bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiology and Clinical Features of Infections Caused by Extended-Spectrum Beta-Lactamase-Producing
Escherichia coli
in Nonhospitalized Patients
Authors: Rodríguez-Baño Jesús , Navarro Maria Dolores , Romero Luisa , Martínez-Martínez Luis , Muniain Miguel A. , Perea Evelio J. , Pérez-Cano Ramón , Pascual Alvaro
Published: March 2004

Infections due to extended-spectrum beta-lactamase (ESBL)-producing
Escherichia coli
(ESBLEC) in nonhospitalized patients seem to be emerging in different countries. Their incidence, epidemiology, and clinical impact in the community have not been studied. We describe the epidemiology and clinical features of infections caused by ESBLEC in nonhospitalized patients in Spain and the results of a case-control study performed to investigate the risk factors associated with the acquisition of these organisms. The clonal relatedness of the organisms was assessed by repetitive extragenic palindromic sequence PCR. The ESBLs and the genes encoding the ESBLs were initially characterized by isoelectric focusing and PCR, respectively. Forty-nine patients (76% with urinary tract infections, 22% with asymptomatic bacteriuria, and 2% with acute cholangitis) were included. Six patients were bacteremic. Diabetes mellitus (odds ratio, 5.5; 95% confidence interval, 1.6 to 18.7), previous fluoroquinolone use (odds ratio, 7.6; 95% confidence interval, 1.9 to 30.1), recurrent urinary tract infections (odds ratio, 4.5; 95% confidence interval, 1.3 to 15.1), a previous hospital admission (odds ratio, 18.2; 95% confidence interval, 5.3 to 61.1), and older age in male patients (odds ratio per year, 1.03; 95% confidence interval, 1.03 to 1.05) were identified as risk factors by multivariate analysis. The ESBLEC isolates were not clonally related. The ESBLs were characterized as members of the CTX-M-9 group, the SHV group, and the TEM group in 64, 18, and 18% of the isolates, respectively. ESBLEC is an emergent cause of urinary tract infections in nonhospitalized patients. There was no evidence of horizontal transmission of ESBLEC strains. Avoidance of fluoroquinolone use in high-risk patients should be considered whenever possible in order to avoid the selection of these organisms.
Evaluation of the Fully Automated BACTEC MGIT 960 System for Testing Susceptibility of
Mycobacterium tuberculosis
to Pyrazinamide, Streptomycin, Isoniazid, Rifampin, and Ethambutol and Comparison with the Radiometric BACTEC 460TB Method
Authors: Scarparo Claudio , Ricordi Paolo , Ruggiero Giuliana , Piccoli Paola
Published: March 2004

The performance of the fully automated BACTEC MGIT 960 (M960) system for the testing of
Mycobacterium tuberculosis
susceptibility to streptomycin (SM), isoniazid (INH), rifampin (RMP), ethambutol (EMB), and pyrazinamide (PZA) was evaluated with 100 clinical isolates and compared to that of the radiometric BACTEC 460TB (B460) system. The agar proportion method and the B460 system were used as reference methods to resolve the discordant results for SM, INH, RMP, and EMB (a combination known as SIRE) and PZA, respectively. The overall agreements were 96.3% for SIRE and 92% for PZA. For SIRE, a total of 26 discrepancies were found and were resolved in favor of the M960 system in 8 cases and in favor of the B460 system in 18 cases. The M960 system produced 8 very major errors (VME) and 10 major errors (ME), while the B460 system showed 4 VME and 4 ME. No statistically significant differences were found. Both systems exhibited excellent performance, but a higher number of VME was observed with the M960 system at the critical concentrations of EMB and SM. For PZA, a total of eight discrepancies were observed and were resolved in favor of the M960 system in one case and in favor of the B460 system in seven cases; no statistically significant differences were found. The M960 system showed four VME and three ME. The mean times to report overall PZA results and resistant results were 8.2 and 9.8 days, respectively, for the M960 system and 7.4 and 8.1 days, respectively, for the B460 system. Statistically significant differences were found. The mean times to report SIRE results were 8.3 days for the M960 system and 8.2 days for the B460 system. No statistically significant differences were found. Twelve strains tested for SIRE susceptibility and seven strains tested for PZA susceptibility had been reprocessed because of contamination. In conclusion, the M960 system can represent a valid alternative to the B460 for
M. tuberculosis
susceptibility testing; however, the frequent contamination of the tests needs to be improved.
Population-Based Case Control Study of Seroprevalence ofMycobacterium paratuberculosisin Patients with Crohn's Disease and Ulcerative Colitis
Authors: Bernstein Charles N. , Blanchard James F. , Rawsthorne Patricia , Collins Michael T.
Published: March 2004

