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PubMed1990

Changes in the spectrum of organisms causing bacteremia and fungemia in immunocompromised patients due to venous access devices.

A significant increase in the use of vascular access devices has changed the spectrum of organisms causing bacteremia and fungemia at Memorial Sloan-Kettering Cancer Center. This paper documents the 1988 laboratory experience with bacteremia and fungemia and contrasts some of that data with information obtained in 1984. In 1988, 439 tunnelled-catheters and 355 ports were inserted in patients; 2,778 organisms were subsequently recovered from 933 episodes of bacteremia and fungemia. Fifty-percent of the episodes of bacteremia and fungemia were vascular access device-related. Compared to 1984, the relative incidence of bacteremia due to gram-positive organisms increased from 33 to 43%, polymicrobic cultures increased from 24 to 27%, and the number of organisms with colony counts greater than 100 cfu/ml increased from 24 to 44%. In 1988, device-related sepsis was often caused by Acinetobacter spp., Bacillus spp., Corynebacterium spp., pseudomonads other than Pseudomonas aeruginosa, and coagulase-negative staphylococci. Infection was also caused by species of flavobacteria, Micrococcus, and Rhodotorula. Efforts required for identification of many of the newer pathogens have escalated material and personnel costs.

Adult↗
PubMed2005

Identification of Lactobacillus ruminus SPM0211 isolated from healthy Koreans and its antimicrobial activity against some pathogens.

The intestinal microbiota are important to the host with regard to resistance they impart against bacterial infections and their involvement in mediating metabolic functions. Lactic acid producing bacteria such as Lactobacillus play an important physiological role in these matters. The aim of the present study was to isolate Lactobacillus sp. that inhibits enteric pathogens. Initially, 17 isolates from healthy Koreans were collected on Lactobacillus selective medium. Resistance of the isolates to antibiotics including rifampicin, streptomycin, clindamycin and vancomycin was measured. One of the isolate was identified as Lactobacillus ruminus on the basis of bacterial cell morphology, cultural characteristic and biochemical characteristics, 16S rRNA sequence analysis and PCR-RAPD. Antimicrobial activity of the bacterium against Vancomycin Intermediate Resistant Staphylococcus aureus (VISA) and Vancomycin-Resistant Enterococci (VRE) was measured. About 10(4) cells of VISA or VRE were mixed with 1, 5, and 9 mL of L. ruminus SPM 0211 and the final volume was adjusted to 10 mL with brain heart infusion (BHI) broth. The cell suspension was incubated for 3, 6, 9, and 24 h, serially diluted and then plated on BHI agar plates. As numbers of L. ruminus SPM 0211 were increased, viable cell count of VISA and VRE decreased. The strongest antimicrobial activity of SPM 0211 was observed after 9 h incubation in any mixture, almost completely inhibiting the growth of these two bacteria. The results suggest that the freshly isolated L. ruminus SPM 0211 may be used as a pro-biotic microbe that prevents the colonization of enteric pathogens and can thereby promote good gastrointestinal health.

Adult↗
PubMed1999

DNA sequences corresponding to the ariel gene family of Entamoeba histolytica are not present in E. dispar.

For the identification of quantitative genetic differences between pathogenic Entamoeba histolytica and the closely related but nonpathogenic species E. dispar, a set of 68 independent probes that had previously been isolated from an E. histolytica cDNA library were hybridized to total genomic DNA of both amoeba species. Besides ehcp5, the sequence that codes for cysteine proteinase 5 and has recently been shown to be missing in E. dispar, only one of the probes exclusively reacted with E. histolytica DNA, whereas the remainder hybridized to DNA of both species. Sequence analysis revealed that the specific probe represents a copy of the multicopy ariel gene family, which has 80% sequence identity to srehp, the gene encoding a serine-rich E. histolytica membrane protein. In contrast to ariel, srehp is present in both amoeba species, suggesting that the ariel gene product might have a particular function in E. histolytica.

Animals↗
PubMed1985

Evaluation and diagnosis of acute infectious diarrhea.

