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Rapid diagnosis of acute pyogenic meningitis by a combined PCR dot-blot assay.

A multiplex PCR was employed to amplify unique conserved sequences of DNA from the pathogens Haemophilus influenzae, Neisseria meningitidis and Streptococcus pneumoniae from cerebrospinal fluid samples of patients suffering from acute pyogenic meningitis. The accurate identification of the PCR amplified product was achieved by hybridizing dot-blots of the PCR products to probes which were specific, biotinylated internal sequences of the amplified target DNA. Detection of the hybrids was done in a colour reaction using streptavidin-alkaline phosphatase conjugate and BCIP/NBT substrates. The entire protocol took only 7 h for the correct identification of the pathogen present in clinical samples of cerebrospinal fluid. The sensitivity and specificity were >95%.

Biotin↗

Rapid carbohydrate fermentation test for confirmation of the pathogenic Neisseria using a Ba(OH)2 indicator.

The Ba(OH)2 indicator system was demonstrated to be a practical procedure in assisting clinical bacteriologists in the accurate and rapid identification of the pathogenic Neisseria from clinical specimens. This system measured the release of CO2, resulting from the metabolism of fermentable carbohydrate, as the precipitated BaCO3, by means of a spectrophotometer, The method was uncomplicated and can be performed in most clinical bacteriology laboratories.

Bacteriological Techniques↗

Isolation and identification of Escherichia coli O157:H7 using different detection methods and molecular determination by multiplex PCR and RAPD.

Escherichia coli O157:H7 is recognized as a significant food-borne pathogen, so rapid identification is important for food hygiene management and prompt epidemiological investigations. The limited prevalence data on Shiga toxin-producing E. coli (STEC) and E. coli O157:H7 in foods and animals in Korea made an assessment of the risks difficult, and the options for management and control unclear. The prevalence of the organisms was examined by newly developed kit-E. coli O157:H7 Rapid kit. For the isolation of E. coli O157:H7, conventional culture, immunomagnetic separation, and E. coli O157:H7 Rapid kit were applied, and multiplex PCR and randomly amplified polymorphic DNA (RAPD) were performed for the molecular determination. There was high molecular relatedness among 11 Korean isolates and 17 U.S. strains at 63% level. Additionally, distinct differentiation between pig and cattle isolates was determined. It implied that RAPD had a capacity to distinguish strains with different sources, however it could not discriminate among isolates according to their differences in the degree of virulence. In antimicrobial susceptibility tests, 45.5% of isolates showed antibiotic resistance to two or more antibiotics. Unlike the isolates from other countries, domestic isolates of E. coli O157:H7 was mainly resistant to ampicillin and tetracyclines. In summary, the application of E. coli O157:H7 Rapid kit may be useful to detect E. coli O157:H7 due to its sensitivity and convenience. Moreover, combinational analysis of multiplex PCR together with RAPD can aid to survey the characteristics of isolates.

Abattoirs↗

[Molecular diagnostics for the detection of prosthetic joint infection].

