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PubMed2002

Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility.

Intact cell mass spectrometry (ICMS) rapidly analyses the surface composition of microorganisms providing rapid, discriminatory fingerprints for identification and subtyping of important nosocomial pathogens such as methicillin resistant Staphylocccus aureus (MRSA). In this study, ICMS using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI TOF/MS) was assessed for the identification and subtyping of MRSA. An intra- and inter-laboratory reproducibility study was carried out and the effects of culture media (an important source of variation for ICMS) were also studied. Several media used for the cultural identification of MRSA were examined using a panel of well-characterised staphylococcal isolates (n=26). Six MRSA isolates were analysed over a 1-month period for intra-laboratory reproducibility on the same instrument and three different culture media. Spectra were consistent for each isolate between the four experiments on the same culture medium. Individual isolates produced different spectral profiles on different culture media. Spectra from organisms grown on Columbia blood agar contained more peaks (approximately 120) compared to Columbia agar (approximately 50) and methicillin mannitol salt agar (approximately 25). All 26 staphylococcal isolates were subjected to an inter-laboratory study on two MALDI instruments. For each isolate, the overall spectral profile was the same for each of the two instruments but the baseline threshold values was adjusted due to instrument differences in detector sensitivities. Differences between certain regions of the spectra reproducibly identified isolates belonging to the two major MRSA strains (EMRSA phage group 15 and 16). These results demonstrate ICMS with appropriate media selection is a rapid and reproducible technique for identification and discrimination of MRSA.

Culture Media↗
PubMed1998

Classification of the genus Legionella.

There are currently 42 described species of legionellae representing 64 serogroups in the family Legionellaceae and the genus Legionella. The phenotypic characteristics of legionellae are described, including growth requirements, and biochemical characteristics. Identification of legionellae by biochemical tests, fatty acid analysis, ubiquinones, protein profiles, carbohydrate analysis, serology, monoclonal antibodies, and molecular techniques is described. The occurrence and description of Legionella-like amebic pathogens are discussed. The problems of identification to the species level are discussed, along with the need for further evaluations of additional strains from all known species using biochemical and molecular techniques.

Humans↗
PubMed2005

A multiplex PCR for detection of Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, and Bordetella pertussis in clinical specimens.

A multiplex PCR was developed that is capable of detecting four of the most important bacterial agents of atypical pneumonia, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, and Bordetella pertussis in uncultured patient specimens. These organisms cause similar symptomologies and are often not diagnosed because they are difficult to identify with classical methods such as culture and serology. Given this, the overall impact of these pathogens on public health may be grossly underestimated. The molecular test presented here provides a simple method for identification of four common, yet diagnostically challenging, pathogens.

Bordetella pertussis↗
PubMed2001

Origin of antiphospholipid antibodies.

Our observations and those from others give further support to our hypothesis that "autoimmune aPL" may be generated by immunization with products from bacteria or viruses after incidental exposure or infection. We also were able to generate an APS-like syndrome in a strain of mice susceptible to autoimmunity, indicating that other factors such as genetic factors are likely to be involved in development of APS. Furthermore, not all aPL generated by immunization with bacterial or viral products were pathogenic. Based on the clinical experience and on the numerous reports indicating the presence of aPL in large number of infectious diseases, it may be expected that not all aPL produced during infection are pathogenic. We hypothesize that a limited number aPL induced by certain viral or bacterial products would be pathogenic in certain groups of predisposed individuals. Identification of those bacterial or viral agents may help to find strategies for the prevention of production of "pathogenic" aPL. Alternatively, free peptides may be used to induce tolerance against aPL production.

Animals↗
PubMed2003

Identification of phenylisoxazolines as novel and viable antibacterial agents active against Gram-positive pathogens.

