bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limitations of DNA Sequencing for Diagnosis of a Mixed Infection by Two Fungi,Phaeoacremonium venezuelenseand aPlectophomellasp., in a Transplant Recipient
Authors: Guarro Josep , Silvestre Agenor Messias , Verkley Gerard , Cano Josep , Gompertz Olga Fischman , Gené Josepa , Ogawa Marília Marufuji , Tomimori-Yamashita Jane , Teixeira Solange Pistori , de Almeida Fernando Augusto 
Published: November 2006

ABSTRACTWe describe a rare case of a subcutaneous infection by bothPhaeoacremonium venezuelenseandPlectophomellasp. in a Brazilian male. Sequencing of a β-tubulin gene fragment allowed us to confirm the identification of the former. However, a similar procedure of sequencing rRNA gene fragments was not useful for the identification of the latter fungus.
Evidence for Indirect Nosocomial Transmission of
Neisseria meningitidis
Resulting in Two Cases of Invasive Meningococcal Disease
Authors: Elias Johannes ,   Health Office in the Rural District Office Wartburgkreis, Claus Heike , Frosch Matthias , Vogel Ulrich 
Published: November 2006

ABSTRACT

Nosocomial transmission of
Neisseria meningitidis
has only rarely been reported. Here, we present a significant spatiotemporal association of two cases of invasive meningococcal disease identified by retrospective cluster analysis with the program SaTScan. The most likely epidemiological link was simultaneous hospitalization, resulting in indirect nosocomial transmission.
Two-Center Collaborative Evaluation of Performance of the BD Phoenix Automated Microbiology System for Identification and Antimicrobial Susceptibility Testing of Gram-Negative Bacteria
Authors: Menozzi Maria Grazia , Eigner Ulrich , Covan Silvia , Rossi Sabina , Somenzi Pietro , Dettori Giuseppe , Chezzi Carlo , Fahr Anne-Marie 
Published: November 2006

ABSTRACT

The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, MD) was assessed for identification (ID) and antimicrobial susceptibility testing (AST) of the majority of clinically encountered bacterial isolates in a European collaborative two-center trial. A total of 494 bacterial isolates including various species of the
Enterobacteriaceae
and 110 nonfermentative gram-negative bacteria were investigated: of these, 385 were single patient isolates, and 109 were challenge strains tested at one center. The performance of the Phoenix extended-spectrum β-lactamase (ESBL) test was also evaluated for 203 strains of
Escherichia coli
,
Klebsiella pneumoniae
, and
Klebsiella oxytoca
included in the study. Forty-two antimicrobial drugs were tested, including members of the following drug classes: aminoglycosides, β-lactam antibiotics, β-lactam/β-lactamase inhibitors, carbapenems, cephems, monobactams, folate antagonists, quinolones, and others. Phoenix system ID results were compared to those of the laboratories' routine ID systems (API 20E and API CHE, ATB ID32E, ID32GN, and VITEK 2 [bioMérieux, Marcy l'Etoile, France]); Phoenix AST results were compared to those of frozen standard broth microdilution (SBM) panels according to NCCLS (now CLSI) guidelines (NCCLS document M100-S9, approved standard M7-A4). Discrepant results were repeated in duplicate. Concordant IDs of 98.4 and 99.1% were observed for the
Enterobacteriaceae
and the nonfermentative group, respectively. For AST results, the overall essential agreement was 94.2%; the category agreement was 97.3%; and the very major error rate, major error rate, and minor error rate were 1.6, 0.6, and 1.9%, respectively. In terms of ESBL detection, Phoenix results were 98.5% concordant with those of the reference system, with 98.0% sensitivity and 98.7% specificity. In conclusion, the Phoenix ID results showed high agreement with results of the systems to which they were being compared: the AST performance was highly equivalent to that of the SBM reference method, and the system proved to be very accurate for the detection of ESBL producers.
Use of the BACTEC Mycobacteria Growth Indicator Tube 960 Automated System for Recovery of Mycobacteria from 9,558 Extrapulmonary Specimens, Including Urine Samples
Authors: Hillemann Doris , Richter Elvira , Rüsch-Gerdes Sabine 
Published: November 2006

