Typing

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

Next-Generation Sequencing for Typing and Detection of Resistance Genes: Performance of a New Commercial Method during an Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli

Abstract: Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131) Escherichia coli infections in a nursing home in The Netherlands. The assay was performed on 56 extended-spectrum-beta-lactamase (ESBL) E. coli isolates collected during 2 prevalence surveys (March and May 2013). Typing results were compared to those of amplified fragment length polymorphism (AFLP), whereby we visually assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP. A microarray was considered the gold standard for detection of resistance genes. AFLP identified a large cluster of 31 indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree showed that all isolates of this outbreak cluster were strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. The BioDetection assay detected ESBL genes in all but 1 isolate (sensitivity, 98%) but was unable to discriminate between ESBL and non-ESBL TEM and SHV beta-lactamases or to specify CTX-M genes by group. The performance of the hospital-acquired infection (HAI) BioDetection System for typing of E. coli isolates compared well with the results of AFLP. Its performance with larger collections from different locations, and for typing of other species, was not evaluated and needs further study.

Comparison of molecular typing methods applied to Clostridium difficile.

Abstract: Since the 1980s the epidemiology of Clostridium difficile infection (CDI) has been investigated by the application of many different typing or fingerprinting methods. To study the epidemiology of CDI, a typing method with a high discriminatory power, typeability, and reproducibility is required. Molecular typing methods are generally regarded as having advantages over phenotypic methods in terms of the stability of genomic markers and providing greater levels of typeability. A growing number of molecular methods have been applied to C. difficile. For the early and rapid detection of outbreak situations, methods such as restriction enzyme analysis, arbitrary primed polymerase chain reaction (PCR), and PCR ribotyping are commonly used. For long-term epidemiology, multilocus sequence typing, multilocus variable number of tandem repeats analysis, and amplified fragment length polymorphism are of interest. Currently, the PCR-ribotyping method and the library of PCR ribotypes in Cardiff are the benchmarks to which most typing studies around the world are compared. Multilocus variable number of tandem repeats analysis is the most discriminative typing method and will contribute significantly to our understanding of the epidemiology of this important nosocomial pathogen.

Comparison of serological and sequence-based methods for typing feline calcivirus isolates from vaccine failures.

Abstract: Feline calicivirus (FCV) can be typed by exploiting antigenic differences between isolates or, more recently, by the sequence analysis of a hypervariable region of the virus's capsid gene. These two methods were used to characterise FCV isolates from 20 vaccine failures which occurred after the use of a commercial, live-attenuated vaccine. Using virus neutralisation, the isolates showed a spectrum of relatedness to the vaccine; depending on the criterion adopted for identity, 10 to 40 per cent of them appeared to be similar to the vaccine virus. Using sequence analysis, the isolates fell into one of two categories; 20 per cent had a similar sequence to the vaccine (0-67 to 2-67 per cent distant), and the remainder had a dissimilar sequence (21-3 to 36-0 per cent distant). Sequence analysis identified one cat that appeared to be infected with two distinct FCVs. The serological and sequence-based typing methods gave the same result in 80 to 95 per cent of individual cases, depending on the criterion adopted for serological identity. It is suggested that molecular typing is a more definitive method for characterising the relatedness of FCV isolates.

Epidemiological typing of MRSA isolates from blood cultures taken in Irish hospitals participating in the European Antimicrobial Resistance Surveillance System (1999–2003)

Abstract: Between 1999 and 2003, meticillin-resistant Staphylococcus aureus (MRSA) isolates recovered from blood cultures in Irish hospitals that participate in the European Antimicrobial Resistance Surveillance System were investigated by epidemiological typing using antibiogram–resistogram (AR) typing, biotyping, and DNA macrorestriction digestion using SmaI followed by pulsed-field gel electrophoresis (PFGE). PFGE patterns were assigned five-digit pulsed-field type (PFT) numbers, and PFTs of apparently related patterns were abbreviated to two-digit PFT groups (PFGs). AR and PFGE typing results were combined to produce AR-PFG types. Representative isolates of each AR-PFG type recovered in 2002 were typed by multilocus sequence typing and staphylococcal cassette chromosome (SCC) mec analysis. Isolates from 1999 and 2000 were also typed by phage typing. The extent to which epidemiological types of MRSA from blood cultures could be extrapolated to the total MRSA population was investigated by comparing results obtained with isolates from the total MRSA population versus those obtained with blood cultures during three study periods. Over the 5 years from 1999 to 2003, 1,580 blood culture isolates from 1,495 patients were analysed. Typeability and discriminatory indices were as follows: AR typing, 1 and 0.97; phage typing, 0.29 and 0.89; PFGE, 0.99 and 0.95; AR-PFG typing, 1 and 0.95. The most frequently occurring AR-PFG types were 06-01, 07-02, 13-00, and 14-00 and were exhibited by 57, 7, 14, and 12% of isolates, respectively. During the study period, the distribution of AR-PFG type changed markedly, with the prevalence of one type (AR-PFG 06-01) increasing by 880%, from 22% (39/181) in 1999 to 80% (343/430) in 2003. Investigation of whether epidemiological types among blood culture isolates of MRSA were representative of the total MRSA population showed that there was no significant difference in most instances. MLST and SCCmec typing showed that AR-PFG types 06-01, 07-02, 13-00, and 14-00 were ST22–MRSA-IV, ST36–MRSA-II, ST8–MRSA-IID, and ST8–MRSA-IIE, respectively.

The effect of key size of touch screen virtual keyboards on productivity, usability, and typing biomechanics.

Abstract: Objective:We investigated whether different virtual keyboard key sizes affected typing force exposures, muscle activity, wrist posture, comfort, and typing productivity.Background:Virtual keyboard use is increasing and the physical exposures associated with virtual keyboard key sizes are not well documented.Method:Typing forces, forearm/shoulder muscle activity, wrist posture, subjective comfort, and typing productivity were measured from 21 subjects while they were typing on four different virtual keyboards with square key sizes, which were 13, 16, 19, and 22 mm on each side with 2-mm between-key spacing.Results:The results showed that virtual keyboard key size had little effect on typing force, forearm muscle activity, and ulnar/radial deviation. However, the virtual keyboard with the 13-mm keys had a 15% slower typing speed (p < .0001), slightly higher static (10th percentile) shoulder muscle activity (2% maximum voluntary contractions, p = .01), slightly greater wrist extension in both hands (2° to 3°...