PURPOSE OF THE STUDY: Ten years after inauguration of the molecular methods into the orthopaedic practice for diagnosing Prosthetic Joint Infection (PJI), this approach is still in the limelight of research and discussion. The aim of the current study was to determine the diagnostic power of our Polymerase Chain Reaction (PCR) protocol for preoperative detection of bacterial nucleic acid in the synovial joint fluid. MATERIAL AND METHODS: Synovial fluids obtained from thirty-five septic hip or knee arthroplasties and sixty-six aseptic controls were investigated by the conventional PCR technique. Two subgroups were established with regard to antibiotic administration before sample collection; with (n=13) and without (n=22) previous antibiotic exposition, respectively. All the surgeries were performed under the identical conditions with strictly established and fulfilled inclusion criteria. The study design applied was a prospective cohort trial. Primers targeting phylogenetically conserved regions of the bacterial gene were used to detect the bacterial 16SrRNA gene in the retrieved samples. If this was positive, a restriction endonuclease treatment of the amplified DNA was performed to reveal the PJI pathogen. Current guidelines were used to evaluate the test performance, including the confidence intervals. The concordance between the culture and PCR identification of PJI pathogens was estimated providing both of the relevant data were available. RESULTS: A qualitative analysis showed the following figures in the subgroup without previous antibiotic exposition: sensitivity (0.64), specificity (0.97), accuracy (0.89), positive predictive value (0.88), negative predictive value (0.89), likelihood ratio for positive result (21.0), and likelihood ratio for negative result (0.38). In the second subgroup the corresponding figures were as follows: 0.85, 0.97, 0.95, 0.85, 0.97, 27.9, and 0.16. The rate of concordance between the microbial and PCR findings was almost identical in both of the subgroups. DISCUSSION: There were large discrepancies in sensitivity and positive predictive values found in the published results. The earlier studies have had various methodological weaknesses, including a lack of strictly formulated inclusion criteria and control groups. In addition, there are differences among research centers in PCR laboratory procedures and specimen retrieval tactics which may potentially have an impact on PCR results. Low sensitivity and high specificity of our PCR technique may be explained by both the intrinsic (DNA extraction protocol, configuration of inner controls, choice of detection threshold, etc.) and extrinsic factors (in particular intra-operative retrieval of specimens). A hypothesis on the inadequacy of PCR techniques for PJI detection still remains to be excluded. CONCLUSION: Based on the current study, the positive results of our PCR technique may be perceived as a mild criterion from the point of power for PJI diagnosis support. However, its clinical utility should be significantly increased in cases with higher pretest probability of PJI, but negative cultures.

Adult↗

Chlamydiae as pathogens--an overview of diagnostic techniques, clinical features, and therapy of human infections.

Chlamydiae are Gram-negative bacteria with obligate intracellular reproduction and disability to synthesize high-energy compounds such as ATP. Their cycle of development is unique among the prokaryotes: the host cells, mainly epithelial cells, are infected by so-called elementary bodies (EB) which undergo reorganization to form metabolically active reticulate bodies (RB). These RB multiply by binary fission, and after transition into infectious EB they are released within 48-72 hours. Chlamydiae cause prolonged subclinical infections of the conjunctiva, lung, cervix, and urethra. Complications in newborns are inclusion conjunctivitis, nasopharyngitis and pneumonia; in females, salpingitis, infertility, and perihepatitis; in male patients, epididymitis and prostatitis; and in both sexes, Chlamydiae-induced arthritis. Identification of the pathogenic agent confirms clinical diagnosis; tissue culture identification remains the diagnostic method of choice. Therapeutical drugs are tetracycline, erythromycin, josamycin, and in certain cases quinolone derivatives.

Animals↗

Antibiotic resistance in nosocomial pulmonary pathogens.

Nosocomial pneumonia is the second most common hospital-acquired infection and are associated with antibiotic-resistant microorganisms. In nosocomial pneumonia, both the diagnosis of the disease and the identification of the pathogen agent are controversial. The lack of standard diagnostic criteria can lead to the inappropriate use of broad-spectrum antibiotic therapy and the emergence of multiresistant bacteria. Moreover, empirical antibiotic treatment must be prescribed after bacteriological sample but before culture results because the majority of nosocomial pneumonias require an urgent antibiotic therapy. Most nosocomial pneumonias are of an endogenous origin, particularly in mechanically ventilated patients, and this is associated with a higher rate of multiresistant methicillin-resistant Staphylococcus aureus, Acinetobacter baumanii, Klebsiella pneumoniae with extended spectrum b-lactamases, and Pseudomonadaceae. Multiple factors influence the frequency of pathogens associated with antibiotic resistance, such as duration of hospital stay, time of onset, prior antibiotic therapy, and local microbial ecology.

Journal Article↗

In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori.

