bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and Specific Detection of
Mycobacterium tuberculosis
from Acid-Fast Bacillus Smear-Positive Respiratory Specimens and BacT/ALERT MP Culture Bottles by Using Fluorogenic Probes and Real-Time PCR
Authors: Miller Nancimae , Cleary Tim , Kraus Günter , Young Andrea K. , Spruill Gina , Hnatyszyn H. James 
Published: October 2002

ABSTRACT

A real-time PCR assay using the LightCycler (LC) instrument for the specific identification of
Mycobacterium tuberculosis complex
(MTB) was employed to detect organisms in 135 acid-fast bacillus (AFB) smear-positive respiratory specimens and in 232 BacT/ALERT MP (MP) culture bottles of respiratory specimens. The LC PCR assay was directed at the amplification of the internal transcribed spacer region of the
Mycobacterium
genome with real-time detection using fluorescence resonance energy transfer probes specific for MTB. The results from the respiratory specimens were compared to those from the Amplicor
M. tuberculosis
PCR test. Specimens from MP culture bottles were analyzed by Accuprobe and conventional identification methods. MTB was cultured from 105 (77.7%) respiratory AFB smear-positive specimens; 103 of these samples were positive by LC PCR and Amplicor PCR. Two samples negative in the LC assay contained rare numbers of organisms; both were positive in the Amplicor assay. Two separate samples negative by Amplicor PCR contained low and moderate numbers of AFB, respectively, and both of these were positive in the LC assay. There were 30 AFB smear-positive respiratory specimens that grew mycobacteria other than tuberculosis (MOTT), and all tested negative in both assays. Of the 231 MP culture bottles, 114 cultures were positive for MTB and all were positive by the LC assay. The remaining 117 culture bottles were negative in the LC assay and grew various MOTT. This real-time MTB assay is sensitive and specific; a result was available within 1 h of having a DNA sample available for testing.
Molecular Characterization of Hepatitis A Virus Isolates from a Transcontinental Shellfish-Borne Outbreak
Authors: Sánchez Glòria , Pintó Rosa M. , Vanaclocha Hermelinda , Bosch Albert 
Published: October 2002

ABSTRACT
One hundred eighty-four serologically confirmed cases of hepatitis A were reported in eastern Spain in 1999. A matched case-control study implicated imported coquina clams complying with European Union shellfish standards as the source of infection; this implication was confirmed by the detection by reverse transcription-PCR of hepatitis A virus (HAV) RNA in shellfish samples. In spite of the recognized low variability of HAV, genetic characterization of the complete capsid region of virus isolates from patient serum samples revealed the existence of both synonymous and nonsynonymous variants. Two antigenic variants were detected, one in a discontinuous epitope defined by monoclonal antibody K3-4C8 and a second in a linear VP1 epitope of the virus. In spite of these antigenic variants, all isolates were assigned to genotype IB, providing further evidence that the outbreak originated from a common source, although multiple strains were likely to be involved.
Increasing Genetic Diversity of
Salmonella enterica
Serovar Typhi Isolates from Papua New Guinea over the Period from 1992 to 1999
Authors: Thong Kwai-Lin , Goh Yee-Ling , Yasin Rohani M. , Lau Ming Guek , Passey Megan , Winston Gibson , Yoannes Mition , Pang Tikki , Reeder John C. 
Published: October 2002

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) of
Xba
I-digested chromosomal DNA was performed on 133 strains of
Salmonella enterica
serovar Typhi obtained from Papua New Guinea, with the objective of assessing the temporal variation of these strains. Fifty-two strains that were isolated in 1992 and 1994 were of one phage type, D2, and only two predominant PFGE profiles, X1 and X2, were present. Another 81 strains isolated between 1997 and 1999 have shown divergence, with four new phage types, UVS I (
n
= 63), UVS (
n
= 5), VNS (
n
= 4), and D1 (
n
= 9), and more genetic variability as evidenced by the multiple and new PFGE
Xba
I profiles (21 profiles; Dice coefficient,
F
= 0.71 to 0.97). The two profiles X1 and X2 have remained the stable, dominant subtypes since 1992. Cluster analysis based on the unweighted pair group method using arithmetic averages algorithm identifies two main clusters (at 87% similarity), indicating that the divergence of the PFGE subtypes was probably derived from some genomic mutations of the X1 and X2 subtypes. The majority of isolates were from patients with mild and moderate typhoid fever and had various
Xba
I profiles. A single isolate from a patient with fatal typhoid fever had a unique X11 profile, while four of six isolates from patients with severe typhoid fever had the X1 pattern. In addition, 12 paired serovar Typhi isolates recovered from the blood and fecal swabs of individual patients exhibited similar PFGE patterns, while in another 11 individuals paired isolates exhibited different PFGE patterns. Three pairs of isolates recovered from three individuals had different phage types and PFGE patterns, indicating infection with multiple strains. The study reiterates the usefulness of PFGE in assessing the genetic diversity of
S. enterica
serovar Typhi for both long-term epidemiology and in vivo stability and instability within an individual patient.
Evaluation of an Enzyme-Linked Immunosorbent Assay (ELISA) with Affinity-Purified Em18 and an ELISA with Recombinant Em18 for Differential Diagnosis of Alveolar Echinococcosis: Results of a Blind Test
Authors: Ito Akira , Xiao Ning , Liance Martine , Sato Marcello O. , Sako Yasuhito , Mamuti Wulamu , Ishikawa Yuji , Nakao Minoru , Yamasaki Hiroshi , Nakaya Kazuhiro , Bardonnet Karine , Bresson-Hadni Solange , Vuitton Dominique A. 
Published: October 2002