ABSTRACT

The BACTEC Mycobacteria Growth Indicator Tube 960 (MGIT 960) system was applied for recovery of mycobacteria from extrapulmonary specimens and compared with solid media (Löwenstein-Jensen and Stonebrink). A total of 9,558 specimens were investigated, comprising 3,074 body fluids, 1,878 tissues, and 2,069 urine samples, from which the recovery of mycobacteria was not yet established for MGIT 960. In total, the MGIT 960 was able to detect 446 (90.3%) of the 494 isolates of
Mycobacterium tuberculosis
complex (MTBC) and 223 (86.0%) out of the 259 isolates of nontuberculous mycobacteria (NTM). In comparison to this, culture on solid medium revealed 358 (72.6%) MTBC isolates and 164 (66.8%) NTM isolates. While 136 (27.6%) of the MTBC isolates and 95 (19.2%) of the NTM isolates were recovered from the MGIT 960 only, 48 (9.7%) of the MTBC isolates and 36 (13.9%) NTM isolates grew only on solid media. Thus, the overall sensitivities for the recovery of mycobacteria from extrapulmonary specimens with MGIT 960 and solid media were 88.8% and 69.3%, respectively. However, the efficiency of the MGIT 960 system can be maximized with additional culture on solid media.
Use of a Combination of Brushing Technique and the Loop-Mediated Isothermal Amplification Method as a Novel, Rapid, and Safe System for Detection of
Helicobacter pylori
Authors: Minami Masaaki , Ohta Michio , Ohkura Teruko , Ando Takafumi , Torii Keizo , Hasegawa Tadao , Goto Hidemi 
Published: November 2006

ABSTRACT

Gastric mucosal biopsy is widely used in the detection of
Helicobacter pylori
but is associated with a number of problems, including false-negative results due to sampling error and massive bleeding after biopsy. Given the extended period required to culture
H. pylori
, detection would be further improved by the use of rapid detection methods such as PCR. Here, we developed a rapid, safe, and convenient method for collecting
H. pylori
which combines endoscopic brushing with the loop-mediated isothermal amplification (LAMP) method. The specificity and sensitivity of LAMP were examined using nine urease-generating non-
H. pylori
bacterial species,
Escherichia coli
,
Clostridium perfringens
,
Campylobacter jejuni
,
Helicobacter hepaticus
, and 51
H. pylori
strains. Results showed that
H. pylori
-specific LAMP primers amplified
H. pylori
DNA only and that the lowest detection limit of the LAMP reaction was 10
2
CFU. Brushing and biopsy samples taken from 200 patients with peptic ulcer at Nagoya University Hospital and a regional health care center were subjected to both LAMP and culturing. No adverse effects such as severe bleeding or penetration occurred during the procedure. By LAMP assay, 123 patients were confirmed as
H. pylori
positive when brushing technique samples were assayed, whereas only 100 were positive when biopsy samples were assayed. Culture assay detected
H. pylori
in 117 patients when it was combined with the brushing technique and in 96 when it was combined with biopsy. Combination of the endoscopic brushing technique with LAMP is considered a useful and safe system for identifying
H. pylori
infection.
Isolation and Characterization of Novel H3N1 Swine Influenza Viruses from Pigs with Respiratory Diseases in Korea
Authors: Shin Jin-Young , Song Min-Suk , Lee Eun Ho , Lee Young-Min , Kim Seok-Yong , Kim Hyong Kyu , Choi Joong-Kook , Kim Chul-Joong , Webby Richard J. , Choi Young-Ki 
Published: November 2006