There is renewed enthusiasm for exploring the possibility thatMycobacterium paratuberculosismay be causative in Crohn's disease (CD). We aimed to determine whether CD subjects are more likely to beM. paratuberculosisseropositive than controls. Using our population-based University of Manitoba Inflammatory Bowel Disease Research Registry, we recruited CD and ulcerative colitis (UC) subjects between 18 and 50 years of age for a study involving detailed questionnaires and venipuncture. We accessed the population-based databases of Manitoba Health (single provincial health insurer) to get age-, gender-, and geography-matched controls to our inflammatory bowel disease (IBD) population. We asked enrolling IBD subjects for potential nonaffected sibling controls. We used an enzyme-linked immunosorbent assay (ELISA) for serum antibodies toM. paratuberculosisinitially developed for cattle but adapted for human use. The rate of positive ELISA results, based on previously published interpretation criteria, was significantly higher for all study groups. There was no difference inM. paratuberculosisseropositivity rate among CD patients (37.8%;n= 283), UC patients (34.7%;n= 144), healthy controls (33.6%;n= 402), and nonaffected siblings (34.1%;n= 138). For siblings, there was no correlation betweenM. paratuberculosisserological status and that of the corresponding IBD affected sibling. None of the demographic or questionnaire variables studied were predictive ofM. paratuberculosisstatus. Subjects with CD and UC were less likely to have ingested unpasteurized milk and less likely to have had a non-tap water source as a primary water source. In conclusion, in this population-based case control study, theM. paratuberculosisseropositivity rate was approximately 35% for all groups and there was no difference in rates between CD patients, UC patients, healthy controls, or nonaffected siblings. The much higher rate of seropositivity for subjects from Manitoba, Canada, than for those from Denmark or Wisconsin cannot be obviously explained. While these data seem to refute any association of CD withM. paratuberculosis, the high seroprevalence in Manitobans raises the possibility that the high rates of CD in Manitoba could be related to high exposure rates forM. paratuberculosis. Hence, the possibility of an association betweenM. paratuberculosisand CD remains inconclusive.
Correlates of Quantitative Measurement of BK Polyomavirus (BKV) DNA with Clinical Course of BKV Infection in Renal Transplant Patients
Authors: Randhawa Parmjeet , Ho Andrew , Shapiro Ron , Vats Abhay , Swalsky P. , Finkelstein Sydney , Uhrmacher John , Weck Karen
Published: March 2004

BK virus-allograft nephropathy (BKVAN) is an increasingly recognized complication after kidney transplantation. Quantitative tests have been advocated to monitor patients, but data demonstrating their efficacy are relatively limited. We developed a real-time PCR assay to quantitate BK virus loads in the setting of renal transplantation, and we correlated the BK virus load with clinical course and with the presence of BK virus in renal biopsy specimens. BK virus loads were measured in urine, plasma, and kidney biopsy samples in three clinical settings: (i) patients with asymptomatic BK viruria, (ii) patients with active BKVAN, and (iii) patients with resolved BKVAN. Active BKVAN was associated with BK viremia greater than 5 × 103 copies/ml and with BK viruria greater than 107 copies/ml in all cases. Resolution of nephropathy led to resolution of viremia, decreased viruria levels, and disappearance of viral inclusions, but low-level viral DNA persisted in biopsy specimens even for patients whose viruria was cleared. All but one patient in the resolved BKVAN group carried a urinary viral load below 107 copies/ml. Viral loads in patients with asymptomatic viruria were generally lower but in some cases overlapped with levels more typical of BKVAN. One patient with asymptomatic viruria and with a viral load overlapping values seen in BKVAN had developed nephropathy by the time of follow-up. In conclusion, serial measurement of viral loads by quantitative PCR is a useful tool in monitoring the course of BK virus infection. The results should be interpreted in conjunction with the clinical picture and biopsy findings.
Hepatitis C Virus Infection in Infants and Children from Argentina
Authors: Gismondi María Inés , Turazza Estela Inés , Grinstein Saúl , Galoppo María Cristina , Preciado María Victoria
Published: March 2004

Hepatitis C virus (HCV) infection is uncommon in children, and its natural history is still unknown. Our aim was to analyze exposure to HCV in 48 infants and children in Argentina and to evaluate consecutive samples in 26 of them to study the outcome of HCV infection in early stages. HCV viremia, as determined by reverse transcription-PCR (RT-PCR) from the 5′ untranslated region, showed continuously positive, occasionally positive, and negative patterns during follow-up. Restriction fragment length polymorphism was performed on RT-PCR-positive samples to evaluate HCV genotype. Genotype 1 turned out to be predominant, and no patient displayed a genotype shift during the observation period. Perinatal HCV infection was predominantly observed in patients born to mothers coinfected with HCV and human immunodeficiency virus. HCV viral load was detected by means of the AMPLICOR MONITOR, version 2.0, kit. No correlation was observed between HCV viral load and alanine aminotransferase and aspartate aminotransferase levels, although we detected a trend towards higher levels among patients displaying consecutive positive HCV RT-PCR results. Our results demonstrate that pediatric HCV infection is characterized by high viral loads and diverse HCV viremia patterns, independent of both age and route of transmission in the population under study. Further research is necessary to determine whether the high rate of HCV replication is related to virus variability or to host immune response.
Detection of Orthopoxvirus DNA by Real-Time PCR and Identification of Variola Virus DNA by Melting Analysis
Authors: Nitsche Andreas , Ellerbrok Heinz , Pauli Georg
Published: March 2004

Although variola virus was eradicated by the World Health Organization vaccination program in the 1970s, the diagnosis of smallpox infection has attracted great interest in the context of a possible deliberate release of variola virus in bioterrorist attacks. Obviously, fast and reliable diagnostic tools are required to detect variola virus and to distinguish it from orthopoxviruses that have identical morphological characteristics, including vaccinia virus. The advent of real-time PCR for the clinical diagnosis of viral infections has facilitated the detection of minute amounts of viral nucleic acids in a fast, safe, and precise manner, including the option to quantify and to genotype the target reliably. In this study a complete set of four hybridization probe-based real-time PCR assays for the specific detection of orthopoxvirus DNA is presented. Melting analysis following PCR enables the identification of variola virus by the PCR product's characteristic melting temperature, permitting the discrimination of variola virus from other orthopoxviruses. In addition, an assay for the specific amplification of variola virus DNA is presented. All assays can be performed simultaneously in the same cycler, and results of a PCR run are obtained in less than 1 h. The application of more than one assay for the same organism significantly contributes to the diagnostic reliability, reducing the risk of false-negative results due to unknown sequence variations. In conclusion, the assays presented will improve the speed and reliability of orthopoxvirus diagnostics and variola virus identification.
Development of a Real-Time PCR Assay for Detection of
Plasmodium falciparum
,
Plasmodium vivax
, and
Plasmodium ovale
for Routine Clinical Diagnosis
Authors: Perandin F. , Manca N. , Calderaro A. , Piccolo G. , Galati L. , Ricci L. , Medici M. C. , Arcangeletti M. C. , Snounou G. , Dettori G. , Chezzi C.
Published: March 2004

