bluuebunny/crossref_metadata_2025 huggingface dataset:
Routes of Transmission of Swine Hepatitis E Virus in Pigs
Authors: Kasorndorkbua C. , Guenette D. K. , Huang F. F. , Thomas P. J. , Meng X.-J. , Halbur P. G.
Published: November 2004

Hepatitis E virus (HEV) is believed to be transmitted by the fecal-oral route in pigs. To date, in experiments, HEV has been transmitted successfully only by the intravenous or intrahepatic route. To assess the route of HEV transmission, 27 pigs were separated into nine groups of three pigs. Positive-control pigs were inoculated intravenously with swine HEV and served as the source of HEV for the other groups. Uninoculated contact pigs were placed in the positive-control group. On three consecutive days, naïve pigs were inoculated using samples collected from the positive-control pigs at 9, 10, and 11 days postinoculation. The tonsils and nasal mucosa of each positive-control pig were swabbed and that swab was used to rub the tonsils and nasal and ocular mucosa of naïve pigs. The positive-control pigs were also injected with bacterin, and the same needle was used to immediately inject naïve pigs. Feces were collected from positive controls and fed by oral gavage to naïve pigs. Weekly fecal and serum samples from each pig were tested for anti-HEV antibodies and HEV RNA. All positive-control pigs shed the virus in feces; two pigs were viremic and seroconverted to anti-HEV. All contact control pigs shed the virus in feces; two seroconverted and one became viremic. One of three pigs in the fecal-oral exposure group shed the virus in feces and seroconverted. Pigs exposed to the contaminated needles or the tonsil and nasal secretion swabs remained negative. This is the first report of experimental fecal-oral transmission of HEV in swine.
Development and Evaluation of an Enzyme-Linked Immunosorbent Assay for Quantifying Antibodies to Japanese Encephalitis Virus Nonstructural 1 Protein To Detect Subclinical Infections in Vaccinated Horses
Authors: Konishi Eiji , Shoda Mizue , Ajiro Naoko , Kondo Takashi
Published: November 2004

Antibodies to Japanese encephalitis virus (JEV) nonstructural 1 (NS1) protein constitute a marker of natural JEV infection among populations vaccinated with inactivated JE vaccine. In Japan, with few recent human JE cases, the natural infection rate is critical to evaluate the necessity of continuing JE vaccination. A sensitive immunochemical staining method for detecting NS1 antibodies in individuals naturally and subclinically infected with JEV was previously established. Here, an enzyme-linked immunosorbent assay (ELISA) to detect NS1 antibodies in equine sera was developed and evaluated as an alternative to immunostaining. By this method, NS1 antigens contained in culture fluids from cells stably transfected with the
NS1
and
NS2A
genes were captured by a rabbit anti-NS1 polyclonal antibody. Three nanograms per well of NS1 antigen, corresponding to 1:2 to 1:8 dilutions of the culture fluid, was sufficient for testing. ELISA values were obtained by a single-serum dilution (1:100), which correlated with ELISA titers obtained by an endpoint method. Under a tentative cutoff value (0.122) statistically calculated from NS1 antibody levels of horses in an area where JEV is not endemic, a high level of qualitative agreement (85.3%) was obtained between the ELISA and immunostaining methods. A significant correlation coefficient (0.799;
P
< 0.001) was also obtained between the two methods. Three experimentally infected horses seroconverted no later than 13 to 23 days postinfection, whereas 4 field horses infected during an epizootic remained positive for NS1 antibodies for at least 40 weeks. Our results indicate that the ELISA used here was sufficiently sensitive to detect subclinical infections in vaccinated equine populations.
Outbreak of Carbapenem-Resistant
Pseudomonas aeruginosa
Producing VIM-8, a Novel Metallo-β-Lactamase, in a Tertiary Care Center in Cali, Colombia
Authors: Crespo M. P. , Woodford N. , Sinclair A. , Kaufmann M. E. , Turton J , Glover J. , Velez J. D. , Castañeda C. R. , Recalde M. , Livermore D. M.
Published: November 2004

The prevalence of imipenem resistance among
Pseudomonas aeruginosa
isolates at a 195-bed tertiary care medical center in Cali, Colombia, rose from 2% in 1996 to 28% in 1997 and to over 40% in 2003. Many isolates showed high-level multiresistance, and phenotypic characterization suggested the spread of a predominant strain with minor variants. Sixty-six resistant isolates collected between February 1999 and July 2003 from hospitalized patients (
n
= 54) and environmental samples (
n
= 12) were subjected to a fuller analysis. Genetic fingerprints were compared by pulsed-field gel electrophoresis (PFGE) of SpeI-digested genomic DNA, and
bla
IMP
and
bla
VIM
genes were sought by PCR. PFGE and serotyping indicated that 52 of the 66 isolates belonged to a single strain, with 82% similarity; the PFGE pattern for this organism was designated pattern A. Two further pairs of isolates represented single strains; the remaining nine isolates were unique, and in the case of one isolate, no satisfactory PFGE profile could be obtained. The pattern A isolates were mostly of serotype O12 and were highly resistant to imipenem (MICs, 32 to >256 μg/ml), with this resistance decreased eightfold or more in the presence of EDTA. They yielded amplicons with
bla
VIM
-specific primers, and sequencing of DNA from a representative isolate revealed
bla
VIM-8
, a novel allele with three polymorphisms compared with the sequence of
bla
VIM-2
. Two of these nucleotide changes were silent, but the third determined a Thr139Ala substitution. Only 4 of 13 resistant isolates (2 clinical isolates and 2 environmental isolates) assigned to other PFGE types carried
bla
VIM
alleles, whereas the others were less multiresistant and mostly had lower levels of imipenem resistance (MICs, ≤32 μg/ml) which was not significantly reduced by EDTA. No
bla
IMP
alleles were detected. During 2003, when the environmental study was undertaken, serotype O12 isolates with
bla
VIM
were recovered from sinks and stethoscopes in the most-affected units, although not from the hands of staff; the problem declined once these reservoirs were disinfected and hygienic precautions were reinforced.
Antimicrobial Susceptibility Testing of
Acinetobacter
spp. by NCCLS Broth Microdilution and Disk Diffusion Methods
Authors: Swenson Jana M. , Killgore George E. , Tenover Fred C.
Published: November 2004