ABSTRACT
Pigs can play an important role in the genetic reassortment of influenza viruses and as a reservoir for another lineage of influenza viruses that have the ability to reassort and be transmitted between species. In March and April 2006, novel H3N1 influenza A viruses were isolated from pigs with respiratory diseases at two different commercial swine farms in Korea. Genetic and phylogenetic analyses of the sequences of all eight viral RNA segments showed that the novel H3N1 swine influenza viruses were reassortants that acquired the hemagglutinin gene from an H3 human-like virus and other genes from swine influenza viruses that are currently circulating in Korea. Serologic and virologic tests in the infected farms suggested that pig-to-pig and farm-to-farm transmissions occurred. Clinical signs in pigs and experimentally infected mice suggest the potential to transmit the virus between swine and other mammalian hosts. To our knowledge, this is the first report of the isolation of the swine H3N1 subtype from domestic pigs under field conditions in Korea. Further surveillance will be needed to determine whether this novel subtype will continue to circulate in the swine population.
Detection of
Brugia
Parasite DNA in Human Blood by Real-Time PCR
Authors: Rao Ramakrishna U. , Weil Gary J. , Fischer Kerstin , Supali Taniawati , Fischer Peter 
Published: November 2006

ABSTRACT

Brugian filariasis (caused by the nematodes
Brugia malayi
and
B. timori
) is an important cause of disability in Southeast Asia. Improved diagnostic tests are needed for filariasis elimination programs (to identify areas of endemicity and to monitor progress) and for diagnosis of the disease in infected individuals. We have developed and evaluated two real-time PCR assays for detecting
Brugia
DNA in human blood and compared the results of these assays to those of “gold standard” assays. One assay uses a TaqMan probe (TaqM) to amplifiy a 320-bp “HhaI repeat” DNA sequence. The other assay uses a minor groove binding probe (MGB) and modified nucleotides in primers (Eclipse MGB) to amplify a 120-bp fragment of the HhaI repeat. This assay detects 22 copies of the target sequence, and it is more sensitive than the TaqM assay. Both assays were evaluated with human blood samples from two different areas of endemicity. The MGB assay was as sensitive as membrane filtration and microscopy for the detection of
B. malayi
infection in 57 blood samples recovered at night from patients in Sulawesi, Indonesia. The MGB assay also detected parasite DNA in 17 of 31 (55%) of microfilaria-negative day blood samples from these subjects. This test was more sensitive than the conventional and the TaqM PCRs (and was almost as sensitive as night blood membrane filtration) for the detection of infection in 52 blood samples recovered at night from individuals in an area of
B. timori
endemicity on Alor Island, Indonesia, where microfilaria-positive individuals had low densities after mass treatment. Thus, the Eclipse MGB real-time PCR assay is a sensitive means of detecting
Brugia
parasite DNA in human blood.
Listeria monocytogenes
Subgroups IIIA, IIIB, and IIIC Delineate Genetically Distinct Populations with Varied Pathogenic Potential
Authors: Liu Dongyou , Lawrence Mark L. , Wiedmann Martin , Gorski Lisa , Mandrell Robert E. , Ainsworth A. Jerald , Austin Frank W. 
Published: November 2006

ABSTRACT

Listeria monocytogenes
lineage III strains belonging to subgroups IIIA (
n
= 8), IIIB (
n
= 5), and IIIC (
n
= 6) were examined along with other known serotype strains (
n
= 11) by PCR and Southern hybridization using several recently described species-, virulence-, and serotype-specific primers and probes. The virulence of seven representative lineage III strains was then evaluated in mice via the intraperitoneal route. The results suggest that subgroup IIIA consists of typical rhamnose-positive avirulent serotype 4a and virulent serotype 4c strains, subgroup IIIC consists of atypical rhamnose-negative virulent serotype 4c strains, and subgroup IIIB consists of atypical rhamnose-negative virulent non-serotype 4a and non-serotype 4c strains, some of which may be related to serotype 7. It is possible that subgroup IIIB (including serotype 7) may represent a novel subspecies within
L. monocytogenes
.
Population-Based Study of Deletions in Five Different Genomic Regions ofMycobacterium tuberculosisand Possible Clinical Relevance of the Deletions
Authors: Kong Y. , Cave M. D. , Zhang L. , Foxman B. , Marrs C. F. , Bates J. H. , Yang Z. H. 
Published: November 2006