Availability of genome sequences of pathogens has provided a tremendous amount of information that can be useful in drug target and vaccine target identification. One of the recently adopted strategies is based on a subtractive genomics approach, in which the subtraction dataset between the host and pathogen genome provides information for a set of genes that are likely to be essential to the pathogen but absent in the host. This approach has been used successfully in recent times to identify essential genes in Pseudomonas aeruginosa. We have used the same methodology to analyse the whole genome sequence of the human gastric pathogen Helicobacter pylori. Our analysis revealed that out of the 1590 coding sequences of the pathogen, 40 represent essential genes that have no human homolog. We have further analysed these 40 genes by the protein sequence databases to list some 10 genes whose products are possibly exposed on the pathogen surface. This preliminary work reported here identifies a small subset of the Helicobacter proteome that might be investigated further for identifying potential drug and vaccine targets in this pathogen.

Anti-Bacterial Agents↗

Use of alpha-aminoadipate and lysine as sole nitrogen source by Schizosaccharomyces pombe and selected pathogenic fungi.

alpha-Aminodipate, an intermediate of the lysine biosynthetic pathway of fungi, or lysine when used as the sole nitrogen source in the medium was growth inhibitory and toxic to Saccharomyces cerevisiae. The fission yeast Schizosaccharomyces pombe and pathogenic fungi Candida albicans, Filobasidiella neoformans and Aspergillus fumigatus grew in the medium containing alpha-aminoadipate as the sole nitrogen source. C. albicans, A. fumigatus, and one of the strains of F. neoformans also grew in the medium containing lysine as the sole nitrogen source. When grown in the alpha-aminoadipate medium, only S. pombe accumulated a significant amount of alpha-ketoadipate in the culture supernatant. Also, 14C-alpha-aminoadipate was converted to 14C-alpha-ketoadipate in vivo. In the ammonium sulfate medium, S. pombe cells converted 14C-alpha-aminoadipate to lysine. The levels of glutamate-alpha-ketoadipate transaminase, an enzyme responsible for the conversion of alpha-aminoadipate to alpha-ketoadipate, and alpha-aminoadipate reductase, an enzyme required for the conversion of alpha-aminoadipate to lysine, were similar in S. pombe cells grown in the alpha-aminoadipate or ammonium sulfate medium. However, the level of homoisocitrate dehydrogenase, an enzyme before the alpha-ketoadipate step, was twelvefold lower in S. pombe cells grown in the alpha-aminoadipate medium compared to the level in cells grown in the ammonium sulfate medium. Pathogenic fungi used in this study did not accumulate alpha-ketoadipate and alpha-aminoadipate-delta-semialdehyde when grown in medium containing alpha-aminoadipate and lysine, respectively, as sole nitrogen source. However, only pathogenic fungi used both lysine and alpha-aminoadipate as sole nitrogen source. This unique metabolic property could be useful for the identification of these pathogens.

2-Aminoadipic Acid↗

Dientamoeba fragilis masquerading as allergic colitis.

BACKGROUND: Dientamoeba fragilis is a rare cause of chronic infectious diarrhea and colitis in children. METHODS: Review of the clinical manifestations, diagnostic methods, and clinical course of D. fragilis infection in our hospital. RESULTS: Eleven pediatric patients are discussed, seven of whom had a history of recent travel. Clinical manifestations of infectious diarrhea included anorexia, intermittent vomiting, abdominal pain, and diarrhea, ranging from 1 to 100 weeks in duration. Peripheral eosinophilia was present in seven patients. One patient with well-documented bovine protein allergy had intermittent episodes of diarrhea and abdominal pain, despite an appropriate elimination diet. Eosinophilic colitis documented by colonoscopy, was due to D. fragilis. Metronidazole was effective in treating five patients, and iodoquinol was effective in treating four others. CONCLUSIONS: D. fragilis should be included in the differential diagnosis of chronic diarrhea and eosinophilic colitis. The identification of this pathogen requires clinical awareness of epidemiologic risk factors and presenting complaints, as well as the laboratory staining procedures essential to its proper identification.