Although both broth microdilution (BMD) and disk diffusion (DD) are listed by NCCLS as acceptable methods for testing
Acinetobacter
spp. for antimicrobial susceptibility, few studies have compared the results generated by the two methods. We tested 196 isolates of
Acinetobacter
spp. from nine U.S. hospitals and from the Centers for Disease Control culture collection by using BMD and DD and clinically appropriate antimicrobial agents. Categorical results for amikacin, ciprofloxacin, gatifloxacin, gentamicin, imipenem, levofloxacin, meropenem, tobramycin, and trimethoprim-sulfamethoxazole were comparable for the two methods: there was only one very major (VM) error, with tobramycin, and only one major (M) error, with meropenem, when DD results were compared with BMD results. However, VM errors were frequent with the β-lactams and β-lactam-β-lactam inhibitor combinations, while M errors were often observed with tetracyclines. For BMD, tests frequently exhibited subtle growth patterns that were difficult to interpret, especially for β-lactams. If subtle growth (i.e., granular, small button, or “starry” growth) was considered positive, error rates between BMD and DD were unacceptably high for ampicillin-sulbactam (VM error, 9.8%; minor [m] error, 16.1%), piperacillin (VM error, 5.7%; m error, 13.5%), piperacillin-tazobactam (VM error, 9.3%; m error, 12.9%), ceftazidime (VM error, 6.2%; m error, 11.4%), cefepime (VM error, 6.2%; m error, 13.0%), cefotaxime (m error, 21.2%), ceftriaxone (m error, 23.3%), tetracycline (M error, 11.4%; m error, 32.1%), and doxycycline (M error, 2.6%). When subtle growth patterns were ignored, the agreement still did not achieve acceptable levels. To determine if the problems with BMD testing occurred in other laboratories, we sent frozen BMD panels containing β-lactam drugs and nine isolates to six labs with experience in performing BMD and DD. Among these laboratories, cefepime MICs ranged from ≤8 to ≥32 μg/ml for four of the nine strains, confirming the problem in interpreting BMD results. Discrepancies between the categorical interpretations of BMD and DD tests were noted primarily with cefepime and piperacillin, for which the BMD results were typically more resistant. Clinical laboratories should be aware of these discrepancies. At present, there are no data to indicate which method provides more clinically relevant information.
Evaluation of a Candidate International Standard Preparation for Human Anti-
Toxoplasma
Immunoglobulin G
Authors: Rigsby Peter , Rijpkema Sjoerd , Guy Edward C. , Francis Janet , Gaines Das Rose
Published: November 2004

A freeze-dried human serum preparation containing immunoglobulin G (IgG) to
Toxoplasma gondii
was assessed for its suitability as an international reference reagent in an international collaborative study by 24 laboratories from 17 countries. This candidate standard was compared with the third international standard (IS) for human anti-
Toxoplasma
serum, TOXM, with the previous second IS, TOXS, and with a range of other serum samples. Samples were tested with the Sabin-Feldman dye test and a range of agglutination assays and enzyme immunoassays. This study emphasizes the need for appropriate standards if intermethod agreement of estimates is to be achieved. On the basis of the results of this study, the preparation was established by the World Health Organization as the first IS for human anti-
Toxoplasma
IgG, with an assigned potency of 20 IU per ampoule of total anti-
Toxoplasma
antibodies.
Emergence, Spread, and Characterization of Phage Variants of Epidemic Methicillin-Resistant
Staphylococcus aureus
16 in England and Wales
Authors: Murchan S. , Aucken H. M. , O'Neill G. L. , Ganner M. , Cookson B. D.
Published: November 2004

Epidemic methicillin-resistant
Staphylococcus aureus
16 (EMRSA-16) and EMRSA-15 are the two most important and prevalent EMRSA strains found in the United Kingdom and have also been found in a number of European countries and the United States. We describe for the first time the spread of an EMRSA strain (EMRSA-16) from its point of origin in one hospital to the surrounding hospitals and regions over the following 2 years. In the first 18 months after its original appearance, 136 hospitals referred EMRSA-16 isolates for typing, and interhospital and intraregional spread were reported: it was more prevalent in males between 60 and 80 years old and was isolated from sputum and throat more often than EMRSA-15. Important characteristics, e.g., carriage of the enterotoxin A (
sea
) and toxic shock syndrome toxin (
tst
) genes and production of urease, are described. Phage-variant strains of EMRSA-16 which share some of the characteristics of the classical strain, including toxin carriage and urease production, emerged, but without genotypic investigations, their relationship could only be inferred. A total of 129 clinical isolates from 52 hospitals, collected between March 1998 and April 1999 and representing classical EMRSA-16 (49 isolates) or phage variants (80 isolates), were compared by phage typing, pulsed-field gel electrophoresis (PFGE) following SmaI macrorestriction, antimicrobial susceptibility testing, urease production, and PCR detection of toxin gene carriage. PFGE analysis revealed 29 profiles, A1 to A29, with A1 representing the prototypic strain, NCTC 13143. All other profiles differed from A1 by 1 to 6 bands, but some differed from each other by up to 10 bands.
Effects of Intrapartum Penicillin Prophylaxis on Intestinal Bacterial Colonization in Infants
Authors: Jauréguy Françoise , Carton Mathieu , Panel Pierre , Foucaud Pierre , Butel Marie-José , Doucet-Populaire Florence
Published: November 2004