The appropriate approach to the diagnosis and management of acute infectious diarrhea is determined by the frequency and setting of the illness, the recognizable causes or syndromes, the cost and yield of available diagnostic tests, and the treatability of the disease. Acute diarrhea affects everyone throughout the world from one to more than six times each year, depending on age, location, and living conditions. The range of identifiable viral, bacterial, and parasitic etiologies is great, and the cost of indiscriminate use of etiologic studies for diagnosis is prohibitive. Because of its insensitivity for many organisms and poor selection of cases for testing, routine stool culture has been one of the most costly and ineffective microbiologic tests; the cost per positive result has traditionally exceeded $900 to $1,000. The appropriate treatment for the vast majority of cases (independent of their cause) is simple and effective: oral glucose- and electrolyte-containing rehydration solution. On the basis of an appropriate history and understanding of pathogenesis, fecal specimens can be selectively obtained and promptly examined for leukocytes and parasites, and the common noninflammatory diarrheas can be separated from the inflammatory infections in order to focus further studies on the latter group. The bacteria for which specific antimicrobial therapy should be considered usually cause inflammatory diarrhea in the United States. Therefore, only when the history or fecal leukocyte findings indicates an inflammatory process is it appropriate to culture for the routine invasive bacterial pathogens. In sporadic inflammatory diarrhea, culture methods should include those for Campylobacter jejuni as well as Salmonella and Shigella. Several special circumstances may prompt a consideration of parasites (including Giardia, Entamoeba, Strongyloides, Cryptosporidium), Vibrio, Yersinia, Clostridium difficile, enterotoxigenic Escherichia coli, food-borne agents, or sexually transmitted pathogens. The practical value of specific identification of rotaviruses (by enzyme-linked immunosorbent assay, Rotazyme, or electron microscopy) is primarily epidemiologic, particularly in hospitalized infants or young children. Using such a selective approach to fecal culture will greatly increase its yield and can reduce the cost per positive result from $1,000 to less than $150.

Acute Disease↗
PubMed1991

Epitopes of the human malaria parasite P. falciparum carried on the surface of HBsAg particles elicit an immune response against the parasite.

The development of recombinant subunit vaccines against pathogenic organisms requires not only the identification of epitopes eliciting a protective immune response but also suitable carriers with adjuvant function. B- and T-cell epitopes of the malaria vaccine candidate gp190 were selected on the basis of a systematic search along the gp190 molecule and by computer prediction based on the amino acid sequence. Using some of the epitopes identified, we have redesigned the surface of the hepatitis B surface antigen lipoprotein particles by replacing the major antigenic determinants with malaria-specific sequences of up to 61 amino acids in length. Upon expression via vaccinia virus the hybrid particles elicit an anti-gp190 immune response in animals. Monoclonal antibodies derived from such infections recognize the native parasite.

Amino Acid Sequence↗
PubMed1994

Detection of respiratory syncytial virus infection in nasal aspirate samples by flow cytometry.

HYPOTHESES: (i) Flow cytometry has the potential for rapid detection of respiratory viral antigens. (ii) This technique can be applied to viral diagnosis in clinical samples. OBJECTIVES AND STUDY DESIGN: (i) To study the identification of six common respiratory viral pathogens by flow cytometry, in virus infected and uninfected cultured cells, as models of positive and negative clinical samples. (ii) To compare flow cytometry with the established techniques of viral isolation and immunofluorescent microscopy in the diagnosis of respiratory syncytial virus infection in 68 naso-pharyngeal aspirates taken from children and sent to the virology laboratory for routine virological diagnosis. RESULTS: (i) For each virus analysed, populations of infected and non-infected cells were clearly discernable, confirming potential for this method in rapid viral diagnosis in clinical samples. (ii) Two definitions were employed for a sample to be positive by flow cytometry, these were compared with the combined established techniques. The sensitivity, specificity, positive and negative predictive values of flow cytometry were 41%, 98%, 92% and 71% for the first definition and 74%, 88%, 80% and 84% for the second definition respectively. CONCLUSIONS: As tested in this study, flow cytometry is less sensitive than established techniques as well as recently developed rapid diagnostic techniques for the diagnosis of respiratory syncytial virus infection. Further evaluation of the potential of flow cytometry in rapid viral diagnosis is warranted.

Journal Article↗
PubMed2006

Heavy metal transporters in Hemiascomycete yeasts.

We have compiled all known heavy metal transporters of the yeast Saccharomyces cerevisiae and identified their orthologs in four other species spanning the entire Hemiascomycete phylum. The 213 transporters belong to 27 distinct phylogenetic families distributed within the three classes: channels, secondary porters (permeases) and transport ATPases. They are present in all cellular membranes: plasma membranes, vacuoles, mitochondria, endoplasmic reticulum, nucleus, Golgi and various cytoplasmic vesicles. The major physiological heavy metals transported are: iron, manganese, zinc, copper, arsenite and cadmium. The major subfamilies that comprise the highest number of transporters are Siderophore-Iron Transporters (SIT) and CT2 (conjugated ABC transporters). They transport heavy metals (iron or cadmium, respectively) conjugated to organic chelators such as siderophores or glutathione. Both subfamilies are considerably amplified in the yeast Yarrowia lipolytica. The pattern of expansion and restriction of the subfamilies during the evolution of the different species is highly variable. The phylogenetic trees of the major transporters subfamilies distinguish homogenous clusters of transporters suggesting that possible different physiological or mechanistic functions evolved independently. We also validated the use of the Hemiascomycetes heavy metal transporters for identification of orthologs transporters in the pathogenic Basidiomycetes Cryptococcus neoformans.