A new and promising group of antibacterial agents, collectively known as the oxazolidinones and exemplified by linezolid (PNU-100766, marketed as Zyvox), have recently emerged as important new therapeutic agents for the treatment of infections caused by Gram-positive bacteria. Because of their significance, extensive synthetic investigations into the structure-activity relationships of the oxazolidinones have been conducted at Pharmacia. One facet of this research effort has focused on the identification of bioisosteric replacements for the usual oxazolidinone A-ring. In this paper we describe studies leading to the identification of antibacterial agents incorporating a novel isoxazoline A-ring surrogate. In a gratifying result, the initial isoxazoline analogue prepared was found to exhibit in vitro antibacterial activity approaching that of the corresponding oxazolidinone progenitor. The synthesis and antibacterial activity profile of a preliminary series of isoxazoline analogues incorporating either a C-C or N-C linkage between their B- and C-rings will be presented. Many of the analogues exhibited interesting levels of antibacterial activity. The piperazine derivative 54 displayed especially promising in vitro activity and in vivo efficacy comparable to the activity and efficacy of linezolid.

Animals↗
PubMed1991

Induction of Arabidopsis defense genes by virulent and avirulent Pseudomonas syringae strains and by a cloned avirulence gene.

We developed a model system to study the signal transduction pathways leading to the activation of Arabidopsis thaliana genes involved in the defense against pathogen attack. Here we describe the identification and characterization of virulent and avirulent Pseudomonas syringae strains that elicit disease or resistance symptoms when infiltrated into Arabidopsis leaves. The virulent and avirulent strains were characterized by determining growth of the pathogen in Arabidopsis leaves and by measuring accumulation of mRNA corresponding to Arabidopsis phenylalanine ammonia-lyase (PAL), beta-1,3-glucanase (BG), and chalcone synthase (CHS) genes in infected leaves. The virulent strain, P. syringae pv maculicola ES4326, multiplied 10(5)-fold in Arabidopsis leaves and strongly elicited BG1, BG2, and BG3 mRNA accumulation but had only a modest effect on PAL mRNA accumulation. In contrast, the avirulent strain, P. syringae pv tomato MM1065, multiplied less than 10-fold in leaves and had only a minimal effect on BG1, BG2, and BG3 mRNA accumulation, but it induced PAL mRNA accumulation. No accumulation of CHS mRNA was found with either ES4326 or MM1065. We also describe the cloning of a putative avirulence (avr) gene from the avirulent strain MM1065 that caused the virulent strain ES4326 to grow less well in leaves and to strongly elicit PAL but not BG1 and BG3 mRNA accumulation. These results suggest that the Arabidopsis PAL and BG genes may be activated by distinct signal transduction pathways and show that differences in plant gene induction by virulent and avirulent strains can be attributed to a cloned presumptive avr gene.

Cloning, Molecular↗
PubMed2000

Fluorescent In situ hybridization allows rapid identification of microorganisms in blood cultures.

Using fluorescent in situ hybridization (FISH) with rRNA-targeted fluorescently labelled oligonucleotide probes, pathogens were rapidly detected and identified in positive blood culture bottles without cultivation and biotyping. In this study, 115 blood cultures with a positive growth index as determined by a continuous-reading automated blood culture system were examined by both conventional laboratory methods and FISH. For this purpose, oligonucleotide probes that allowed identification of approximately 95% of those pathogens typically associated with bacteremia were produced. The sensitivity and specificity of these probes were 100%. From all 115 blood cultures, microorganisms were grown after 1 day and identification to the family, genus, or species level was achieved after 1 to 3 days while 111 samples (96.5%) were similarly identified by FISH within 2.5 h. Staphylococci were identified in 62 of 62 samples, streptococci and enterococci were identified in 19 of 20 samples, gram-negative rods were identified in 28 of 30 samples, and fungi were identified in two of two samples. Thus, FISH is an appropriate method for identification of pathogens grown in blood cultures from septicemic patients.

Bacteremia↗
PubMed1999

Development and evaluation of a 24 well microtitre plate method for isolation of Listeria spp. or Listeria monocytogenes from foods.

A rapid and simple method (24M) using 24 well microtitre plates was developed to determine the presence of Listeria monocytogenes or Listeria spp. in food samples. The 24M was composed of two 24 well microtitre plates connected with a yellow tip. The 24M was evaluated with pathogen cocktails and ground beef samples and compared with the conventional method for presumptive identification of Listeria spp. Only food-borne pathogen cocktails and ground beef samples containing L. monocytogenes or Listeria spp. showed a positive reaction in 24M after 24 h incubation at 35 degrees C. Test results were the same with the conventional method and the 24M method and showed high efficiency for recovery of Listeria spp. from foods. This new, convenient and economical method can isolate Listeria spp. simultaneously from 24 different food samples.

