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1.  DNA fingerprinting of Shiga-toxin producing Escherichia coli O157 based on Multiple-Locus Variable-Number Tandem-Repeats Analysis (MLVA) 
Background
The ability to react early to possible outbreaks of Escherichia coli O157:H7 and to trace possible sources relies on the availability of highly discriminatory and reliable techniques. The development of methods that are fast and has the potential for complete automation is needed for this important pathogen.
Methods
In all 73 isolates of shiga-toxin producing E. coli O157 (STEC) were used in this study. The two available fully sequenced STEC genomes were scanned for tandem repeated stretches of DNA, which were evaluated as polymorphic markers for isolate identification.
Results
The 73 E. coli isolates displayed 47 distinct patterns and the MLVA assay was capable of high discrimination between the E. coli O157 strains. The assay was fast and all the steps can be automated.
Conclusion
The findings demonstrate a novel high discriminatory molecular typing method for the important pathogen E. coli O157 that is fast, robust and offers many advantages compared to current methods.
doi:10.1186/1476-0711-2-12
PMCID: PMC317353  PMID: 14664722
VNTR fingerprinting; Escherichia coli; STEC; capillary electrophoresis; PFGE; AFLP
2.  Mutations in the 23S rRNA gene are associated with clarithromycin resistance in Helicobacter pylori isolates in Brazil 
Background
Resistance of Helicobacter pylori to clarithromycin has been associated with A2142G and A2143G point mutations in the 23S rRNA gene. Thus, the purpose of the present study was to determine the prevalence of each mutation in 52 clarithromycin-resistant H. pylori strains and to characterize the influence each type of mutation on the MIC.
Methods
The MIC for clarithromycin was determined by the agar dilution method, and the point mutations of H. pylori were detected by PCR followed by restriction fragment length polymorphism.
Results
Clarithromycin MICs ranged from 2 to >256 microgram ml-1 among the 52 strains included in this study. Both the A2142G and the A2143G mutations were present in 94.2% of clarithromycin-resistant H. pylori strains examined. A relationship was observed between the presence of the A2142G mutation and the highest MIC values (p = 0.01).
Conclusion
In an H. pylori-infected population, the A2142G mutation may incur to a greater probability of treatment failure if clarithromycin is used.
doi:10.1186/1476-0711-2-11
PMCID: PMC305369  PMID: 14633281
3.  Comparison of the accelerated and classic vaccination schedules against Hepatitis B: three-week Hepatitis B vaccination schedule provides immediate and protective immunity 
Background
Hepatitis B virus infection although preventable by vaccination remains an important health issue throughout the world due to its morbidity, mortality and economical losses. Early seroprotection is desirable for people at high risk of exposure. The aim of this study was to determine whether three-week hepatitis B vaccination (on days 0, 10 and 21) provide seroprotection or not.
Methods
The 120 subjects enrolled into the study were divided into two groups and vaccinated by the classic (months 0, 1, and 2) or the accelerated (days 0, 10, and 21) schedules and antibody response determined on days 30, 60, and 90 and, if below 10 mIU/ml-1, again on day 180. For each individual in the classic group (B) three subjects were enrolled in the accelerated group (A). Recombinant hepatitis B vaccine (Gen-Hevac B, Pasteur) was given as 20 micrograms intramuscular injections via the deltoid muscle. A booster dose on day 365 was administered for each group. Family members of hepatitis B carriers and volunteer health personnel were enrolled into group A. To the B group only volunteers who wanted vaccination against hepatitis B were included.
Results
After three doses of vaccine, Anti-HBs titers reached protective levels in both groups. The number of vaccinees with seroprotective levels of Anti-HBs (≥10 mIU/ml-1) on day 30 was 53 (58.9%) in group A and 9 (30.0%) in group B (p < 0.05). On day 60, there was no difference between group A and B, with response rates of 84.4% (n = 76) and 80.0% (n = 24) respectively (p > 0.05). On day 90 there was no difference between group B and group A; with 26 (86.7%) and 79 (87.7%) responders respectively. In both groups those with Anti-HBs levels <10 mIU/ml-1 attained protective levels by day 180.