ABSTRACTRegions of difference (RDs) have been described in clinical isolates ofMycobacterium tuberculosis, but the potential epidemiological and clinical relevance of the genotypes of these RDs remains to be investigated. We screened a population-based sample of 648 isolates for the deletion of five RDs, designated RD105, RD181, RD142, RD150, and RD239, using microarray-based hybridization, PCR, and DNA sequencing and assessed the associations between the RD deletions and the clinical characteristics of the patients using chi-square analysis and multivariate logistic regression model. Of the 648 isolates, 18 (2.8%) had the RD239 deletion and 39 (6.0%) had the RD105 deletion. The deletions of RD142, RD150, and RD181 subdivided the isolates with the RD105 deletion into four groups comprising a group with concurrent deletions of RD105, RD181, and RD142 (n= 13); a group with concurrent deletions of RD105, RD181, and RD150 (n= 5); a group with concurrent deletions of RD105 and RD181 (n= 13); and a group with a deletion of RD105 only (n= 8). Extrathoracic tuberculosis is statistically significantly associated with infection with the isolates with concurrent deletions of RD105, RD181, and RD142 (adjusted odds ratio [OR] = 3.05; 95% confidence interval [CI] = 1.58, 5.90) and the isolates with concurrent deletions of RD105, RD181, and RD150 (adjusted OR = 11.09; 95% CI = 4.27, 28.80), after controlling for the previously identified risk factors for extrathoracic tuberculosis (human immunodeficiency virus serostatus, race, gender, and the genotype of theplcDgene). These two combinations of RD deletions have the potential for predicting the clinical presentation ofM. tuberculosisinfection in the human host.
Group A Streptococci from Invasive-Disease Episodes in Poland Are Remarkably Divergent at the Molecular Level
Authors: Szczypa Katarzyna , Sadowy Ewa , Izdebski Radoslaw , Strakova Lenka , Hryniewicz Waleria 
Published: November 2006

ABSTRACT

Forty-one clinical isolates of group A streptococcus (GAS) were recovered in Poland from patients with severe invasive infections and were analyzed by phenotypic and genotypic techniques. All isolates were characterized by determining their susceptibilities to antimicrobial agents and by determining their types by pulsed-field gel electrophoresis, multilocus sequence typing,
emm
typing, and the detection of five streptococcal pyrogenic exotoxin genes (
speA
,
speB
,
speC
,
speF
,
ssa
). The isolates studied were fully susceptible to penicillin G, levofloxacin, quinupristin-dalfopristin, and linezolid. Resistance to tetracycline, chloramphenicol, and erythromycin was detected in 46.3, 12.1, and 9.8% of the isolates, respectively. A total of 23 different
emm
sequence types were identified, of which
emm1
and
emm12
(19.5% each) were the most common, followed by
emm81
,
emm44/61
, and
emm85
. All the
emm1
isolates had the
speA2
allele. Twenty-three unrelated sequence types (STs) were identified, with the most frequent STs, ST28 and ST36, corresponding to
emm1
and
emm12
, respectively. Six newly found STs (STs 375, 376, 377, 378, 379, and 385) corresponded to
emm
types 74, 102, 77, 76, 84 and 63, respectively. The
emm1
type and the presence of
speA2
gene were associated with the severity of GAS infections. This work presents the first molecular study on Polish invasive GAS isolates.
Beijing Genotype of
Mycobacterium tuberculosis
Is Significantly Associated with Human Immunodeficiency Virus Infection and Multidrug Resistance in Cases of Tuberculous Meningitis
Authors: Caws Maxine , Thwaites Guy , Stepniewska Kasia , Lan Nguyen Thi Ngoc , Duyen Nguyen Thi Hong , Phuong Nguyen Thi , Huyen Mai Nguyet Thu , Duy Phan Minh , Loc Tran Huu , Chau Tran Thi Hong , van Soolingen Dick , Kremer Kristin , Chau Nguyen Van Vinh , Chinh Nguyen Tran , Farrar Jeremy 
Published: November 2006

