spp. Representatives of six species of Listeria were studied. Five isolates of L. innocua and four isolates of L. seeligeri were all distinguishable from one another, but the four isolates of L. ivanovii tested, although distinguishable from other Listeria spp., were not differentiated. Among L. monocytogenes serovars 1/2a (eight isolates), 1/2b (eight isolates) and 4b (10 isolates), at least six, three and six RAPD patterns were observed, respectively. Fourteen neonatal cross-infection sets of L. monocytogenes isolates, shown to be indistinguishable by serotyping and phage typing, were examined with three different primers. With one primer, three of the sets were shown to consist of closely related, but distinguishable, strains. In the other 11 cases, each set of strains was indistinguishable with all three primers. These preliminary data indicate that RAPD analysis has promise as a method for typing Listeria spp.

Utility of Mycobacterial Interspersed Repetitive Unit Typing for Differentiating Multidrug-Resistant Mycobacterium tuberculosis Isolates of the Beijing Family

Abstract: Mycobacterial interspersed repetitive unit (MIRU) typing has been found to allow rapid, reliable, high-throughput genotyping of Mycobacterium tuberculosis and may represent a feasible approach to study global M. tuberculosis molecular epidemiology. To evaluate the use of MIRU typing in discriminating drug-resistant M. tuberculosis strains of the Beijing genotype family, 102 multidrug-resistant (MDR) clinical isolates and 253 randomly selected non-MDR isolates collected from 2000 to 2003 in Hong Kong were subjected to 12-locus MIRU typing, spoligotyping, and IS6110 restriction fragment length polymorphism (RFLP) typing. Spoligotyping showed that 243 (68.5%) of 355 isolates belonged to Beijing family genotype. MIRU typing showed lower discrimination in differentiating between the Beijing family strains (Hunter-Gaston discriminative index [HGI] of 0.8827) compared with the IS6110 RFLP method (HGI = 0.9979). For non-Beijing strains, MIRU typing provided discrimination (HGI = 0.9929) comparable to that of the RFLP method (HGI = 0.9961). There was no remarkable difference in discrimination power between the two methods in differentiating both within and between MDR and non-MDR strains of M. tuberculosis. Dendrograms constructed with the MIRU typing data showed a clear segregation between the Beijing and non-Beijing genotype. Addition of RFLP to MIRU typing offered a higher discrimination ability (92.6%) than did addition of MIRU typing to RFLP (40.0%). This supported the potential use of this method to analyze the global genetic diversity of MDR M. tuberculosis strains that may be at different levels of evolutionary divergence.

Rapid serotyping of human rotavirus strains by solid-phase immune electron microscopy.

Abstract: Nine cell culture-adapted, as well as 30 clinical, human rotavirus (HRV) strains from fecal extracts of children with primary HRV infection were typed by rapid solid-phase immune electron microscopy with protein A and absorbed DS-1 (HRV serotype 2), Wa (serotype 1), and VA70 (assumed serotype 3) rabbit immune sera. As a reference typing test for cell culture-adapted strains, the neutralization assay was used, whereas for noncultivatable strains typing was done for comparison, indirectly, based upon the differential neutralization reactivity of convalescent-phase serum samples from patients with primary HRV infection versus the three reference HRV serotypes. Typing results by solid-phase immune electron microscopy for all strains examined were in complete agreement with those obtained by the neutralization assay, both on cell culture-adapted strains with the three reference rabbit antisera and on three reference HRV strains with human convalescent-phase serum samples. Since adaptation to growth in cell cultures of clinical HRV strains from stool specimens is a time-consuming procedure and is often unsuccessful, solid-phase immune electron microscopy is preferred over the neutralization assay, giving results in about 16 h and also allowing typing of HRV strains from stool specimens low in virus particles. In addition, HRV strains reacting differently from the three reference serotypes may be easily selected by solid-phase immune electron microscopy for further characterization, as was the case for one strain in this study.