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PubMed2003

Chronic granulomatous pleuritis caused by nocardia: PCR based diagnosis by nocardial 16S rDNA in pathological specimens.

Nocardiosis is an uncommon infection caused by the aerobic actinomycete nocardia. Identification of the pathogen is essential for the definitive diagnosis and for an effective treatment. This report describes a case of chronic granulomatous pleuritis caused by nocardia. A 59 year old Japanese man had a history of repeated pyothorax. Right pleural decortication and thoracic drainage were performed. Microbiological examinations of the drained fluid failed to identify a pathogen. Pathological examinations revealed Gram positive filamentous and branching bacilli in the granulomatous lesion of the pleura. Sequencing of the 971 bp 16S ribosomal DNA extracted and amplified from paraffin wax embedded sections identified the microorganism as Nocardia sp. IFM 0860. The patient received sulfamethoxazol/trimethoprim and minocycline. Although the presence of a brain abscess was disclosed by systemic examination, the clinical course has been favourable. In this patient, polymerase chain reaction analysis of 16S ribosomal DNA in pathological specimens was useful in making an accurate diagnosis of nocardiosis and in determining the appropriate treatment.

DNA, Bacterial↗

PubMed2006

The prevalence of proline iminopeptidase negative Neisseria gonorrhoeae throughout England and Wales.

BACKGROUND: The accurate laboratory identification of Neisseria gonorrhoeae is an essential element of the diagnosis of gonorrhoea and is particularly important for medicolegal cases. The detection of proline iminopeptidase (Pip) activity is widely used as a marker for gonococci, although Pip negative N gonorrhoeae isolates have been shown to generate false negative identifications when using biochemical kits. This study aimed to determine the frequency of Pip negative gonococci in England and Wales. METHODS: A total of 2055 isolates were collected from consecutive patients attending 26 genitourinary medicine centres as part of the Gonococcal Resistance to Antimicrobials Surveillance Programme (GRASP). Upon receipt the identity of all isolates was confirmed using N gonorrhoeae specific monoclonal antibodies and the Pip status was determined using the Gonochek II kit. RESULTS: The overall prevalence of Pip negative isolates was found to be 4.33%. Significant geographical variation was observed between isolates from centres outside London (p< or =0.001). Variation was also observed within London between the nine different clinics submitting isolates (p = 0.025). There was also a higher frequency of these isolates among men who have sex with men (p< or =0.001), which may account for geographical variations. CONCLUSION: Pip negative N gonorrhoeae isolates are a very serious cause for concern as currently all biochemical test kits available within the United Kingdom require the presence of the Pip enzyme for an unambiguous identification of this pathogen. Raising awareness of the current prevalence of Pip negative N gonorrhoeae isolates is critical for the successful control of gonorrhoea.

Aminopeptidases↗

PubMed1981

Ophthalmia neonatorum due to Branhamella (Neisseria) catarrhalis. Case reports.

In two cases of conjunctivitis in neonates Branhamella (Neisseria) catarrhalis was identified as the causative organism. A misdiagnosis of gonococcal ophthalmia neonatorum would have been made in both cases if the diagnosis had been based on morphological grounds alone. Thus, full identification of the pathogen in cases of neonatal conjunctivitis is important to avoid the medical and social consequences of a misdiagnosis of gonorrhoea.

Bacterial Infections↗

PubMed2002

Development of oligonucleotide primers for the specific PCR-based detection of the most frequent Enterobacteriaceae species DNA using wec gene templates.

Oligonucleotide primers were designed for the PCR-based detection of the wec gene cluster involved in the biosynthetic pathway leading to the production of enterobacterial common antigen (ECA). Escherichia coli DNA was detected using wec A, wec E, and wec F gene primers. The wec A primers were specific for E. coli. The wec E and wec F primers enabled the detection of the most frequent species of the Enterobacteriaceae found in blood and urine specimens as well as in water. The sensitivity of the assay was approximately 1.2 x 102 bacteria/mL of water. Thus, these primers represent an important step in the molecular diagnosis of major Enterobacteriaceae infections. Their role in the routine testing of contamination in drinking water and food may prove to be very useful. The DNA of Enterobacteriaceae species is detected in a first step PCR, followed by specific identification of important pathogens like E. coli O157, Shigella spp., Salmonella spp., and Yersinia spp.

Blood↗

PubMed1998

Cypress canker: a pandemic in progress.