Abdominal Pain↗

Serum and peripheral blood mononuclear cells infectious burden: correlation to inflammation and atherosclerosis in haemodialysis patients.

BACKGROUND: Infectious agents may be implicated in the inflammatory atherosclerotic process. Not only specific microorganisms but also the infectious burden, defined as the number of pathogens to which a patient is exposed, has been associated with atherosclerosis. In the present study, the infectious burden, determined directly (by identification of viable pathogens in peripheral blood mononuclear cells (PBMC)) and indirectly (by serum antibodies detection) is correlated to the inflammatory and atherosclerotic status in haemodialysis (HD) patients, a population at high risk for cardiovascular disease. METHODS: The viable forms of four microorganisms (Chlamydia pneumoniae, herpes virus 1 and 2 and cytomegalovirus) were identified in patients PBMC by cell cultures and subsequent polymerase chain reaction. Serum IgG against the above pathogens and Helicobacter pylori were also determined. Inflammation was assessed by measurement of C-reactive protein (CRP), serum amyloid A (SAA), three pro- and one anti-inflammatory cytokines and four adhesion molecules. Atherosclerosis was defined by a scoring system using medical history data. RESULTS: The number of viable pathogens identified in PBMC in the 122 HD patients included in the study were zero in 22.1% of them, one in 33.6%, two in 43.4% and three in one patient. The number of IgG antibodies determined was one in 6.6% of patients, two in 32%, three in 48.4% and four in 13.1%. Seropositivity was not significantly different between patients with or without the respective viable pathogen identified in PBMC. Atherosclerosis was present in 40.2% of patients, and CRP, SAA and interleukin-6 were all increased in these patients. Neither inflammatory indexes nor atherosclerosis were significantly different in patients with a higher number of viable pathogens detected in PBMC or in those with a higher antibodies number. CONCLUSIONS: The direct infectious burden determination (the number of viable pathogens in PBMC) does not coincide with the serum (by IgG detection) infectious burden. Although inflammation correlates to atherosclerosis, neither PBMC nor the serum infectious burden is associated with these two entities in the inflamed and atherosclerotic HD patients.

Adolescent↗

New perspectives for a new century: implications of pathogen responses for the future of antimicrobial therapy.

Although the discovery of new classes of antibiotics has lagged behind in the last three decades, the incidence of life-threatening nosocomial infections that are resistant to multiple antibacterial agents has increased steadily. Recent advances in bacterial pathogenicity through the identification of a number of virulence factors and the bacterial genetics behind it have opened the way to a clearer understanding of the pathogen-host relationship. Bacteria communicate with each other through specific signaling chemicals to act as a community rather than individual cells to achieve a critical density or a "quorum." Establishment of quorum is the initiating signal for turning on a variety of virulence factors essential for the pathogenicity and dissemination of pathogens through the host. Pathogenic bacteria use a variety of biochemical mediators, collectively called "virulence factors," to invade and attack host tissues and to avoid detection and elimination by the host immune system. Delineating the specific responses the host immune system elicits in response to specific virulence factors and quorum-sensing molecules is essential to the development of new diagnostic methods for early detection of an infection and the prognosis to a given antibacterial therapy. Identification of inhibitors of virulence factors will represent new antimicrobial therapeutic modalities, and this can be used synergistically with current antibiotic therapy because they act through independent prokaryotic pathways to inhibit bacterial growth and survival.

Anti-Bacterial Agents↗

Molecular reidentification of human pathogenic Trichoderma isolates as Trichoderma longibrachiatum and Trichoderma citrinoviride.

Several species of the well-known saprophytic genus Trichoderma have been identified as the cause of infections in immunosuppressed humans. Because the differentiation and identification of Trichoderma species based on morphological characters only, is very difficult, two molecular approaches were applied for species identification. Six human pathogenic Trichoderma isolates were investigated by PCR-fingerprinting and analysis of ribosomal DNA internal transcribed spacer (ITS) sequences and compared with the corresponding data sets established for described species of the genus. Five of these strains were identified as T. longibrachiatum, whereas one single strain turned out to be T. citrinoviride. Both species are very closely related and belong to Trichoderma section Longibrachiatum. These data indicate that the occurrence of pathogenic Trichoderma strains may be restricted to species of section Longibrachiatum.