Early-onset group B streptococcal (GBS) infections remain a leading cause of morbidity and mortality in infants. To prevent the vertical transmission of GBS and neonatal GBS infection, guidelines recommend intrapartum penicillin or amoxicillin prophylaxis. This intrapartum antibiotic prophylaxis (IAP) is suspected to favor colonization by antibiotic-resistant bacteria. However, the effects of this prophylaxis on the patterns of acquisition of gastrointestinal bacterial flora in infants have never been studied. We collected stool samples from 3-day-old infants born to mothers who received intrapartum amoxicillin (antibiotic-exposed group;
n
= 25) and to untreated mothers (non-antibiotic-exposed group;
n
= 25). The groups were matched for factors known to affect intestinal microbial colonization: gestational age, type of delivery, and type of feeding. Qualitative and quantitative differential analyses of the bacterial flora in stool samples were performed. Similar numbers of infants in the non-antibiotic-exposed and antibiotic-exposed groups were colonized by aerobic bacteria and amoxicillin-resistant enterobacteria (75 and 77%, respectively) (
P
= 0.79). In contrast, significantly fewer infants in the antibiotic-exposed group than in the non-antibiotic-exposed group were colonized by anaerobic bacteria, especially
Clostridium
(12 and 40%, respectively) (
P
< 0.05). Regarding intestinal bacterial colonization, the differences between antibiotic-exposed and non-antibiotic-exposed infants were remarkably few. The only statistically significant effect was the reduced initial bacterial colonization by
Clostridium
in the antibiotic-exposed group. In our study, the use of IAP did not favor colonization by β-lactam-resistant bacteria. However, further evaluations are required to highlight the potential risks of the widespread use of antibiotics to prevent early-onset GBS infection.
Genetic Recombination between Two Genotypes of Genogroup III Bovine Noroviruses (BoNVs) and Capsid Sequence Diversity among BoNVs and Nebraska-Like Bovine Enteric Caliciviruses
Authors: Han Myung Guk , Smiley Jeffrey R. , Thomas Christopher , Saif Linda J.
Published: November 2004

To determine the genogroups and genotypes of bovine enteric caliciviruses (BECVs) circulating in calves, we determined the complete capsid gene sequences of 21 BECVs. The nucleotide and predicted amino acid sequences were compared phylogenetically with those of known human and animal enteric caliciviruses. Based on these analyses, 15 BECVs belonged to
Norovirus
genogroup III and genotype 2 (GIII/2) and were genetically distinct from human
Norovirus
GI and GII. Six BECVs had capsid gene sequences similar to that of the unclassified Nebraska (NB)-like BECV. The 15 bovine noroviruses (BoNVs) were more closely related to Bo/NLV/Newbury-2/76/UK (GIII/2) and other known genotype 2 BoNVs than to genotype 1 Bo/NLV/Jena/80/DE. The BoNV Bo/CV521-OH/02/US showed high nucleotide and amino acid identities (84 and 94%, respectively) with the capsid gene of Bo/NLV/Newbury-2/76/UK, whereas the nucleotide and amino acid sequences of the RNA polymerase gene were more closely related to those of Bo/NLV/Jena/80/DE (77 and 87% identities, respectively) than to those of Bo/NLV/Newbury-2/76/UK (69 and 69% identities, respectively), suggesting that Bo/CV521-OH/02/US is a genotype 1-2 recombinant. Gene conversion analysis by the recombinant identification program and SimPlot also predicted that Bo/CV521-OH/02/US was a recombinant. Six NB-like BECVs shared 88 to 92% nucleotide and 94 to 99.5% amino acid identities with the NB BECV in the capsid gene. The results of this study demonstrate genetic diversity in the capsid genes of BECVs circulating in Ohio veal calves, provide new data for coinfections with distinct BECV genotypes or genogroups, and describe the first natural BoNV genotype 1-2 recombinant, analogous to the previously reported human norovirus recombinants.
Validation of the Use of Middlebrook 7H10 Agar, BACTEC MGIT 960, and BACTEC 460 12B Media for Testing the Susceptibility of
Mycobacterium tuberculosis
to Levofloxacin
Authors: Sanders Cynthia A. , Nieda Rachel R. , Desmond Edward P.
Published: November 2004

