We investigated group A rotavirus (GARV) antigenemia and genomia in children with rotavirus gastroenteritis. A total of 16 patients (2-29 months old), who received a diagnosis of GARV gastroenteritis using a commercial rapid test, were enrolled in this study. The sera from the patients were tested for the presence of GARV antigen and the VP7 and NSP3 genes using an enzyme-linked immunosorbent assay (ELISA) and reverse transcription-polymerase chain reaction, respectively. Furthermore, when the VP7 gene was amplified, G type was identified and compared with that of GARV from the fecal samples of the patients. GARV antigen was detected in 12 of 16 serum samples (75.0%). No GARV antigen was found in infants that were 6 months old or younger. Thirteen of 16 serum samples (81.3%) were positive for GARV genes. In cases where both antigen and gene analyses were conducted, either GARV antigens or genes, or both, were detected in all cases. The GARV antigen levels of serum collected at 2 days of illness or more were significantly higher than were the levels in the samples obtained from the 1st day. Furthermore, the ELISA optical density values of patients with convulsion were significantly higher than were those of patients without convulsion, suggesting that the antigen level is associated with disease severity.

Although phenotypic resistance testing provides more direct measurement of antiretroviral drug resistance than genotypic testing, it is costly and time-consuming. However, genotypic resistance testing has the advantages of being simpler and more accessible, and it might be possible to use the data obtained for predicting quantitative drug susceptibility to interpret complex mutation combinations. This study applied the Artificial Neural Network (ANN) system to predict the HIV-1 resistance phenotype from the genotype. A total of 7,598 pairs of HIV-1 sequences, with their corresponding phenotypic fold change values for 14 antiretroviral drugs, were trained, validated, and tested in ANN modeling. The results were compared with the HIV-SEQ and Geno2pheno interpretation systems. The prediction performance of the ANN models was measured by 10-fold cross-validation. The results indicated that by using the ANN, with an associated set of amino acid positions known to influence drug resistance for individual antiretroviral drugs, drug resistance was accurately predicted and generalized for individual HIV-1 subtypes. Therefore, high correlation with the experimental phenotype may help physicians choose optimal therapeutic regimens that might be an option, or supporting system, of FDA-approved genotypic resistance testing in heavily treatment-experienced patients.

In the present study, we aimed to assess the rate and effect of device-associated nosocomial infections (DANIs), as well as the rate of antibiotic resistance, in the medical-surgical intensive care unit (ICU) of a research and training hospital in Turkey, and to compare our results with those reported by the National Nosocomial Infections Surveillance (NNIS) system and International Nosocomial Infection Control Consortium (INICC). A total of 509 patients were followed up within a 1-year period from 1 November 2007 to 1 November 2008. The total patient days were 4,087, the number of DANIs was 181. The ventilator-associated pneumonia rate in 1,000 ventilator days was 27.1, the rate of central venous catheter (CVC)-associated blood circulation infections in 1,000 CVC days was 11.8, and the rate of urinary catheter-associated urinary tract infections in 1,000 urinary catheter days was 9.6. The most frequently isolated microorganisms were Pseudomonas aeruginosa and Acinetobacter spp. Of the infections caused by Staphylococcus aureus, 81.2% were due to methicillin-resistant strains. Of the Enterobacteriaceae isolates, 53.5% were found to be resistant to ceftriaxone, while 29% of the P. aeruginosa isolates were found to be resistant to ciprofloxacin. The rates of use of devices such as ventilators, CVCs, and urinary catheters were 0.87, 0.93, and 0.98, respectively, which are higher than the rates reported by NNIS and INICC. On the other hand, the present DANI rate was higher than that reported by NNIS, but close to that reported by INICC. We conclude that the indications for and duration of device use should be reviewed.

The T-SPOT.TB test does not cross-react with Bacille Calmette-Guérin or most non-tuberculosis mycobacterium species, and is based on IFN-gamma responses to Mycobacterium tuberculosis-specific antigens. The objective of this study was to compare tuberculin skin test (TST) with T-SPOT.TB results used in the diagnosis of active tuberculosis (TB) as well as latent tuberculosis infection (LTBI). A total of 136 subjects participated in three different groups (47 patients with active pulmonary TB, 47 healthy persons without M. tuberculosis exposure, and 42 hospital members with a history of close contact with active TB patients). The T-SPOT.TB sensitivity (83.0%) and the negative predictive value (NPV) (82.6%) in the diagnosis of active TB were significantly higher than those of TST. The sensitivity and NPV of the TST were 38.3 and 60.8%, respectively. The T-SPOT.TB specificity (80.9%) and positive predictive value (81.3%) were lower than those of TST (95.7 and 90.0%, respectively). The performance of T-SPOT.TB and TST for diagnosing LTBI was the same (54.8%). T-SPOT.TB was superior in terms of sensitivity (83.0%); TST detected only 18, whereas T-SPOT.TB test detected 39 out of 47 patients with active TB. T-SPOT.TB is thought to have better performance than TST due to false-negative results in diagnosing active TB. However, it is considered that large prospective longitudinal studies are needed for diagnosing LTBI.