Ascomycota↗
PubMed2004

TROSPA, an Ixodes scapularis receptor for Borrelia burgdorferi.

The Lyme disease agent Borrelia burgdorferi naturally persists in a cycle that primarily involves ticks and mammals. We have now identified a tick receptor (TROSPA) that is required for spirochetal colonization of Ixodes scapularis. B. burgdorferi outer surface protein A, which is abundantly expressed on spirochetes within the arthropod and essential for pathogen adherence to the vector, specifically bound to TROSPA. TROSPA mRNA levels in ticks increased following spirochete infestation and decreased in response to engorgement, events that are temporally linked to B. burgdorferi entry into and egress from the vector. The blockade of TROSPA by TROSPA antisera or by the repression of TROSPA expression via RNA interference reduced B. burgdorferi adherence to the I. scapularis gut in vivo, thereby preventing efficient colonization of the vector and subsequently reducing pathogen transmission to the mammalian host. Identification of an I. scapularis receptor for B. burgdorferi is the first step toward elucidating arthropod ligands that are required for survival of spirochetes in nature.

Amino Acid Sequence↗
PubMed2004

Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva.

We describe the generation of an auto-annotated index of genes that are expressed in the salivary glands of four-day fed female adult Rhipicephalus appendiculatus ticks. A total of 9162 EST sequences were derived from an uninfected tick cDNA library and 9844 ESTs were from a cDNA library from ticks infected with Theileria parva, which develop in type III salivary gland acini. There were no major differences between abundantly expressed ESTs from the two cDNA libraries, although there was evidence for an up-regulation in the expression of some glycine-rich proteins in infected salivary glands. Gene ontology terms were also assigned to sequences in the index and those with potential enzyme function were linked to the Kyoto encyclopedia of genes and genomes database, allowing reconstruction of metabolic pathways. Several genes code for previously characterized tick proteins such as receptors for myokinin or ecdysteroid and an immunosuppressive protein. cDNAs coding for homologs of heme-lipoproteins which are major components of tick hemolymph were identified by searching the database with published N-terminal peptide sequence data derived from biochemically purified Boophilus microplus proteins. The EST data will be a useful resource for construction of microarrays to probe vector biology, vector-host and vector-pathogen interactions and to underpin gene identification via proteomics approaches.

Amino Acid Sequence↗
PubMed2004

Cellular targets of anti-alpha-enolase autoantibodies of patients with autoimmune retinopathy.

Autoantibodies against alpha-enolase are often associated with visual loss in patients with autoimmune retinopathy. Anti-recoverin autoantibodies have been the most extensively studied for their pathologic association with cancer-associated retinopathy (CAR). It has been shown that anti-recoverin antibodies penetrate retinal layers corresponding to the cellular location of recoverin and cause the death of photoreceptors and bipolar cells. However, the pathogenic effects of anti-alpha-enolase antibodies have not been studied. In this study, we tested the labeling and apoptotic effects of such autoantibodies on retinal cells. Serum antibodies against alpha-enolase from patients with autoimmune retinopathy were tested ex vivo and in vivo in Sprague-Dawley rats. Autoantibodies to alpha-enolase specifically labeled the retinal ganglion cells and inner nuclear layer cells. Using ex vivo experiments and intravitreal injections, we observed that antibodies were capable of penetrating retinal tissue to target ganglion cell and inner nuclear layers and, consequently, were able to induce cell death through an apoptotic process. The apoptotic nuclei detected by a DNA fragmentation assay and caspase 3-positive cells were co-localized in the ganglion cell layer and inner nuclear layer. The results showed that antibodies against alpha-enolase target antigens in these layers and induce the apoptotic death of sensitive cells. Rat retinal explants and the intravitreal injection of antibodies provide us with a good model to identify antibody pathogenic targets in the retina. Such identification may help explain the complex of clinical symptoms for autoimmune retinopathy mediated by autoantibody and may help guide treatment strategies.

Animals↗
PubMed2007

Prospective comparison of R-mix shell vial system with direct antigen tests and conventional cell culture for respiratory virus detection.