Levofloxacin, the active
l
-isomer of the quinolone ofloxacin, is now widely accepted for treatment of multidrug-resistant tuberculosis. Because the drug is now widely used, we sought to establish susceptibility test conditions for
Mycobacterium tuberculosis
against levofloxacin by the traditional reference method, agar proportion (AP), the commonly used BACTEC 460 radiometric system, and the newer BACTEC MGIT 960 method. To determine the stability of levofloxacin in the two newer test systems (BACTEC 460 and BACTEC MGIT 960), media containing subinhibitory levels of levofloxacin were prepared and stored at 4 and 37°C for 14 days. The stored media were inoculated with H37Rv, and the drug activity was compared to freshly prepared media. Results show that levofloxacin is stable over the course of testing. Next, optimum levofloxacin test concentrations were determined for AP, BACTEC 460, and BACTEC MGIT 960 methods. MICs were determined for 32 pan-susceptible isolates of
M. tuberculosis
obtained from presumably untreated patients and 14 quinolone-resistant isolates. The levofloxacin-resistant strains either were isolated from patients who remained culture-positive despite treatment with a quinolone agent (six strains) or contained known mutations in
gyrA
(eight strains). Levofloxacin MICs resulted in a bimodal pattern with values for resistant strains consistently higher than those for pan-susceptible strains. Results show that levofloxacin concentrations of 2 μg/ml (BACTEC 460 and BACTEC MGIT 960) and 1 μg/ml (AP) inhibited the growth of all pan-susceptible strains while permitting the growth of all levofloxacin-resistant strains. Confirmatory tests with a subset of pan-susceptible and levofloxacin-resistant isolates validated the selected test concentrations.
Type III Secretion Phenotypes of
Pseudomonas aeruginosa
Strains Change during Infection of Individuals with Cystic Fibrosis
Authors: Jain Manu , Ramirez Daniel , Seshadri Roopa , Cullina Joanne F. , Powers Catherine A. , Schulert Grant S. , Bar-Meir Maskit , Sullivan Christine L. , McColley Susanna A. , Hauser Alan R.
Published: November 2004

Pseudomonas aeruginosa
is a frequent cause of respiratory exacerbations in individuals with cystic fibrosis. An important virulence determinant of this pathogen is its type III protein secretion system. In this study, the type III secretion properties of 435
P. aeruginosa
respiratory isolates from 56 chronically infected individuals with cystic fibrosis were investigated. Although it had been previously reported that 75 to 90% of
P. aeruginosa
isolates from patients with hospital-acquired pneumonia secreted type III proteins, only 12% of isolates from cystic fibrosis patients did so, with nearly all of these isolates secreting ExoS and ExoT but not ExoU. Despite the low overall prevalence of type III protein-secreting isolates, at least one secreting isolate was cultured from one-third of cystic fibrosis patients. Interestingly, the fraction of cystic fibrosis patient isolates capable of secreting type III proteins decreased with duration of infection. Although 90% of isolates from the environment, the presumed reservoir for the majority of
P. aeruginosa
strains that infect patients with cystic fibrosis, secreted type III proteins, only 49% of isolates from newly infected children, 18% of isolates from chronically infected children, and 4% of isolates from chronically infected adults with cystic fibrosis secreted these proteins. Within individual patients, isolates of clonal origin differed in their secretion phenotypes, indicating that as strains persisted in cystic fibrosis patient airways, their type III protein secretion properties changed. Together, these findings indicate that following infection of cystic fibrosis patient airways,
P. aeruginosa
strains gradually change from a type III protein secretion-positive phenotype to a secretion-negative phenotype.
Usefulness of Routine Epicardial Pacing Wire Culture for Early Prediction of Poststernotomy Mediastinitis
Authors: Mekontso-Dessap Armand , Honoré Stéphanie , Kirsch Matthias , Houël Rémi , Loisance Daniel , Brun-Buisson Christian
Published: November 2004

Poststernotomy mediastinitis (PSM) is one of the most serious complications of cardiac surgery, and its associated morbidity and mortality demand early recognition for emergency therapy. In this study, we investigated the usefulness of epicardial pacing wire (EPW) cultures for the prediction of PSM. Among 2,200 patients who underwent a cardiac surgical procedure at our hospital between 1 January 1999 and 31 December 2001, 82 (3.7%) had PSM;
Staphylococcus aureus
was the organism (45.1%) most frequently isolated at the time of surgical debridement. EPWs from 1,607 (73.0%) patients, 73 (4.5%) of whom developed PSM, were cultured. EPW cultures from 466 (29.0%) were positive, most often (74.9%) for coagulase-negative
Staphylococci
. EPW cultures were truly positive in 26 cases, truly negative in 1,106 cases, falsely positive in 428 cases, and falsely negative in 47 cases (with sterile cultures in 35 cases and a culture positive for an organism different from that isolated at the time of debridement in 12 cases). EPW culture had a positive predictive value of only 5.7% and a high negative predictive value (95.9%) for the diagnosis of PSM, with an accuracy of 70.4%. However, the likelihood ratio of positive (1.27) and negative (0.89) tests indicated only small changes in pretest-to-posttest probability. Therefore, a strategy of routine culture of EPWs to predict PSM seems questionable.
Selective Discrimination of
Listeria monocytogenes
Epidemic Strains by a Mixed-Genome DNA Microarray Compared to Discrimination by Pulsed-Field Gel Electrophoresis, Ribotyping, and Multilocus Sequence Typing
Authors: Borucki Monica K. , Kim So Hyun , Call Douglas R. , Smole Sandra C. , Pagotto Franco
Published: November 2004

