bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution of
Giardia duodenalis
Genotypes and Subgenotypes in Raw Urban Wastewater in Milwaukee, Wisconsin
Authors: Sulaiman Irshad M. , Jiang Jianlin , Singh Ajaib , Xiao Lihua 
Published: June 2004

ABSTRACT

Giardia
cysts in 131 raw wastewater samples from Milwaukee, Wis., were genotyped by sequence analysis of the triosephosphate isomerase gene which showed the presence of two distinct genotypes (assemblages A and B) of
Giardia duodenalis
. Of the 131 samples, 111 belonged to assemblage A, and the remaining samples belonged to assemblage B. A high degree of genetic polymorphism was evident within the assemblage B cluster, with 10 distinct subgenotypes identified, eight of which have not been reported before.
Stable Carbon Isotopic Fractionations Associated with Inorganic Carbon Fixation by Anaerobic Ammonium-Oxidizing Bacteria
Authors: Schouten Stefan , Strous Marc , Kuypers Marcel M. M. , Rijpstra W. Irene C. , Baas Marianne , Schubert Carsten J. , Jetten Mike S. M. , Sinninghe Damsté Jaap S. 
Published: June 2004

ABSTRACT

Isotopic analyses of
Candidatus
“Brocadia anammoxidans,” a chemolithoautotrophic bacterium that anaerobically oxidizes ammonium (anammox), show that it strongly fractionates against
13
C; i.e., lipids are depleted by up to 47‰ versus CO
2
. Similar results were obtained for the anammox bacterium
Candidatus
“Scalindua sorokinii,” which thrives in the anoxic water column of the Black Sea, suggesting that different anammox bacteria use identical carbon fixation pathways, which may be either the Calvin cycle or the acetyl coenzyme A pathway.
Insertions, Deletions, and Single-Nucleotide Polymorphisms at Rare Restriction Enzyme Sites Enhance Discriminatory Power of Polymorphic Amplified Typing Sequences, a Novel Strain Typing System for
Escherichia coli
O157:H7
Authors: Kudva Indira T. , Griffin Robert W. , Murray Megan , John Manohar , Perna Nicole T. , Barrett Timothy J. , Calderwood Stephen B. 
Published: June 2004

ABSTRACT

Polymorphic amplified typing sequences (PATS) for
Escherichia coli
O157:H7 (O157) was previously based on indels containing XbaI restriction enzyme sites occurring in O-island sequences of the O157 genome. This strain-typing system, referred to as XbaI-based PATS, typed every O157 isolate tested in a reproducible, rapid, straightforward, and easy-to-interpret manner and had technical advantages over pulsed-field gel electrophoresis (PFGE). However, the system was less discriminatory than PFGE and was unable to differentiate fully between unrelated isolates. To overcome this drawback, we enhanced PATS by using another infrequently cutting restriction enzyme, AvrII (also known as BlnI), to identify additional polymorphic regions that could increase the discriminatory ability of PATS typing. Referred to as AvrII-based PATS, the system identified seven new polymorphic regions in the O157 genome. Unlike XbaI, polymorphisms involving AvrII sites were caused by both indels and single-nucleotide polymorphisms occurring in O-island and backbone sequences of the O157 genome. AvrII-based PATS by itself provided poor discrimination of the O157 isolates tested. However, when primer pairs amplifying the seven polymorphic AvrII sites were combined with those amplifying the eight polymorphic XbaI sites (combined PATS), the discriminatory power of PATS was enhanced. Combined PATS matched related O157 isolates better than PFGE while differentiating between unrelated isolates. PATS typed every O157 isolate tested and directly targeted polymorphic sequences responsible for differences in the restriction digest patterns of O157 genomic DNA, utilizing PCR rather than relying on gel electrophoresis. This enabled PATS to resolve the ambiguity in PFGE typing, including that arising from the “more distantly related” and “untypeable” profiles.
Relationship of MIC and Bactericidal Activity to Efficacy of Vancomycin for Treatment of Methicillin-Resistant
Staphylococcus aureus
Bacteremia
Authors: Sakoulas George , Moise-Broder Pamela A. , Schentag Jerome , Forrest Alan , Moellering Robert C. , Eliopoulos George M. 
Published: June 2004