A TaqMan-based real-time PCR qualitative assay for the detection of three species of malaria parasites—
Plasmodium falciparum
,
P. ovale
, and
P. vivax
—was devised and evaluated using 122 whole-blood samples from patients who had traveled to areas where malaria is endemic and who presented with malaria-like symptoms and fever. The assay was compared to conventional microscopy and to an established nested-PCR assay. The specificity of the new assay was confirmed by sequencing the PCR products from all the positive samples and by the lack of cross-reactivity with
Toxoplasma gondii
and
Leishmania infantum
DNA. Real-time PCR assay showed a detection limit (analytical sensitivity) of 0.7, 4, and 1.5 parasites/μl for
P. falciparum
,
P. vivax
, and
P. ovale
, respectively. Real-time PCR, like nested PCR, brought to light errors in the species identification by microscopic examination and revealed the presence of mixed infections (
P. falciparum
plus
P. ovale
). Real-time PCR can yield results within 2 h, does not require post-PCR processing, reduces sample handling, and minimizes the risks of contamination. The assay can therefore be easily implemented in routine diagnostic malaria tests. Future studies are warranted to investigate the clinical value of this technique.
Performance Assessment of the Fecal Leukocyte Test for Inpatients
Authors: Granville L. A. , Cernoch P. , Land G. A. , Davis J. R.
Published: March 2004

Traditionally, fecal leukocyte testing detects large bowel inflammation or disruption, conditions that allow leukocytes into the stool. However, test usefulness with inpatients is unclear. Two hundred five inpatients who had undergone one to three tests were identified, and their FLT results were compared to their gastrointestinal disease diagnoses at time of discharge. A specificity of 92% for detecting intact colonic mucosae in inpatients was found.
Long-Term Preservation of Fungal Isolates in Commercially Prepared Cryogenic Microbank Vials
Authors: Espinel-Ingroff A. , Montero D. , Martin-Mazuelos E.
Published: March 2004

Since 1994, 6,198 yeasts and 391 molds belonging to 25 and 37 species, respectively, were stored in Microbank cryogenic vials at ≥−130°C in liquid nitrogen and at −70°C in a freezer. All of the isolates, with the exception of 45 yeasts and 15 dermatophytes, were recovered from both storage temperatures. Good reproducibility was demonstrated for amphotericin B, fluconazole, and voriconazole MICs determined for random isolates.
Resistance of Group B Streptococcus to Selected Antibiotics, Including Erythromycin and Clindamycin
Authors: Heelan Judith S. , Hasenbein Meredith E. , McAdam Alexander J.
Published: March 2004

Resistance of group B streptococcus (GBS) to antibiotics, particularly erythromycin and clindamycin, was studied. Erythromycin resistance was present in 22% of GBS isolates, and these isolates were constitutively resistant, inducibly resistant, or sensitive to clindamycin. Erythromycin and clindamycin MICs were related to the presence of
ermA
,
ermB
, or
mefA
genes.
Comparative Analysis of
agr
Locus Diversification and Overall Genetic Variability among Bovine and Human
Staphylococcus aureus
Isolates
Authors: Gilot Philippe , van Leeuwen Willem
Published: March 2004

The accessory gene regulator (
agr
) is a central system that controls the expression of
Staphylococcus aureus
virulence factors. In this study, the distribution of
agr
alleles, defined by
agr
restriction fragment length polymorphism within
agr
interference groups, among
S. aureus
isolates from bovine and human origin was measured with PCR-based techniques. Statistically highly significant associations of some
agr
alleles with the infection of a specific host were found. The genetic difference between the two
S. aureus
populations was further stressed after analysis of their genetic background by binary typing.
Evaluation of
groEL
Gene Analysis for Identification of
Borrelia burgdorferi
Sensu Lato
Authors: Park Hyo-Soon , Lee Jung-Hee , Jeong Eun-Ju , Koh Seong-Eun , Park Tae-Kyu , Jang Won-Jong , Park Kyung-Hee , Kim Bum-Joon , Kook Yoon-Hoh , Lee Seung-Hyun
Published: March 2004

The nucleotide sequences of the
groEL
genes, the flagellin genes, and the 16S rRNA genes from 22 reference strains of
Borrelia
were compared.
groEL
sequence analysis is useful not only in interspecies differentiation but also in intraspecies differentiation of
Borrelia afzelii
and
Borrelia garinii
isolates.
Comparison of the Denka Seiken Slide Agglutination Method to the Quellung Test for Serogrouping of
Streptococcus pneumoniae
Isolates
Authors: Shutt Cheryl K. , Samore Matthew , Carroll Karen C.
Published: March 2004

This study compared a slide agglutination test (Denka Seiken, Tokyo, Japan) to the “gold standard” quellung reaction (Pneumotest; Statens Serum Institut, Copenhagen, Denmark) for the serogrouping of pneumococci. Two hundred clinical isolates of
Streptococcus pneumoniae
were used for the comparison. Each assay was performed according to the manufacturer's instructions. There was an overall agreement of 95.7% between the two methods. Only 4 of 10 isolates of serogroup 22 were detected with the slide agglutination assay. Two isolates that were untypeable by the Pneumotest method were typed as serogroups 6 and 31 by the slide agglutination method. The Pneumotest method was unable to type 22 isolates, and the slide agglutination method was unable to type 16 isolates. The slide agglutination method compares favorably with the Pneumotest method and is easier to perform and to interpret.
Type III Secretion System Genes in Clinical
Aeromonas
Isolates
Authors: Chacón M. R. , Soler L. , Groisman E. A. , Guarro J. , Figueras M. J.
Published: March 2004

