bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical and Prognostic Importance of Serotyping
Mycobacterium avium-Mycobacterium intracellulare
Complex Isolates in Human Immunodeficiency Virus-Negative Patients
Authors: Maekura Ryoji , Okuda Yoshinari , Hirotani Atsusi , Kitada Seigo , Hiraga Touru , Yoshimura Kenji , Yano Ikuya , Kobayashi Kazuo , Ito Masami
Published: July 2005

We studied whether the serotypes of
Mycobacterium avium-Mycobacterium intracellulare
complex (MAC) isolates determine the prognosis for pulmonary MAC disease. We prospectively monitored a cohort of 68 patients with pulmonary MAC disease for whom the serotype-specific glycopeptidolipids in isolates were identified using thin-layer chromatography and fast atom bombardment mass-spectrometry in 1990 and 1995. Serovar 4
Mycobacterium avium
was detected in 40/68 patients (58.8%). Other serotypes were serotypes 1 (five cases), 6 (three cases), 8 (seven cases), 9 (three cases), 14 (four cases), and 16 (six cases). Patients with serovar 4 were significantly (
P
< 0.01) younger (63.0 ± 9.8 years) than patients with other serotypes (71.8 ± 10.3). Patients who failed treatment had a significantly poorer prognosis than other patients. There were no cases of MAC-related death in the cured group. Chest radiographic findings progressively worsened in 36 (90%) of patients with serotype 4, and 14/36 died from respiratory failure caused by pulmonary
Mycobacterium avium
disease. The patients with serotype 4 had a significantly poorer prognosis than patients with other serotypes. These results show that both the outcome of chemotherapy and the serotypes of MAC isolates are important for assessing the prognosis of pulmonary MAC disease.
Purification and Characterization of Nipah Virus Nucleocapsid Protein Produced in Insect Cells
Authors: Eshaghi Majid , Tan Wen Siang , Ong Swee Tin , Yusoff Khatijah
Published: July 2005

The nucleocapsid (N) protein of Nipah virus (NiV) is a major constituent of the viral proteins which play a role in encapsidation, regulating the transcription and replication of the viral genome. To investigate the use of a fusion system to aid the purification of the recombinant N protein for structural studies and potential use as a diagnostic reagent, the NiV N gene was cloned into the pFastBacHT vector and the His-tagged fusion protein was expressed in Sf9 insect cells by recombinant baculovirus. Western blot analysis of the recombinant fusion protein with anti-NiV antibodies produced a band of approximately 62 kDa. A time course study showed that the highest level of expression was achieved after 3 days of incubation. Electron microscopic analysis of the NiV recombinant N fusion protein purified on a nickel-nitrilotriacetic acid resin column revealed different types of structures, including spherical, ring-like, and herringbone-like particles. The light-scattering measurements of the recombinant N protein also confirmed the polydispersity of the sample with hyrdrodynamic radii of small and large types. The optical density spectra of the purified recombinant fusion protein revealed a high
A
260
/
A
280
ratio, indicating the presence of nucleic acids. Western blotting and enzyme-linked immunosorbent assay results showed that the recombinant N protein exhibited the antigenic sites and conformation necessary for specific antigen-antibody recognition.
Cysticercosis Immunodiagnosis Using 18- and 14-Kilodalton Proteins from
Taenia crassiceps
Cysticercus Antigens Obtained by Immunoaffinity Chromatography
Authors: Espíndola Noeli Maria , Iha Alberto Hiroshi , Fernandes Irene , Takayanagui Osvaldo Massaiti , Machado Luís dos Ramos , Livramento José Antônio , Mendes Maia Antônio Augusto , Peralta José Mauro , Vaz Adelaide José
Published: July 2005

Monoclonal antibodies (MAb) against
Taenia crassiceps
and
Taenia solium
cysticerci were produced and showed cross-reactivity with a 14-kDa protein from
T. solium
and with 18- and 14-kDa proteins from
T. crassiceps
. These MAbs and antibodies from cerebrospinal fluid (CSF) as well as serum samples from patients with neurocysticercosis (NC) reacted with 18- and 14-kDa
T. crassiceps
proteins purified by immunoaffinity chromatography using a Sepharose column coupled with MAbs (anti-excretory/secretory or anti-vesicular fluid antigens). Immunoaffinity-purified 18- and 14-kDa proteins were used in the design of a diagnostic enzyme-linked immunosorbent assay (ELISA) to detect antibodies in 23 CSF and 20 serum samples from patients with NC, showing 100% sensitivity. The test specificity was determined using 42 noninflammatory CSF samples and 70 inflammatory CSF samples from patients with other neurological disorders (OND), showing 100% and 99.1% (confidence interval, 97.3% to 100%) specificity, respectively. A false-positive CSF sample result in the OND group was from a human immunodeficiency virus-positive patient with meningoencephalitis. By using serum samples from 194 healthy individuals, the specificity was 100%. Analysis of an additional 16 serum samples from individuals with other parasitic diseases (13 with intestinal parasitosis and 3 with schistosomiasis) showed negative results. Three (10%) serum samples from patients with hydatidosis were positive in our ELISA and in ELISA with
T. solium
cysticerci antigens. Two of them were also positive by immunoblotting. The use of 18- and 14-kDa
T. crassiceps
immunoaffinity-purified proteins for detection of anti-cysticercus antibodies in CSF and/or serum samples using an ELISA system showed a good performance and high specificity for serum samples, dispensing with the use of confirmatory tests, such as immunoblotting, for checking specificity.
Genomic Deletions Classify the Beijing/W Strains as a Distinct Genetic Lineage of
Mycobacterium tuberculosis
Authors: Tsolaki Anthony G. , Gagneux Sebastien , Pym Alexander S. , Goguet de la Salmoniere Yves-Olivier L. , Kreiswirth Barry N. , Van Soolingen Dick , Small Peter M.
Published: July 2005

