Typing

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

Bacteriocins as tools in analysis of nosocomial Klebsiella pneumoniae infections.

Abstract: Epidemiological analysis of isolates from nosocomial infections caused by Klebsiella pneumoniae was improved by the use of bacteriocins in addition to capsular serotyping. Screening for bacteriocins produced by 77 reference strains for capsular serotyping identified 39 strains, and 8 of these strains were selected as a typing set. Using this set, we found that 241 to 259 (91%) nonepidemic clinical isolates of K. pneumoniae were inhibited by one or more of the eight producers. Of the most frequent bacteriocin type there were 31 examples (12%). High reproducibility of typing patterns (83.3%) and easy practicability of typing were achieved with a streak-and-point method avoiding the use of suspensions of bacteriocins and the risk of instability. The Klebsiella bacteriocins were active also on Enterobacter and Shigella species and on Escherichia coli strains, but were ineffective on other Enterobacteriacae.

In vivo stability and discriminatory power of methicillin-resistant Staphylococcus aureus typing by restriction endonuclease analysis of plasmid DNA compared with those of other molecular methods.

Abstract: We evaluated test discriminatory power and DNA type alterations among methicillin-resistant Staphylococcus aureus strains by testing 199 sequential isolates from 39 patients collected over 30 to 228 days Isolates were typed by one or three different methods (restriction endonuclease analysis of plasmid DNA [REAP] with or without pulsed-field gel electrophoresis of genomic DNA [PFGE] and immunoblotting [IB]) REAP was highly discriminatory compared with PFGE and IB However, the initial isolates from 4 of the 39 patients lacked detectable plasmid DNA and could not be typed by REAP Typing of individual patient isolates showed that a different REAP type was identified only once every 138 days Among 25 comparisons, seven sequential isolate pairs demonstrating REAP differences were also different by PFGE and IB This likely represented the presence of more than one strain Eighteen other pairs with REAP differences were identical or related to one another by PFGE and IB typing, and 17 of these differences were likely caused by a single genetic alteration within the same strain or clone The rate of PFGE differences explicable by single genetic alterations among sequential isolates identical by REAP was similar to the overall rate for REAP differences in the whole collection We conclude that REAP and PFGE typing differences explicable by single genetic alterations are relatively infrequent but not rare These isolates should be examined by alternative typing systems to further support or refute clonality

A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis

Abstract: Among enterococci, Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections. The high genetic plasticity of E. faecalis complicates both molecular investigations and phylogenetic analyses. Whole-genome sequencing (WGS) enables unraveling of epidemiological linkages and putative transmission events between humans, animals, and food. Core genome multilocus sequence typing (cgMLST) aims to combine the discriminatory power of classical multilocus sequence typing (MLST) with the extensive genetic data obtained by WGS. By sequencing a representative collection of 146 E. faecalis strains isolated from hospital outbreaks, food, animals, and colonization of healthy human individuals, we established a novel cgMLST scheme with 1,972 gene targets within the Ridom SeqSphere+ software. To test the E. faecalis cgMLST scheme and assess the typing performance, different collections comprising environmental and bacteremia isolates, as well as all publicly available genome sequences from the NCBI and SRA databases, were analyzed. In more than 98.6% of the tested genomes, >95% good cgMLST target genes were detected (mean, 99.2% target genes). Our genotyping results not only corroborate the known epidemiological background of the isolates but exceed previous typing resolution. In conclusion, we have created a powerful typing scheme, hence providing an international standardized nomenclature that is suitable for surveillance approaches in various sectors, linking public health, veterinary public health, and food safety in a true One Health fashion.

Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation

Abstract: Background Ochrobactrum anthropi is a versatile bacterial species with strains living in very diverse habitats. It is increasingly recognized as opportunistic pathogen in hospitalized patients. The population biology of the species particularly with regard to the characteristics of the human isolates is being investigated. To address this issue, we proposed a polyphasic approach consisting in Multi-Locus Sequence Typing (MLST), multi-locus phylogeny, genomic-based fingerprinting by pulsed-field gel electrophoresis (PFGE) and antibiotyping.

Comparison of PCR Binary Typing (P-BIT), a New Approach to Epidemiological Subtyping of Campylobacter jejuni, with Serotyping, Pulsed-Field Gel Electrophoresis, and Multilocus Sequence Typing Methods

Abstract: To overcome some of the deficiencies with current molecular typing schema for Campylobacter spp., we developed a prototype PCR binary typing (P-BIT) approach. We investigated the distribution of 68 gene targets in 58 Campylobacter jejuni strains, one Campylobacter lari strain, and two Campylobacter coli strains for this purpose. Gene targets were selected on the basis of distribution in multiple genomes or plasmids, and known or putative status as an epidemicity factor. Strains were examined with Penner serotyping, pulsed-field gel electrophoresis (PFGE; using SmaI and KpnI enzymes), and multilocus sequence typing (MLST) approaches for comparison. P-BIT provided 100% typeability for strains and gave a diversity index of 98.5%, compared with 97.0% for SmaI PFGE, 99.4% for KpnI PFGE, 96.1% for MLST, and 92.8% for serotyping. Numerical analysis of the P-BIT data clearly distinguished strains of the three Campylobacter species examined and correlated somewhat with MLST clonal complex assignations and with previous classifications of "high" and "low" risk. We identified 18 gene targets that conferred the same level of discrimination as the 68 initially examined. We conclude that P-BIT is a useful approach for subtyping, offering advantages of speed, cost, and potential for strain risk ranking unavailable from current molecular typing schema for Campylobacter spp.