We have identified the genes
ascF
and
ascG
, which encode components of a putative type III secretion system (TTSS) in
Aeromonas
. We investigated the distribution of these and other TTSS genes in 84 clinical isolates and found hybridizing sequences in 50% of the strains, with a higher prevalence in
Aeromonas hydrophila
and
Aeromonas veronii
than in
Aeromonas caviae
.
Real-Time Multiplex PCR Assay for Detection of
Brucella
spp.,
B. abortus
, and
B. melitensis
Authors: Probert William S. , Schrader Kimmi N. , Khuong Nhi Y. , Bystrom Susan L. , Graves Margot H.
Published: March 2004

The identification of
Brucella
can be a time-consuming and labor-intensive process that places personnel at risk for laboratory-acquired infection. Here, we describe a real-time PCR assay for confirmation of presumptive
Brucella
isolates. The assay was designed in a multiplex format that will allow the rapid identification of
Brucella
spp.,
B. abortus
, and
B. melitensis
in a single test.
Stability of Polymorphic GC-Rich Repeat Sequence-Containing Regions of
Mycobacterium tuberculosis
Authors: Richardson Madalene , van der Spuy Gian D. , Sampson Samantha L. , Beyers Nulda , van Helden Paul D. , Warren Robin M.
Published: March 2004

Mycobacterium tuberculosis
cultures were subjected to DNA fingerprinting with IS
6110-
and polymorphic GC-rich sequence (PGRS)-containing probes. The PGRS banding patterns remained highly stable during multiple cultures of specimens from one disease episode (0.5% changed) and during transmission in patients with close contact (1.9% changed). Characteristic PGRS-restriction fragment length polymorphism motifs for different strain groupings may indicate distant evolutionary events leading to the differentiation of
M. tuberculosis
strain lineages.
First Isolation of
Borrelia lusitaniae
from a Human Patient
Authors: Collares-Pereira M. , Couceiro S. , Franca I. , Kurtenbach K. , Schäfer S. M. , Vitorino L. , Gonçalves L. , Baptista S. , Vieira M. L. , Cunha C.
Published: March 2004

The first human isolate of
Borrelia lusitaniae
recovered from a Portuguese patient with suspected Lyme borreliosis is described. This isolate, from a chronic skin lesion, is also the first human isolate of
Borrelia
in Portugal. Different phenotypic and molecular methods are used to characterize it.
Sensitivity of a Novel Stool Antigen Test for Detection of
Helicobacter pylori
in Adult Outpatients before and after Eradication Therapy
Authors: Weingart Vincens , Rüssmann Holger , Koletzko Sibylle , Weingart Josef , Höchter Wilhelm , Sackmann Michael
Published: March 2004

We investigated whether a novel monoclonal stool antigen test for detection of
Helicobacter pylori
performs with the same accuracy as the
13
C-urea breath test (UBT) for adult outpatients in the setting of a private office. The two tests showed identical levels of sensitivity when used to identify
H. pylori
-infected patients before and after eradication therapy.
Concordance of Prevalence of Human Papillomavirus DNA in Anogenital and Oral Infections in a High-Risk Population
Authors: Cañadas M. Paz , Bosch F. Xavier , Junquera M. Luisa , Ejarque Maijo , Font Rebeca , Ordoñez Elena , de Sanjosé Silvia
Published: March 2004

The concordance of the prevalence of human papillomavirus (HPV) DNA in 188 sex workers in five different locations was investigated. HPV was found in 43.6% of the women, and its prevalence at genital sites was similar. Prevalence was highest among women aged 20 years or younger but declined thereafter in specimens from all anogenital sites.
A Canine Parvovirus Mutant Is Spreading in Italy
Authors: Martella Vito , Cavalli Alessandra , Pratelli Annamaria , Bozzo Giancarlo , Camero Michele , Buonavoglia Domenico , Narcisi Donato , Tempesta Maria , Buonavoglia Canio
Published: March 2004

By antigenic and genetic characterization of canine parvovirus type 2 (CPV-2) strains collected in 2001 and 2002 in Italy, it was possible to observe the spread of viruses with an unusual mutation, Glu-426, affecting a major antigenic epitope of CPV-2. Out of 67 strains analyzed, 49 (73.13%) were characterized as CPV-2a, 6 (8.95%) were characterized as CPV-2b, and 12 (17.91%) were characterized as the Glu-426 mutant.
Human Papillomavirus, Cytomegalovirus, and Adeno-Associated Virus Infections in Pregnant and Nonpregnant Women with Cervical Intraepithelial Neoplasia
Authors: Grce M. , Husnjak K. , Matovina M. , Milutin N. , Magdic L. , Husnjak O. , Pavelic K.
Published: March 2004

Two hundred eight cervical specimens from two groups of subjects, 165 nonpregnant women and 53 pregnant women with cervical intraepithelial neoplasia (CIN) of grades I to III, were positive by PCR analyses for human papillomaviruses (HPVs), adeno-associated virus type 2 (AAV 2), and human cytomegalovirus (HCMV) in 67, 6, and 4.1% of the cases, respectively. The presence of AAV 2 infection was more frequently associated with pregnancy (17 versus 2.4%) and HPV-positive cervices (odds ratio = 6.358) than HCMV was. Increased HPV infection was strongly associated (
P
< 0.001) with a higher CIN grade, but there is no evidence that AAV 2 and HCMV infections have any impact on CIN development.
Detection of Human Herpesvirus 7 DNA by Loop-Mediated Isothermal Amplification
Authors: Yoshikawa Tetsushi , Ihira Masaru , Akimoto Shiho , Usui Chie , Miyake Fumi , Suga Sadao , Enomoto Yoshihiko , Suzuki Ryota , Nishiyama Yukihiro , Asano Yoshizo
Published: March 2004