Beijing/W strains of
Mycobacterium tuberculosis
are geographically widespread and hypervirulent. To enhance our understanding of their origin and evolution, we sought phylogenetically informative large sequence polymorphisms (LSPs) within the Beijing/W family. Comparative whole-genome hybridization of Beijing/W strains revealed 21 LSPs, 7 of which were previously unreported. We show that some of these LSPs are unique event polymorphisms that can be used to define and subdivide the Beijing/W family. One LSP (RD105) was seen in all Beijing/W strains and thus serves as a useful marker for the identification of this family of strains. Additional LSPs (RD142, RD150, and RD181) further divided this family into four monophyletic subgroups, demonstrating a deeper population structure than previously appreciated. All Beijing/W strains were also observed to have an intact
pks15/1
gene that is involved in the biosynthesis of a phenolic glycolipid, a putative virulence factor. A simple PCR assay using these Beijing/W strain-defining deletions will facilitate molecular epidemiological studies and may assist in the identification of the molecular basis of phenotypes associated with this important lineage of
M. tuberculosis
.
Genotyping of Methicillin-Resistant
Staphylococcus aureus
Strains from Two Hospitals in Bangalore, South India
Authors: Arakere Gayathri , Nadig Savitha , Swedberg Göte , Macaden Ragini , Amarnath Satish K. , Raghunath Dasarathy
Published: July 2005

Methicillin-resistant
Staphylococcus aureus
(MRSA) is a major nosocomial pathogen in India, and up to 70% methicillin resistance has been reported from hospitals in various parts of India. Hospitals use phenotyping for the most part, and molecular genotyping is not done. Here we report on the genotyping of 82 single-patient isolates from two hospitals in Bangalore, South India, for the first time. Most of the strains possessed type III or IIIA staphylococcal cassette chromosome (
SCCmec
) cassettes, and we did not detect strains with type I, IA, or II cassettes. Most isolates also contained the type III cassette chromosome recombinase (
ccr
) AB region. Multilocus sequence typing (MLST) and staphylococcal protein A (
spa
) typing of a selected number of isolates have been carried out. Although most isolates that were chosen for MLST and
spa
typing had the same patterns, they were quite diverse in their pulsed-field gel electrophoresis (PFGE) patterns. PFGE, MLST, and
spa
typing of the Indian strains revealed that they are related to the previously described Hungarian and Brazilian clones.
Characterization of a Novel P[25],G11 Human Group A Rotavirus
Authors: Rahman Mustafizur , Matthijnssens Jelle , Nahar Sharifun , Podder Goutam , Sack David A. , Azim Tasnim , Van Ranst Marc
Published: July 2005

A novel rotavirus strain (Dhaka6) isolated from a 21-year-old Bangladeshi male patient was characterized by sequence analysis of its VP7 and VP4 gene segments. Phylogenetic analysis of the VP7 gene of the Dhaka6 strain revealed a common evolutionary lineage with porcine G11 rotavirus strains. This isolate is the first reported G11 rotavirus strain infecting a human host. Comparison of the VP4 gene sequences with all currently recognized 24 different P genotypes revealed only low nucleotide (54 to 71%) and amino acid (52 to 76%) sequence identities. This lack of high sequence similarity in the VP4 gene indicates that the Dhaka6 isolate represents a new group A rotavirus P genotype, to which we propose assignment of the designation P[25].
Characterization of a Shiga Toxin-, Intimin-, and Enterotoxin Hemolysin-Producing
Escherichia coli
ONT:H25 Strain Commonly Isolated from Healthy Cattle
Authors: Sheng Haiqing , Davis Margaret A. , Knecht Hannah J. , Hancock Dale D. , Van Donkersgoed Joyce , Hovde Carolyn J.
Published: July 2005

Among bovine fecal and recto-anal mucosal swab samples cultured in our laboratory for
Escherichia coli
O157:H7, we frequently isolated
E. coli
organisms that were phenotypically similar to the O157:H7 serotype as non-sorbitol fermenting and negative for β-glucuronidase activity but serotyped O nontypeable:H25 (ONT:H25). This study determined the prevalence and virulence properties of the
E. coli
ONT:H25 isolates. Among dairy and feedlot cattle (
n
= 170) sampled in Washington, Idaho, and Alberta, Canada, the percentage of animals culture positive for
E. coli
ONT:H25 ranged from 7.5% to 22.5%, compared to the prevalence of
E. coli
O157:H7 that ranged from 0% to 15%. A longitudinal 8-month study of dairy heifers (
n
= 40) showed that 0 to 15% of the heifers were culture positive for
E. coli
O157:H7, while 15 to 22.5% of the animals were culture positive for
E. coli
ONT:H25. As determined by a multiplex PCR, the
E. coli
ONT:H25 isolates carried a combination of virulence genes characteristic of the enterohemorrhagic
E. coli
, including intimin, translocated intimin receptor, Stx2, and hemolysin (
eae-
β,
tir
,
stx
2vh-a
, and
hly
).
E. coli
ONT:H25 isolates from diverse geographic locations and over time were fingerprinted by separating XbaI-restricted chromosomal DNA by pulsed-field gel electrophoresis (PFGE) separation. Two strains of
E. coli
ONT:H25 were highly similar by PFGE pattern. Experimental inoculation of cattle showed that
E. coli
ONT:H25, like
E. coli
O157:H7, colonized the bovine recto-anal junction mucosa for more than 4 weeks following a single rectal application of bacteria.
Comparative Recovery of Microorganisms from BacT/ALERT Plastic and Glass FA and FN Blood Culture Bottles
Authors: Riley J. A. , Heiter B. J. , Bourbeau P. P.
Published: July 2005

