bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feasibility of Freeze-Dried Sera for Serological and Molecular Biological Detection of Hepatitis B and C Viruses
Authors: Ohishi Waka , Fujiwara Saeko , Suzuki Gen , Kishi Takeshi , Sora Misae , Matsuura Shinsuke , Hakoda Masayuki , Tatsukawa Yoshimi , Yamada Michiko , Chayama Kazuaki 
Published: December 2006

ABSTRACT
We compared hepatitis B virus (HBV) surface antigen, anti-hepatitis C virus (HCV) antibody, and HCV RNA quantification in frozen and freeze-dried serum samples to assess the usefulness of freeze-dried sera for detection of HBV and HCV. The results indicated that freeze-dried sera as well as frozen sera can be useful for serological and molecular biological analyses of HBV and HCV.
Characterization of aBrucellasp. Strain as a Marine-Mammal Type despite Isolation from a Patient with Spinal Osteomyelitis in New Zealand
Authors: McDonald W. L. , Jamaludin R. , Mackereth G. , Hansen M. , Humphrey S. , Short P. , Taylor T. , Swingler J. , Dawson C. E. , Whatmore A. M. , Stubberfield E. , Perrett L. L. , Simmons G. 
Published: December 2006

ABSTRACTNaturally acquired infection of humans with a marine mammal-associatedBrucellasp. has only been reported once previously in a study describing infections of two patients from Peru. We report the isolation and characterization of a strain ofBrucellafrom a New Zealand patient that appears most closely related to strains previously identified from marine mammals. The isolate was preliminarily identified asBrucella suisusing conventional bacteriological tests in our laboratory. However, the results profile was not an exact match, and the isolate was forwarded to four international reference laboratories for further identification. The reference laboratories identified the isolate as eitherB. suisorB. melitensisby traditional bacteriological methods in three laboratories and by a molecular test in the fourth laboratory. Molecular characterization by PCR, PCR-restriction fragment length polymorphism, and DNA sequencing of thebp26gene; IS711; theompgenesomp25,omp31,omp2a, andomp2b; IRS-PCR fragments I, III, and IV; and five housekeeping gene fragments was conducted to resolve the discrepant identification of the isolate. The isolate was identified to be closely related to aBrucellasp. originating from a United States bottlenose dolphin (Tursiops truncatus) and common seals (Phoca vitulina).
Specific Primers for Rapid Detection ofMicrosporum audouiniiby PCR in Clinical Samples
Authors: Roque H. D. , Vieira R. , Rato S. , Luz-Martins M. 
Published: December 2006

ABSTRACTThis report describes application of PCR fingerprinting to identify common species of dermatophytes using the microsatellite primers M13, (GACA)4, and (GTG)5. The initial PCR analysis rendered a specific DNA fragment forMicrosporum audouinii, which was cloned and sequenced. Based on the sequencing data of this fragment, forward (MA_1F) and reverse (MA_1R) primers were designed and verified by PCR to establish their reliability in the diagnosis ofM. audouinii. These primers produced a singular PCR band of 431 bp specific only to strains and isolates ofM. audouinii, based on a global test of 182 strains/isolates belonging to 11 species of dermatophytes. These findings indicate these primers are reliable for diagnostic purposes, and we recommend their use in laboratory analysis.
Predominance of Clones Carrying Panton-Valentine Leukocidin Genes among Methicillin-Resistant
Staphylococcus aureus
Strains Isolated in Japanese Hospitals from 1979 to 1985
Authors: Ma Xiao Xue , Ito Teruyo , Chongtrakool Piriyaporn , Hiramatsu Keiichi 
Published: December 2006

ABSTRACT

We examined 97 strains of methicillin-resistant
Staphylococcus aureus
(MRSA) isolated between 1979 and 1985, the period of time when the appearance of MRSA strains increased, and we determined that these strains are distinct from the MRSA clones predominating in today's Japanese hospitals. Type IV staphylococcal cassette chromosome
mec
(SCC
mec
) strains were the most frequent, comprising 53.6% of all strains, followed by type I (22.7%) and type II (21.6%) SCC
mec
strains. Among the type IV SCC
mec
strains, the frequencies of two new subtypes, type IV.3 (IVc) and type IV.4 (IVd), were very high, comprising 38.1 and 10.3% of all strains, respectively. Forty-four of the 97 strains (45.3%) were Panton-Valentine leukocidin (PVL) positive. Among the PVL-positive strains, sequence type 30 (ST30)-SCC
mec
type IV strains producing type 4 coagulase were the most frequent. This is in striking contrast to the MRSA strains isolated in the 1990s, most of which were ST5-SCC
mec
type II strains producing type 2 coagulase and positive for the toxic shock syndrome toxin 1 gene. We also identified a new PVL-carrying prophage lysogenized in a type IV.3 SCC
mec
strain, 81/108. φ108PVL was distinct from the three extant PVL-carrying phages and was presumed to be carried by ST30-type IV.3 SCC
mec
strains isolated in Japan. These results provide genetic bases for the transition of MRSA clones in Japan that is commonly considered the transition from coagulase type 4 MRSA strains to coagulase type 2 MRSA strains. The results also suggested that MRSA strains that predominated between 1979 and 1985 were generated from PVL-positive methicillin-susceptible
S. aureus
strains through the integration of SCC
mec
elements.
Phylogenetic Analysis of “CandidatusMycoplasma turicensis” Isolates from Pet Cats in the United Kingdom, Australia, and South Africa, with Analysis of Risk Factors for Infection
Authors: Willi Barbara , Tasker Séverine , Boretti Felicitas S. , Doherr Marcus G. , Cattori Valentino , Meli Marina L. , Lobetti Remo G. , Malik Richard , Reusch Claudia E. , Lutz Hans , Hofmann-Lehmann Regina 
Published: December 2006