ABSTRACT

We attempted to find a relationship between the microbiological properties of bloodstream isolates of methicillin-resistant
Staphylococcus aureus
(MRSA) and the efficacy of vancomycin in the treatment of bacteremia. Vancomycin susceptibility testing was performed, and bactericidal activity was determined for 30 isolates from 30 different patients with MRSA bacteremia for whom clinical and microbiological outcome data were available. The majority of these patients had been previously enrolled in multicenter prospective studies of MRSA bacteremia refractory to conventional vancomycin therapy. Logistic regression found a statistically significant relationship between treatment success with vancomycin and decreases in both vancomycin MICs (≤0.5 μg/ml versus 1.0 to 2.0 μg/ml;
P
= 0.02) and degree of killing (reduction in 1og
10
CFU/milliliter) by vancomycin over 72 h of incubation in vitro (
P
= 0.03). For MRSA isolates with vancomycin MICs ≤ 0.5 μg/ml, vancomycin was 55.6% successful in the treatment of bacteremia whereas vancomycin was only 9.5% effective in cases in which vancomycin MICs for MRSA were 1 to 2 μg/ml. Patients with MRSA that was more effectively killed at 72 h by vancomycin in vitro had a higher clinical success rate with vancomycin therapy in the treatment of bacteremia (log
10
< 4.71 [
n
= 9], 0%; log
10
4.71 to 6.26 [
n
= 13], 23.1%; log
10
> 6.27 [
n
= 8], 50%). We conclude that a significant risk for vancomycin treatment failure in MRSA bacteremia begins to emerge with increasing vancomycin MICs well within the susceptible range. Elucidating the mechanisms involved in intermediate-level glycopeptide resistance in
S. aureus
should begin by examining bacteria that begin to show changes in vancomycin susceptibility before the development of obvious resistance. Prognostic information for vancomycin treatment outcome in MRSA bacteremia may also be obtained by testing the in vitro bactericidal potency of vancomycin.
Molecular Characterization of Rifampin- and Isoniazid-Resistant
Mycobacterium tuberculosis
Strains Isolated in Poland
Authors: Sajduda Anna , Brzostek Anna , Popławska Marta , Augustynowicz-Kopeć Ewa , Zwolska Zofia , Niemann Stefan , Dziadek Jarosław , Hillemann Doris 
Published: June 2004

ABSTRACT

A total of 105 rifampin (RMP)- and/or isoniazid (INH)-resistant strains of
Mycobacterium tuberculosis
isolated from different parts of Poland in 2000 were screened for mutations associated with resistance to these drugs by two molecular methods, namely sequence analysis and real-time PCR technology. Three loci associated with drug resistance were selected for characterization: they were
rpoB
(RMP),
katG
, and the regulatory region of
inhA
(INH). Nineteen different mutations were identified in 64 RMP-resistant strains, and five new alleles were described. The most common point mutations were in codons 531 (41%), 516 (16%), and 526 (9%) of the
rpoB
gene. Mutations were not found in two (3%) of the isolates. In the case of resistance to INH, six different mutations in the
katG
gene of 83 resistant strains were detected. Fifty-seven (69%) isolates exhibited nucleotide substitutions at codon 315. One strain harbored a mutation affecting codon 279 (Gly279Thr). Twelve of 26 INH-resistant strains with the wild-type codon 315 (14.5% of all strains tested) had the mutation −15C→T in the regulatory region of
inhA
. A full correlation between the DNA sequence analysis and real-time PCR data was obtained. We conclude that the real-time PCR method is fast and reliable for the detection of RMP and INH resistance-associated mutations in
M. tuberculosis
clinical isolates.
Rapid Quantification of Hepatitis B Virus DNA by Automated Sample Preparation and Real-Time PCR
Authors: Stelzl Evelyn , Muller Zsofia , Marth Egon , Kessler Harald H. 
Published: June 2004