bioMerieux, Inc., has recently introduced plastic bottles to replace glass bottles for use in the BacT/ALERT blood culture system. We compared the performance of the plastic to the glass bottles in a large clinical evaluation. Two blood cultures were collected from each patient, one using glass FA (aerobic) and FN (anaerobic) bottles and one using plastic FA and FN bottles. Of the 4,040 sets of four bottles collected, 3,110 contained the recommended 8 to 12 ml of blood, yielding 524 microorganisms with 359 judged to be clinically significant. Of the 359 significant organisms, 255 were recovered in either one or two bottles from both pairs of bottles in a set while 56 organisms were recovered only from the glass bottles and 48 were recovered only from the plastic bottles (
P
, not significant [NS]). Of the 286 significant organisms recovered only in the FA bottles (glass and plastic), 180 were recovered in both bottles, 57 in the plastic bottles only, and 49 in the glass bottles only (
P
, NS). Of the 303 significant organisms recovered in the FN bottles only (glass and plastic), 212 were recovered in both bottles, 46 in the plastic bottles only, and 45 in the glass bottles only (
P
, NS). For individual organisms, the only significant difference in recovery was obtained for
Escherichia coli
, with more isolates recovered in the FN plastic than in the FN glass bottles (
P
= 0.02). These data suggest that recovery of microorganisms with plastic FA/FN bottles is at least equal to that with glass FA/FN bottles while offering greater safety for users.
Characterization of Vancomycin-Resistant
Enterococcus faecium
Isolates from Broiler Poultry and Pig Farms in England and Wales
Authors: Garcia-Migura L. , Pleydell E. , Barnes S. , Davies R. H. , Liebana E.
Published: July 2005

This study aimed to investigate the occurrence and molecular epidemiology of vancomycin-resistant
Enterococcus faecium
(VREF) isolates on poultry and pig farms in England and Wales. A total of 217 VREF isolates were obtained from fresh feces and environmental swabs collected from conventional and organic farms. A predominant pulsed-field gel electrophoresis (PFGE) profile was found for each VREF-positive farm, together with less frequent types. All isolates presented the
vanA
genotype and were
esp
negative. Seventy-six percent of the VREF isolates were additionally resistant to nine or more antimicrobials, presenting a diverse range of resistance phenotypes. The multiresistance traits did not appear to be specific to individual farms or sample types (i.e., environmental or fecal), nor did they correlate with any specific PFGE type. Ninety-three percent of the isolates were resistant to penicillin, 89% were resistant to tetracycline, 87.5% were resistant to erythromycin, and 50% were resistant to quinupristin-dalfospristin (Synercid). The lack of clonality among these populations may suggest the horizontal transfer of resistance genes and/or a dynamic replacement of clonal lines rather than persistence.
Sensitive and Rapid Detection of Herpes Simplex Virus and Varicella-Zoster Virus DNA by Loop-Mediated Isothermal Amplification
Authors: Kaneko Hisatoshi , Iida Tomohiro , Aoki Koki , Ohno Shigeaki , Suzutani Tatsuo
Published: July 2005

Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method in which reagents react rapidly and efficiently, with a high specificity, under isothermal conditions. We used a LAMP assay for the detection of herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), and varicella-zoster virus (VZV). The virus specificities of primers were confirmed by using 50 HSV-1, 50 HSV-2, and 8 VZV strains. The assay was performed for 45 min at 65°C. The LAMP assay had a 10-fold higher sensitivity than a PCR assay. An analysis of nucleotide sequence variations in the target and primer regions used for the LAMP assay indicated that 3 of 50 HSV-1 strains had single nucleotide polymorphisms. No HSV-2 or VZV strains had nucleotide polymorphisms. Regardless of the sequence variation, there were no differences in sensitivity with the HSV-1-specific LAMP assay. To evaluate the application of the LAMP assay for clinical diagnosis, we tested clinical samples from 40 genital herpes patients and 20 ocular herpes patients. With the LAMP assay, 41 samples with DNA extraction and 26 direct samples without DNA extraction were identified as positive for HSV-1 or HSV-2, although 37 samples with DNA extraction and just one without DNA extraction were positive by a PCR assay. Thus, the LAMP assay was less influenced than the PCR assay by the presence of inhibitory substances in clinical samples. These observations indicate that the LAMP assay is very useful for the diagnosis of HSV-1, HSV-2, and VZV infections.
Enterobacter hormaechei
subsp.
oharae
subsp. nov.,
E. hormaechei
subsp.
hormaechei
comb. nov., and
E. hormaechei
subsp.
steigerwaltii
subsp. nov., Three New Subspecies of Clinical Importance
Authors: Hoffmann Harald , Stindl Sibylle , Ludwig Wolfgang , Stumpf Anita , Mehlen Andre , Monget Daniel , Pierard Denis , Ziesing Stefan , Heesemann Jürgen , Roggenkamp Andreas , Schleifer Karl H.
Published: July 2005

Six species and six additional genovars are combined within the so-called
Enterobacter cloacae
complex, with one of them being the species
Enterobacter hormaechei
. In a recent population genetic study, two genetic clusters were found in close phylogenetic proximity to the genetic cluster of
E. hormaechei
. In order to prove the hypothesis that these three genetic clusters belong to the same species, we performed cross-hybridization experiments in microplates with DNAs of representatives of each genetic cluster. The close phylogenetic relationship among the clusters was reflected by their relatively low Δ

T
m

values, ranging from 0.3 to 4.8, confirming the hypothesis that the clusters are parts of the same species. These clusters can be distinguished from the other species of the
E. cloacae
complex, which have Δ