ABSTRACT

Alveolar echinococcosis (AE) is the most potentially lethal parasitic zoonosis of the nontropical areas in the northern hemisphere, where cystic echinococcosis (CE) is also endemic. Both AE and CE are highly endemic in China, and both serologic detection of echinococcosis, either AE or CE, and differentiation of AE from CE are crucial problems. Evaluation of Western blot analysis (WB) and enzyme-linked immunosorbent assay (ELISA) for the Em18 antigen, using affinity-purified and recombinant Em18, was carried out “blindly” using 60 human sera from patients diagnosed in France. The results were compared with those obtained using a commercially available
Echinococcus
WB immunoglobulin G (IgG) kit developed in France. The Em18 WB and
Echinococcus
WB IgG showed very similar results for detection of AE. Both affinity-purified Em18 or a recombinant Em18 WB and
Echinococcus
WB IgG seem useful for identification of AE, and the latter seems appropriate for both AE and CE, whereas affinity-purified Em18 ELISA and the newly developed recombinant Em18 ELISA appear to be suitable for detection of AE, especially for epidemiological surveys.
Evaluation of the ICT Malaria P.f/P.v and the OptiMal Rapid Diagnostic Tests for Malaria in Febrile Returned Travellers
Authors: Playford E. Geoffrey , Walker John 
Published: October 2002

ABSTRACT

Rapid diagnostic tests (RDTs) are less reliant on expert microscopy and have the potential to reduce errors in malaria diagnosis but have not been extensively evaluated in nonimmune persons or in countries where infection is not endemic. We evaluated the ICT P.f/P.v (ICT-Amrad, Sydney, Australia) and OptiMal (Flow Inc., Portland, Oreg.) assays prospectively for the diagnosis of malaria in 158 specimens from 144 febrile returned travellers in Australia by using expert microscopy and PCR as reference standards. Malaria was diagnosed in 93 specimens from 87 patients by expert microscopy, with 3 additional specimens from recently treated patients testing positive for
Plasmodium falciparum
by PCR. For the diagnosis of asexual-stage
P. falciparum
malaria, the sensitivity and specificity of the ICT P.f/P.v assay were 97 and 90%, respectively, and those of the OptiMal assay were 85 and 96%, respectively. The ICT P.f/P.v assay missed one infection with a density of 45 parasites/μl, whereas the OptiMal assay missed infections up to 2,500/μl; below 1,000/μl, its sensitivity was only 43%. For the diagnosis of
P. vivax
malaria, the sensitivity and specificity of the ICT P.f/P.v assay were 44 and 100%, respectively, and those of the OptiMal assay were 80 and 97%, respectively. Both assays missed infections with parasite densities over 5,000/μl: up to 10,000/μl with the former and 5,300/μl with the latter. Despite the high sensitivity of the ICT P.f/P.v assay for
P. falciparum
malaria, caution is warranted before RDTs are widely adopted for the diagnosis of malaria in nonimmune patients or in countries where malaria is not endemic.
Single and Combination Antibiotic Susceptibilities of Planktonic, Adherent, and Biofilm-Grown
Pseudomonas aeruginosa
Isolates Cultured from Sputa of Adults with Cystic Fibrosis
Authors: Aaron Shawn D. , Ferris Wendy , Ramotar Karam , Vandemheen Katherine , Chan Francis , Saginur Raphael 
Published: October 2002