The reliability of loop-mediated isothermal amplification (LAMP), initially developed for the detection of human herpesvirus 7 (HHV-7), was evaluated in this study. Although a LAMP product was detected in HHV-7 DNA, neither HHV-6 nor human cytomegalovirus DNA produced a product. When agarose gel electrophoresis was used for the detection of LAMP products, the sensitivity of a 30-min HHV-7 LAMP reaction reached 250 copies/tube. The use of turbidity for the detection of the LAMP products gave a sensitivity of 500 and 250 copies/tube for 30- and 60-min reactions, respectively. Following these initial validation studies, clinical samples collected from two patients with primary HHV-7 infections were examined by HHV-7 LAMP. By use of agarose gel electrophoresis, HHV-7 LAMP products could be detected in acute-phase plasma samples but no LAMP product was detectable in convalescent-phase plasma samples from either patient. Since a turbidity assay is less sensitive than agarose gel electrophoresis, no HHV-7 LAMP product could be detected in plasma samples after a 30-min LAMP reaction. After a 60-min LAMP reaction, HHV-7 LAMP product could be detected in acute-phase plasma samples.
Detection of Ehrlichial DNA in
Haemaphysalis
Ticks Recovered from Dogs in Japan That Is Closely Related to a Novel
Ehrlichia
sp. Found in Cattle Ticks from Tibet, Thailand, and Africa
Authors: Inokuma Hisashi , Beppu Takeshi , Okuda Masaru , Shimada Yojiro , Sakata Yoshimi
Published: March 2004

Tick DNA samples from dogs in Japan were examined for
Ehrlichia
infection by 16S rRNA gene-based PCR and sequencing. Three positive samples were detected from
Haemaphysalis
ticks, and higher levels of similarity (98.46 to 99.06%) were found to recently detected
Ehrlichia
spp. from cattle ticks in Tibet, Thailand, and Africa.
Cryptococcus neoformans
Shows a Remarkable Genotypic Diversity in Brazil
Authors: Barreto de Oliveira M. T. , Boekhout T. , Theelen B. , Hagen F. , Baroni F. A. , Lazera M. S. , Lengeler K. B. , Heitman J. , Rivera I. N. G. , Paula C. R.
Published: March 2004

The genotypic diversity of Brazilian
Cryptococcus neoformans
strains was analyzed. The majority of the samples were αA (65%), followed by αB (17.5%), αD (9%), αAaD hybrids (5%), and αC (3.5%). A considerable genotypic diversity occurred within
C. neoformans
var.
grubii
, and a new amplified fragment length polymorphism genotype, 1B, was recognized.
Legionella pneumophila
Serogroup 4 Isolated from Joint Tissue
Authors: Linscott Andrea J. , Poulter Melinda D. , Ward Kevin , Bruckner David A.
Published: March 2004

We report the isolation of
Legionella pneumophila
serogroup 4 from synovial tissue obtained from an 80-year-old female with chronic swelling of her right metacarpophalangeal joint. Synovial tissue infections caused by
L. pneumophila
are rare. Interestingly, this isolate was recovered from chocolate agar after 5 days of incubation.
Molecular Epidemiology of Sequential Outbreaks of
Acinetobacter baumannii
in an Intensive Care Unit Shows the Emergence of Carbapenem Resistance
Authors: Zarrilli Raffaele , Crispino Margherita , Bagattini Maria , Barretta Elena , Di Popolo Anna , Triassi Maria , Villari Paolo
Published: March 2004

The molecular epidemiology of multidrug-resistant
Acinetobacter baumannii
was investigated in the medical-surgical intensive care unit (ICU) of a university hospital in Italy during two window periods in which two sequential
A. baumannii
epidemics occurred. Genotype analysis by pulsed-field gel electrophoresis (PFGE) of
A. baumannii
isolates from 131 patients identified nine distinct PFGE patterns. Of these, PFGE clones B and I predominated and occurred sequentially during the two epidemics.
A. baumannii
epidemic clones showed a multidrug-resistant antibiotype, being clone B resistant to all antimicrobials tested except the carbapenems and clone I resistant to all antimicrobials except ampicillin-sulbactam and gentamicin. Type 1 integrons of 2.5 and 2.2 kb were amplified from the chromosomal DNA of epidemic PFGE clones B and I, respectively, but not from the chromosomal DNA of the nonepidemic clones. Nucleotide analysis of clone B integron identified four gene cassettes:
aacC1
, which confers resistance to gentamicin; two open reading frames (ORFs) coding for unknown products; and
aadA1a
, which confers resistance to spectinomycin and streptomycin. The integron of clone I contained three gene cassettes:
aacA4
, which confers resistance to amikacin, netilmicin, and tobramycin; an unknown ORF; and
bla
OXA-20
, which codes for a class D β-lactamase that confers resistance to amoxicillin, ticarcillin, oxacillin, and cloxacillin. Also, the
bla
IMP
allele was amplified from chromosomal DNA of
A. baumannii
strains of PFGE type I. Class 1 integrons carrying antimicrobial resistance genes and
bla
IMP
allele in
A. baumannii
epidemic strains correlated with the high use rates of broad-spectrum cephalosporins, carbapenems, and aminoglycosides in the ICU during the study period.
Analysis of the Serotype and Genotype Correlation of VP1 and the 5′ Noncoding Region in an Epidemiological Survey of the Human Enterovirus B Species
Authors: Thoelen Inge , Moës Elien , Lemey Philippe , Mostmans Sara , Wollants Elke , Lindberg A. Michael , Vandamme Anne-Mieke , Van Ranst Marc
Published: March 2004

