The purpose of this study was to investigate the use of decision tree for the classification of antimicrobial peptides. The classification was based on the activities of known antimicrobial peptides against common microbes including Escherichia coli and Staphylococcus aureus. A feature selection was employed to select an effective subset of features from available attribute sets.Sequential applications of decision tree with 17 nodes with 9 leaves and 13 nodes with 7 leaves provided the classification rates of 76.74% and 74.66% against E. coli and S. aureus, respectively. Angle subtended by positively charged face and the positive charge commonly gave higher accuracies in both E. coli and S. aureus datasets. In this study, we describe a successful application of decision tree that provides the understanding of the effects of physicochemical characteristics of peptides on bacterial membrane.
Classification* ; Dataset ; Decision Trees* ; Escherichia coli ; Membranes ; Peptides ; Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common nosocomial pathogens. In April 1997, there were five MRSA-infected patients among 16 patients in the Neonatal Intensive Care Unit (NICU), Seoul National University Hospital, which is a tertiary-care hospital with 1,500 beds. The infections had spread from twin patients with MRSA who had transferred from Hospital C. MRSA was isolated from the axilla of 15 (94%) of the 16 patients, including the two patients with obvious infections. Three (19%) of 16 doctors and nine (30%) of 30 nurses had MRSA colonization of the anterior nares. Six different PFGE patterns (A through F) were identified in the 53 isolates of MRSA tested. Twelve of 13 isolates from infected sites of five patients showed pattern F. Three MRSA strains obtained from hospital C showed closely or possibly related pattern F. MRSA of type F was isolated from three of 16 patients' axilla, and one of 3 doctors' and three of 30 nurses' nasal swabs. The antibiogram code for 12 of 13 MRSA isolates from five infected patients was 66,754. PFGE patterns of these isolates were either F, F1, F2 or Fa. Only one of three strains isolated from clinical specimens of patients in Hospital C showed the antibiogram code 66754, although they were all PFGE types F1 and Fa. In conclusion, the presumptive sources of the outbreak of MRSA infection in NICU were the twin patients transferred from hospital C. Antibiogram correlated reasonably well to the PFGE type. An effective notification system is needed when a MRSA-infected patient is transferred to another hospital to control the spread of the infection.
Bacterial Typing Techniques* ; Electrophoresis, Gel, Pulsed-Field* ; Human ; Methicillin Resistance/physiology* ; Microbial Sensitivity Tests* ; Staphylococcus aureus/physiology* ; Staphylococcus aureus/classification*

Deep infection is the most serious complication of total hip arthroplasty with difficulty to treat and occasionally results into catastrophic consequences. The treatment methods are antibiotics, incision & drainage of the hip, debridement & modified Girdlestone resection arthroplasty, one stage revision to total hip arthroplasty, two stage revision and hip disarticulation. The purpose of this report is to consider the treatment of the infected total hip arthroplasty. Since 1979, we have treated 12 cases of infected arthroplasty including 6 cases from other hopital. Duration of interval between primary hip arthroplasty and diagnosis of infection were average 42,4 months(minimum 2 months to maximum 16 years). The results were as follows; 1. The incidence rate of the infected total hip arthroplasty was 1.3%. 2. By Fitzgerald classification, 2 cases were in acute stage, 6 cases in delayed stage and 4 cases in late stage. 3. The causative organisms were coagulase negative Staphylococcus aureus in 6 cases, Staphylococcus hemolyticus in 2 cases, Pseudomonas in 1 case and negative culture in 3 cases. 4. Increased uptake on Bone Scan in all 12 cases and increased ESR ranged from 28mm/hr to 82mm/hr. 5. Our treatment methods were secondary revision to total hip arthroplasty with cement bead insertion in 4 cases, primary revision in 1 case, incision & drainage of hip in 1 case, debridement & modified Girdlestone resection arthroplasty in 2 cases and hip disarticulation in 2 cases. And the rest 2 cases have been followed up after modified Girdlestone resection arthroplasty because of the remained infection. In our experience, two stage revision to total hip arthroplasty with antibiotics mixed cement bead was more useful in the treatment of the infected total hip arthroplasty.
Anti-Bacterial Agents ; Arthroplasty ; Arthroplasty, Replacement, Hip ; Classification ; Coagulase ; Debridement ; Diagnosis ; Disarticulation ; Drainage ; Hip ; Incidence ; Pseudomonas ; Staphylococcus ; Staphylococcus aureus

