Letter to the editor: Suspected discrepancies due to inadequate quality of an in vitro analysis revealed by an in silico analysis.

The author's in vitro analysis results were compared with those of an in silico structure analysis of the relevant sequences obtained from the author's entire genome sequence data. It was speculated that the in silico results together with author's phylogenetic results demonstrate problems in the authors' published in vitro data, which were presumably due to an inadequate accuracy of an in vitro assay. It was fortuitously suggested that alignment images to an excess repeat structure of the same locus provide a improved speculation of a number of repeats and that accurate in vitro assays are expected to complementarily provide reliable insights in the era of whole genome sequencing.

Comparison of a variable-number tandem-repeat (VNTR) method for typing Mycobacterium avium with mycobacterial interspersed repetitive-unit-VNTR and IS1245 restriction fragment length polymorphism typing.

Mycobacterium avium complex (MAC) infections are increasing annually in various countries, including Japan, but the route of transmission and pathophysiology of the infection remain unclear. Currently, a variable-number tandem-repeat (VNTR) typing method using the Mycobacterium avium tandem repeat (MATR) loci (MATR-VNTR) is employed in Japan for epidemiological studies using clinical isolates of M. avium.

[Usefulness of variable numbers of tandem repeats typing in clinical strains of Mycobacterium avium].

Objectives: We evaluated the usefulness of Variable Numbers of Tandem Repeats (VNTR) analysis, which was recently reported as a new typing method of Mycobacterium avium strains of animal origin, for strain differentiation of clinical isolates of M. avium in comparison with the standard IS1245-RFLP typing method. In addition, forty M.

[Molecular epidemiology of tuberculosis by the use of IS6110 restriction fragment length polymorphism: a study from 2001 to 2003].

Objective: To analyze the situation of tuberculosis infection by DNA fingerprinting in the middle and eastern part of Osaka, Japan.

Design: We performed IS6110 restriction fragment length polymorphism (RFLP) on 1200 isolates from tuberculosis patients who visited our hospital from January 2001 to December 2003. A cluster was defined as a series of isolates with more than 90% similarity by IS6110 RFLP and those with the same drug-susceptibility pattern.

The artAB genes encode a putative ADP-ribosyltransferase toxin homologue associated with Salmonella enterica serovar Typhimurium DT104.

Many bacterial pathogens encode ADP-ribosyltransferase toxins. The authors identified an ADP-ribosyltransferase toxin homologue (ArtA, ArtB) in Salmonella enterica serovar Typhimurium (S. typhimurium) DT104.

Experimental transmission of ovine herpesvirus-2 in sheep.

Transmission of ovine herpesvirus-2 (OvHV-2) in sheep via natural contact and nasal secretions was examined. OvHV-2-free lambs were produced by separating newborn lambs from their mothers within 5 days of birth and raising them in an isolation facility. Transmission experiments via natural contact were conducted by keeping OvHV-2-free lambs with OvHV-2-infected sheep of different ages.

Molecular characterization of a prophage of Salmonella enterica serotype Typhimurium DT104.

Isolates of the Salmonella enterica serotype Typhimurium definitive phage type (DT104) were found to contain the same prophage (designated phage ST104). The complete sequence of the DNA genome of prophage ST104 was determined. The entire DNA sequence consisted of 41,391 bp, including 64 open reading frames, and exhibited high similarity to P22 and to phage type conversion phage ST64T.

Comparison of Salmonella enterica serovar Abortusequi isolates of equine origin by pulsed-field gel electrophoresis and fluorescent amplified-fragment length polymorphism fingerprinting.

Equine paratyphoid is caused by Salmonella enterica serovar Abortusequi, and manifests mainly as abortion in the mare. We compared S. Abortusequi strains isolated in Japan and other countries using pulsed-field gel electrophoresis (PFGE) and fluorescent amplified-fragment length polymorphism (FAFLP) analysis.

Development of a shuttle polymerase chain reaction for the detection of bovine herpesvirus 2.

Three different polymerase chain reaction (PCR) protocols were evaluated for their ability to detect bovine herpesvirus 2 (BoHV-2): single-step PCR with 3 reaction stages (denaturation, annealing and extension), 2 reaction stages (denaturation and annealing/extension; shuttle PCR), and semi-nested PCR with 3 reaction stages. All the PCR protocols showed the same sensitivity (detection limit of 0.4 TCID(50)).