Listeria monocytogenes
can cause serious illness in humans, and subsequent epidemiological investigation requires molecular characterization to allow the identification of specific isolates.
L. monocytogenes
is usually characterized by serotyping and is subtyped by using pulsed-field gel electrophoresis (PFGE) or ribotyping. DNA microarrays provide an alternative means to resolve genetic differences among isolates, and unlike PFGE and ribotyping, microarrays can be used to identify specific genes associated with strains of interest. Twenty strains of
L. monocytogenes
representing six serovars were used to generate a shotgun library, and subsequently a 629-probe microarray was constructed by using features that included only potentially polymorphic gene probe sequences. Fifty-two strains of
L. monocytogenes
were genotyped by using the condensed array, including strains associated with five major listeriosis epidemics. Cluster analysis of the microarray data grouped strains according to phylogenetic lineage and serotype. Most epidemiologically linked strains were grouped together, and subtyping resolution was the same as that with PFGE (using AscI and ApaI) and better than that with multilocus sequence typing (using six housekeeping genes) and ribotyping. Additionally, a majority of epidemic strains were grouped together within phylogenetic Division I. This epidemic cluster was clearly distinct from the two other Division I clusters, which encompassed primarily sporadic and environmental strains. Discriminant function analysis allowed identification of 22 probes from the mixed-genome array that distinguish serotypes and subtypes, including several potential markers that were distinct for the epidemic cluster. Many of the subtype-specific genes encode proteins that likely confer survival advantages in the environment and/or host.
Characterization of “
Candidatus
Piscichlamydia salmonis” (Order
Chlamydiales
), a Chlamydia-Like Bacterium Associated With Epitheliocystis in Farmed Atlantic Salmon (
Salmo salar
)
Authors: Draghi Andrew , Popov Vsevolod L. , Kahl Melissa M. , Stanton James B. , Brown Corrie C. , Tsongalis Gregory J. , West A. Brian , Frasca Salvatore
Published: November 2004

To characterize intracellular gram-negative bacteria associated with epitheliocystis in farmed Atlantic salmon (
Salmo salar
), gills with proliferative lesions were collected for histopathology, conventional transmission and immunoelectron microscopy, in situ hybridization, and DNA extraction during epitheliocystis outbreaks in Ireland and Norway in 1999 and 2000, respectively, and compared by ultrastructure and immunoreactivity to nonproliferative gills from Ireland archived in 1995. Genomic DNA from proliferative gills was used to amplify 16S ribosomal DNA (rDNA) for molecular phylogenetic analyses. Epitheliocystis inclusions from proliferative gills possessed variably elongate reticulate bodies, examples of binary fission, and vacuolated and nonvacuolated intermediate bodies, whereas inclusions in nonproliferative gills had typical chlamydial developmental stages plus distinctive head-and-tail cells. Immunogold processing using anti-chlamydial lipopolysaccharide antibody labeled reticulate bodies from proliferative and nonproliferative gills. 16S rDNA amplified directly from Irish (1999) and Norwegian (2000) gill samples demonstrated 99% nucleotide identity, and riboprobes transcribed from cloned near-full-length 16S rDNA amplicons from Norwegian gills hybridized with inclusions in proliferative lesions from Irish (1999) and Norwegian (2000) sections. A 1,487-bp consensus 16S rRNA gene sequence representing the chlamydia-like bacterium (CLB) from proliferative gills had the highest percent nucleotide identity with endosymbionts of
Acanthamoeba
spp. (order
Chlamydiales
). Molecular phylogenetic relationships inferred from 16S rRNA gene sequences using distance and parsimony indicated that the CLB from proliferative gills branched with members of the order
Chlamydiales
. “
Candidatus
Piscichlamydia salmonis” is proposed for the CLB associated with epitheliocystis from proliferative gills of Atlantic salmon, which exhibits developmental stages different from those identified in nonproliferative gills.
Mapping of Antigenic Sites on the Nucleocapsid Protein of the Severe Acute Respiratory Syndrome Coronavirus
Authors: He Yuxian , Zhou Yusen , Wu Hao , Kou Zhihua , Liu Shuwen , Jiang Shibo
Published: November 2004

Antigenic sites on the nucleocapsid (N) protein of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) were mapped by Pepscan analysis with overlapping peptides that span the N protein sequence. Two major immunodominant epitopes located in the C-terminal region (amino acids [aa] 362 to 412) and middle region (aa 153 to 178) reacted with more than 75% of sera from SARS patients. Several minor immunodominant epitopes were reactive with about 50% of the SARS sera. Antisera from mice immunized with inactivated SARS-CoV recognized the two major immunodominant epitopes and one antigenic site located adjacent to the N-terminal region (aa 76 to 101), which did not react with the sera from SARS patients. Several monoclonal antibodies against SARS-CoV bound to the N- or C-terminal antigenic sites. These results suggest that the above antigenic sites on the N protein are important in eliciting humoral immune response against SARS-CoV in humans and animals and can be used as antigens for developing diagnostic tests.
Phaeohyphomycotic Soft Tissue Infections Caused by the Coelomycetous Fungus
Microsphaeropsis arundinis
Authors: Pendle Stella , Weeks Kerry , Priest Michael , Gill Anthony , Hudson Bernard , Kotsiou George , Pritchard Robert
Published: November 2004

Microsphaeropsis arundinis
is an anamorphic fungal plant inhabitant belonging to the form class
Coelomycetes
. We describe two cases of
M. arundinis
soft tissue infections in immunosuppressed patients. This organism has not previously been described as causing disease in humans. It was identified on the basis of its typical ostiolate pycnidial conidiomata, ampulliform conidiogenous cells, and small, smooth-walled, brown, cylindrical conidia.
Molecular Detection of Linezolid Resistance in
Enterococcus faecium
and
Enterococcus faecalis
by Use of 5′ Nuclease Real-Time PCR Compared to a Modified Classical Approach
Authors: Werner Guido , Strommenger Birgit , Klare Ingo , Witte Wolfgang
Published: November 2004

A nucleotide transversion from guanine to uracil in the 23S rRNA confers linezolid resistance. We describe a real-time PCR using two Taqman probes that detects a single mutated allele among the genomes of
Enterococcus faecium
and
Enterococcus faecalis
. Results were confirmed by a classical approach involving LabChip technology assayed with an Agilent Bioanalyzer 2100.
Convenience of Serum for Visceral Leishmaniasis Diagnosis by PCR
Authors: Fissore Cristel , Delaunay Pascal , Ferrua Bernard , Rosenthal Eric , Del Giudice Pascal , Aufeuvre Jean-Pierre , Le Fichoux Yves , Marty Pierre
Published: November 2004