ABSTRACT

Evidence suggests that
Pseudomonas aeruginosa
bacteria form biofilms within the airways of adults with cystic fibrosis (CF). The objective of this study was to determine whether clinical isolates of
P. aeruginosa
recovered from adults with CF have similar susceptibilities to individual antibiotics and to antibiotic combinations when grown as adherent monolayers or as biofilms compared to when they are grown using planktonic methods. Twelve multiresistant
P. aeruginosa
isolates, one mucoid and one nonmucoid from each of six CF patients, were grown conventionally under planktonic conditions, as adherent bacterial monolayers, and as biofilms. Each bacterial isolate remained genotypically identical despite being cultured under planktonic, adherent, or biofilm growth conditions. Isolates grown as adherent monolayers and as biofilms were less susceptible to bactericidal killing by individual antibiotics compared to those grown planktonically. More importantly, biofilm-grown bacteria, but not adherent monolayer-grown bacteria, were significantly less susceptible to two- and three-drug combinations of antibiotics than were planktonically grown bacteria (
P
= 0.005). We conclude that biofilm-grown bacteria derived from patients with CF show decreased susceptibility to the bactericidal effects of antibiotic combinations than do adherent and planktonically grown bacteria.
Epidemiological Features of Invasive
Kingella kingae
Infections and Respiratory Carriage of the Organism
Authors: Yagupsky Pablo , Peled Nechama , Katz Orna 
Published: October 2002

ABSTRACT

The age, sex, and seasonal distributions of invasive
Kingella kingae
infections in southern Israel were examined and compared to the epidemiology of respiratory carriage of the organism. Medical records of all patients diagnosed between 1988 and 2002 were reviewed, and 2,044 oropharyngeal specimens were cultured on selective media during two periods (February to May and October to December) in 2001. Invasive infections significantly affected children (73 of 74 patients [98.6%] were younger than 4 years), 50 patients (67.8%) were males (
P
= 0.045), and 55 episodes (74.3%) occurred between July and December (
P
= 0.004). Carriage was higher in the 0- to 3-year-old group and decreased with increasing age (
P
for trend = 0.0008). Carriage rates were similar in both sexes and did not significantly differ between the February-to-May and October-to-December periods. The highest rate of carriage of
K. kingae
coincided with the age (less than 4 years) at which invasive infections were especially frequent. The peculiar sex and seasonal distributions of invasive disease, however, cannot be readily explained by the epidemiology of respiratory carriage. Viral infections and other yet-to-be-defined cofactors may play a role in the causation of invasive
K. kingae
infections.
Rate of Occurrence and Pathogenic Effect of Enteroaggregative
Escherichia coli
Virulence Factors in International Travelers
Authors: Jiang Zhi-Dong , Greenberg David , Nataro James P. , Steffen Robert , DuPont Herbert L. 
Published: October 2002

ABSTRACT

One or more putative enteroaggregative
Escherichia coli
(EAEC) virulence factors (
aggA, aggR, aspU,
or
aafA
) were identified in 60 (70%) of 86 EAEC isolates from travelers with diarrhea compared with a rate of 7 (8%) of 90 in patients with diarrhea who were infected with nonadherent
E. coli
(odds ratio, 27.36; 95% confidence interval, 11.30 to 65.91). The presence of
aggR
or one or more virulence factors in EAEC from patients with diarrhea was associated with a statistically increased concentration of interleukin-8 (IL-8) in feces compared with that in EAEC negative for these factors: for
aggR
positive (9 of 12 [75%]; median, 800 pg/ml) versus
aggR
negative (5 of 18 [28%]; median, 0),
P
< 0.05; and for isolates positive for ≥1 virulence factor (13 of 21 [62%]; median, 360 pg/ml) versus those negative for ≥1 virulence factor (1 of 9 [11%]; median, 0),
P
< 0.05. Other fecal cytokines (IL-1β and IL-1ra) were found in increased concentrations (
P
< 0.05 when at least one EAEC virulence factor was present compared with the concentrations when EAEC negative for multiple virulence factors was found in patients with diarrhea. Putative virulence factors were commonly found in EAEC from patients with diarrhea, and the pathogenicity of many strains was suggested by showing an association between the presence of plasmid-borne virulence factors and the presence of fecal cytokines. The different patterns of virulence factors of EAEC revealed several clusters demonstrating diversity among the isolates from the various regions.
Novel Allelic Variants of Mycobacteria Isolated in Brazil as Determined by PCR-Restriction Enzyme Analysis of
hsp65
Authors: da Silva Rocha A. , Werneck Barreto A. M. , Dias Campos C. E. , Villas-Bôas da Silva M. , Fonseca L. , Saad M. H. , Degrave W. M. , Suffys P. N. 
Published: October 2002