BACKGROUND AND OBJECTIVES: Conventional cell culture (CC) has limited clinical utility as a result of the extended incubation period often required for virus isolation. Alternative methodologies have been introduced in an effort to improve turnaround times. One such system, the R-mix shell vial is discussed herein. The study objectives were: (a) to establish R-mix testing parameters as compared to direct antigen testing (DAT) and CC, and (b) to assess technical aspects and cost of R-mix in a high volume clinical virology laboratory. STUDY DESIGN: A prospective analysis of respiratory samples submitted to the clinical virology laboratory between November 2004 and April 2005 was performed. All specimens were inoculated onto R-mix shell vials (SV) and CC tubes; and a subset also underwent DAT for influenza A and B and/or RSV. A retrospective estimated cost analysis was made. RESULTS: A total of 563 samples were included in the study, which collectively revealed a total of 207 viruses. Sensitivity of R-mix for seven major respiratory viruses ranged from 45% to 83% compared to CC and DAT, while mean time to detection (TTD) varied from 1.1 to 1.4 days. In addition to these viruses, 23 picornaviruses, 11 CMV isolates and 5 HSV isolates were detected by CC alone. CONCLUSIONS: The R-mix system has similar sensitivity as CC for the detection of parainfluenza 1-3 and influenza A/B while dramatically reducing the TTD. Furthermore, it is significantly more sensitive and produces more timely results for RSV than CC; yet, neither method offers a diagnostic benefit over rapid DAT for RSV detection. The sensitivity of R-mix for adenovirus appears to be significantly lower than that of CC. Lastly, methodologies other than R-mix must remain in place under circumstances where identification of other potential viral respiratory pathogens, including herpesviruses and picornaviruses, is desired.

Adenoviruses, Human↗
PubMed2004

Determination of species-specific sequences of superoxide dismutase A encoding gene sodA and chaperonin 60 encoding gene cpn60 for identification and phylogenetic analysis of Streptococcus phocae.

Species-specific PCR tests, based on the manganese-dependent superoxide dismutase A encoding gene (sodA) and the chaperonin 60 encoding gene (cpn60), were developed for the identification of Streptococcus phocae, a bacterial pathogen of seals. The selection of both oligonucleotide primer pairs was performed after amplification and sequencing of internal parts of both genes using universal oligonucleotide primers. The sequence studies of both genes additionally confirmed that S. phocae could taxonomically be classified to the pyogenic group of the genus Streptococcus.

Animals↗
PubMed2003

Naturally processed measles virus peptide eluted from class II HLA-DRB1*03 recognized by T lymphocytes from human blood.

This is the first report of the direct identification of a HLA-DRB1*03 measles-derived peptide from measles virus infected EBV-transformed B cells. We purified HLA-DR3-peptide complexes from EBV-B cells infected with measles virus (Edmonston strain) and sequenced the HLA-DR3-peptides by mass spectrometry. A class II peptide, derived from a measles phosphoprotein, ASDVETAEGGEIHELLRLQ (P1, residues 179-197), exhibited the capacity to stimulate peripheral blood mononuclear cells to proliferate. Our data provides direct evidence that the antigenic peptide of measles virus was processed by antigen-presenting cells, presented in the context of HLA class II molecules, and was recognized by peripheral blood T cells from healthy individuals previously immunized with measles vaccine. The approach described herein provides a useful methodology for the future identification of HLA-presented pathogen-derived epitopes using mass spectrometry. The study of cell-mediated immune responses to the measles-derived peptide in immune persons should provide significant insight into the design and development of new vaccines.

Adolescent↗
PubMed2001

A rapid method for the identification and differentiation of Helicoverpa nucleopolyhedroviruses (NPV Baculoviridae) isolated from the environment.

A diagnostic method is described for the identification and differentiation of nucleopolyhedrovirus (NPV) pathogens of Helicoverpa species (Lepidoptera: Noctuidae) isolated from the environment. The method is based on the polymerase chain reaction (PCR) used in conjunction with restriction fragment length polymorphism (RFLP) analysis and comprises three parts. The first part describes procedures for obtaining PCR quality viral DNA from individual diseased H. armigera cadavers recovered during bioassay analyses of soil and other types of environmental sample. These procedures were modified from standard techniques used for the routine purification and dissolution of NPV polyhedra and provided an overall PCR success rate of 95% (n=60). The second part describes the design of several sets of PCR primers for generating DNA amplification products from closely and distantly related NPVs. These PCR primers were designed from published DNA sequence data and from randomly cloned genomic DNA fragments isolated from a reference H. armigera SNPV (HaSNPV) isolate. The final part of the method describes how specific PCR products when digested with specific restriction endonuclease enzymes, can be used to generate diagnostic DNA profiles (haplotypes) that can be used both to identify heterologous NPVs e.g. Autographa californica MNPV and related viruses, and to differentiate genotypic variants of Helicoverpa SNPV. In the latter case, only two PCR products and four restriction digests were required to differentiate a reference set of 10 Helicoverpa SNPV isolates known to differ 0.1--3.5% at the nucleotide level. The diagnostic method described below marks the second part of a two-phase quantitative-diagnostic protocol that is now being applied to a variety of ecological investigations. In particular, its application should lead to a significant improvement in our understanding of the distribution and population genetics of Helicoverpa SNPVs in the Australian environment, as well as providing a sound basis for the design of pre- and post-release monitoring systems for genetically enhanced bioinsecticides. It is also likely that this method can be adapted readily to the study of other insect pathogen associations important economically.