ABSTRACTTwo hemotropic mycoplasmas have been recognized in cats,Mycoplasma haemofelisand “CandidatusMycoplasma haemominutum.” We recently described a third feline hemoplasma species, designated “CandidatusMycoplasma turicensis,” in a Swiss cat with hemolytic anemia. This isolate induced anemia after experimental transmission to two specific-pathogen-free cats and analysis of the 16S rRNA gene revealed its close relationship to rodent hemotropic mycoplasmas. The agent was recently shown to be prevalent in Swiss pet cats. We sought to investigate the presence and clinical importance of “CandidatusMycoplasma turicensis” infection in pet cats outside of Switzerland and to perform the molecular characterization of isolates from different countries. A “CandidatusMycoplasma turicensis”-specific real-time PCR assay was applied to blood samples from 426 United Kingdom (UK), 147 Australian, and 69 South African pet cats. The 16S rRNA genes of isolates from different countries were sequenced and signalment and laboratory data for the cats were evaluated for associations with “CandidatusMycoplasma turicensis” infection. Infections were detected in samples from UK, Australian, and South African pet cats. Infection was associated with the male gender, and “CandidatusMycoplasma haemominutum” andM. haemofeliscoinfection. Coinfected cats exhibited significantly lower packed cell volume (PCV) values than uninfected cats. Phylogenetic analyses revealed that some Australian and South African “CandidatusMycoplasma turicensis” isolates branched away from the remaining isolates. In summary, “CandidatusMycoplasma turicensis” infection in pet cats exists over a wide geographical area and significantly decreased PCV values are observed in cats coinfected with other feline hemoplasmas.
Phaeoacremonium krajdenii
, a Cause of White Grain Eumycetoma
Authors: Hemashettar B. M. , Siddaramappa B. , Munjunathaswamy B. S. , Pangi A. S. , Pattan Jayashree , Andrade A. T. , Padhye A. A. , Mostert Lizel , Summerbell R. C. 
Published: December 2006

ABSTRACT

We describe the first case of white grain pedal eumycetoma caused by
Phaeoacremonium krajdenii
in a 41-year-old man from Goa, India. Based on histological examination of biopsy tissue showing serpentine granules, a culture of the granules yielding phaeoid fungal colonies, and morphological characteristics and sequence comparison of the partial β-tubulin gene with the ex-type isolate of
P. krajdenii
, the causal agent was identified as
P. krajdenii
.
Vulvovaginal-Swab or First-Catch Urine Specimen To Detect
Chlamydia trachomatis
in Women in a Community Setting?
Authors: Skidmore Sue , Horner Paddy , Herring Alan , Sell Joanne , Paul Ian , Thomas Jane , Caul E. Owen , Egger Matthias , McCarthy Anne , Sanford Emma , Salisbury Chris , Macleod John , Sterne Jonathan A. C. , Low Nicola 
Published: December 2006

ABSTRACT

Screening for chlamydia in women is widely recommended. We evaluated the performance of two nucleic acid amplification tests for detecting
Chlamydia trachomatis
in self-collected vulvovaginal-swab and first-catch urine specimens from women in a community setting and a strategy for optimizing the sensitivity of an amplified enzyme immunoassay on vulvovaginal-swab specimens. We tested 2,745 paired vulvovaginal-swab and urine specimens by PCR (Roche Cobas) or strand displacement amplification (SDA; Becton Dickinson). There were 146 women infected with chlamydia. The assays detected 97.3% (95% confidence interval [CI], 93.1 to 99.2%) of infected patients with vulvovaginal-swab specimens and 91.8% (86.1 to 95.7%) with urine specimens. We tested 2,749 vulvovaginal-swab specimens with both a nucleic acid amplification test and a polymer conjugate-enhanced enzyme immunoassay with negative-gray-zone testing. The relative sensitivities obtained after retesting specimens in the negative gray zone were 74.3% (95% CI, 62.8 to 83.8%) with PCR and 58.3% (95% CI, 46.1 to 69.8%) with SDA. In community settings, both vulvovaginal-swab and first-catch urine specimens from women are suitable substrates for nucleic acid amplification tests, but enzyme immunoassays, even after negative-gray-zone testing, should not be used in screening programs.
Comparison of Mannitol Salt Agar and Blood Agar Plates for Identification and Susceptibility Testing of
Staphylococcus aureus
in Specimens from Cystic Fibrosis Patients
Authors: Sharp Susan E. , Searcy Cindy 
Published: December 2006