The sequence identity of the enterovirus VP1 gene has been shown to correlate with the serotype concept. Enterovirus molecular typing methods are therefore often based on sequencing of the VP1 genomic region and monophyletic clustering of VP1 sequences of a homologous serotype. For epidemiological surveillance, 342 enterovirus samples obtained from patients with aseptic meningitis in Belgium from 1999 to 2002 were first diagnosed as being enterovirus positive by amplification of the 5′ noncoding region (5′NCR) by reverse transcription (RT)-PCR. Subsequently, samples were molecularly typed by RT-nested PCR amplification and sequencing of a portion of the VP1 gene. Phylogenetic analyses were performed to investigate enteroviral evolution and to examine the serotype and genotype correlation of the two genomic regions. Our typing results demonstrated echovirus 30, echovirus 13, echovirus 18, and echovirus 6 to be the most predominant types. Echoviruses 13 and 18 were considered to be emerging human serotypes since 2000 and 2001, respectively, as they had been rarely reported before. Several serotypes existed as multiple genotypes (subtypes) from 1999 to 2002, but genomic differences mainly resided at synonymous sites; these results strongly suggest that the subtypes exhibit similar antigenic properties. Phylogenetic analyses confirmed that VP1 is an adequate region for molecular typing. Serotype-specific clusters are not observed commonly in phylogenetic trees based on the 5′NCR, and the phylogenetic signal in the 5′NCR was found to be particularly low. However, some substructure in the 5′NCR tree made a tentative prediction of the enterovirus type possible and was therefore helpful in PCR strategies for VP1 (e.g., primer choice), provided some background knowledge on the local spectrum of enteroviruses already exists.
Preclinical Evaluation of Two Real-Time, Reverse Transcription-PCR Assays for Detection of the Severe Acute Respiratory Syndrome Coronavirus
Authors: Bressler Adam M. , Nolte Frederick S.
Published: March 2004

We verified the analytical performance characteristics of a previously described real-time reverse transcription-PCR (RT-PCR) assay targeting the open reading frame (ORF) 1b region of the severe acute respiratory syndrome coronavirus (SARS-CoV) with RNA transcripts. We then compared it to a novel nucleocapsid gene real-time RT-PCR assay with genomic RNA. The assays differed only in the primer and probe sequences and final concentrations. A commercially available armored RNA (Ambion, Austin, Tex.) was evaluated as positive control for the ORF 1b assay. The analytical sensitivity, reproducibility, amplification efficiency, and dynamic range of the assays were similar. Both were specific for SARS-CoV as determined by testing against human CoV 229E and OC43, specimens from patients without SARS, and by BLAST searches of GenBank for primer and probe sequence homology. The armored RNA was found to be a suitable positive control for the ORF 1b assay that could be reliably recovered and amplified from a variety of clinical specimens.
Molecular Epidemiology of Coagulase-Negative Staphylococci Causing Sepsis in a Neonatal Intensive Care Unit over an 11-Year Period
Authors: Krediet Tannette G. , Mascini Ellen M. , van Rooij Ellen , Vlooswijk Judith , Paauw Armand , Gerards Leo J. , Fleer André
Published: March 2004

Coagulase-negative staphylococci (CoNS) are the major causative microorganisms in neonatal nosocomial sepsis. Previous studies have shown that CoNS sepsis in the neonatal intensive care unit (NICU) is caused by predominant molecular types that are widely distributed among both neonates and staff. Some of these molecular types may persist in the NICU for years. The purpose of the present study was to determine the dynamic behavior of CoNS strains causing sepsis over a prolonged period of time by determining the molecular types of all blood isolates from septicemic infants over a period of 11 years (1991 to 2001). The results show that neonatal CoNS sepsis is increasingly caused by a few predominant molecular clusters. The most striking finding was that in recent years one molecular cluster emerged as the predominant cause of neonatal CoNS sepsis, responsible for no less than 31% (20 of 65) of blood isolates in 2001. Antibiotic resistance, particularly beta-lactam resistance, is probably an important selective force considering the high
mecA
gene carriage of CoNS blood isolates (70 to 92%). We conclude that neonatal CoNS sepsis is increasingly caused by a limited number of predominant molecular CoNS types and that antibiotic resistance is probably a major selective force.
Comparison of Conventional Bacteriology with Nucleic Acid Amplification (Amplified Mycobacterium Direct Test) for Diagnosis of Tuberculous Meningitis before and after Inception of Antituberculosis Chemotherapy
Authors: Thwaites Guy E. , Caws Maxine , Chau Tran Thi Hong , Dung Nguyen Thi , Campbell James I. , Phu Nguyen Hoan , Hien Tran Tinh , White Nicholas J. , Farrar Jeremy J.
Published: March 2004