Evolution, Molecular ; Methicillin Resistance ; Staphylococcus aureus ; classification ; drug effects ; genetics ; isolation & purification

Child ; Cross Infection ; microbiology ; Disease Outbreaks ; Humans ; Methicillin-Resistant Staphylococcus aureus ; classification ; drug effects ; genetics

BACKGROUND: Multiple-locus variable-number tandem-repeat fingerprinting (MLVF) is based on multiplex PCR, utilizing variable number tandem repeat. Our goal was to compare the performance of MLVF in distinguishing clinical Staphylococcus aureus isolates with that of pulsed-field gel electrophoresis (PFGE), which has traditionally been the gold standard. METHODS: Sixty-three clinically significant S. aureus isolates were tested using both PFGE and MLVF. Multiplex PCR for MLVF was performed using PCR primers for clfA, clfB, sdrCDE, sspA, and spa. PFGE was performed with genomic DNA fragments generated by SmaI endonuclease digestion. Banding patterns of MLVF or PFGE were analyzed using InfoQuestFP software. RESULTS: The hands-on time of our modified method was about 3 h, on average, for each of 18 isolates. PFGE (80% cutoff) or MLVF (75% cutoff) separated all of the 63 isolates into 13 and 12 types, respectively. Three types generated by PFGE were identical to those generated by MLVF. PFGE and MLVF yielded similar Simpson's diversity indices, indicating similar discriminatory power. The overall concordance between PFGE and MLVF was low, as represented by adjusted Rand indices (0.266-0.278). PFGE predicted MLVF type better than MLVF predicted PFGE type, as reflected by Wallace coefficients (PFGE cutoff 80% vs. MLVF cutoff 75%, 0.389 vs. 0.233). Analysis of the relationship between a pair of isolates showed 91.0% concordance between the PFGE (80% cutoff) and MLVF (75% cutoff). CONCLUSIONS: Our simple, low-cost, modified MLVF protocol can effectively discriminate between S. aureus clinical isolates. MLVF can replace PFGE for the hospital infection control of S. aureus.
Bacterial Typing Techniques/*methods ; *DNA Fingerprinting ; DNA, Bacterial/analysis ; *Electrophoresis, Gel, Pulsed-Field ; Genotype ; Humans ; Methicillin-Resistant Staphylococcus aureus/classification/genetics/isolation & purification ; Multiplex Polymerase Chain Reaction ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/*classification/*genetics/isolation & purification

Methicillin-resistant Staphylococcus aureus (MRSA) strains may cause serious nosocomial infections, including pneumonia and septicemia. The rate of methicillin-resistance among S. aureus isolates in Korea is over 50%. In this study, 90 MRSA isolates from Kyung Hee University Hospital were characterized employing bacteriophage typing, pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility testing. Eighty percent of the strains could be phage-typed. The largest group or 40% of the strains belonged to lyso group III, followed by 32% of the isolates which produced a reaction with regional additional phages. Phage type 83A was most frequently encountered, followed by phage type D11. PFGE patterns confirmed the presence of two major clusters, which comprise the isolates belonging to lyso group III and the strains that were typable with regional additional phages. The latter group also contained a number of strains that were nontypable with bacteriophages. The resistance rates to ciprofloxacin, erythromycin, tetracycline, gentamicin and clindamycin were over 94%. Strains with intermediate resistance to vancomycin strains or resistance to mupirocin were not found. In conclusion, this study demonstrates that the results of phage typing are confirmed and supplemented by PFGE data.
Bacteriophage Typing ; Electrophoresis, Gel, Pulsed-Field ; Human ; *Methicillin Resistance ; Microbial Sensitivity Tests ; Staphylococcus aureus/*classification/drug effects