In this retrospective study, the usefulness of a PCR performed on serum for primary diagnosis and monitoring of Mediterranean visceral leishmaniasis (MVL) was assessed. In the case of primary diagnosis of MVL, the serum PCR showed a sensitivity of 97% and a specificity of 95%, with positive and negative predictive values of 94 and 97%, respectively.
Utility of Molecular Identification in Opportunistic Mycotic Infections: a Case of Cutaneous
Alternaria infectoria
Infection in a Cardiac Transplant Recipient
Authors: Lo Cascio G. , Ligozzi M. , Maccacaro L. , Fontana R.
Published: November 2004

We report on a case of cutaneous infection caused by
Alternaria infectoria
in a cardiac transplant recipient. A rapid molecular diagnosis was obtained by sequence analysis of the internal transcribed spacer domain of the 5.8S ribosomal DNA region amplified from colonies developed on Sabouraud medium. Treatment consisted of a combination of systemic antifungal therapy, first with amphotericin B and then with itraconazole.
Mycobacterium avium
subsp.
paratuberculosis
Strains Isolated from Crohn's Disease Patients and Animal Species Exhibit Similar Polymorphic Locus Patterns
Authors: Ghadiali Alifiya H. , Strother Megan , Naser Saleh A. , Manning Elizabeth J. B. , Sreevatsan Srinand
Published: November 2004

Analysis of short sequence repeats of
Mycobacterium avium
subsp.
paratuberculosis
isolated from Crohn's disease patients identified two alleles, both of which clustered with strains derived from animals with Johne's disease. Identification of a limited number of genotypes among human strains implies the existence of human disease-associated genotypes and strain sharing with animals.
Monitoring for Presence of Potentially Xenotic Viruses in Recipients of Pig Islet Xenotransplantation
Authors: Garkavenko O. , Croxson M. C. , Irgang M. , Karlas A. , Denner J. , Elliott R. B.
Published: November 2004

This study represents a long-term follow-up of human patients receiving pig islet xenotransplantation. Eighteen patients had been monitored for up to 9 years for potentially xenotic pig viruses: pig endogenous retrovirus, pig cytomegalovirus, pig lymphotropic herpesvirus, and pig circovirus type 2. No evidence of viral infection was found.
Fibronectin-Binding Protein Gene Recombination and Horizontal Transfer between Group A and G Streptococci
Authors: Towers Rebecca J. , Gal Daniel , McMillan David , Sriprakash Kadaba S. , Currie Bart J. , Walker Mark J. , Chhatwal Gursharan S. , Fagan Peter K.
Published: November 2004

We report evidence of interspecies gene transfer between the important virulence factor genessfbIandgfbA. Because the identified group G streptococcusgfbAtypes possess DNA cassettes that can be identified in a number of group A streptococcus strains, it appears that homologous recombination is occurring between these species.
Characterization of a West Nile Virus Isolate from a Human on the Gulf Coast of Texas
Authors: Granwehr Bruno P. , Li Li , Davis Charles T. , Beasley David W. C. , Barrett Alan D. T.
Published: November 2004

Genetic characterization of a human cerebrospinal fluid West Nile virus isolate from Beaumont, Texas, revealed several nucleotide changes and amino acid substitutions that differentiated it from all other North American strains isolated to date, suggesting that isolates from the Texas Gulf Coast may form a unique genetic group among North American strains.
Clonal Spread of IMP-1-Producing
Pseudomonas aeruginosa
in Two Hospitals in Singapore
Authors: Koh Tse Hsien , Wang Grace Chee Yeng , Sng Li-Hwei
Published: November 2004

Thirty-six isolates of carbapenem-resistant
Pseudomonas aeruginosa
were studied. Pulsed-field gel electrophoresis revealed the presence of two clones. One clone carried a
bla
IMP-1
gene identical to that first described in Japan. The other clone carried a
bla
IMP-1
variant containing four silent mutations. One isolate with a unique pulsed-field gel electrophoresis pattern contained
bla
IMP-7
.
Interstitial Pneumonitis and Coinfection of Human Herpesvirus 6 and
Pneumocystis carinii
in a Patient with Hypogammaglobulinemia
Authors: Vuorinen Tytti , Kotilainen Pirkko , Lautenschlager Irmeli , Kujari Harry , Krogerus Leena , Oksi Jarmo
Published: November 2004

Human herpesvirus 6 (HHV-6) has occasionally been associated with cases of interstitial pneumonitis, mainly in individuals with impaired cellular immunity. Here we report for the first time severe interstitial pneumonitis with simultaneous HHV-6 and
Pneumocystis carinii
infections in the lung tissue of a young patient with hypogammaglobulinemia.
Fatal Cerebral Phaeohyphomycosis Due to
Curvularia lunata
in an Immunocompetent Patient
Authors: Carter Elliot , Boudreaux Carole
Published: November 2004

Curvularia
infections in humans are relatively uncommon despite the ubiquitous presence of this soil-dwelling dematiaceous fungus in the environment. Originally thought to be solely a pathogen of plants,
Curvularia
has been described as a pathogen of humans and animals in the last half-century, causing respiratory tract, cutaneous, and corneal infections. Only three previous cases of central nervous system involvement by
Curvularia
have been documented in the medical literature. We report a fatal case of cerebral
Curvularia
infection in which there was no known history of immunocompromise or prior respiratory tract or sinus infection in the patient.
Aeromonas popoffii
Urinary Tract Infection
Authors: Hua Huy Thong , Bollet Claude , Tercian Stephane , Drancourt Michel , Raoult Didier
Published: November 2004