Animals↗
PubMed1991

Differentiation of pathogenic from nonpathogenic Entamoeba histolytica by restriction fragment analysis of a single gene amplified in vitro.

We previously reported the identification of homologous cDNA clones derived from a pathogenic isolate and a nonpathogenic isolate of Entamoeba histolytica, which had been designated cEh-P1 and cEh-NP1, respectively. Sequence analysis of both clones had revealed 10% nucleic acid substitutions, which were dispersed over the entire sequence. This genetic difference had been found to be conserved between all four pathogenic and all five nonpathogenic laboratory strains of E. histolytica tested. On the basis of nucleic acid substitutions, we have now developed a sensitive assay to distinguish pathogenic from nonpathogenic forms of E. histolytica by using fresh clinical isolates. Comparing the sequence of cEh-P1 and cEh-NP1, we identified a 482-bp segment that contained identical 5' and 3' ends but differed in internal cleavage sites for restriction endonucleases. By using oligonucleotide primers corresponding to the 5' and 3' ends of this segment, the corresponding gene was amplified by the polymerase chain reaction. Endonuclease digestion of the amplified DNA yielded restriction fragments that are characteristic for pathogenic and nonpathogenic forms. This assay allows the detection and classification of fewer than 10 amoebae within a few hours. The differentiation of 48 isolates into pathogenic and nonpathogenic strains by using this method corresponded to the clinical status of the infected individuals and to the classification obtained by isoenzyme determination. The results further support the concept that pathogenic and nonpathogenic strains of E. histolytica constitute distinct subspecies.

Animals↗
PubMed2004

Identification and characterisation of hyaluronate lyase from Streptococcus suis.

Hyaluronate lyase, which catalyses the degradation of hyaluronic acid (HA), has been described from several pathogenic streptococcal species. We describe, for the first time, identification and purification of hyaluronate lyase from the zoonotic pig pathogen Streptococcus suis. We have cloned the hyaluronate lyase gene from S. suis and used it to generate an allelic replacement knock-out mutant of S. suis serotype 7 that can no longer biosynthesise the enzyme. Interestingly, a limited strain survey indicates that hyaluronate lyase activity is not present in all disease isolates of S. suis. Polyclonal anti-hyaluronate lyase anti-serum raised against our recombinant hyaluronate lyase has been used in Western blots, showing that hyaluronate lyase activity is always associated with the presence of protein of the expected size, whereas lack of hyaluronate lyase activity is due to truncation or absence of the enzyme. We show that hyaluronate lyase activity is required for S. suis to use HA polymer as a carbon source and that supplying exogenous recombinant hyaluronate lyase to all S. suis strains tested allowed fermentation of the resultant HA breakdown products.

Blotting, Western↗
PubMed2006

Regional community-acquired urinary tract infections in Israel: diagnosis, pathogens, and antibiotic guidelines adherence: a prospective study.

INTRODUCTION: The identification and treatment of hospitalized patients with community-acquired urinary tract infections (CAUTI) may be a challenge. The pathogens causing the infection and their relative proportions vary geographically and with time. This observational prospective study had three primary goals: (1) to estimate the likelihood of diagnosis of CAUTI upon admission; (2) to evaluate adherence to the institutional recommendations; (3) to assess the compatibility of the current local antibiotic recommendations with a pathogen's distribution and with its drug sensitivities. METHODS AND RESULTS: Two hundred and twenty-three patients with positive urinary cultures fulfilling criteria for CAUTI were studied. Only 54 (24.2%) were diagnosed as having a urinary tract infection upon admission. Approximately 90% of the patients, who were correctly diagnosed, received the institutional recommended antibiotic therapy (ofloxacin or cefuroxime). Gram-negative intestinal flora comprised 86.1% (192 patients) of the causative microorganisms. Of these, 20.3% of the pathogens demonstrated resistance to ofloxacin and 19.8% to cefuroxime. The prevalence of Escherichia coli, the most common pathogen of UTI, significantly declined in the current study, from 70.5% in 1991 to 56% in 2000. CONCLUSIONS: We observed a low sensitivity in diagnosing community-acquired urinary tract infections upon admission. In patients correctly diagnosed, the use of recommended antibiotics was high. A substantial percentage of the pathogens were resistant to the recommended antibiotics. This study stresses the need for frequent re-evaluation of the prevalence of pathogens involved in regional community-acquired urinary tract infections and the adjustment of the empirical first-line treatment accordingly.