T
m

values of 5.6 to 10.3. Forty-eight
E. hormaechei
strains from the different genetic clusters were phenotypically characterized with 129 biochemical tests. In this way,
E. hormaechei
could be differentiated from the other species of the
E. cloacae
complex because it tests negative in the 3-hydroxy-butyrate test. The three genetic clusters of
E. hormaechei
could also be differentiated from each other by using phenotypic tests. Hence, we propose three new subspecies of
E. hormaechei
corresponding to genetic clusters VI, VII, and VIII of the
E. cloacae
complex.
E. hormaechei
subsp.
hormaechei
comb. nov. corresponds to the original species description, as it gives negative results for the adonitol,
d
-arabitol,
d
-sorbitol, and
d
-melibiose tests and a positive result for the dulcitol test.
E. hormaechei
subsp.
oharae
subsp. nov. gives negative results for the dulcitol, adonitol, and
d
-arabitol tests and positive results for the
d
-sorbitol and
d
-melibiose tests.
E. hormaechei
subsp.
steigerwaltii
subsp. nov. gives a negative result for the dulcitol test and positive results for the adonitol,
d
-arabitol,
d
-sorbitol, and
d
-melibiose tests. Among the members of the
E. cloacae
complex,
E. hormaechei
seems to be the species most frequently recovered from clinical specimens.
Use of a Locked-Nucleic-Acid Oligomer in the Clamped-Probe Assay for Detection of a Minority
Pfcrt
K76T Mutant Population of
Plasmodium falciparum
Authors: Senescau Alice , Berry Antoine , Benoit-Vical Françoise , Landt Olfert , Fabre Richard , Lelièvre Joël , Cassaing Sophie , Magnaval Jean-François
Published: July 2005

Given the emergence of drug resistance and the high rate of polyclonal microorganism infections, the availability of a fast and sensitive test to detect minority mutant populations would be an improvement in the diagnosis of infectious diseases. A clamped-probe real-time PCR assay to diagnose the
Plasmodium falciparum
K76T mutation in clone populations was developed, using a wild-type-specific locked-nucleic-acid-containing oligomer to suppress wild-type PCR amplification and to enhance melting analysis with a mutation-specific detection probe.
Identification of Two Distinct Hybridization Groups in the Genus
Hafnia
by 16S rRNA Gene Sequencing and Phenotypic Methods
Authors: Janda J. Michael , Abbott Sharon L. , Bystrom Sue , Probert Will S.
Published: July 2005

A collection of 52 strains belonging to the
Hafnia alvei
complex were subjected to molecular (16S rRNA gene sequencing) and biochemical analysis. Based upon 16S rRNA gene sequencing results, two genetic groups were identified which correspond with previously recognized DNA hybridization group 1 (ATCC 13337
T
and ATCC 29926;
n
= 23) and DNA hybridization group 2 (ATCC 29927;
n
= 29). Of 46 biochemical tests used to characterize hafniae, 19 reactions (41%) yielded variable results. Of these 19 tests, 6 were determined to have discriminatory value in the separation of DNA groups 1 and 2, with malonate utilization found to be the most differential test. Test results of malonate utilization alone correctly assigned 90% of
Hafnia
isolates to their correct DNA group.
Multilocus DNA Sequence Comparisons Rapidly Identify Pathogenic Molds
Authors: Rakeman Jennifer L. , Bui Uyen , LaFe Karen , Chen Yi-Ching , Honeycutt Rhonda J. , Cookson Brad T.
Published: July 2005

The increasing incidence of opportunistic fungal infections necessitates rapid and accurate identification of the associated fungi to facilitate optimal patient treatment. Traditional phenotype-based identification methods utilized in clinical laboratories rely on the production and recognition of reproductive structures, making identification difficult or impossible when these structures are not observed. We hypothesized that DNA sequence analysis of multiple loci is useful for rapidly identifying medically important molds. Our study included the analysis of the D1/D2 hypervariable region of the 28S ribosomal gene and the internal transcribed spacer (ITS) regions 1 and 2 of the rRNA operon. Two hundred one strains, including 143 clinical isolates and 58 reference and type strains, representing 43 recognized species and one possible new species, were examined. We generated a phenotypically validated database of 118 diagnostic alleles. DNA length polymorphisms detected among ITS1 and ITS2 PCR products can differentiate 20 of 33 species of molds tested, and ITS DNA sequence analysis permits identification of all species tested. For 42 of 44 species tested, conspecific strains displayed >99% sequence identity at ITS1 and ITS2; sequevars were detected in two species. For all 44 species, identifications by genotypic and traditional phenotypic methods were 100% concordant. Because dendrograms based on ITS sequence analysis are similar in topology to 28S-based trees, we conclude that ITS sequences provide phylogenetically valid information and can be utilized to identify clinically important molds. Additionally, this phenotypically
validated database of ITS sequences will be useful for identifying new species of pathogenic molds.
Use of an Automated Multiple-Locus, Variable-Number Tandem Repeat-Based Method for Rapid and High-Throughput Genotyping of
Staphylococcus aureus
Isolates
Authors: Francois Patrice , Huyghe Antoine , Charbonnier Yvan , Bento Manuela , Herzig Sébastien , Topolski Ivan , Fleury Bénédicte , Lew Daniel , Vaudaux Pierre , Harbarth Stephan , van Leeuwen Willem , van Belkum Alex , Blanc Dominique S. , Pittet Didier , Schrenzel Jacques
Published: July 2005

Fast and reliable genotyping methods that allow real-time epidemiological surveillance would be instrumental to monitoring of the spread of methicillin-resistant
Staphylococcus aureus
. We describe an automated variable-number tandem repeat-based method for the rapid genotyping of
Staphylococcus aureus
. Multiplex PCR amplifications with eight primer pairs that target gene regions with variable numbers of tandem repeats were resolved by microcapillary electrophoresis and automatically assessed by cluster analysis. This genotyping technique was evaluated for its discriminatory power and reproducibility with clinical isolates of various origins, including a panel of control strains previously characterized by several typing methods and collections from either long-term carriers or defined nosocomial outbreaks. All steps of this new procedure were developed to ensure a rapid turnaround time and moderate cost. The results obtained suggest that this rapid approach is a valuable tool for the genotyping of
S. aureus
isolates in real time.
Dissemination of Methicillin-Resistant Staphylococci among Healthy Japanese Children
Authors: Hisata Ken , Kuwahara-Arai Kyoko , Yamanoto Munetaka , Ito Teruyo , Nakatomi Yasuo , Cui Longzhu , Baba Tadashi , Terasawa Masahiko , Sotozono Chie , Kinoshita Shigeru , Yamashiro Yuichiro , Hiramatsu Keiichi
Published: July 2005