Aeromonas popoffii
is a recently described species isolated mainly from freshwater. An isolate of
Aeromonas popoffii
was found to be responsible for a urinary tract infection in a 13-year-old boy suffering from spina bifida with enterocystoplasty. This is the first reported case of human infection attributed to this species.
Catheter-Related Bloodstream Infection Caused by
Mycobacterium brumae
Authors: Lee Stephanie A. , Raad Issam I. , Adachi Javier A. , Han Xiang Y.
Published: November 2004

Mycobacterium brumae
is a rapidly growing environmental mycobacterial species identified in 1993; so far, no infections by this organism have been reported. Here we present a catheter-related
M. brumae
bloodstream infection in a 54-year-old woman with breast cancer. The patient presented with high fever (39.7°C), and >1,000 colonies of
M. brumae
grew from a quantitative culture of blood drawn through the catheter. A paired peripheral blood culture was negative, however, suggesting circulational control of the infection. The patient was treated empirically with meropenem and vancomycin, and the fever resolved within 24 h. The catheter was removed a week later, and from the tip
M. brumae
was isolated a second time, suggesting catheter colonization. The organism was identified by colonial morphology, sequence analysis of the 16S rRNA gene, and biochemical tests.
The role of ultraviolet radiation in structuring epilithic algal communities in Rocky Mountain montane lakes: evidence from pigments and taxonomy
Authors: Tank Suzanne E , Schindler David W
Published: November 2004

We investigated changes in the community structure of epilithic (rock-dwelling) algae brought about by ultraviolet-A and -B radiation (UV-A and UV-B, respectively), using measurements of biovolume of individual taxa, and taxonomically diagnostic photosynthetic pigments. We undertook our study in four Canadian Rocky Mountain montane lakes, where downwelling ultraviolet radiation (UVR) can be intense. Although taxonomic counts revealed significant decreases in algal community diversity under UV-A and UV-B exposure, they revealed no other significant trends in algal community composition. Instead, redundancy analysis using these counts suggested that variations in nutrient concentrations were most important in structuring these communities. Photosynthetic pigments decreased significantly under UV-A and UV-B exposure. This decrease was much more striking for carotenoid than for chlorophyll concentrations, despite the photoprotective properties of many carotenoid pigments. Grazed carotenoids have been shown to be more resistant to degradation than grazed chlorophylls. We suggest that an observed increase in grazing pressure in our UVR-shielded communities counteracted increases in algal growth, but that increased algal growth rates were reflected by increased concentrations of slowly degrading carotenoids. Our study suggests that other factors, such as nutrients and grazers, are more important than UVR for structuring epilithic algal communities in our study lakes.
Effects of sediment nutrients and depth on small-scale spatial heterogeneity of submersed macrophyte communities in Lake Pleasant, Pennsylvania
Authors: Johnson R K , Ostrofsky M L
Published: November 2004

Sediment concentrations of total and available nitrogen (N), phosphorus (P), and potassium (K) and organic matter from the littoral zone of Lake Pleasant, Pennsylvania, were highly variable. Only organic matter and total N were correlated with depth, however. This result suggests the existence of more complex environmental gradients than the prevailing paradigm of monotonic changes in sediment characteristics with increasing depth. The spatial heterogeneity of submersed aquatic plant communities was significantly correlated with depth, and available N and P. Canonical correspondence analysis demonstrated that these three factors explained 38% of the variance in community structure. Other sediment characteristics (available K, organic matter, and total N, P and K) were not significant by themselves, but all variables combined explained 63% of community-structure variance. Cluster analysis identified species or groups of species typical of endpoints on the depth versus nutrient axes. Myriophyllum exalbescens was typical of deep sites with relatively nutrient-rich sediments, whereas deep nutrient-poor sites were dominated by Vallisneria americana and Megalodonta beckii. Shallow nutrient-rich sites were dominated by several species of Potamogeton and Elodea canadensis, and shallow nutrient-poor sites were dominated by Heteranthera dubia and Najas flexilis. These results demonstrate the importance of sediment characteristics in determining macrophytes' community structure within lakes.
Over-winter lipid depletion and mortality of age-0 rainbow trout (Oncorhynchusmykiss)
Authors: Biro Peter A , Morton Ashley E , Post John R , Parkinson Eric A
Published: November 2004

In this study we identify the size-dependent risk of winter starvation mortality as a strong selective pressure on age-0 rainbow trout (Oncorhynchus mykiss) that could promote the risk-taking behaviour and allocation of energy to lipids previously observed in young trout cohorts. Age-0 trout subjected to simulated winter starvation conditions gradually depleted lipid reserves to a critical minimum lipid content below which death occurred. Small fish with lower lipid content exhausted lipid reserves earlier, and experienced high mortality rates sooner, than larger fish with greater lipid content. Consequently, winter starvation endurance was dependent upon size-dependent lipid reserves and winter duration. To validate the laboratory findings in the field, we stocked several size classes of hatchery-raised trout with known lipid content at the start of winter into two experimental lakes, and estimated survival and lipid depletion at winter's end. Larger age-0 trout had greater initial lipid reserves than smaller trout. Individuals depleted most of their lipid reserves over the winter, and experienced mortality that ranged from just under 60% for the largest individuals to just over 90% of the smallest individuals. Many survivors had lipid contents near, but none were below, the minimum lipid content determined in the laboratory.
Changes in the δ13C of pelagic food webs: the influence of lake area and trophic status on the isotopic signature of whitefish (Coregonus lavaretus)
Authors: Perga Marie-Elodie , Gerdeaux Daniel
Published: November 2004