ABSTRACT

Human isolates of
Mycobacterium
collected in 16 different states of Brazil were submitted to PCR-restriction analysis (PRA) of a 439-bp fragment of the
hsp65
gene with
Hae
III and
Bst
EII. Fourteen allelic variants not described in clinical isolates so far were observed among 36 (10%) of 356 Brazilian strains, including a new pattern for
Mycobacterium scrofulaceum
,
M. intracellulare
, and
M. flavescens
, two new patterns for
M. fortuitum
, three new patterns each for
M. gordonae
and
M. terrae
, and one new pattern for
M
.
avium
complex-like strains. Two unidentified strains each also presented a new pattern, strongly suggesting that
Mycobacterium
genotypes are distributed biogeographically. The PRA procedure was also performed with 43 reference isolates belonging to 34 species, adding a further six new patterns to the identification algorithm. A database containing the normalized restriction patterns of both enzymes was constructed. Patterns available on the Internet can be introduced into this database, which will make possible the comparison of genotypes from isolates from different parts of the world.
Heterogeneity and Seroprevalence of a Newly Identified Avian Hepatitis E Virus from Chickens in the United States
Authors: Huang F. F. , Haqshenas G. , Shivaprasad H. L. , Guenette D. K. , Woolcock P. R. , Larsen C. T. , Pierson F. W. , Elvinger F. , Toth T. E. , Meng X. J. 
Published: October 2002

ABSTRACT
We recently identified and characterized a novel virus, designated avian hepatitis E virus (avian HEV), from chickens with hepatitis-splenomegaly syndrome (HS syndrome) in the United States. Avian HEV is genetically related to but distinct from human and swine HEVs. To determine the extent of genetic variation and the seroprevalence of avian HEV infection in chicken flocks, we genetically identified and characterized 11 additional avian HEV isolates from chickens with HS syndrome and assessed the prevalence of avian HEV antibodies from a total of 1,276 chickens of different ages and breeds from 76 different flocks in five states (California, Colorado, Connecticut, Virginia, and Wisconsin). An enzyme-linked immunosorbent assay using a truncated recombinant avian HEV ORF2 antigen was developed and used to determine avian HEV seroprevalence. About 71% of chicken flocks and 30% of chickens tested in the study were positive for antibodies to avian HEV. About 17% of chickens younger than 18 weeks were seropositive, whereas about 36% of adult chickens were seropositive. By using a reverse transcription-PCR (RT-PCR) assay, we tested 21 bile samples from chickens with HS syndrome in California, Connecticut, New York, and Wisconsin for the presence of avian HEV RNA. Of the 21 bile samples, 12 were positive for 30- to 35-nm HEV-like virus particles by electron microscopy (EM). A total of 11 of the 12 EM-positive bile samples and 6 of the 9 EM-negative bile samples were positive for avian HEV RNA by RT-PCR. The sequences of a 372-bp region within the helicase gene of 11 avian HEV isolates were determined. Sequence analyses revealed that the 11 field isolates of avian HEV had 78 to 100% nucleotide sequence identities to each other, 79 to 88% identities to the prototype avian HEV, 76 to 80% identities to chicken big liver and spleen disease virus, and 56 to 61% identities to other known strains of human and swine HEV. The data from this study indicated that, like swine and human HEVs, avian HEV isolates are genetically heterogenic and that avian HEV infection is enzoonotic in chicken flocks in the United States.
Molecular Methods for Cytomegalovirus Surveillance in Bone Marrow Transplant Recipients
Authors: Weinberg Adriana , Schissel Debra , Giller Roger 
Published: October 2002