Conclusion
In this study, the three-week vaccination provided protective antibody titers within a shorter time compared to the classic schedule. Therefore, in order to provide rapid antibody production against hepatitis B virus, the accelerated vaccination schedule seems to be a good preference.
doi:10.1186/1476-0711-2-10
PMCID: PMC293476  PMID: 14622443
Hepatitis B; vaccination; accelerated schedule
4.  Recurrent pneumococcal meningitis in a splenectomised HIV-infected patient 
Background
Streptococcus pneumoniae is a major cause of human disease, especially in pre-school children and elderly people, as well as in special risk groups such as asplenic, antibody deficient patients, or presenting disruption of natural barriers. The occurrence of pneumococcal disease has increased with the onset of the HIV epidemic and the emergence of drug-resistance.
Case presentation
We report the case of an HIV-1-infected patient who experienced three episodes of recurrent pneumococcal meningitis over a 4-year period, despite chemoprophylaxis and capsular vaccination.
Conclusions
Efficacy of anti-pneumococcal chemoprophylaxis and vaccination in HIV-infected patients are discussed in the light of this particular case.
doi:10.1186/1476-0711-2-9
PMCID: PMC521196  PMID: 14613586
5.  Performance of CHROMAGAR candida and BIGGY agar for identification of yeast species 
Background
The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species.
Methods
A total number of 270 yeast strains including 169 Candida albicans, 33 C. tropicalis, 24 C. glabrata, 18 C. parapsilosis, 12 C. krusei, 5 Trichosporon spp., 4 C. kefyr, 2 C. lusitaniae, 1 Saccharomyces cerevisiae and 1 Geotrichum candidum were included. The strains were first identified by germ tube test, morphological characteristics on cornmeal tween 80 agar and Vitek 32 and API 20 C AUX systems. In parallel, they were also streaked onto CHROMagar Candida and bismuth sulphite glucose glycine yeast agar plates. The results were read according to the color, morphology of the colonies and the existance of halo around them after 48 hours of incubation at 37°C.
Results
The sensitivity and specificity values for C. albicans strains were found to be 99.4, 100% for CHROMagar Candida and 87.0, 75.2% for BiGGY agar, respectively. The sensitivity of CHROMagar Candida to identify C. tropicalis, C. glabrata and C. krusei ranged between 90.9 and 100% while the specificity was 100%. The sensitivity rates for BiGGY agar were 66.6 and 100% while the specificity values were found to be 95.4 and 100% for C. tropicalis and C. krusei, respectively.
Conclusions
It can be concluded that the use of CHROMagar Candida is an easy and reliable method for the presumptive identification of most commonly isolated Candida species especially C. albicans, C. tropicalis and C. krusei. The lower sensitivity and specificity of BiGGY agar to identify commonly isolated Candida species potentially limits the clinical usefulness of this agar.
doi:10.1186/1476-0711-2-8
PMCID: PMC280667  PMID: 14613587
6.  Prescribing patterns of antibiotics and sensitivity patterns of common microorganisms in the Internal Medicine ward of a teaching hospital in Western Nepal: a prospective study 
Background
Information about antibiotic use and resistance patterns of common microorganisms are lacking in hospitals in Western Nepal. Excessive and inappropriate use of antibiotics contributes to the development of bacterial resistance. The parameter: Defined daily dose/100 bed-days, provides an estimate of consumption of drugs among hospital in-patients. This study was carried out to collect relevant demographic information, antibiotic prescribing patterns and the common organisms isolated including their antibiotic sensitivity patterns.
Methods
The study was carried out over a 3-month period (01.04.2002 to 30.06.2002) at the Manipal Teaching Hospital, Western Nepal. The median number of days of hospitalization and mean ± SD cost of antibiotics prescribed during hospital stay were calculated. The use of antibiotics was classified for prophylaxis, bacteriologically proven infection or non-bacteriologically proven infection. Sensitivity patterns of the common organisms were determined. Defined daily dose/100 bed-days of the ten most commonly prescribed antibiotics were calculated.
Results
203 patients were prescribed antibiotics; 112 were male. Median duration of hospitalization was 5 days. 347 antibiotics were prescribed. The most common were ampicillin, amoxicillin, metronidazole, ciprofloxacin and benzylpenicillin. Mean ± SD cost of antibiotics was 16.5 ± 13.4 US$. Culture and sensitivity testing was carried out in 141 patients. The common organisms isolated were H. influenzae, E. coli, K. pneumoniae and S. aureus.