Over the past 70 years a destructive blight of Cupressus macrocarpa and other Cupressaceae, caused by Seiridium cardinale, has spread worldwide from California, devastating forests, plantations, and ornamental cypresses. The epidemic has been particularly severe in the Mediterranean region, on C. sempervirens. A similar destructive blight induced by Lepteutypa cupressi, which caused serious losses to Monterey cypresses in East Africa in the 1940s, has now also spread to distant continents, albeit to a lesser extent. There is yet a third wave of canker disease induced by S. unicorne, although this is a milder type. This review deals with problems related to identification of the pathogens, their taxonomy, pathogenesis and role of fungal toxins, and early screening of cypress clones or hybrids for resistance to the pathogens and tolerance to their toxins.

Journal Article↗

PubMed2001

Diagnostic yield of CT-guided percutaneous aspiration procedures in suspected spontaneous infectious diskitis.

PURPOSE: To evaluate the diagnostic yield of computed tomography (CT)-guided percutaneous needle aspiration procedures in the setting of suspected spontaneous infectious diskitis and to assess the usefulness of concurrent cytologic examination as a supplement to microbiologic evaluation. MATERIALS AND METHODS: A retrospective study was performed to evaluate 105 consecutive CT-guided percutaneous disk space aspiration procedures in 92 patients suspected of having spontaneous (non-postoperative) infectious diskitis. Our criterion standard for the presence of active infection was the identification of a pathogen either from the CT-guided aspiration specimen or from a surgical specimen. All cases had microbiologic analysis, 78 cases had cytopathologic analysis, and 31 cases had open surgery. RESULTS: Microbiologic analysis of the CT-guided percutaneous aspiration specimens was positive in 39 of 43 cases proved to have active infections, with four false-negative and no false-positive cases (sensitivity, 91%; specificity, 100%). The false-negative cases were all active fungal infections identified from surgical specimens. Adding cytopathologic analysis to microbiologic analysis improved sensitivity but reduced specificity. The most common pathogens were species of Staphylococcus, Streptococcus, Candida, and Mycobacterium. All 30 active bacterial infections were identified with the CT-guided procedures, but only five of nine fungal infections were identified. CONCLUSION: CT-guided percutaneous needle aspiration is an accurate method for identifying active bacterial disk space infections but is less reliable for identifying fungal infections.

Adolescent↗

PubMed2004

Evaluation on the use of beta-lactamase and aminoglycoside modifying enzyme gene sequences as markers for the early detection of antibiotic resistance profile of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is one of the major causes of infections including the hospital acquired (Nosocomial) infections. Detection of them and their antibiotic resistance profile by conventional method takes about three days. Recently, DNA based diagnostic methods are being used for the identification of the pathogens. Hence we have tested a rapid and sensitive method using DNA sequences as markers for detecting the presence of three genes coding for the enzymes that inactivate the two most commonly used Anti-pseudomonadal drugs such as beta-lactam antibiotics (Penicillin, and its derivatives) and Aminoglycosides such as Gentamicin, Tobramycin, Amikacin, Streptomycin. The internal region of these genes were used for designing and synthesizing primers and these primers were used in Polymerase Chain Reaction (PCR) to screen for the presence of these genes in the clinical isolates and to label them non-radioactively with Biotin. They in turn were used to detect the presence of the antibiotic resistance genes in the clinical isolates by hybridization. The specificity (ratio of positive results obtained in both methods and the sensitivity (the minimum amount of sample DNA and the labeled probe required for the tests) were evaluated.

Amikacin↗

PubMed2001

[Hereditary colorectal carcinomas - reflection on preventive surgery].

Nonpolyposis Colorectal Cancer (HNPCC) accounts for about 5% of all colorectal cancers and is the most frequent familial form; familial adenomatous polyposis coli accounts for about 1%. Prerequisitive for individually tailored surveillance is the identification of the pathogenic germline mutation. In classical FAP, surgical standard is a restorative proctocolectomy while in HNPCC there is no surgical standard other than standard oncological resection due to missing evidence. In HNPCC, prophylactic colectomy before the onset of the first colorectal cancer is not recommended. Main arguments for the extension of the resection in the case of the first colorectal carcinoma in HNPCC are the rate of metachronous colorectal carcinomas of 40-45% in a 10-year interval and rapid tumor progression. In HNPCC, in the case of first colon cancer a subtotal colectomy seems to be indicated. A proctocolectomy or, if indicated, a restorative proctocolectomy may be considered in the case of carcinomas in the lower rectum. These considerations should be evaluated in a prospective clinical trial. Counselling, molecular diagnosis and surgery in patients with hereditary colorectal cancers should only be performed in interdisciplinary centers.