The role of nucleic acid amplification techniques in the rapid diagnosis of tuberculous meningitis remains uncertain. We compared the performance of Ziehl-Neelsen (ZN) staining, the Gen-Probe amplified
Mycobacterium tuberculosis
direct test (MTD), and culture with 341 cerebrospinal fluid specimens from 152 adults (73 with and 79 without tuberculous meningitis) before and after inception of antituberculosis chemotherapy. The sensitivity, specificity, and positive and negative predictive values of ZN staining before treatment were 34/66 (52%), 79/79 (100%), 34/34 (100%), and 79/111 (71%), compared with 25/66 (38%), 78/79 (99%), 25/26 (96%), and 79/120 (66%) for MTD. The sensitivity of combined ZN staining and MTD (either positive) was 45/66 (68%). The sensitivity of staining and culture fell more rapidly than that of MTD after the start of treatment: after 5 to 15 days of treatment, MTD was more sensitive than ZN staining (12/43 [28%] versus 2/43 [2%];
P
= 0.013). Slower bacterial clearance was observed if
M. tuberculosis
was resistant to isoniazid and/or streptomycin: resistant organisms were more likely to be cultured from cerebrospinal fluid after 2 to 5 days of treatment than fully sensitive organisms (
P
< 0.001). The sensitivities of ZN staining, MTD, and the two tests combined were improved by repeated sampling to 38/59 (64%), 35/59 (59%), and 49/59 (83%), respectively. In conclusion, ZN staining of the cerebrospinal fluid is at least as good as MTD for the rapid diagnosis of tuberculosis and is much faster and less expensive. However, the combination of these methods on serial samples detects more cases. Alternative tests are still urgently required.
The timing of Proterozoic magmatism in the Pinware terrane of southeast Labrador, easternmost Quebec and northwest Newfoundland
Authors: Heaman L M , Gower C F , Perreault S
Published: March 2004

The Pinware terrane is located in the easternmost Grenville Province and contains crust of Labradorian (17101600 Ma), Pinwarian (15201460 Ma), Elsonian (14601230 Ma), Grenvillian (1080985 Ma), and late- to post-Grenvillian (985955 Ma) age. Newly obtained UPb geochronological data enhance understanding of all these evolutionary stages. A Labradorian age of 1632 ± 8 Ma has been obtained for the Brador River granite, thereby establishing the presence of mid- to late- Labradorian rocks in the southernmost part of the region. A maximum age of ~1600 Ma obtained for the Ten Mile Lake granite indicates for the first time that Labradorian crust could continue into the northern Long Range Inlier of western Newfoundland. Pinwarian activity is indicated by ages of ~15261504, 1500 ± 14, 1467 ± 44, and 1466 ± 8 Ma from granitoid rocks at Rivière St-Paul, West St. Modeste, Diable Bay, and Pinware, respectively. The first evidence for late Elsonian mafic magmatism in this region is provided by a concordant baddeleyite date of 1248 ± 5 Ma from gabbronorite at Lourdes-de-Blanc-Sablon. This study has also identified an early post-tectonic, high-level, maficanorthositicsyenitic magmatic event between 985 and 975 Ma. Recognition of the event relies on previous results and newly obtained ages of 979.5 ± 2.8 Ma from the Red Bay gabbro, 974.5 ± 1.8 Ma from the Vieux Fort anorthosite, and 969 ± 11 Ma from the Lower Pinware River alkali-feldspar syenite. Time, composition, and fabric criteria distinguish these rocks from late-post-tectonic monzonite, syenite and granite emplaced between 966 and 956 Ma.
A new species of the ptilodontid multituberculate Prochetodon (Mammalia, Allotheria) from the Paleocene Paskapoo Formation of Alberta, Canada
Authors: Scott Craig S
Published: March 2004

A new species of the ptilodontid multituberculate genus Prochetodon (Mammalia, Allotheria) from the Paleocene Paskapoo Formation of Alberta, Canada, is described. Prochetodon speirsae sp. nov. is the oldest discovered species of the genus, extending the temporal range of Prochetodon earlier into the Paleocene. It exhibits a mosaic of primitive and derived dental features suggestive of a position phylogenetically intermediate between Ptilodus and Prochetodon. Newly discovered specimens from the late Paleocene Gao Mine locality are referred tentatively to Prochetodon foxi. The occurrence of a primitive form of Prochetodon in sediments of early Tiffanian age suggests the evolutionary history of the genus is more complex than previously appreciated. Prochetodon joins a number of well-documented, progressive mammalian taxa making their first appearance in the Western Interior of North America at higher latitudes, well before their first known occurrence in the United States, suggesting a possible origin and immigration from currently unsampled habitats.
Regional unconformities and the sedimentary architecture of the Oak Ridges Moraine area, southern Ontario
Authors: Sharpe David , Pugin André , Pullan Susan , Shaw John
Published: March 2004

Seismic stratigraphy, geometry, and sediment facies within the Oak Ridges Moraine (ORM) area of Ontario record major structural elements and surfaces of the Quaternary sedimentary sequence. The derived stratigraphic architecture can be used to identify the key elements of a regional erosional surface, represented by an unconformity in the subsurface, and associated overlying channel sediments. The erosional surface  unconformity forms a distinct time datum in the Quaternary sequence, which provides an important aid to lithostratigraphic correlation. The architecture also gives improved understanding of the effects of erosion on the late-glacial landscape. The surfaces of erosional drumlins and intervening troughs, and the beds and banks of meltwater channels in the ORM area, define the regional unconformity, highlighted by seismic profiles linked to continuously cored boreholes. These features are attributed to regional-scale, subglacial meltwater flow events. The sculpted surfaces, which are analogous to water-eroded forms, the presence of boulder lags and coarse-grained deposits on the regional erosional surface, and the channels with undulating profiles provide the vital supporting evidence for a meltwater interpretation. The inter-regional extent of the unconformity is inferred from the coherence of regional paleoflows and the extent of drumlinized uplands, tunnel channels, and scoured bedrock terrain across ~75% of the landscape from the ORM area east and south to the Finger Lakes, New York. The implied magnitude of erosion suggests a pressing need for directed sedimentological study in those ocean basins that were probable depositional sites for flood deposits.
The origin and identity of invertebrate organisms being transported to Canada's Pacific coast by ballast water
Authors: Levings C D , Cordell J R , Ong S , Piercey G E
Published: March 2004