DNA Fingerprinting↗

Gastrointestinal infections in children.

New pathogens that cause gastroenteritis in children are being recognized. Even well-recognized pathogens, such as Clostridium difficile, may require more extensive testing than was previously thought necessary. Several new tests have emerged that allow for faster identification of these pathogens so that same-day results may be possible. Probiotic therapy has emerged as a novel strategy for the treatment of gastroenteritis. New vaccines against both viral and bacterial causes of gastroenteritis are being developed. The most exciting recent advance in vaccine development may be the creation of edible vaccines.

Journal Article↗

Serial analysis of gene expression in eukaryotic pathogens.

The tag-based method of serial analysis of gene expression (SAGE) has been used to measure mRNA abundance and differential expression in a variety of organisms including several parasites and fungal pathogens. SAGE is based on the collection of short sequence tags as a measure of transcript abundance and the method provides an alternative, and in some instances, complementary approach to array-based methods of measuring differential gene expression. These methods are being used to improve our molecular understanding of the pathogenesis of eukaryotic microbes and SAGE in particular presents valuable opportunities for gene discovery and genome annotation. For eukaryotic pathogens, the SAGE method has been employed for the parasites Plasmodium falciparum, Toxoplasma gondii and Giardia lamblia, as well as fungal pathogens of plants (Magnaporthe grisea, Blumeria graminis, Ustilago maydis) and humans (Cryptococcus neoformans, Coccidiodes posadasii, Trichophyton rubrum). The accumulating information promises to speed the identification of key pathogen functions for virulence and proliferation in the host with the hope that some of these will represent important targets for drug and vaccine development.

Animals↗

[Nosocomial infections in a university hospital. Results of a prospective study of infections in a medical and surgical ward and a surgical intensive care unit].

The results of an 11-month pilot study of surveillance of nosocomial infections are reported. Prospective surveillance was performed by daily examination of the microbiology reports and daily visits by the infection control nurse to the ward for the review of charts and Kardex of all patients for detection of "infection clues". Work sheets were used to collect all data during the daily rounds. Infection rates were calculated by dividing the the total number of hospital-acquired infections by the total number of discharges during the surveillance period. Active surveillance was performed for 6 months in the surgical intensive care unit (SCIU), 5 months in the surgical ward (SW) and 9 months in the medical ward (MW). Of 1527 patients discharged from these wards, nosocomial infections developed in 158 patients (10.4%). The overall infection rate was 14% (214 nosocomial infections). The infection rate varied greatly from ward to ward due to different patient populations, invasive procedures and severity of underlying diseases. Incidence infection rates were 42.5% for the SICU, 19.6% for the SW and 4.1% for the MW. The major sites affected were surgical wounds (42%), urinary tract (23%), respiratory tract (19%) and bloodstream (8%). The major etiologic agents associated with these nosocomial infections were E. coli, Pseudomonas aeruginosa, enterococci and Staphylococcus aureus. Conclusions drawn from the results of surveillance are discussed. The major benefits of an effective surveillance program for nosocomial infections are (a) estimates of the endemic levels of nosocomial infection, (b) identification of the nosocomial pathogens commonly encountered within a given institution, (c) identification of risk factors and (d) prompt recognition of epidemics. These data provide the necessary basis for an effective infection control program.

Cross Infection↗

Opportunistic fusarial infections in humans.