Adenomatous Polyposis Coli↗

PubMed1995

Simultaneous detection of Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis by a rapid PCR method.

The identification of periodontal pathogens by conventional methods is time-consuming and difficult. Therefore, a multiplex PCR method for simultaneous detection of Actinobacillus actinomycetemcomitans (A.a.) and Porphyromonas gingivalis (P.g.) was developed for rapid and easy determination of these risk-indicator bacteria in human periodontal disease. The PCR primers were designed to hybridize to various regions of 16S rRNA genes, and a hot-start technique was used to obtain maximum sensitivity and specificity. This method can detect both of these bacteria in subgingival plaque samples at concentrations as low as 5 to 50 cells per sample. The sensitivity, however, was even 10 times better when the bacteria were analyzed in a water suspension. Since the only step between sample collection and the actual analysis is a brief centrifugation of the patient sample, the detection can be readily carried out in four hours. The performance of the method was studied with 36 patient samples. The results showed that the PCR method detected A.a. (44% vs. 25%, respectively) and P.g. (56% vs. 42%, respectively) more often than the conventional culture in plaque samples. Thus, our multiplex PCR method is rapid and more effective than conventional protocols in detecting these periodontal pathogens.

Aggregatibacter actinomycetemcomitans↗

PubMed1996

Management of otitis media with effusion in young children.

OBJECTIVE: To summarize and critique the Agency for Health Care Policy and Research (AHCPR) Clinical Practice Guideline for the management of otitis media with effusion (OME) in children. DATA SOURCES: The AHCPR Clinical Practice Guideline, Otitis Media with Effusion in Young Children; the Quick Reference Guide for Clinicians, Managing Otitis Media with Effusion in Young Children; and the Parent Guide, Middle Ear Fluid in Young Children, were the primary data sources. The AHCPR developed the Guideline based on a comprehensive literature review from multiple bibliographic databases, including the National Library of Medicine. Data were also collected during open hearings and from unpublished sources derived from a call in the Federal Register. Additional citations from the biomedical literature were used for supporting evidence. STUDY SELECTION: Peer-reviewed reports of controlled, randomized studies were preferred, but other study designs were considered. Over 3000 abstracts were identified, of which 378 articles were used for data extraction, and an additional 100 articles were included from bibliography review and panel recommendations. An expert panel reviewed the data and incorporated clinical expertise into the development of consensus statements. DATA EXTRACTION: Data were extracted to apply to a base case with OME to narrow the scope of the Guideline. The base case was defined as a child who is 1-3 years old, is otherwise healthy, and has no underlying craniofacial, neurologic, or sensory conditions. Multiple meta-analyses were done to help the panel come to conclusions on several issues. DATA SYNTHESIS: The Guideline documents carefully outlined treatment algorithms for the management of OME in otherwise healthy children. The main areas that need to be further clarified are the role of more aggressive identification of causative pathogens, when antimicrobial therapy should be initiated, and which antimicrobial agents are preferred for the treatment of OME. There are many vague areas in the Guideline that allow for multiple interpretations. Data regarding the use of corticosteroids were influenced heavily by the expert opinion of the panel rather than the literature-based evidence and potential cost implications. The Guideline provided specific recommendations for the surgical management of OME. Confounding patient factors that would affect decisions on management of OME, such as underlying disease states and physical or mental abnormalities, were not addressed in the Guideline. CONCLUSIONS: The documents were well organized and provide detailed explanation of the recommendations. The Guideline provides specific criteria for the surgical management of OME, but is vague in its recommendations on the medical management of OME with antibiotics, corticosteroids, and the use of invasive tympanocentesis in the evaluation of OME in otherwise healthy children.

Anti-Bacterial Agents↗

PubMed2006

Prevalences of Pneumocystis jiroveci, Mycobacterium tuberculosis and Streptococcus pneumoniae infection in children with severe pneumonia, in a tertiary referral hospital in northern Tanzania.