ABSTRACT

Multidrug-resistant tuberculous meningitis is fatal without rapid diagnosis and use of second-line therapy. It is more common in human immunodeficiency virus (HIV)-positive patients. Beijing genotype strains of
Mycobacterium tuberculosis
are associated with drug resistance, particularly multidrug resistance, and their prevalence is increasing worldwide. The prevalence of Beijing genotype strains among
Mycobacterium tuberculosis
isolates from the cerebrospinal fluid of HIV-positive (
n
= 35) and HIV-negative (
n
= 187) patients in Ho Chi Minh City was determined. The Beijing genotype was significantly associated with HIV status (odds ratio [OR] = 2.95 [95% confidence interval {CI}, 1.38 to 6.44];
P
= 0.016), resistance to any drug (OR = 3.34 [95% CI, 1.87 to 5.95];
P
< 0.001) and multidrug resistance (Fisher's exact test;
P
= 0.001). The association of the Beijing genotype with drug resistance was independent of HIV status. This is the first report of Beijing genotype association with HIV status, which may be an association unique to tuberculous meningitis.
Molecular Characterization of Novel G5 Bovine Rotavirus Strains
Authors: Park Sung-Hee , Saif Linda J. , Jeong Cheol , Lim Guem-Ki , Park Sang-Ik , Kim Ha-Hyun , Park Su-Jin , Kim You-Jung , Jeong Jae-Ho , Kang Mun-Il , Cho Kyoung-Oh 
Published: November 2006

ABSTRACT
Group A rotaviruses are a major cause of acute gastroenteritis in young children as well as many domestic animals. The rotavirus genome is composed of 11 segments of double-stranded RNA and can undergo genetic reassortment during mixed infections, leading to progeny viruses with novel or atypical phenotypes. The aim of this study was to determine if the bovine group A rotavirus strains KJ44 and KJ75, isolated from clinically infected calves, share genetic features with viruses obtained from heterologous species. All 11 genes sequences of the KJ44 and KJ75 strains were sequenced and analyzed. The KJ44 VP4 had 91.7% to 96.3% deduced amino acid identity to the bovine related P[1] strain, whereas the KJ75 strain was most closely related to the bovine related P[5] strain (91.9% to 96.9% amino acid identity). Both KJ44 and KJ75 strains also contained the bovine related VP3 gene. The remaining 9 segments were closely related to porcine group A rotaviruses. The KJ44 and KJ75 strains showed high amino acid identity to the G5 rotaviruses, sharing 90.4% to 99.0% identity. In addition, these strains belonged to the NSP4 genotype B, which is typical of porcine rotaviruses and subgroup I, with the closest relationship to the porcine JL-94 strain. These results strongly suggest that bovine rotavirus strains with the G5 genotype occur in nature as a novel G genotype in cattle as a result of a natural reassortment between bovine and porcine strains.
Detection of Severe Acute Respiratory Syndrome Coronavirus in Stool Specimens by Commercially Available Real-Time Reverse Transcriptase PCR Assays
Authors: Louie L. , Simor A. E. , Chong S. , Luinstra K. , Petrich A. , Mahony J. , Smieja M. , Johnson G. , Gharabaghi F. , Tellier R. , Willey B. M. , Poutanen S. , Mazzulli T. , Broukhanski G. , Jamieson F. , Louie M. , Richardson S. ,   Ontario Laboratory Working Group for the Rapid Diagnosis of Emerging Pathogens
Published: November 2006

ABSTRACT
Three commercially available real-time reverse transcriptase PCR assays (the Artus RealArt HPA coronavirus LightCycler, the Artus RealArt HPA coronavirus Rotor-Gene, and the EraGen severe acute respiratory syndrome coronavirus POL assay) and three RNA extraction methodologies were evaluated for the detection of severe acute respiratory syndrome coronavirus RNA from 91 stool specimens. The assays' sensitivities were highest (58% to 75%) for specimens obtained 8 to 21 days after symptom onset. The assays were less sensitive when specimens were obtained less than 8 days or more than 21 days after the onset of symptoms. All assays were 100% specific.
Differentiation of Mycobacterial Species by
hsp65
Duplex PCR Followed by Duplex-PCR-Based Restriction Analysis and Direct Sequencing
Authors: Kim Hyun-Ju , Mun Ho-Suk , Kim Hong , Oh Eun-Ju , Ha Youngju , Bai Gill-Han , Park Young-Gil , Cha Chang-Yong , Kook Yoon-Hoh , Kim Bum-Joon 
Published: November 2006