Animals↗
PubMed2003

Extraction methods for lipopolysaccharides from Escherichia coli ATCC 25922 for quantitative analysis by capillary electrophoresis.

Lipopolysaccharides (LPS) are major constituents of the cell wall of Gram-negative bacteria. Capillary zone electrophoresis (CZE) was applied to distinguish between lipopolysaccharides extracted from Escherichia coli ATCC 25922 with various techniques. Extraction methods proposed by Westphal and Jann [Methods Carbohydr. Chem. 5 (1965) 83], Galanos et al. [Eur. J. Biochem. 9 (1969) 245], Ni Eidhin and Mouton [FEMS Microbiol. Lett. 110 (1993) 133] and Nichols [Infect. Immun. 62 (1994) 3753] for LPS preparation were evaluated. Electrophoresis buffers with varying pHs were applied to assess the structure stability of the extracted LPS samples. Variations in structural breakdown were apparent demonstrating that different extraction methods removed different LPS molecules. Furthermore, the results obtained proved the CZE useful as an analytical technique for LPS evaluation. The LPS removed with the Nichols extraction procedure presented a unique electrophorogram that could in future be applied in the rapid identification of Gram-negative foodborne pathogens.

Electrophoresis, Capillary↗
PubMed2003

Reduced amounts of LPS affect both stress tolerance and virulence of Salmonella enterica serovar Dublin.

Signature-tagged mutagenesis (STM) is a widely used technique for identification of virulence genes in bacterial pathogens. While this approach often generates a large number of mutants with a potential reduction in virulence a major task is subsequently to determine the mechanism by which the mutations influence virulence. Presently, we have characterised a Salmonella enterica serovar Dublin STM mutant that, in addition to having reduced virulence, was also impaired when growing under various stress conditions. The mutation mapped to the manC (rfbM) gene of the O-antigen gene cluster involved in O-antigen synthesis. The O-antigen is a component of the lipopolysaccharide (LPS) forming a unique constituent of the outer membrane of Gram-negative bacteria. While mutations in the O-antigen genes usually eliminate the entire O-antigen side chain we found that the transposon mutant produced intact O-antigen, however, the mutation reduced the amount of LPS.

Animals↗
PubMed2003

Laboratory diagnosis of invasive mycoses.

Rising numbers of immunocompromised patients have led to an ever-increasing population at risk of invasive fungal disease. Much has been achieved in the laboratory diagnosis of these infections, such as advances in blood culture systems, and the development of new biochemical, antigen detection assays, and molecular methodologies. More standardized susceptibility testing guidelines provide for better therapeutic interventions. In an era of economic cutbacks in health care, future challenges include the development of cost-effective and technically simplified systems, which provide early detection and identification of common and emerging fungal pathogens. It will, however, take some time to establish the clinical relevance of these new methodologies in different patient populations.

Culture Media↗
PubMed2002

The use of direct cDNA selection to rapidly and effectively identify genes in the fungus Aspergillus fumigatus.

Aspergillus fumigatus is one of the causes of invasive lung disease in immunocompromised individuals. To rapidly identify genes in this fungus, including potential targets for chemotherapy, diagnostics, and vaccine development, we constructed cDNA libraries. We began with non-normalized libraries, then to improve this approach we constructed a normalized cDNA library using direct cDNA selection. Normalization resulted in a reduction of the frequency of clones with highly expressed genes and an enrichment of underrepresented cDNAs. Expressed sequence tags generated from both the original and the normalized libraries were compared with the genomes of Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans, indicating that a large proportion of A. fumigatus genes do not have orthologs in these fungal species. This method allowed the expeditious identification of genes in a fungal pathogen. The same approach can be applied to other human or plant pathogens to rapidly identify genes without the need for genomic sequence information.

Aspergillus fumigatus↗