Conclusions
Antibiotic resistance is becoming a problem in the Internal Medicine ward. Formulation of a policy for hospital antibiotic use and an educational programme especially for junior doctors is required.
doi:10.1186/1476-0711-2-7
PMCID: PMC179888  PMID: 12904265
Antibiotics; Drug utilization; Internal Medicine ward
7.  Multifocal tuberculosis presenting with osteoarticular and breast involvement 
Background
Polyarticular involvement, wrist and ankle arthritis are uncommon presentation of skeletal tuberculosis. Tuberculosis of the breast is also extremely rare.
Case Presentation
Wrist, ankle and breast involvement were detected in the same patient. Mycobacterium tuberculosis was isolated from both synovial and breast biopsy specimen cultures.
Conclusions
In general, tuberculosis arthritis is a frequently missed diagnosis, especially in different clinical patterns. A high level of suspicion is required particularly in high-risk populations and endemic areas.
doi:10.1186/1476-0711-2-6
PMCID: PMC153487  PMID: 12685934
8.  Retrospective analysis of antibiotic susceptibility patterns of respiratory isolates of Pseudomonas aeruginosa in a Turkish University Hospital 
Background
Lower respiratory tract infections due to Pseudomonas aeruginosa have a high mortality rate. Antibacterial activity of various antibiotics against P. aeruginosa isolated from each hospital depends on the variety or amount of antibiotics used in each hospital.
Method
A total of 249 respiratory isolates of Pseudomonas aeruginosa in Sivas (Turkey) were included between January-1999 and January-2002. Isolates were tested against 14 different antibiotics by a disc diffusion method or standardized microdilution technique.
Results
Organisms were cultured from the following specimens: sputum (31.3%), transtracheal/endotracheal aspirates (37.8%), and bronchial lavage (30.9%). Isolates in bronchial lavage were highly susceptible to cefoperazone and aminoglycosides. Resistance to ampicillin/sulbactam was 98.8%, ticarcillin 40.1%, ticarcillin/clavulanic acid 11.2%, piperacillin 21.8%, aztreonam 66.6%, cefotaxim 75.4%, ceftriaxone 84.2%, cefoperazone 39.0%, ceftazidime 50.8%, gentamicin 57.5%, tobramycin 58.4%, amikacin 25.4%, ciprofloxacin 16.1%, and imipenem/cilastatin 21.6%. The term multidrug-resistant P. aeruginosa covered resistance to imipenem, ciprofloxacin, ceftazidime, gentamicin, and piperacillin. 1.2% of isolates were multidrug-resistant.
Conclusions
These findings suggest that amikacin resistance increases progressively in Turkey. Piperacillin and ticarcillin/clavulanate were the most active agents against both imipenem- and ciprofloxacin-resistant isolates in our region.
doi:10.1186/1476-0711-2-5
PMCID: PMC152644  PMID: 12665428
9.  Prevalence of genotypic HIV-1 drug resistance in Thailand, 2002 
Background
The prices of reverse transcriptase (RT) inhibitors in Thailand have been reduced since December 1, 2001. It is expected that reduction in the price of these inhibitors may influence the drug resistance mutation pattern of HIV-1 among infected people. This study reports the frequency of HIV-1 genetic mutation associated with drug resistance in antiretroviral-treated patients from Thailand.
Methods
Genotypic resistance testing was performed on samples collected in 2002 from 88 HIV-1 infected individuals. Automated DNA sequencing was used to genotype the HIV-1 polymerase gene isolated from patients' plasma.
Results
Resistance to protease inhibitors, nucleoside and non-nucleoside reverse transcriptase inhibitors were found in 10 (12%), 42 (48%) and 19 (21%) patients, respectively. The most common drug resistance mutations in the protease gene were at codon 82 (8%), 90 (7%) and 54 (6%), whereas resistant mutations at codon 215 (45%), 67 (40%), 41 (38%) and 184 (27%) were commonly found in the RT gene. This finding indicates that genotypic resistance to nucleoside reverse transcriptase inhibitors was prevalent in 2002. The frequency of resistant mutations corresponding to non-nucleoside reverse transcriptase inhibitors was three times higher-, while resistant mutation corresponding to protease inhibitors was two times lower than those frequencies determined in 2001.