ABSTRACT

Antimicrobial susceptibilities of
Staphylococcus aureus
strains can be determined accurately by using isolates from mannitol salt agar, and yellow isolates on mannitol salt agar at quantities of >1+ can be reported as
S. aureus
. These methods decrease the time to identification/antimicrobial susceptibility testing of
S. aureus
and decrease costs through eliminating additional testing.
Rapid Simultaneous Detection by Real-Time PCR of Cytomegalovirus UL97 Mutations in Codons 460 and 520 Conferring Ganciclovir Resistance
Authors: Göhring Katharina , Mikeler Elfriede , Jahn Gerhard , Hamprecht Klaus 
Published: December 2006

ABSTRACT
Ganciclovir (GCV) resistance is an emerging problem for transplant recipients. A sensitive and rapid real-time PCR approach for simultaneous and semiquantitative detection of human cytomegalovirus (HCMV) UL97 mutations in codons 460/520 was established by LightCycler and confirmed by restriction fragment length polymorphism and sequencing. Results from HCMV laboratory strains were compared with results from 11 GCV-resistant clinical isolates.
Optimizing Antigen Cocktails for Detection ofMycobacterium bovisin Herds with Different Prevalences of Bovine Tuberculosis: ESAT6-CFP10 Mixture Shows Optimal Sensitivity and Specificity
Authors: Aagaard C. , Govaerts M. , Meikle V. , Vallecillo A. J. , Gutierrez-Pabello J. A. , Suarez-Güemes F. , McNair J. , Cataldi A. , Espitia C. , Andersen P. , Pollock J. M. 
Published: December 2006

ABSTRACTBovine tuberculosis is a major problem in many countries; hence, new and better diagnostic tools are urgently needed. In this work, we have tested ESAT6, CFP10, PE13, PE5, MPB70, TB10.4, and TB27.4 for their potentials as diagnostic markers in field animals from Northern Ireland, Mexico, and Argentina, regions with low, medium, and high prevalences of bovine tuberculosis, respectively. At all three sites, ESAT6 and CFP10 were superior diagnostic antigens, while their combination performed even better at the two sites where the combination was tested, providing the best coverage for the detection of diseased populations. The high sensitivity in the skin test reactor groups, combined with the high specificity in the tuberculosis-free groups, indicated that a diagnosis could correctly be made for 85% of the infected animals, based on their responses to these two antigens. Furthermore, TB10.4, PE13, and PE5 have the potential to supplement ESAT6 and CFP10 in a future five-component diagnostic cocktail.
Blood Culture Contamination in Tanzania, Malawi, and the United States: a Microbiological Tale of Three Cities
Authors: Archibald Lennox K. , Pallangyo Kisali , Kazembe Peter , Reller L. Barth 
Published: December 2006

ABSTRACT

We conducted retrospective, comparative analyses of contamination rates for cultures of blood obtained in the emergency rooms of Muhimbili National Hospital (MNH) in Dar es Salaam, Tanzania; Lilongwe Central Hospital (LCH) in central Malawi; and the Duke University Medical Center (DUMC) in the United States. None of the emergency room patients had indwelling intravascular devices at the time that the blood samples for cultures were obtained. In addition, we reviewed the contamination rates for a cohort of patients already hospitalized in the DUMC inpatient medical service, most of whom had indwelling intravascular devices. The bloodstream infection rates among the patients at MNH (
n
= 513) and LCH (
n
= 486) were similar (∼28%); the contamination rates at the two hospitals were 1.3% (7/513) and 0.8% (4/486), respectively. Of 54 microorganisms isolated from cultures of blood collected in the DUMC emergency room, 26 (48%) were identified as skin contaminants. Cultures of blood collected in the DUMC emergency room were significantly more likely to yield growth of contaminants than the cultures of blood collected in the emergency rooms at MNH and LCH combined (26/332 versus 11/1,003;
P
< 0.0001) or collected in the DUMC inpatient medical service (26/332 versus 7/283;
P
< 0.01). For the MNH and LCH blood cultures, lower contamination rates were observed when skin was disinfected with isopropyl alcohol plus tincture of iodine rather than isopropyl alcohol plus povidone-iodine. In conclusion, blood culture contamination was minimized in sub-Saharan African hospitals with substantially limited resources through scrupulous attention to aseptic skin cleansing and improved venipuncture techniques. Application of these principles when blood samples for culture are obtained in U.S. hospital emergency rooms should help mitigate blood culture contamination rates and the unnecessary microbiology workup of skin contaminants.
Prevalence and Sequence Variants of IS
481
in
Bordetella bronchiseptica
: Implications for IS
481
-Based Detection of
Bordetella pertussis
Authors: Register Karen B. , Sanden Gary N. 
Published: December 2006