To clarify the route and source of Enterobacter sakazakii infection in a basic study, we analyzed powder infant formula milk (PIF), which may be an important source of infantile infection, regarding contamination with Enterobacteriaceae including this type of bacteria, and conducted drug sensitivity tests with various antimicrobial agents. Enterobacteriaceae was isolated 36 (24.2%) of 149 PIF samples. These comprised of 12 (19.7%) of 61 domestically produced samples and 24 (27.3%) of 88 imported samples. E. sakazakii was isolated in 9 (6.6%) of the 149 PIF samples. These comprised 4 (6.6%) of 61 domestically produced samples and 5 (5.7%) of 88 imported samples. In 8 of the 9 samples in which E. sakazakii was isolated, the bacterial levels were estimated to be 0.36 MPN/100 g. However, one imported sample showed a bacterial level of 0.91 MPN/100 g. In the drug sensitivity tests of E. sakazakii isolated from PIF, we compared the MIC₉₀ values. E. sakazakii was highly sensitive to 9 agents: cefotaxime, ceftriaxone, cefoperazone, ceftazidime, cefpirome, cefozopran, gentamicin, meropenem, and ciprofloxacin, and moderately sensitive to 5 agents: piperacillin, erythromycin, minocycline, chloramphenicol, and rifampicin. However, it was resistant to 2 agents, ampicillin and lincomycin.

In 2007, a large outbreak of pertussis occurred at a university in Japan. Initially, a student, suffering from nocturnal cough and post-tussive vomiting for 3 weeks was diagnosed with pertussis. During the subsequent outbreak, 361 university students and staff members presented with a primary complaint of a cough. In the present study, we analyzed bacterial agglutinin titers against two Bordetella pertussis strains, Yamaguchi (epidemic strain) and Tohama (vaccine strain), in 310 patients with a cough and evaluated its diagnostic accuracy for adolescent and adult pertussis. These serological analyses showed a significant difference (P<0.001) in the levels of Yamaguchi agglutinin titer, but not in those of Tohama agglutinin titer, between patient and healthy adult groups. Therefore, the bacterial agglutination assay against strain Yamaguchi may be a useful tool for diagnosis of adolescent and adult pertussis, especially in young adults, when an agglutinin titer cutoff value of ≥160x is used in combination with clinical symptoms and other clinical laboratory tests.

A total of 312 uropathogenic Escherichia coli strains were isolated from clinical specimens in 7 hospitals in Aichi Prefecture, Japan. Among them, 113 strains were resistant to quinolone, and 49 strains were resistant to fluoroquinolone. Phylogenetic group B2 was most prevalent in both susceptible strains (148 of 199 strains, 74.4%) and resistant strains (quinolone-resistant strains, 73 of 113 strains, 64.6%; fluoroquinolone-resistant strains, 40 of 49 strains, 81.6%). The resistant strains showed a significantly lower prevalence of virulence genes papA, hlyA, and cnf1 than did the susceptible strains, and this observation was further obvious when compared within B2 group strains. Among the 40 fluoroquinolone-resistant strains belonging to group B2, 37 (92.5%) strains carried PAIusp subtype IIa, 36 strains of which carried E84V mutation in parC, whereas none of the 9 strains belonging to group D carried PAIusp subtype IIa, and only one strain carried the mutation. These observations indicate that the differences of phenotypes including resistance of quinolone and carriage of virulence genes are associated with the complex context of genetic background, including the phylogenetic group and PAIusp subtype.

We subtyped 117 Vibrio vulnificus isolates from 85 V. vulnificus sepsis patients and 32 environmental samples by performing automated ribotyping for the purpose of molecular epidemiological study. Although there was one indistinguishable ribotype among the four human isolates and one environmental isolate, taken as a whole, the ribotypes were highly diverse regardless of sample sources. We report here for the first time the assorted ribotypes of V. vulnificus human and environmental isolates in Korea.

Ethidium monoazide (EMA) and propidium monoazide (PMA) have been utilized for selective PCR amplification of DNA from viable bacterial cells. In this study, we compared the abilities of EMA and PMA, together with real-time PCR, to specifically distinguish dead Legionella cells from viable cells. Several experiments showed that PMA or EMA treatment could specifically prevent the PCR amplification of DNA from dead Legionella cells in water samples. However, a 4-fold higher concentration of PMA than EMA was required to achieve this effect. EMA may therefore be more useful for practical environmental investigations of Legionella.