Fusarium species are common hyaline soil saprophytes and plant pathogens which have frequently been reported as etiologic agents of opportunistic infections in humans. These infections have usually been limited to superficial mycoses, but recently the number of infections of deep tissues and disseminated infections has greatly increased, especially in patients with an underlying immunosuppressive condition. The characteristic signs of these infections are disseminated skin nodules, fungemia and multiorgan involvement. Frequently, myalgia is also present. Skin involvement occurred in over 80% of cases of disseminated infections. These lesions are significant because they are readily accessible for biopsy and culture, thus permitting an early diagnosis. The therapy and outcome are dependent on the degree of invasion of the organisms and the status of the host. Identification of the pathogen to genus level is not difficult, but identification to species level requires a greater degree of expertise. Up to now, 15 species of Fusarium have been reported to cause infections in humans and animals. Few patients with disseminated fusarial infections have survived, even after receiving an adequate dosage of amphotericin B, the only antifungal agent that has some effect against these fungi. In vitro susceptibility to amphotericin B is a poor predictor of the clinical outcome of invasive fungal infections. Recovery of the phagocytic mechanisms in the form of rising neutrophil counts appears to be mandatory for clinical resolution. The resolution of neutropenia may be aided by the use of exogenous growth factors. Outside the USA, the majority of cases of disseminated fusarial infection have been reported from Mediterranean or tropical countries.

Fusarium↗

New emerging zoonoses: a challenge and an opportunity for the veterinary profession.

The concept of emerging infectious diseases appeared in the late 1980s, when major outbreaks occurred around the globe and surprised many scientists who considered infectious diseases to be maladies of the past or limited to the under-developed world. Several reports identified erosion of the public health infrastructure among the factors contributing to new and re-emerging infectious diseases. As indicated by Morse, "Disease emergence often follows ecological changes caused by human activities such as agriculture or agricultural change, migration, urbanization, deforestation, or dam building". "Among these new diseases, surprisingly, most emergent viruses and many emergent bacteria are zoonotic". Several new zoonoses have been recently identified. Many of these diseases were either unknown, because we were not able to isolate the infectious agent or to distinguish them from other clinical syndromes, or discovered accidentally. Much of the recent identification of new pathogens has been based on new molecular biology tools or epidemiological studies. For all these diseases or infections, veterinarians played a key role in their identification, isolation of the causative organisms and understanding of the epidemiology of the infection. The role of the veterinary profession is very important in public health and on the rise again in the U.S.A., as it should be in many other countries. Surveillance, clinical curiosity and awareness, epidemiology and laboratory training are the essential tools and competency that the veterinary profession must use to meet the challenge of new emerging zoonoses.

Animals↗

Surveillance of pediatric infections in a teaching hospital in Mato Grosso do Sul, Brazil.

Nosocomial infections (NI) result in considerably high mortality and morbidity rates, especially among pediatric patients. Considering current worldwide changes, information about the occurrence of pathogens and susceptibility tests are now seen as decisive for optimizing treatment. The purpose of this research was to determine the frequency of microorganisms, antimicrobial and genetic profiles, and risk factors associated with nosocomial infections in a teaching hospital in Campo Grande, Mato Grosso do Sul. From January 1998 to December 1999, 108 patients were characterized as having nosocomial infection, from which 137 pathogens were isolated. Identification and antimicrobial susceptibility was determined by conventional and automated techniques. Staphylococcus aureus and Klebsiella pneumoniae strains were characterized by Pulsed Field Gel Electrophoresis (PFGE). Pathogens were most often isolated from infants one-month old or younger, and bloodstream infections were the most frequent. The main isolated agents isolated were: coagulase-negative staphylococci (38), Pseudomonas aeruginosa (19), S. aureus (26), K. pneumoniae (18), and Candida spp. (13). The risk conditions that were most closely related to NI acquisition were: prolonged hospital stays (69.4%), prematurity (60.9%) and exposure to high-risk device procedures (95.4%). Ciprofloxacin and imipenem were the most effective drugs, inhibiting all or almost all of the Enterobacteriaceae, P. aeruginosa and Acinetobacter calcoaceticus isolates. Only 23% of the S. aureus samples were resistant to oxacillin. Genomic typing revealed 10 distinct patterns for S. aureus and 13 for K. pneumoniae, suggesting that most them did not belong to the same clone. PFGE was effective in differentiating the strains.

Age Factors↗