Methicillin-resistant
Staphylococcus aureus
(MRSA), regarded as a tenacious pathogen in the hospital, has recently become increasingly prevalent as a community pathogen. We evaluated the prevalence and characteristics of methicillin-resistant staphylococci in the Japanese community by testing nasal samples of 818 children of five day care centers and two kindergartens in three districts. We found that methicillin-resistant staphylococci are already prevalent among healthy children. Among 818 children, 35 children (4.3%) carried MRSA and 231 children (28.2%) carried methicillin-resistant coagulase-negative staphylococci (MRC-NS). The types of staphylococcal cassette chromosome
mec
(SCC
mec
) found among 44 MRSA isolates were as follows: type IIa, 11 isolates; type IIb, 19 isolates; and type IV, 14 isolates. The type IIb SCC
mec
element was a new SCC
mec
element found in this study. Eleven (25%) strains which belonged to clonal complex 5 (CC5) carried type IIa SCC
mec
, and they produced type 2 coagulase and toxic shock syndrome toxin 1. They were indistinguishable from health care-associated MRSA (H-MRSA) strains in Japan, represented by strain N315. On the other hand, 33 (75%) strains, most of which belonged to CC78 or CC91, carried small SCC
mec
elements, such as type IIb or type IV, and they produced type 1 or type 3 coagulase and exfoliative toxin. The data indicated that MRSA clones distinct from H-MRSA have disseminated in healthy children. The fact that MRC-NS strains were prevalent in the community suggested that they might serve as a reservoir for the SCC
mec
element carried by MRSA strains disseminated in the community.
Characterization of a New Species of Adenovirus in Falcons
Authors: Schrenzel Mark , Oaks J. Lindsay , Rotstein Dave , Maalouf Gabriel , Snook Eric , Sandfort Cal , Rideout Bruce
Published: July 2005

In 1996, a disease outbreak occurred at a captive breeding facility in Idaho, causing anorexia, dehydration, and diarrhea or sudden death in 72 of 110 Northern aplomado falcons (
Falco femoralis septentrionalis
) from 9 to 35 days of age and in 6 of 102 peregrine falcons (
Falco peregrinus
) from 14 to 25 days of age. Sixty-two Northern aplomado and six peregrine falcons died. Epidemiologic analyses indicated a point source epizootic, horizontal transmission, and increased relative risk associated with cross-species brooding of eggs. Primary lesions in affected birds were inclusion body hepatitis, splenomegaly, and enteritis. The etiology in all mortalities was determined by molecular analyses to be a new species of adenovirus distantly related to the group I avian viruses, serotypes 1 and 4,
Aviadenovirus
. In situ hybridization and PCR demonstrated that the virus was epitheliotropic and lymphotropic and that infection was systemic in the majority of animals. Adeno-associated virus was also detected by PCR in most affected falcons, but no other infectious agents or predisposing factors were found in any birds. Subsequent to the 1996 epizootic, a similar disease caused by the same adenovirus was found over a 5-year period in orange-breasted falcons (
Falco deiroleucus
), teita falcons (
Falco fasciinucha
), a merlin (
Falco columbarius
), a Vanuatu peregrine falcon (
Falco peregrinus nesiotes
), and gyrfalcon × peregrine falcon hybrids (
Falco rusticolus
/
peregrinus
) that died in Wyoming, Oklahoma, Minnesota, and California. These findings indicate that this newly recognized adenovirus is widespread in western and midwestern North America and can be a primary pathogen in different falcon species.
Development of a Novel Protein Microarray Method for Serotyping
Salmonella enterica
Strains
Authors: Cai H. Y. , Lu L. , Muckle C. A. , Prescott J. F. , Chen S.
Published: July 2005

An antibody microarray assay was developed for
Salmonella
serotyping based on the Kauffmann-White scheme. A model (8 by 15) array was constructed using 35 antibodies for identification of 20 common
Salmonella
serovars and evaluated using 117 target and 73 nontarget
Salmonella
strains. The assay allowed complete serovar identification of 86 target strains and partial identification of 30 target strains and allowed exclusion of the 73 nontarget strains from the target serovars.
Comparison of Conventional Susceptibility Testing, Penicillin-Binding Protein 2a Latex Agglutination Testing, and
mecA
Real-Time PCR for Detection of Oxacillin Resistance in
Staphylococcus aureus
and Coagulase-Negative
Staphylococcus
Authors: Miller Melissa B. , Meyer Heather , Rogers Elaine , Gilligan Peter H.
Published: July 2005

Penicillin-binding protein (PBP) 2a latex agglutination was compared with conventional susceptibility testing and
mecA
real-time PCR for the detection of oxacillin resistance in
Staphylococcus aureus
. Inoculum volume and induction with oxacillin were PBP 2a testing variables. For coagulase-negative
Staphylococcus
, an increased inoculum volume of 10 μl greatly reduced the number of isolates requiring induction.
Repeated Occurrence of Diverse Extended-Spectrum β-Lactamases in Minor Serotypes of Food-BorneSalmonella entericasubsp.enterica
Authors: Politi L. , Tassios P. T. , Lambiri M. , Kansouzidou A. , Pasiotou M. , Vatopoulos A. C. , Mellou K. , Legakis N. J. , Tzouvelekis L. S.
Published: July 2005

Screening of Greek nontyphoid salmonellae from 2000 to 2002 yielded three extended-spectrum β-lactamase (ESBL)-producing human isolates.Salmonella entericaserotype Brandenburg harbored a multiresistant SHV-5 gene-carrying plasmid.S. entericaserotype Blockley andS. entericaserotype Hadar harbored a TEM-52 gene-carrying plasmid. AnS. entericaserotype Virchow strain producing plasmid-mediated CTX-M-32 was isolated twice from poultry end products. All ESBL plasmids were self-transferable and carried by clones currently common in Greece.
Evaluation of Real-Time Reverse Transcriptase PCR and Real-Time Loop-Mediated Amplification Assays for Severe Acute Respiratory Syndrome Coronavirus Detection
Authors: Poon Leo L. M. , Wong Bonnie W. Y. , Chan Kwok H. , Ng Stella S. F. , Yuen Kwok Y. , Guan Yi , Peiris J. S. Malik
Published: July 2005