ABSTRACT
Two different methods for detection of cytomegalovirus (CMV), PCR and hybrid capture (HC), were compared by using plasma, peripheral blood leukocytes (PBLs), and whole blood (WB) from allogeneic bone marrow transplant recipients. One hundred specimens were obtained from nine children over an 18-month surveillance period. PCR of plasma for CMV was used for clinical management. The proportions of samples positive for CMV DNA by PCR with plasma, HC with WB, and PCR with PBLs were 21, 28, and 37%, respectively. Among 44 samples that were tested by all three methods, 68% had concordant results. By using a robust definition of true-positive samples (positivity by two or more methods or positivity of sequential samples by one method), the sensitivities of PCR with plasma, HC with WB, and PCR with PBLs were 50, 67, and 83%, respectively, and the specificities were 100, 96, and 96%, respectively. Two patients developed CMV-associated end-organ disease (one developed respiratory disease, and one developed gastrointestinal disease). CMV DNA was not detected in the plasma 1 week prior to the development of symptoms in either patient, whereas HC with WB was positive for both patients and PCR with PBLs was for one patient. These data suggest that WB or PBLs might be the preferred sample for use for surveillance for CMV in immunocompromised patients.
Performance Characteristics and Utilization of Rapid Antigen Test, DNA Probe, and Culture for Detection of Group A Streptococci in an Acute Care Clinic
Authors: Chapin Kimberle C. , Blake Patricia , Wilson Claire D. 
Published: October 2002

ABSTRACT
Group A streptococcus (GAS) antigen testing has become a routine point-of-care (POC) test in acute care settings. Concern about performance parameters (PP) of these tests as well as inappropriate antibiotic use has resulted in various recommendations regarding diagnosis of GAS. There were two objectives in this study. The first was to evaluate the rapid GAS antigen test presently in use (Thermo BioStar, Boulder, Colo.) and the GAS Direct probe test (Gen-Probe, San Diego, Calif.) compared to culture. The second was to define the optimal use of these technologies in a large acute care pediatric clinic. A total of 520 consecutive pediatric patients presenting with symptoms of pharyngitis at any of three Lahey Clinic acute care facilities were evaluated. Pharyngeal specimens were collected using a double-swab collection device (Copan, Corona, Calif.). One swab was used for the antigen test, the second was used for the probe test, and the pledget was placed in the collection device for culture on 5% sheep blood agar, incubated for 48 h anaerobically, and subsequently placed in Todd-Hewitt broth. After discrepant analysis, sensitivity, specificity, and positive and negative predictive values were as follows: 94.8, 100, 100, and 96.9% for the probe test and 86.1, 97.1, 93.7, and 93.4% for the antigen test, respectively. Sensitivity using an enhanced culture technique was 99.4% (163 of 164). False-positive (FP) antigen results were often seen from patients previously diagnosed and/or treated for GAS. No FP results were seen with the probe test. Colony counts for the false-negative (FN) antigen tests were higher than those for the FN probe tests. Compared to culture and DNA probe, the rapid antigen test (RAT) offered a result at the time of the patient's visit, with acceptable PP when prevalence of disease is high. Follow-up testing with the RAT of GAS patients who previously tested as positive should be avoided due to increased FP results. The probe test was comparable to culture in performance. Results indicate the probe test can be used as the primary test or as a backup to negative antigen tests. The probe test offers the advantage over culture of same-day reporting of a final result but, in contrast to a POC test, necessitates follow-up communication to the patient. Preliminary data show the specificity of the probe test to be greater than that of the RAT for patients previously diagnosed with GAS.
Optimal DNA Isolation Method for Detection of Bacteria in Clinical Specimens by Broad-Range PCR
Authors: Rantakokko-Jalava Kaisu , Jalava Jari 
Published: October 2002

ABSTRACT
Broad-range amplification of bacterial DNA from clinical specimens has proved useful for the diagnosis of various bacterial infections, especially during antimicrobial treatment of the patient. Optimal sample processing protocols for diagnostic broad-range bacterial PCR should release DNA from an array of target organisms with equal efficiencies and wash out inhibitory factors from various sample types without introducing bacterial DNA contamination to the amplification reaction. In the present study, two physical cell wall disintegration methods, bead beating and sonication, for enhanced detection of organisms with difficult-to-lyse cell walls were studied. The analytical sensitivities of several commercially available DNA purification kits, which were used with and without additional cell disintegration steps, were compared by using dilution series of model bacteria. Selected purification methods were used to process routine clinical specimens in parallel with the standard phenol-ether DNA extraction, and the results obtained by bacterial PCR and sequencing with the two template preparations were compared. The method with the DNA isolation kit with the lowest detection limits from the bacterial suspensions (Masterpure) did not prove to be superior to the standard method when the two methods were applied to 69 clinical specimens. For another set of 68 clinical specimens, DNA purified with a glass fiber filter column (High Pure) with an additional sonication step yielded results well in accord with those obtained by the standard method. Furthermore, bacterial DNA was detected in four samples that remained PCR negative by the standard method, and three of these contained DNA from gram-positive pathogens. Three samples were positive by the standard method only, indicating the limitations of applying any single method to all samples.