ABSTRACT
Monitoring of hepatitis B virus (HBV) DNA in serum by molecular methods has become the standard for assessment of the replicative activity of HBV. Several molecular assays for the detection and quantification of HBV DNA have been described. However, they usually lack automated sample preparation. Moreover, those assays, which are based on PCR, are limited by a short dynamic range (2 to 3 log units). In the present study, the use of RealArt HBV LC PCR Reagents in conjunction with automated extraction on the COBAS AMPLIPREP analyzer was evaluated. Members of an HBV proficiency program panel were tested; linearity, interassay, and intra-assay variations were determined. The performance of the assay in a routine clinical laboratory was evaluated with a total of 117 clinical specimens. When members of the HBV proficiency program panel were tested by the new molecular assay, the results were found to be within ±0.5 log unit of the results obtained by reference laboratories. Determination of linearity resulted in a quasilinear curve over more than 6 log units. The interassay variation of the RealArt HBV LC PCR Reagents by use of the automated sample preparation protocol ranged from 16 to 73%, and the intra-assay variation ranged from 9 to 40%. When clinical samples were tested by the new assay with the automated sample preparation protocol and the results were compared with those obtained by the COBAS AMPLICOR HBV MONITOR Test with manual sample preparation, the results for 76% of all samples with positive results by both tests were found to be within ±0.5 log unit and the results for another 18% were found to be within between 0.5 and 1.0 log unit. In conclusion, the real-time PCR assay with automated sample preparation proved to be suitable for the routine molecular laboratory and required less hands-on time.
Comparison of Quantitative and Semiquantitative Enzyme-Linked Immunosorbent Assays for Immunoglobulin G against
Chlamydophila pneumoniae
to a Microimmunofluorescence Test for Use with Patients with Respiratory Tract Infections
Authors: Hermann Corinna , Gueinzius Katja , Oehme Albrecht , von Aulock Sonja , Straube Eberhard , Hartung Thomas 
Published: June 2004

ABSTRACT

We previously reported a high degree of variation in the sensitivities of serodiagnostic kits for the detection of
Chlamydophila pneumoniae
in sera from healthy donors. Since a low predictive value of a test can impair its diagnostic value, we have extended our studies to samples from patients with pneumonia. We focused on the most promising enzyme-linked immunosorbent assays (ELISAs) (SeroCP and SeroCP Quant; Savyon) identified in our previous study and included a new ELISA (sELISA; Medac). The agreement between all ELISAs for immunoglobulin G (IgG) and a reference microimmunofluorescence (MIF) test for IgG (SeroFIA; Savyon) was ≥90% for a collective of 80 patients. The positive predictive values were all ≥93%. The negative predictive values ranged from 68 to 83%. False-negative results were obtained only for samples that had low titers in the MIF test. The correlation of the IgG antibody titers determined by the MIF and SeroCP Quant tests was high (
r
sp
= 0.9). Since the semiquantitative SeroCP and quantitative SeroCP Quant ELISAs achieved the highest sensitivities, they were evaluated further by using a second batch of sera from 50 patients with predominantly medium and low antibody titers in the MIF test and a control collection of sera from 80 children with negative MIF results. Again, the tests showed a high concordance with the MIF results (96%), and the antibody titers in the SeroCP Quant and MIF tests correlated well (
r
sp
= 0.8). The specificities determined with the negative sera were ≥99% for the SeroCP Quant test and 86% for the SeroCP test. These results show that ELISAs that are fast and objective deliver seroprevalence results, sensitivities, and specificities that are very similar to those of the MIF test.
Dengue Virus Serotyping Based on Envelope and Membrane and Nonstructural Protein NS1 Serotype-Specific Capture Immunoglobulin M Enzyme-Linked Immunosorbent Assays
Authors: Shu Pei-Yun , Chen Li-Kuang , Chang Shu-Fen , Su Chien-Ling , Chien Li-Jung , Chin Chuan , Lin Ting-Hsiang , Huang Jyh-Hsiung 
Published: June 2004

ABSTRACTEnvelope and membrane (E/M) and nonstructural protein NS1 serotype-specific capture Immunoglobulin M (IgM) enzyme-linked immunosorbent assays (ELISAs) were developed to differentiate four dengue virus serotypes. A total of 93 anti-dengue virus IgM-positive serum samples collected between days 5 and 45 of illness from 59 confirmed dengue patients were analyzed. The results showed that positive serotype specificity could be identified for 86.1 and 47.6% of serum samples tested for E/M-specific IgM antibodies versus 83.3 and 42.9% of serum samples tested for NS1-specific IgM antibodies from patients with primary and secondary dengue virus infections, respectively. Dual analyses with both E/M and NS1 serotype-specific capture IgM ELISAs showed that positive serotype specificity could be correctly identified for 98.6 and 61.9% of all of the primary and secondary serum samples tested, respectively. These findings suggested that E/M and NS1 serotype-specific capture IgM ELISAs have the potential to be of use in dengue virus serotyping.
Molecular Epidemiologic Evaluation of Endocarditis Due to
Oerskovia turbata
and CDC Group A-3 Associated with Contaminated Homograft Valves
Authors: McNeil Michael M. , Brown June M. , Carvalho Michelle E. , Hollis Dannie G. , Morey Roger E. , Reller L. Barth 
Published: June 2004