We compared the performance of a recently established real-time loop-mediated amplification (LAMP) assay with the one from a highly sensitive quantitative PCR assay. None of these assays produced false-positive results in this study. For samples isolated from patients within the first 3 days of disease onset, the detection rate of the quantitative PCR assay was higher (14 of 15 were positive) than the LAMP assay (9 of 15 were positive). By contrast, the detection rates of these assays toward specimens sampled from patients with more than 3 days of illness were similar (32 of 44 for PCR and 33 of 44 for LAMP were positive). The simpler operation of LAMP might be a possible solution for on-site diagnosis.
Use of PCR Analyses To Define the Distribution of
Ralstonia
Species Recovered from Patients with Cystic Fibrosis
Authors: Coenye Tom , Spilker Theodore , Reik Rebecca , Vandamme Peter , LiPuma John J.
Published: July 2005

Two new PCR assays (for
Ralstonia
species and
Ralstonia respiraculi
), together with previously published PCR assays, were used to assess
Ralstonia
isolates recovered from 111 cystic fibrosis patients.
Ralstonia mannitolilytica
accounted for 46% of isolates, while
R. respiraculi
and
Ralstonia pickettii
accounted for 19% and 18%, respectively.
Ralstonia basilensis
and
Ralstonia metallidurans
, species not previously recovered from human samples, were also identified.
Age-Related Prevalence and Distribution of Nontuberculous Mycobacterial Species among Patients with Cystic Fibrosis
Authors: Pierre-Audigier Catherine , Ferroni Agnès , Sermet-Gaudelus Isabelle , Le Bourgeois Muriel , Offredo Catherine , Vu-Thien Hoang , Fauroux Brigitte , Mariani Patricia , Munck Anne , Bingen Edouard , Guillemot Didier , Quesne Gilles , Vincent Véronique , Berche Patrick , Gaillard Jean-Louis
Published: July 2005

We studied the prevalence and species distribution of nontuberculous mycobacteria (NTM) in relation to age in 385 patients with cystic fibrosis (CF) (mean age ± standard deviation [range], 12.0 ± 6.1 [1 to 24] years; sex ratio, 0.53) attending three Parisian centers. The overall prevalence of NTM in sputum was 8.1% (31 out of 385). The following NTM were isolated (
n
= 33):
Mycobacterium abscessus
(
n
= 13, 39.4%),
Mycobacterium avium
complex (MAC) (
n
= 7, 21.2%),
Mycobacterium gordonae
(
n
= 6, 18.2%), and other (
n
= 7, 21.2%). Sixteen patients met the American Thoracic Society microbiological criteria for NTM infection, including 11 patients positive for
M. abscessus
, 4 for MAC, and 1 for MAC and
Mycobacterium kansasii
. The overall prevalence of NTM was significantly lower in patients under 15 years old than for patients equal to or more than 15 years old (4.8 versus 14.9%, respectively;
P
= 0.001).
M. abscessus
was isolated at all ages, while MAC was not recovered before 15 years (prevalence of 0.0 and 5.2% in patients aged 1 to 14 and 15 to 24, respectively;
P
= 0.001).
Possible Tick-Borne Human Enterovirus Resulting in Aseptic Meningitis
Authors: Freundt Eric C. , Beatty Douglas C. , Stegall-Faulk Teresa , Wright Stephen M.
Published: July 2005

Enterovirus-specific genetic sequences were isolated from two
Amblyomma americanum
tick pools. Identical genetic sequences were later obtained from cerebrospinal fluid of a patient with aseptic meningitis and a recent history of tick attachment. These observations suggest the possibility of an emerging tick-borne human enterovirus associated with aseptic meningitis.
Multiplex PCR for Identification of Seven
Streptococcus pneumoniae
Serotypes Targeted by a 7-Valent Conjugate Vaccine
Authors: O'Halloran Damien M. , Cafferkey Mary T.
Published: July 2005

Here we describe a
Streptococcus pneumoniae
one-step multiplex PCR assay which identifies by amplicon size the seven capsular polysaccharide serotypes targeted by the 7-valent conjugate vaccine. The multiplex PCR assay was used to blindly assay clinical isolates recovered during 1999 in the Republic of Ireland from cases of invasive disease whose serotypes were previously determined by classical methods.
Molecular Evidence that Nasal Carriage of
Staphylococcus aureus
Plays a Role in Respiratory Tract Infections of Critically Ill Patients
Authors: Corne Philippe , Marchandin Hélène , Jonquet Olivier , Campos Josiane , Bañuls Anne-Laure
Published: July 2005

The relationship between nasal
Staphylococcus aureus
carriage and lower respiratory tract infections was studied in 16 critically ill patients.
S. aureus
strains from nasal and bronchial samples were characterized by pulsed-field gel electrophoresis. In all but one case, nasal and bronchial strains were genetically identical in the same patients.
Intra- and Interpatient Variability of the
hsp65
and 16S-23S Intergenic Gene Region in
Mycobacterium abscessus
Strains from Patients with Cystic Fibrosis
Authors: König Brigitte , Tammer Ina , Sollich Veronika , König Wolfgang
Published: July 2005

To establish the exact pathogenic role of
Mycobacterium abscessus
in cystic fibrosis (CF), molecular tests are required for accurate identification. Forty-eight
M. abscessus
isolates from seven patients with CF were analyzed by sequence analysis for sequence variants within the
hsp65
gene and the 16S-23S intergenic sequence (ITS). We detected two different
hsp65
genes and correspondingly two ITS sequevars belonging to
M. abscessus
type I and type II.
Identification of
Vibrio parahaemolyticus
Pandemic Group-Specific DNA Sequence by Genomic Subtraction
Authors: Okura Masatoshi , Osawa Ro , Arakawa Eiji , Terajima Jun , Watanabe Haruo
Published: July 2005