ABSTRACT

Here we describe a novel duplex PCR method which can differentiate
Mycobacterium tuberculosis
and nontuberculosis mycobacteria (NTM) strains by amplifying
hsp65
DNAs of different sizes (195 and 515 bp, respectively). The devised technique was applied to 54 reference and 170 clinical isolates and differentiated all strains into their respective groups with 100% sensitivity and specificity. Furthermore, a duplex PCR-restriction analysis (duplex PRA) and a direct sequencing protocol were developed to differentiate NTM strains at the species and subspecies levels based on previously reported
hsp65
DNA sequences (H. Kim et al., Int. J. Syst. Evol. Microbiol. 55:1649-1656, 2005) and then applied to 105 NTM clinical isolates. All NTM isolates were clearly differentiated at the species and subspecies levels by subsequent procedures (PRA or direct sequencing) targeting 515-bp NTM duplex PCR amplicons. Our results suggest that novel duplex PCR-based methods are sensitive and specific for identifying mycobacterial culture isolates at the species level.
Cholera Due to Altered El Tor Strains of
Vibrio cholerae
O1 in Bangladesh
Authors: Nair G. Balakrish , Qadri Firdausi , Holmgren Jan , Svennerholm Ann-Mari , Safa Ashrafus , Bhuiyan Nurul A. , Ahmad Q. Shafi , Faruque Shah M. , Faruque A. S. G. , Takeda Yoshifumi , Sack David A. 
Published: November 2006

ABSTRACT

We determined the types of cholera toxin (CT) produced by a collection of 185
Vibrio cholerae
O1 strains isolated in Bangladesh over the past 45 years. All of the El Tor strains of
V. cholerae
O1 isolated since 2001 produced CT of the classical biotype, while those isolated before 2001 produced CT of the El Tor biotype.
First Reported Case of Dialysis-Related Peritonitis Due to
Escherichia vulneris
Authors: Senanayake Sanjaya N. , Jadeer Assad , Talaulikar Girish S. , Roy Jhumur 
Published: November 2006

ABSTRACT

Escherichia vulneris
is a recently identified environmental organism that can colonize humans and animals. To date, very few infections with
E. vulneris
have been reported. This is the first reported case of peritonitis due to
E. vulneris
in the setting of peritoneal dialysis.
Comparison between the Gen-Probe Transcription-Mediated Amplification
Trichomonas vaginalis
Research Assay and Real-Time PCR for
Trichomonas vaginalis
Detection Using a Roche LightCycler Instrument with Female Self-Obtained Vaginal Swab Samples and Male Urine Samples
Authors: Hardick Andrew , Hardick Justin , Wood Billie Jo , Gaydos Charlotte 
Published: November 2006

ABSTRACT

This study compared two assays for
Trichomonas vaginalis
detection, Gen-Probe's transcription-mediated amplification (TMA) assay for
Trichomonas vaginalis
and BTUB FRET PCR, using self-obtained clinical samples from 611 patients. Infection status was defined as two positive results by two different tests. The initial TMA assay sensitivity was 96.7%; specificity was 97.5%. The TMA assay was comparable to BTUB FRET PCR.
Identification of a
Streptococcus agalactiae
Serotype III Subtype 4 Clone in Association with Adult Invasive Disease in Hong Kong
Authors: Ip Margaret , Cheuk Edmund S. C. , Tsui Michelle H. Y. , Kong Fanrong , Leung T. N. , Gilbert Gwendolyn L. 
Published: November 2006

ABSTRACT

Characterization of
Streptococcus agalactiae
serotype III isolates revealed a subtype 4 clone that has an indistinguishable pulsed-field gel electrophoresis pattern and possesses a C-α protein, IS
1381
, and a novel sequence type (ST), ST 283, by multilocus sequence tagging. This clone was significantly associated with diseases caused by invasive strains from nonpregnant adults (
P
≤ 0.01, chi-square test) and was not present in the genital tracts of pregnant mothers.