Conclusion
This study shows that the frequencies of RT inhibitor resistance mutations have been increased after the reduction in the price of RT inhibitors since December 2001. We believe that this was an important factor that influenced the mutation patterns of HIV-1 protease and RT genes in Thailand.
doi:10.1186/1476-0711-2-4
PMCID: PMC153426  PMID: 12657161
10.  Central venous catheter related infections: Risk factors and the effect of glycopeptide antibiotics 
Backround
We undertook a prospective study of all new central venous catheters inserted into patients in the intensive care units, in order to identify the risk factors and to determine the effect of glycopeptide antibiotics on catheter – related infections.
Methods
During the study period 300 patients with central venous catheters were prospectively studied. The catheters used were nontunneled, noncuffed, triple lumen and made of polyurethane material. Catheters were cultured by semiquantitative method and blood cultures done when indicated. Data were obtained on patient age, gender, unit, primary diagnosis on admission, catheter insertion site, duration of catheterization, whether it was the first or a subsequent catheter and glycopeptide antibiotic usage.
Results
Ninety-one (30.3%) of the catheters were colonized and infection was found with 50 (16.7%) catheters. Infection was diagnosed with higher rate in catheters inserted via jugular vein in comparison with subclavian vein (95% CI: 1.32–4.81, p = 0.005). The incidence of infection was higher in catheters which were kept in place for more than seven days (95% CI 1.05–3.87, p = 0.03). The incidence of infection was lower in patients who were using glycopeptide antibiotic during catheterization (95% CI: 1.49–5.51, p = 0.005). The rate of infection with Gram positive cocci was significantly lower in glycopeptide antibiotic using patients (p = 0.01). The most commonly isolated organism was Staphylococcus aureus (n = 52, 37.1%).
Conclusion
Duration of catheterization and catheter insertion site were independent risk factors for catheter related infection. Use of glycopeptide antibiotic during catheterization seems to have protective effect against catheter related infection.
doi:10.1186/1476-0711-2-3
PMCID: PMC151687  PMID: 12643811
Central venous catheter; infection; risk; glycopeptide
11.  Arthritis and Osteomyelitis due to Aspergillus fumigatus: A 17 years old boy with chronic granulomatous disease 
Background
Invasive Aspergillus infections are frequently seen in immunocompromised patients but arthritis is a rare complication of Aspergillus infections in the absence of immune suppressive therapy, trauma or surgical intervention.
Case presentation
A 17 years old male patient with arthritis and patellar osteomyelitis of the left knee whose further investigations revealed chronic granulomatous disease as the underlying disease is followed. Aspergillus fumigatus was isolated from the synovial fluid and the tissue samples cultures. He was treated with Amphotericin B deoxicolate 0.7 mg/kg/day. Also surgical debridement was performed our patient. Amphotericin B nephrotoxicity developed and the therapy switched to itraconazole 400 mg/day. Itraconazole therapy were discontinued at the 6th month. He can perform all the activities of daily living including.
Conclusion
We think that, chronic granulomatous disease should be investigated in patients who have aspergillar arthritis and osteomyelitis.
doi:10.1186/1476-0711-2-2
PMCID: PMC150380  PMID: 12605719
12.  Hypersensitivity vasculitis induced by cefoperazone/sulbactam 
Background
Cefoperazone has not been reported to cause vasculitic complications before. Here, we report a case of hypersensitivity vasculitis associated with cefoperazone/sulbactam.
Case presentation
A 13-year-old girl with appendicitis developed hypersensitivity vasculitis on the fifth day of cefoperazone/sulbactam therapy. Hypersensitivity vasculitis resolved gradually after removal of the agent on the seventh day and did not recur. Although hypersensitivity vasculitis has multiple causes, coexistence of hypersensitivity vasculitis and cefoperazone treatment, and the quite resolution of the disease after removal of the drug, strongly favours a causative relationship.
Conclusion
To our knowledge, this is the first report of a hypersensitivity vasculitis associated with cefoperazone.
doi:10.1186/1476-0711-2-1
PMCID: PMC149382  PMID: 12556245
Hypersensitivity vasculitis; cefoperazone

Results 1-12 (12)