A genomic subtraction between a pandemic
Vibrio parahaemolyticus
and a nonpandemic strain that seemed to be clonally related was performed. A subtractive DNA fragment was identified to be a part of a 16-kbp insertion sequence which was present in almost all pandemic strains but not in nonpandemic strains tested.
Toxoplasmosis after Renal Transplantation: Implications of a Missed Diagnosis
Authors: Wulf M. W. H. , van Crevel R. , Portier R. , ter Meulen C. G. , Melchers W. J. G. , van der Ven A. , Galama J. M. D.
Published: July 2005

We describe a renal transplant patient with a primary
Toxoplasma gondii
infection presenting as pneumonitis, with subsequent chorioretinitis and encephalitis. The diagnostic challenges of
T. gondii
infection in immunocompromised patients are discussed.
Fatal Reactivation of Postnatal Cytomegalovirus Infection with Rapid Emergence of Ganciclovir Resistance in an Infant after Allogeneic Stem Cell Transplantation
Authors: Voigt Sebastian , Michel Detlef , Kershaw Olivia , Kühl Jörn-Sven , Mertens Thomas , Ebell Wolfram , Meisel Helga
Published: July 2005

Human cytomegalovirus (HCMV) can cause serious problems after hematopoietic stem cell transplantation. The death of a pediatric transplant recipient after reactivation of a postnatal HCMV infection with bilateral retinitis and pneumonitis is described. Sequencing of the HCMV UL97 region revealed a compartment-specific mutation (H520Q) in urine conferring ganciclovir resistance.
Transmission ofMycobacterium tuberculosisfrom Human to Cattle
Authors: Ocepek Matjaž , Pate Mateja , Žolnir-Dovč Manca , Poljak Mario
Published: July 2005

We describe the first transmission ofMycobacterium tuberculosisfrom human to cattle confirmed by molecular typing of isolates involved in the transmission. IS6110-based restriction fragment length polymorphism analysis showed that the isolates from the cattle and farm worker who suffered from pulmonary tuberculosis 1 year prior to this case were the same strains.
Simultaneous Detection of “
Rickettsia mongolotimonae
” in a Patient and in a Tick in Greece
Authors: Psaroulaki Anna , Germanakis Antonis , Gikas Achilleas , Scoulica Efstathia , Tselentis Yannis
Published: July 2005

Rickettsia conorii
, a spotted fever group rickettsia which is transmitted by
Rhipicephalus
sp. complex ticks, was considered until now the only pathogenic rickettsia prevalent in Greece. Here, we report the presence of “
Rickettsia mongolotimonae
” (proposed name) detected simultaneously in a patient and in a
Hyalomma anatolicum excavatum
tick, sampled on the patient.
Discordant Rise in Galactomannan Antigenemia in a Patient with Resolving Aspergillosis, Renal Failure, and Ongoing Hemodialysis
Authors: El Saleeby Chadi M. , Allison Kim J. , Knapp Katherine M. , Walsh Thomas J. , Hayden Randall T.
Published: July 2005

We describe the case of a patient with improving invasive aspergillosis and paradoxically rising serum galactomannan levels in the presence of chronic renal failure and ongoing hemodialysis. Dialysate tested negative for galactomannan, demonstrating the inability of treatments such as hemodialysis to clear
Aspergillus
antigen from serum. In patients with renal failure and aspergillosis, rising serum galactomannan levels may not necessarily signify progressive infection.
Bacteremia Caused by an Undescribed Species of
Janibacter
Authors: Loubinoux Julien , Rio Bernard , Mihaila Liliana , Foïs Elena , Le Fleche Anne , Grimont Patrick A. D. , Marie Jean-Pierre , Bouvet Anne
Published: July 2005

A yellow-pigmented rod- to coccoid-shaped coryneform microorganism was isolated from the blood of a patient with acute myeloid leukemia. It was identified by 16S rRNA gene sequencing as a previously undescribed species of
Janibacter
. The isolate was susceptible to penicillins, aminoglycosides, fluoroquinolones, and glycopeptides.
Involvement of Streptococcal Mitogenic Exotoxin Z in Streptococcal Toxic Shock Syndrome
Authors: Yang Lily , Thomas Mark , Woodhouse Andrew , Martin Diana , Fraser John D. , Proft Thomas
Published: July 2005

We report a nonfatal case of streptococcal toxic shock syndrome (STSS) caused by a
Streptococcus pyogenes emm118
strain encoding a novel variant of streptococcal mitogenic exotoxin Z (SMEZ-34). This variant was responsible for the major mitogenic activity in the cell culture supernatant. Patient sera showed seroconversion toward SMEZ, implying a role for this toxin in STSS.
SELF-ORGANIZING MAP-BASED DISCOVERY AND VISUALIZATION OF HUMAN ENDOGENOUS RETROVIRAL SEQUENCE GROUPS
Authors: OJA MERJA , SPERBER GÖRAN O. , BLOMBERG JONAS , KASKI SAMUEL
Published: July 2005

About 8 per cent of the human genome consists of human endogenous retroviral sequences (HERVs), which are remains from ancient infections. The HERVs may give rise to transcripts or affect the expression of human genes. The first step in understanding HERV function is to classify HERVs into families. In this work we study the relationships of existing HERV families and detect potentially new HERV families. A Median Self-Organizing Map (SOM), a SOM for non-vectorial data, is used to group and visualize a collection of 3661 HERVs. The SOM-based analysis is complemented with estimates of the reliability of the results. A novel trustworthiness visualization method is used to estimate which parts of the SOM visualization are reliable and which not. The reliability of extracted interesting HERV groups is verified by a bootstrap procedure suitable for SOM visualization-based analysis. The SOM detects a group of epsilonretroviral sequences and a group of ERV9, HERVW, and HUERSP3 sequences which suggests that ERV9 and HERVW sequences may have a common origin.
MULTI/INFINITE DIMENSIONAL NEURAL NETWORKS, MULTI/INFINITE DIMENSIONAL LOGIC THEORY
Authors: MURTHY GARIMELLA RAMA
Published: July 2005