At the Kilimanjaro Christian Medical Centre, a tertiary referral hospital in northern Tanzania, both the number of paediatric cases of lower respiratory-tract infection (LRTI) and the associated mortality increased between 2000 and 2001. Molecular diagnostic tools were used to enhance the identification of the pathogens responsible for this perceived increase. All 72 children aged between 2 and 60 months who were admitted with LRTI over a 3-month period were enrolled in the study. Induced sputum was collected from each child and, if the parents consented, the subjects were also tested for HIV. The sputum samples were each checked for bacteria by culture and, in amplification assays, for the DNA of Pneumocystis jiroveci, Mycobacterium tuberculosis and Streptococcus pneumoniae. Twenty-two (50%) of the 44 children tested for HIV had HIV-1 antibodies. Although only two children, both aged <6 months, were found PCR-positive for P. jiroveci, and only one was found positive for M. tuberculosis, 46 (including one of those found positive for P. jiroveci and the child found positive for M. tuberculosis) were found PCR-positive for S. pneumoniae. It therefore appears that most paediatric cases of LRTI who present at the hospital are attributable to S. pneumoniae, and that infections with this pathogen are entirely responsible for the observed increase in the incidence of LTRI in the local children. The increase seen in LRTI-associated mortality among the children may be the result of pneumococcal antibiotic resistance.

Anti-Bacterial Agents↗

PubMed2005

Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing.

BACKGROUND: Precise identification of bacterial pathogens at the strain level is essential for epidemiological purposes. In Streptococcus pneumoniae, the existence of 90 different serotypes makes the typing particularly difficult and requires the use of highly informative tools. Available methods are relatively expensive and cannot be used for large-scale or routine typing of any new isolate. We explore here the potential of MLVA (Multiple Loci VNTR Analysis; VNTR, Variable Number of Tandem Repeats), a method of growing importance in the field of molecular epidemiology, for genotyping of Streptococcus pneumoniae. RESULTS: Available genome sequences were searched for polymorphic tandem repeats. The loci identified were typed across a collection of 56 diverse isolates and including a group of serotype 1 isolates from Africa. Eventually a set of 16 VNTRs was proposed for MLVA-typing of S. pneumoniae. These robust markers were sufficient to discriminate 49 genotypes and to aggregate strains on the basis of the serotype and geographical origin, although some exceptions were found. Such exceptions may reflect serotype switching or horizontal transfer of genetic material. CONCLUSION: We describe a simple PCR-based MLVA genotyping scheme for S. pneumoniae which may prove to be a powerful complement to existing tools for epidemiological studies. Using this technique we uncovered a clonal population of strains, responsible for infections in Burkina Faso. We believe that the proposed MLVA typing scheme can become a standard for epidemiological studies of S. pneumoniae.

Bacterial Typing Techniques↗

PubMed2003

New sinus culture applicator (Yariktas applicator).

Identification of the pathogen is crucial for the selection of an appropriate antibiotic in the management of sinusitis. We describe an original instrument that provides contamination-free culture from the sinus in endoscopic sinus surgery.

Humans↗

PubMed1997

Salmonella lung involvement in patients with HIV infection.

STUDY OBJECTIVE: To determine the frequency, clinical features, and outcome of lung involvement in HIV-infected patients having nontyphoid strains of Salmonella bacteremia. DESIGN: A retrospective clinical study. PATIENTS AND SETTING: We studied the records of all HIV-infected patients with Salmonella bacteremia diagnosed at a university tertiary hospital from January 1987 to December 1995. RESULTS: Lung involvement was found in 18 (35.3%) of 51 HIV-infected individuals with Salmonella bacteremia. Six of 18 (33.3%) were diagnosed as having definite Salmonella pulmonary infection by isolation of Salmonella from respiratory specimens, while probable Salmonella lung disease was considered in two patients who developed lung abscesses without the identification of any pathogen. Predisposing factors for focal disease, such as prior lung disease or Salmonella serotype, were equally prevalent regardless of the presence of Salmonella pulmonary involvement. Cavitary infiltrates or abscess formation were seen in five of the eight patients. With the exception of one patient coinfected with Nocardia asteroides who died 1 month later, all patients were cured with antibiotic treatment. Superinfection with other pulmonary pathogens (10 cases, 56%) was more frequent than Salmonella pneumonia; the most frequent alternative diagnosis was Pneumocystis carinii pneumonia (5 cases, 28%), pyogenic bacterial infection (17%), and tuberculosis (11%). CONCLUSIONS: In HIV-infected patients with Salmonella bacteremia, lung involvement is frequent, although there were no significant factors to explain this association. Cavitary disease was the most common radiologic pattern, and focal lung disease due to Salmonella does not seem to be associated with a worse prognosis. Coinfection and superinfection with other respiratory pathogens are more common than isolated Salmonella lung disease, and therefore, additional diagnostic procedures must be considered in the evaluation of these patients.

AIDS-Related Opportunistic Infections↗

PubMed2006

A review of current and future molecular diagnostic tests for use in the microbiology laboratory.

Nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratories. Similar to conventional tests, the first-generation deoxyribonucleic acid assays determined only a single analyte. Recent improvements in detection technologies have paved the way for the development of multiparameter assays using macroarrays or micro-arrays, while the introduction of closed-tube real-time polymerase chain reaction systems has resulted in the development of rapid microbial diagnostics with a reduced contamination risk. The use of these new molecular technologies is not restricted to detection and identification of microbial pathogens but also can be used for genotyping, allowing one to determine antibiotic resistance or to perform microbial fingerprinting.

Bacteria↗

PubMed2004

Griseofulvin versus terbinafine in the treatment of tinea capitis: a meta-analysis of randomized, clinical trials.

OBJECTIVE: Tinea capitis, a common pediatric infection in the United States, is caused mainly by Trichophyton species and affects many urban children. Although the current treatment of choice is oral griseofulvin, terbinafine has been shown to be variably effective in several comparative, randomized trials. The purpose of this study was to perform a meta-analysis of randomized, clinical trials comparing the efficacies of oral terbinafine and oral griseofulvin for the treatment of childhood tinea capitis. METHODS: The Medline database was searched for randomized, clinical studies comparing griseofulvin and terbinafine for the treatment of tinea capitis. Acceptance criteria included oral administration of griseofulvin for at least 6 weeks and the identification of a pathogenic dermatophyte from the scalp at the time of enrollment in the study. Scalp culture status at least 8 weeks after enrollment was used as the outcome. The common odds ratio (OR) with 95% confidence intervals (CIs), the Cochran-Mantel-Haenszel test for significance, and the Breslow-Day test for homogeneity were calculated. RESULTS: Six articles that satisfied all inclusion criteria were identified. These studies were combined by using outcomes at 12 to 16 weeks after enrollment. The common OR was 0.86 (95% CI: 0.57-1.27). When the 5 studies that identified Trichophyton species as the predominant pathogen were combined, using outcomes 12 weeks after enrollment, the results nearly favored terbinafine (OR: 0.65 [95% CI: 0.42-1.01]). For outcomes at 8 weeks after enrollment, no difference was found between the agents (OR: 0.84 [95% CI: 0.54-1.32]). Consclusions.A 2- to 4-week course of terbinafine is at least as effective as a 6- to 8-week course of griseofulvin for the treatment of Trichophyton infections of the scalp. Griseofulvin is likely to be superior to terbinafine for the rare cases caused by Microsporum species.

Antifungal Agents↗

PubMed1977

[Meningitis caused by primary lymphoma of the central nervous system. Report of a case].

The case of a 17 years-old woman, with clinical findings of meningites, without identification of a pathogenic agent is reported. The pacient received treatment for tuberculous and fungi meningitis. In the clinical course were found neoplastic cells in the spinal fluid. Despite the radiologic investigation, the original site of the tumor was not found in life. In the post-mortem examination, a small tumor was discovered in the 4th ventricle. The hystologic examination revealed a primary central nervous system lymphoma, diffuse infiltration of the meninges by tumor cells and proliferation into the central nervous system through the Virchow-Robin space. The clinical course, laboratory investigation and anatomical findings of the tumor are presented. A short revision about the pathogenesis of neoplastic meningites and primary central nervous system lymphoma is made.

Adolescent↗

PubMed2005

Molecular characterization of Mycobacterium kansasii isolates in the State of São Paulo between 1995-1998.

Mycobacterium kansasii is the most common cause of pulmonary nontuberculous mycobacteria infection and classical identification of this pathogen needs a time consuming phenotypic tests. Polymerase chain reaction-restriction fragment length polymorphism analysis (PRA) of the gene enconding for the 65 kDa heat shock (hsp65) protein offers an easy, rapid, and inexpensive procedure to identify and subtype M. kansasii isolates. In the present study, we performed a retrospective analysis of patients who had mycobacteria identified on the basis of phenotypic tests by means of a review of database at Mycobacteria Laboratory of the Instituto Adolfo Lutz in the period 1995-1998. A total of 9381 clinical isolates were analyzed of which 7777 (82.9%) were identified as M. tuberculosis complex and 1604 (17.1%) as nontuberculous mycobacteria. Of the 296 M. kansasii isolates, 189 (63.8%) isolates obtained from 119 patients were viable and were analyzed by PRA-hsp65. Hundred eight two (98.9%) were classified as M. kansasii type I. Two isolates were classified as type II and III and five isolates were characterized as other Mycobacterium species. Clinical isolates of M. kansasii in the state of Sao Paulo was almost exclusively subtype I regardless of HIV status.

Bacterial Proteins↗