We investigated the microbial contamination of suction tubes attached to wall-type suction instruments. Microbial contamination of suction tubes used for endoscopy or sputum suction in hospital wards was examined before and after their disinfection. In addition, disinfection and washing methods for suction tubes were evaluated. Suction tubes (n=33) before disinfection were contaminated with 10²-10⁸ colony-forming units (cfu)/tube. The main contaminants were Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. The suction tubes were disinfected with sodium hypochlorite (n=11) or hot water (n=11), or by an automatic tube cleaner (n=11). After 2-h immersion in 0.1% (1,000 ppm) sodium hypochlorite, 10³-10⁷ cfu/tube of bacteria were detected in all 11 tubes examined. After washing in hot running water (65℃), 10³-10⁷ cfu/tube were detected in 3 of the 11 examined tubes. The bacteria detected in the suction tubes after disinfection with sodium hypochlorite or hot water were P. aeruginosa, A. baumannii, and S. maltophilia. On the other hand, after washing with warm water (40℃) using the automatic tube cleaner, contamination was found to be <20 cfu/tube (lower detection limit, 20 cfu/tube) in all 11 tubes examined. These results suggest the usefulness of washing with automatic tube cleaners.

Acute bacterial meningitis is an important cause of mortality and morbidity with high rates of long-term neurological sequelae. To determine the clinical presentation, complications, and outcome of acute meningitis in Yemen, a retrospective study in patients 15 years or older with acute bacterial meningitis who were admitted into Al-Thawra Teaching Hospital in Sana'a from January 2006 to December 2007 was carried out. There were 121 patients with acute bacterial meningitis. Lumbar puncture was performed in 112 (92.6%). The most common pathogen was Streptococcus pneumoniae found in 47.4% of positive cultures, Neisseria meningitidis in 33.9%, and Haemophilus influenzae in 10.2%. The classical triad of acute bacterial meningitis was found in 65% of cases. The mortality rate was 22.3%, with 27 patients dying during hospitalization. S. pneumoniae had a case fatality rate of 35.7%. Frequent complications were impaired consciousness, recurrent convulsion, and chest infection, which occurred in 30.6, 16.5, and 10.7% of the patients, respectively. Risk factors for death among those with acute bacterial meningitis included older age (>/=45 years), altered mental status, chest infection, and S. pneumoniae infection. This study highlights the importance of bacterial meningitis as a serious disease of adults in Yemen and the need for effective methods to prevent its complications.

To analyze the association of several types of malignant lymphomas in different anatomical sites with the Epstein-Barr virus (EBV) infection status, 127 cases of formalin-fixed paraffin-embedded samples of malignant lymphomas were investigated with in situ hybridization detecting EBV-encoded small RNA (EBER) in tumor cells. Forty-six out of 108 non-Hodgkin lymphoma (NHL) cases were positive for EBER (42.6%). The EBER-positivity rate of NHL in the nasal cavity and nasopharynx (35/60 cases, 58.3%) was higher than that of NHL in stomach (9/30 cases, 30%) and in the superficial lymph nodes (2/18 cases, 11.1%) (P<0.05). The EBER-positivity rate of Hodgkin lymphoma in the superficial lymph nodes was 26.3% (5/19 cases). These findings suggest that the EBV-positivity rate in lymphomas is related to their histological types and locations.

Entamoeba moshkovskii and Entamoeba dispar are impossible to differentiate microscopically from the pathogenic species Entamoeba histolytica. There are limited data on the prevalence of these commensal parasites in Iran. We utilized a single-round PCR assay to determine the prevalence of E. moshkovskii, E. dispar, and E. histolytica in stool samples from Iranian patients infected with gastrointestinal disorders. After culturing of microscopy-positive isolates and extraction of DNA, PCR was carried out to differentiate the Entamoeba isolates. Out of 3,825 stool samples examined by microscopy, 58 specimens (1.52%) were infected with E. histolytica, E. dispar, or E. moshkovskii. By PCR, 2 E. histolytica (3.45%), 53 E. dispar (91.37%), 2 E. moshkovskii (3.45%), and one mixed E. dispar/E. moshkovskii infection (1.73%) were detected. In view of the reporting of E. moshkovskii in this study in Iran and the difficulty in discriminating this ameba from two similar Entamoeba spp. by microscopy, we recommend the single-round PCR assay as an alternative tool in routine diagnosis and in epidemiological studies of amebiasis.