We assessed the colonization risk of invertebrate nonindigenous species (NIS) in ballast water being brought into Canada's Pacific coast by indirect and direct methods. Initially we mapped the locations in the northern Pacific Ocean where ships coming into Vancouver Harbour had performed mid-ocean exchange (MOE). Exchange transects (the distance between the start and end positions for the onset and end of MOE) were on average about 400 km long. Samples were also taken from ballast tanks after filling at a northwestern Pacific port and then again after MOE in the mid-Pacific. Invertebrate communities were different pre- and post-MOE, but some coastal organisms were still present after flushing. In addition, samples were obtained from ballast tanks aboard ships in Vancouver Harbour. In "low" salinity samples (<25), 13 different taxa were found, and 52 taxa were found in "high" salinity samples (>25). Risks could be reduced if MOE was performed in the southerly subtropical domain, south of the subarctic domain and transition zone in the mid-Pacific, or well offshore for northsouth shipping routes. For voyages on the west coast of North America, colonization risk of invertebrate NIS is likely higher for ballast water from harbours already colonized by NIS.
Managing fishing power: the case of Alaska red king crab (Paralithodes camtschaticus)
Authors: Briand Genevieve , Heckelei Thomas , Matulich Scott C , Mittelhammer Ron C
Published: March 2004

Because of concern about the inability to manage the Bristol Bay red king crab (Paralithodes camtschaticus) fishery in Alaska and, in particular, to use in-season fishery performance to close the fishery at or near the preseason guideline harvest level, increasingly stringent pot limits were adopted to elongate the collapsing seasons. This paper provides a rigorous examination of the effect that pot limits had on season elongation and whether a redistribution of wealth occurred between large and small fishing vessels as a result of the policy. A simulation model of the fishery shows that pot limits did not elongate the season sufficiently to improve in-season management. Moreover, the policy allowed vessels to capture efficiency gains arising from an industry-wide reduction in fishing capacity. Both vessel size classes benefited from mutual gear reduction in all years except 1992. Redistribution of wealth was found to occur only in one year of the five years examined.
Trophic structure and energy flow in backwater lakes of two large floodplain rivers assessed using stable isotopes
Authors: Herwig Brian R , Soluk Daniel A , Dettmers John M , Wahl David H
Published: March 2004

Carbon and nitrogen stable isotopes (δ13C and δ15N, respectively) were measured for locally abundant primary producers, detritus, aquatic invertebrates, and fish in backwater lakes of two large floodplain rivers in an effort to understand patterns of energy dependence and trophic structure within these habitats. We observed trophic enrichment values for15N that were within the ranges observed for other aquatic systems but were often considerably lower than the 3.4 typically assumed in stable isotope studies. Production based on benthic and terrestrial material, combined with planktonic production for larval fish, appears to be an important energy source supporting consumers in backwater lakes of large floodplain rivers. Our isotopic data challenge the conventional wisdom that macrophytes are centrally involved in supplying carbon to aquatic consumers in shallow lakes and that food webs in most lakes are sustained almost exclusively by carbon fixed by phytoplankton.
An estimate of chinook salmon (Oncorhynchus tshawytscha) spawning habitat and redd capacity upstream of a migration barrier in the upper Columbia River
Authors: Hanrahan Timothy P , Dauble Dennis D , Geist David R
Published: March 2004

Chief Joseph Dam on the Columbia River is the upstream terminus for anadromous fish because of its lack of fish passage facilities. Management agencies are currently evaluating the feasibility of reintroducing anadromous fish upriver of Chief Joseph Dam. We evaluated the physical characteristics of potential fall chinook salmon (Oncorhynchus tshawytscha) spawning habitat in the upper section of Chief Joseph Reservoir. The objectives were to estimate the location and quantity of potential spawning habitat and to determine the redd capacity of the area based on spawning habitat characteristics. The suitability of the study area was estimated through the use of geomorphic analysis, empirical physical data, and modeled hydraulic data. We estimated that 5% (48.7 ha) of the study area contains potentially suitable fall chinook salmon spawning habitat. Potential spawning habitat is primarily limited by deep water and low water velocities, resulting in 20% (9.6 ha) of the potential spawning habitat being characterized as high quality. Estimates of redd capacity within potential spawning habitat range from 207 to 1599 redds. The results of our study provide fisheries managers with useful information for evaluating the complex issue of reintroducing anadromous fish to the Columbia River upstream of Chief Joseph Dam.
Test fishery indices for sockeye salmon (Oncorhynchus nerka) as affected by age composition and environmental variables
Authors: Flynn Lucy , Hilborn Ray
Published: March 2004

In this paper, we explore sources of variability in test fishing indices for sockeye salmon (Oncorhynchus nerka) and illustrate potential solutions. For our analysis, we use the Port Moller test fishery in Bristol Bay, Alaska. The traditional model used to forecast run size using Port Moller test fishery data is based on a simple linear regression of total returns to the fishing districts against the cumulative test fishery catch-per-unit-effort (CPUE) index on a given date. We show that much of the inaccuracy of recent forecasts based on test fishery indices is due to the variable age composition of sockeye runs and the unequal vulnerability of respective age classes to the test fishing gear. We also illustrate solutions to the problems presented by variability in migration route and variability in return timing. In warmer years, we found that there was an increase in effective vulnerability to the test fishing gear and that the strength of this relationship increased linearly with the average body length of age classes. Retrospective analysis shows that correcting for age composition, migration route, and timing provides an in-season index of abundance with an average error of 6.7 million fish or 21%, compared with 33% for previous models.