ABSTRACT

Oerskovia turbata
is an unusual bacterial cause of endocarditis and septicemia in immunocompromised patients. In this study, we compared 12 isolates from a 1975 medical center cluster, 11 originally identified as
O. turbata
(four from the blood of a homograft aortic valve-associated endocarditis patient and seven from contaminated homograft valves) and one CDC group A-3 strain from the blood of a second endocarditis patient with fatal outcome, with eight control strains from unrelated locations. The control strains included type and reference strains of
O. turbata
,
Cellulomonas hominis
, and CDC group A-3. The four blood isolates from the first patient and six of the valve isolates shared identical biochemical, antimicrobial susceptibility, and BglI ribotype patterns that differed from the second patient's isolate and control strains. The blood isolate from the second patient and the remaining valve isolate shared a phenotypic and genotypic profile and were phenotypically identical to, but epidemiologically different from, the CDC group A-3 reference strain with the strain-specific enzyme. Also, these isolates differed from the type strain and the other reference strains of
C. hominis
and
O. turbata
. Our results indicate that the four blood isolates from the first patient and six of the homograft valve isolates represent a single clone of
O. turbata
associated with endocarditis. Additionally, our results indicate that the blood isolate from the second patient and one of the homograft valve isolates differ from
O. turbata
and
C. hominis
and represent a unique clone of CDC group A-3 associated with fatal endocarditis.
Characterization of
Chlamydia trachomatis omp1
Genotypes Detected in Eye Swab Samples from Remote Australian Communities
Authors: Stevens Matthew P. , Tabrizi Sepehr N. , Muller Rosanne , Krause Vicki , Garland Suzanne M. 
Published: June 2004

ABSTRACT

Chlamydia trachomatis
conjunctival samples collected over a 6-month period from individuals with clinical signs of trachoma and located in remote communities in the Australian Northern Territory were differentially characterized according to serovar and variants. The rationale was to gain an understanding of the epidemiology of an apparent increased prevalence of acute trachoma in areas thought to be less conducive to this disease. Characterization was performed through sequencing of a region of the
omp1
gene spanning the four variable domains and encoding the major outer membrane protein. Nucleotide and deduced amino acid sequences were genotyped by using a BLAST similarity search and were examined by phylogenetic analyses to illustrate evolutionary relationships between the clinical and GenBank reference strains. The predominant genotype identified corresponded to that of serovar C (87.1%), followed by the genotype corresponding to serovar Ba (12.9%). All nucleotide and amino acid sequences exhibited minor levels of variation with respect to GenBank reference sequences. The
omp1
nucleotide sequences of the clinical samples best aligned with those of the conjunctival
C
.
trachomatis
reference strains C/TW-3/OT and Ba/Apache-2. All clinical samples (of serovar C) exhibited four or five nucleotide changes compared with C/TW-3/OT, while all serovar Ba samples had one or two nucleotide differences from Ba/Apache-2. Phylogenetic analyses revealed close relationships between these Northern Territory chlamydial samples and the respective reference strains, although the high proportion of sequence variants suggests an evolutionarily distinct
C
.
trachomatis
population causing eye infections in Australia. Given that such genotypic information has gone unreported, these findings provide knowledge and a foundation for trachoma-associated
C
.
trachomatis
variants circulating in the Northern Territory.
Multifocal Detection of Multidrug-Resistant
Pseudomonas aeruginosa
Producing the PER-1 Extended-Spectrum β-Lactamase in Northern Italy
Authors: Pagani Laura , Mantengoli Elisabetta , Migliavacca Roberta , Nucleo Elisabetta , Pollini Simona , Spalla Melissa , Daturi Rossana , Romero Egidio , Rossolini Gian Maria 
Published: June 2004