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most frequent agents of hospital infections. The aim of this study was to evaluate the polymorphism of MRSA strains from our hospital by pulsed-field gel electrophoresis (PFGE) and ribotyping, and to compare effectiveness of two methods for epidemiologic investigation. METHODS: A total of 40 MRSA isolates were studied. All strains were isolated from patients from October 1990 to May 1995: 13 isolates from NS ward, 9 from GS and OS ward, 11 from medical ward, and 7 from other medical centers. All strains were analyzed and classified by ribotyping and PFGE patterns. RESULTS: Eight different ribotypes (H1-H8) and ten ribotypes (E1-E10) were seen by HindIII and EcoRI digestion. The problem was that some isolates showed discordance between classifications by HindIII and EcoRI digestion and three isolates from other medical centers had same ribotypes with that of our hospital strains. PFGE analysis revealed 19 different types (A to S). The PFGE analysis showed ward specificity, 54% of isolates from NS ward and 54% of isolates from medical ward were PFGE types D and J respectively, and 33% of isolates from GS and OS ward was H type and 33% was G type. CONCLUSIONS: PFGE was a more effective epidemiological tool for the typing of MRSA strains but a combination with ribotyping could provide more detailed strain differentiation.
Classification ; Cross Infection ; Digestion ; Electrophoresis, Gel, Pulsed-Field* ; Epidemiologic Studies* ; Humans ; Methicillin Resistance* ; Methicillin-Resistant Staphylococcus aureus* ; Ribotyping* ; Sensitivity and Specificity

OBJECTIVETo analyze multilocus sequence typing (MLST) of methicillin-resistant Staphylococcus aureus (MRSA) strains in 2000 and 2005, and get a primary knowledge of MLST Characterization of MRSA.

METHODSSequence analysis was conducted on seven allelic genes of 29 methicillin-resistant Staphylococcus aureus strains and 2 methicillin-sensitive Staphylococcus aureus (MSSA) strains and the allelic profiles were gained from internet database.

RESULTSAll 12 MRSA strains in 2000 were sequence type (ST) 239 and 10 MRSA strains in 2005 were ST239, while 7 MRSA strains in 2005 were new types, ST5 (41.18%, 7/17). ST6 and ST630 were allelic profiles of 2 MSSA strains. ST239 was the most prevalent allelic profile (75.86%, 22/29), while ST5 was the second prevalent allelic profile (24.14%, 7/29) among all isolates.

CONCLUSIONST239 and ST5 are the most prevalent MRSA clones in this research. MRSA strains have different allelic profile from MSSA strains. MLST might provide an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the internet. Further studies need to be taken by increasing strains.

BACKGROUND: Methicillin-resistant Staphylococcus aureus(MRSA) is an increasingly common cause of nosocomial infections worldwide. Epidemiologic investigation of MRSA outbreaks and identification of pathways of nosocomial MRSA spread require the ability to distinguish individual MRSA strains. We applied molecular tap ing of the methicillin-resistant determinant (mec) and coagulase typing in the investigation of a nosocomial MRSA infections. METHODS: We randomly selected 79 strains of mecA positive MRSA isolated from patients who visited Dong-A university Hospital from Dec. 1995 to Oct. 1996. Molecular typing of MRSA was performed by comparing the size of the mac-associated hypervariable region amplified by the polymerase chain reaction (PCR). Coagulase typing with type I-VIII antisera was also used for classification of MRSA based on its phenotype. Each isolates were classified by the combination of molecular analyses and coagulase type. RESULTS: The 79 MRSA isolates were grouped Into sin hypervariable legion (HVR) genotypes on the basis of the size of the PGR products. In coagulase typing, the most predominant type was II(46.8%) and type V was not found. Nine strains were not typable. The combination of HVR genotypes and coagulase types showed 23 different types in 79 MRSA Isolates. The strains which were repeatedly isolated from the same patients showed the same HYR genotypes and coagulate types. CONCLUSION: The combination of HVR genotypes and coagulase types is thought to be useful in epidemiolgical Investigation of nosocomial infections caused by MRSA ,because of its simplicity and reproducibility.
Classification ; Coagulase* ; Cross Infection* ; Disease Outbreaks ; Genotype ; Humans ; Immune Sera ; Methicillin Resistance* ; Methicillin-Resistant Staphylococcus aureus* ; Molecular Typing* ; Phenotype ; Polymerase Chain Reaction ; Staphylococcus