Aged↗
PubMed1993

Update on laboratory tests for the diagnosis of pulmonary disease in HIV-1-infected individuals.

Various diagnostic tests, both specific and nonspecific, are available in the clinical laboratories for diagnosing human immunodeficiency virus-1 (HIV-1) infection and associated respiratory pathogens. Pneumocystis carinii pneumonia remains the most common pulmonary disease in HIV-1-infected individuals and there have been no significant advances in the laboratory diagnosis of the pathogen beyond the traditional microscopic examination of specimens. In contrast, the greatest revolution in laboratory diagnostic testing has been for mycobacteria, with major advances resulting in significant reduction in the time necessary for isolation and identification to the species level. The application of the polymerase chain reaction for the identification of a variety of pulmonary pathogens observed in HIV-1 infected individuals is discussed.

Enzyme-Linked Immunosorbent Assay↗
PubMed2003

Reverse vaccinology.

Whole-genome sequencing of bacteria and advances in bioinformatics have revolutionized the vaccinology field, leading to the identification of potential vaccine candidates without the need for cultivating the pathogen. This approach, termed "reverse vaccinology", reduces the time and cost required for the identification of candidate vaccines and provides new solutions for those diseases for which conventional approaches have failed. The first example of the potential of reverse vaccinology has been the identification of novel antigens of meningococcus B as potential candidates for a novel and effective vaccine. The same approach has been successfully applied to other important human pathogens, demonstrating the feasibility to develop vaccines against any infectious disease. This review focuses on some recent advances in the identification of vaccine candidates by mining the genomic sequences of pathogenic bacteria.

Animals↗
PubMed2006

Identification and structural basis of binding to host lung glycogen by streptococcal virulence factors.

The ability of pathogenic bacteria to recognize host glycans is often essential to their virulence. Here we report structure-function studies of previously uncharacterized glycogen-binding modules in the surface-anchored pullulanases from Streptococcus pneumoniae (SpuA) and Streptococcus pyogenes (PulA). Multivalent binding to glycogen leads to a strong interaction with alveolar type II cells in mouse lung tissue. X-ray crystal structures of the binding modules reveal a novel fusion of tandem modules into single, bivalent functional domains. In addition to indicating a structural basis for multivalent attachment, the structure of the SpuA modules in complex with carbohydrate provides insight into the molecular basis for glycogen specificity. This report provides the first evidence that intracellular lung glycogen may be a novel target of pathogenic streptococci and thus provides a rationale for the identification of the streptococcal alpha-glucan-metabolizing machinery as virulence factors.

Amino Acid Sequence↗
PubMed2000

Aerococcus urinae in urinary tract infections.

Aerococcus urinae is a rarely reported pathogen, possibly due to difficulties in the identification of the organism. A. urinae is a gram-positive coccus that grows in pairs and clusters, produces alpha-hemolysis on blood agar, and is negative for catalase and pyrrolidonyl aminopeptidase. Some of these characteristics and its being absent from the databases of most commercial identification systems could allow A. urinae to be misidentified as a streptococcus, enterococcus, or staphylococcus. We report two cases of urinary tract infection (UTI) caused by A. urinae and characterize these isolates by morphology, biochemical testing, whole-cell fatty acid analysis, 16S rRNA gene sequencing, and antibiotic susceptibilities. Most patients infected with A. urinae are elderly males with predisposing conditions who present initially with UTI. Because A. urinae is resistant to sulfonamides, treatment could be inappropriate, with infections resulting in serious complications, including death. It is important for the clinician and the microbiologist to consider A. urinae a potential pathogen and proceed with thorough microbiological identification.

Aged↗
PubMed1989

Evaluation of the Cobas-Bact system for direct and rapid identification and antimicrobial susceptibility testing of gram-negative rods from positive blood culture broths.