We investigated the relationships between the pattern of variation of δ13C in pelagic food webs and various morphologic and trophic characteristics of peri-alpine lakes. We used the δ13C of whitefish (Coregonus lavaretus), a long-lived zooplanktivorous fish, to assess the isotope ratio of dissolved inorganic carbon (DIC) at the origin of the pelagic food web. The δ13C of DIC depends on its origin, which may be the atmosphere or the mineralization of organic matter. A synchronic study of 22 peri-alpine lakes shows that the surface area of the lake accounts for much of the variability of the δ13C in pelagic food webs (r2 = 0.76). The δ13C increases with lake size, which suggests that the origin of the DIC integrated into the pelagic food web depends on lake size. To differentiate the influence of trophic status from morphological effects, a diachronic study was performed on the δ13C of fish scales collected over the 20-year re-oligotrophication of Lake Geneva. The δ13C of whitefish increased with phosphorus concentration (r2 = 0.71). This pattern is related to the growing demand for atmospheric DIC as primary production increases.
Temporal changes in nitrogen and phosphorus codeficiency of plankton in lakes of coastal and interior British Columbia
Authors: Davies John-Mark , Nowlin Weston H , Mazumder Asit
Published: November 2004

Plankton nutrient limitation and deficiency were assessed in six coastal and four interior lakes and reservoirs in British Columbia. Ultimate nutrient limitation was defined as occurring over longer time scales (months to years) and represented the potential attainable biomass or yield. Proximate nutrient deficiency reflected plankton physiological status and, therefore, represented potential limitations of instantaneous growth rates. All lakes and reservoirs were considered to be ultimately P-limited according to total N to total P ratios (TN:TP). However, both P and N deficiencies were found to occur at the same time, suggesting that when deficiency occurs, codeficiency is common. The <3 µm size fraction accounted for a large proportion of P debt, whereas the >3 µm size fraction accounted for most of the ammonium-enhanced response. Thus, plankton size is important for understanding nutrient deficiencies in plankton communities. Our results stress (i) the importance of measuring proximate deficiencies at greater temporal resolution, (ii) that N and P were commonly found to be codeficient, (iii) the need to define nutrient limitation and deficiency in the context of the method used, and (iv) that several concurrent measures of deficiency are required to assess the nutrient status of plankton communities.
Movement patterns in inland cutthroat trout (Oncorhynchus clarki utah): management and conservation implications
Authors: Schrank Amy J , Rahel Frank J
Published: November 2004

Knowledge of movement patterns is critical to the management and conservation of inland salmonids. We studied the movements of Bonneville cutthroat trout (Oncorhynchus clarki utah) in a drainage in western Wyoming, USA. Our objectives were to (i) characterize the postspawning movement patterns of adult Bonneville cutthroat trout, (ii) contrast postspawning and summer movement patterns, and (iii) identify factors that disrupt the movements of Bonneville cutthroat trout. Our data showed that postspawning movements of Bonneville cutthroat trout formed a continuum, with fish moving from 0.5 to 82.0 km. Postspawning distance was positively related to fish length. Despite the wide range of movement observed during the spring, fish did not move more than 0.5 km during the summer. A road culvert and an irrigation diversion dam did not seem to pose barriers to the upstream movement of Bonneville cutthroat trout to headwater spawning areas in the spring. However, 23% of radio-tagged fish in 2000 moved into the irrigation diversion ditch as they moved downstream after spawning and subsequently died there. Maintaining drainage connectivity is an important conservation concern for trout populations such as this one, where fish move between complementary spawning and summer habitats.
A hierarchical approach to determining reference points for Pandalid shrimp
Authors: Cadrin Steven X , Boutillier James A , Idoine Josef S
Published: November 2004

Reference points for harvesting Pandalid shrimp are categorized into five general approaches: historical proxies, biomass dynamics models, dynamic pool models, stockrecruit models, and demographic production models. Each of these approaches has different data requirements and underlying assumptions. Estimation of biological reference points from these methods can be viewed as a hierarchy, using data-poor proxies in the lowest tier to applying more informative demographic production models in the highest. Based on a review of Pandalid life histories, precautionary-approach reference points, and methodologies for estimating reference points and their applications to Pandalid shrimp stocks, we advocate a progression from proxies to more informative models and the requisite advancement of research programs to develop reliable reference points for Pandalid shrimp stocks.
Biological reference points for invertebrate fisheries: introduction
Authors: Smith Stephen J , Sainte-Marie Bernard
Published: November 2004

In the context of applying the precautionary approach to fisheries management, much of the current attention on developing reference points has been focussed on finfish species. However, at present the largest marine fisheries in Canada in terms of landings and value are those for invertebrate species. A workshop on reference points for invertebrate fisheries was held in Halifax, Nova Scotia, Canada, from 2 to 5 December 2002 to address the particular needs of fisheries on this diverse group of species. Seven of the papers presented at that workshop were published as a group in this issue of the Canadian Journal of Fisheries and Aquatic Science. Reproduction and recruitment were identified by all of these papers as key elements of population resilience and productivity that needed to be monitored in some way. The monitoring of reproductive capacity should be extended to aspects important in the mating systems, such as local densities, spatial patterns of agesize structure, and spatial and temporal patterns of breeding areas for broadcast spawners with poorly mobile or sessile adults. Similarly, such monitoring would also include female and male size and the number of female reproductive opportunities for crustacean species with copulating adults.