ABSTRACT

Forty-four nonreplicate clinical isolates of
Pseudomonas aeruginosa
that were resistant to extended-spectrum cephalosporins (ceftazidime and cefepime) and aztreonam, that putatively produced an acquired extended- spectrum β-lactamase (ESBL), according to the results of a double-disk synergy test, and that had been involved in nosocomial outbreaks were obtained from six different hospitals in northern Italy and screened for the presence of
bla
PER
ESBL determinants. Twenty isolates, associated with nine independent outbreaks that occurred in five hospitals in the Milan area and its surroundings during 1995-2000, were found to carry an acquired
bla
PER-1
gene. PER-1 producers representative of the nine outbreaks exhibited a multidrug resistance (MDR) phenotype, including resistance to extended-spectrum cephalosporins, aztreonam, meropenem, aminoglycosides, and in most cases, imipenem and ciprofloxacin. An analysis of macrorestriction profiles of their genomic DNAs by pulsed-field gel electrophoresis revealed an overall clonal diversity of the PER-1 producers, although interhospital clonal spread was also observed. The
bla
PER-1
gene was not transferable and appeared to be chromosomally located. An analysis of the EcoRI and EcoRV restriction fragment length polymorphisms of the
bla
PER-1
locus revealed identical patterns for all isolates, and the characterization of a 1.9-kb region containing
bla
PER-1
revealed a conserved structure in representatives of the various clonal lineages. The present findings indicate that MDR
P. aeruginosa
clones producing the PER-1 ESBL are endemic to this area of northern Italy, where they have been circulating since the mid-1990s and have been associated with several nosocomial outbreaks.
Characterization of G10P[11] Rotaviruses Causing Acute Gastroenteritis in Neonates and Infants in Vellore, India
Authors: Iturriza Gómara Miren , Kang Gagandeep , Mammen Ajit , Jana Atanu Kumar , Abraham Mary , Desselberger Ulrich , Brown David , Gray Jim 
Published: June 2004

ABSTRACTRotavirus G10P[11] strains, which are commonly found in cattle, have frequently been associated with asymptomatic neonatal infections in India. We report the finding of G10P[11] strains associated with severe disease in neonates in Vellore, southern India. Rotavirus strains from 43 fecal samples collected from neonates with or without gastrointestinal symptoms between 1999 and 2000 were genotyped by reverse transcription-PCR. Forty-one neonates (95%) were infected with G10P[11] rotavirus strains, and 63% of the infections were in children who had gastrointestinal symptoms, including acute watery diarrhea. G10P[11] strains were also seen infecting older children with dehydrating gastroenteritis in Vellore. Characterization of the genes encoding VP7, VP4, VP6, and NSP4 of these strains revealed high sequence homology with the corresponding genes of the asymptomatic neonatal strain I321, which in turn is very closely related to bovine G10P[11] strains circulating in India. No significant differences were seen in the sequences obtained from strains infecting symptomatic neonates or children and asymptomatic neonates.
Serological and Genetic Diversity of Capsular Polysaccharides in
Enterococcus faecalis
Authors: Hufnagel Markus , Hancock Lynn E. , Koch Stefanie , Theilacker Christian , Gilmore Michael S. , Huebner Johannes 
Published: June 2004

ABSTRACT

Enterococci possess capsular carbohydrate antigens that are targets of opsonic antibodies. These antigens may be used to develop alternative options for the treatment and prevention of enterococcal infections. The present study was done to analyze the diversity of capsular polysaccharides in
Enterococcus faecalis
. Four type-specific sera were used in an enzyme-linked immunosorbent assay format to detect polysaccharide antigen extracted from bacterial cell walls. A total of 55% of a collection of 29
E. faecalis
strains could be grouped into one of four serogroups. Additional analysis of the strains by opsonophagocytic assays revealed agreement between the results of the two methods for 72% of the isolates. An additional four strains could be assigned to a serogroup on the basis of opsonic killing by sera with antibodies against the four prototypes strains, provisionally named CPS-A to CPS-D. The results of the two methods disagreed for one strain (4%). When the results of both methods were combined, 66% of the strains could be classified. One strain had to be assigned to two serogroups. The assignments to the four serogroups were confirmed by analysis of the genetic organization of the biosynthetic capsular polysaccharide (
cps
) locus. All strains grouped into serotypes CPS-A and CPS-B possessed only the
cpsA
and
cpsB
genes, while all strains grouped into serogroups CPS-C and CPS-D possessed an additional eight or nine genes. Our results suggest the existence of a limited number of
E. faecalis
capsule serotypes, and we provisionally propose four serotypes, named CPS-A to CPS-D, and the respective prototype strains for these families.