A direct antimicrobial susceptibility test and a direct identification of positive blood culture broths for gram-negative rods confirmed with Gram stain by using a new instrument, Cobas-Bact, were compared with the conventional Kirby-Bauer agar diffusion disk method and with the in-house set of identification or API 20E, respectively. The bacterial pellet of centrifuged positive blood culture broth was used to inoculate a Cobas-Bact susceptibility and identification rotor. Bacteria from 206 cases of monomicrobial septicemia due to members of the family Enterobacteriaceae were tested. In 198 episodes (96%), direct identification and antimicrobial susceptibility testing results were obtained for the same bacterial pathogen within 5 h of detection. Of 204 direct identifications obtained, 177 (86.6%) were "high-confidence" correct identifications (percentage of likelihood [P] greater than or equal to 80%) and 25 (12.5%) "low-confidence" correct identifications (P less than 80%), whereas only 2 misidentifications occurred (1 Escherichia coli and 1 Proteus mirabilis). Direct susceptibility testing was performed in 199 episodes (96%), providing 1,885 antibiotic-microorganism combinations. Full agreement reached 86.3%, and essential agreement reached 92.8%. Minor discrepancies were found in 120 (6.5%) of the tests, major discrepancies were found in 127 (6.8%) tests, and very major discrepancies were found in only 7 (0.4%) tests. Subsequent MIC determinations in cases of major or very major discrepancies reduced the number of major discrepancies involving cephalosporins from 60 to 16, whereas all those involving aminoglycosides remained. Overall, this direct and rapid Cobas-Bact identification and susceptibility testing procedure offered accurate information with 5 to 6 h after the laboratory detection of bacteremia and septicemia due to members of the Enterobacteriacease.

Bacteriological Techniques↗
PubMed2003

Viral origin of antiphospholipid antibodies: endothelial cell activation and thrombus enhancement by CMV peptide-induced APL antibodies.

Our observations and those from others, give further support to our hypothesis that "autoimmune aPL" may be generated by immunization with products from bacteria or viruses after incidental exposure or infection. We also were able to generate APS-like syndrome in a strain of mice susceptible to autoimmunity, indicating that other factors such as genetics are likely to be involved in the development of APS. Furthermore, not all aPL antibodies generated by immunization with bacterial or viral products are pathogenic. Based on the clinical experience and on the numerous reports indicating presence of aPL in a large number of infectious diseases, it may be expected that not all aPL antibodies produced during infection will be pathogenic. We hypothesize that a limited number aPL antibodies induced by certain viral/bacterial products would be pathogenic in certain groups of predisposed individuals. Identification of these bacterial and/ or viral agents may help to find strategies for the prevention of production of aPL "pathogenic" antibodies. Alternatively, free peptides may be used to induce tolerance against aPL production.

Animals↗
PubMed2002

Identification and phylogenetic analysis of a glucose transporter gene family from the human pathogenic yeast Candida albicans.

We have identified a large family of glucose transporter genes (HGT1 to HGT20) from the human pathogenic yeast Candida albicans by screening of genomic sequences, reverse-transcription PCR assays, and phylogenetic analyses. The putative glucose transporter ORF sequences share among themselves 10-93% pairwise sequence identity and, in comparative analyses of predicted amino acid sequences, exhibit similarities to human and yeast transporters of the major facilitator superfamily (MFS): the predicted 12-transmembrane domains and sugar transporter signatures align closely to those of HXT transporters of Saccharomyces cerevisiae and GLUT transporters of humans, with amino acid residues at certain positions highly conserved throughout the families. Reverse-transcription PCR analyses demonstrated that the majority of the glucose transporters was transcribed in culture medium containing 2% glucose, while several were transcribed in the presence of low (0.2%) and/or high (5%) concentrations of glucose. Phylogenetic analyses revealed that there were three distinct clades of 20 HGT genes, which might represent three possible subfamilies. Additionally, HGT18 and HGT20 show a high overall sequence identity to the human GLUTs, indicating a possible functional convergence. We conclude that glucose transporters in C. albicans comprise a family of 20 known members, with variable transcription in response to glucose concentration.

Amino Acid Sequence↗