A mathematical model of an arbitrary multi-dimensional neural network is developed and a convergence theorem for an arbitrary multi-dimensional neural network represented by a fully symmetric tensor is stated and proved. The input and output signal states of a multi-dimensional neural network/logic gate are related through an energy function, defined over the fully symmetric tensor (representing the connection structure of a multi-dimensional neural network). The inputs and outputs are related such that the minimum/maximum energy states correspond to the output states of the logic gate/neural network realizing a logic function. Similarly, a logic circuit consisting of the interconnection of logic gates, represented by a block symmetric tensor, is associated with a quadratic/higher degree energy function. Infinite dimensional logic theory is discussed through the utilization of infinite dimension/order tensors.
THE COMBINED USE OF SELF-ORGANIZING MAPS AND ANDREWS' CURVES
Authors: GARCÍA-OSORIO C. , FYFE C.
Published: July 2005

The use of self-organizing maps to analyze data often depends on finding effective methods to visualize the SOM's structure. In this paper we propose a new way to perform that visualization using a variant of Andrews' Curves. Also we show that the interaction between these two methods allows us to find sub-clusters within identified clusters. Perhaps more importantly, using the SOM to pre-process data by identifying gross features enables us to use Andrews' Curves on data sets which would have previously been too large for the methodology. Finally we show how a three way interaction between the human user and these two methods can be a valuable exploratory data analysis tool.
A BAYESIAN RECURRENT NEURAL NETWORK FOR UNSUPERVISED PATTERN RECOGNITION IN LARGE INCOMPLETE DATA SETS
Authors: ORRE ROLAND , BATE ANDREW , NORÉN G. NIKLAS , SWAHN ERIK , ARNBORG STEFAN , EDWARDS I. RALPH
Published: July 2005

A recurrent neural network, modified to handle highly incomplete training data is described. Unsupervised pattern recognition is demonstrated in the WHO database of adverse drug reactions. Comparison is made to a well established method, AutoClass, and the performances of both methods is investigated on simulated data. The neural network method performs comparably to AutoClass in simulated data, and better than AutoClass in real world data. With its better scaling properties, the neural network is a promising tool for unsupervised pattern recognition in huge databases of incomplete observations.
GRADIENT DOMAIN CONTEXT ENHANCEMENT FOR FIXED CAMERAS
Authors: ILIE ADRIAN , RASKAR RAMESH , YU JINGYI
Published: July 2005

We propose a class of enhancement techniques suitable for scenes captured by fixed cameras. The basic idea is to increase the information density in a set of low quality images by extracting the context from a higher-quality image captured under different illuminations from the same viewpoint. For example, a night-time surveillance video can be enriched with information available in daytime images. We also propose a new image fusion approach to combine images with sufficiently different appearance into a seamless rendering. Our method ensures the fidelity of important features and robustly incorporates background contexts, while avoiding traditional problems such as aliasing, ghosting and haloing. We show results on indoor as well as outdoor scenes.
CLUSTERING MULTIPLE IMAGE SEQUENCES WITH A SEQUENCE-TO-SEQUENCE SIMILARITY MEASURE
Authors: SHAN YING , SAWHNEY HARPREET S. , POPE ART
Published: July 2005

We propose a novel similarity measure of two image sequences based on shapeme histograms. The idea of shapeme histogram has been used for single image/texture recognition, but is used here to solve the sequence-to-sequence matching problem. We develop techniques to represent each sequence as a set of shapeme histograms, which captures different variations of the object appearances within the sequence. These shapeme histograms are computed from the set of 2D invariant features that are stable across multiple images in the sequence, and therefore minimizes the effect of both background clutter, and 2D pose variations. We define sequence similarity measure as the similarity of the most similar pair of images from both sequences. This definition maximizes the chance of matching between two sequences of the same object, because it requires only part of the sequences being similar. We also introduce a weighting scheme to conduct an implicit feature selection process during the matching of two shapeme histograms. Experiments on clustering image sequences of tracked objects demonstrate the efficacy of the proposed method.
ESTIMATING APPROXIMATE AVERAGE SHAPE AND MOTION OF DEFORMING OBJECTS WITH A MONOCULAR VIEW
Authors: KIM TAEONE , HONG KI-SANG
Published: July 2005

With a monocular view, the nonrigid recovery of 3D motion and time-varying shapes of a deforming object may be impossible without any prior information, because ambiguous, multiple solutions exist for motion and shapes which produce the same projection image. In this paper, as a preceding step to the nonrigid recovery of a deforming object, we develop an approach for estimating the approximate average shape and motion of the object. This reasonably solves the ambiguity problem in nonrigid recovery. By investigating the internal structures of nonrigid objects, we introduce a novel concept, called DoN (Degree of Nonrigidity). Based on this, we propose an iterative certainty reweighted factorization method. In addition, we refine and improve the method by reformulating it in a robust manner to cope with outliers existing in the tracked features. Finally, we present some experimental results on both synthetic data and a real video sequence.
SUBSPACE-BASED FACE RECOGNITION: OUTLIER DETECTION AND A NEW DISTANCE CRITERION
Authors: CHEN PEI , SUTER DAVID
Published: July 2005

Illumination effects, including shadows and varying lighting, make the problem of face recognition challenging. Experimental and theoretical results show that the face images under different illumination conditions approximately lie in a low-dimensional subspace, hence principal component analysis (PCA) or low-dimensional subspace techniques have been used. Following this spirit, we propose new techniques for the face recognition problem, including an outlier detection strategy (mainly for those points not following the Lambertian reflectance model), and a new error criterion for the recognition algorithm. Experiments using the Yale-B face database show the effectiveness of the new strategies.