ABSTRACT

We report the prevalence in
Bordetella bronchiseptica
of IS
481
, a frequent target for diagnosis of
Bordetella pertussis
, as approximately 5%. However, PCR amplicons of the predicted size were detectable in 78% of IS
481
-negative strains. Our results suggest that PCR targeting IS
481
may not be sufficiently specific for reliable identification of
B. pertussis
.
First Case of
Staphylococcus pseudintermedius
Infection in a Human
Authors: Van Hoovels Lieve , Vankeerberghen Anne , Boel An , Van Vaerenbergh Kristien , De Beenhouwer Hans 
Published: December 2006

ABSTRACT

We present the first clinical report of a
Staphylococcus pseudintermedius
infection in a human. Biochemically,
S. pseudintermedius
can be easily misidentified as
S. aureus
. Therefore, the final microbiological identification requires the combination of phenotypic and genotypic tests.
Relationship between Preexisting Anti-Varicella-Zoster Virus (VZV) Antibody and Clinical VZV Reactivation in Hematopoietic Stem Cell Transplantation Recipients
Authors: Onozawa Masahiro , Hashino Satoshi , Takahata Mutsumi , Fujisawa Fumie , Kawamura Takahito , Nakagawa Masao , Kahata Kaoru , Kondo Takeshi , Ota Shuichi , Tanaka Junji , Imamura Masahiro , Asaka Masahiro 
Published: December 2006

ABSTRACT

Reactivation of latent varicella-zoster virus (VZV), presenting as localized zoster or as disseminated infection, is a common and potentially serious complication in hematopoietic stem cell transplantation (HSCT) recipients. We retrospectively studied anti-VZV immunoglobulin G titers by the immune adherence hemagglutination method after HSCT and also studied VZV DNA by real-time PCR during clinical VZV reactivation using cryopreserved serum samples. No significant difference was found between anti-VZV titers in 13 patients with VZV infection (localized zoster in 11 patients and disseminated zoster in 2 patients) and in 13 subjects without VZV infection at each time point after HSCT. Preexisting anti-VZV titers of disseminated zoster cases tended to be lower than those of localized zoster cases (
P
= 0.10). Serum VZV DNA copy numbers at the onset of disseminated zoster cases tended to be higher than those of localized zoster cases (
P
= 0.09). A strong inverse correlation was found between preexisting anti-VZV titer and serum VZV DNA at onset (
r
= −0.90,
P
= 0.006). In HSCT recipients, preexisting antibody does not prevent the development of VZV reactivation but may contribute to decreased viral load at onset, resulting in a mild clinical course.
Identification of New Genetic Regions More Prevalent in Nontypeable
Haemophilus influenzae
Otitis Media Strains than in Throat Strains
Authors: Xie Jingping , Juliao Patricia C. , Gilsdorf Janet R. , Ghosh Debashis , Patel Mayuri , Marrs Carl F. 
Published: December 2006

ABSTRACT

Nontypeable (NT)
Haemophilus influenzae
strains cause significant respiratory illness and are isolated from up to half of middle ear aspirates from children with acute otitis media. Previous studies have identified two genes,
lic2B
and
hmwA
, that are associated with NT
H. influenzae
strains isolated from the middle ears of children with otitis media but that are not associated with NT
H. influenzae
strains isolated from the throats of healthy children, suggesting that they may play a role in virulence in otitis media. In this study, genomic subtraction was used to identify additional genetic regions unique to middle ear strains. The genome of NT
H. influenzae
middle ear strain G622 was subtracted from that of NT
H. influenzae
throat strain 23221, and the resultant gene regions unique to the middle ear strain were identified. Subsequently, the relative prevalence of the middle ear-specific gene regions among a large panel of otitis media and throat strains was determined by dot blot hybridization. By this approach, nine genetic regions were found to be significantly more prevalent in otitis media strains. Classification tree analysis of
lic2B
,
hmwA
, and the nine new potential otitis media virulence genes revealed two
H. influenzae
pathotypes associated with otitis media.
Direct Detection of
Mycobacterium tuberculosis
Complex DNA and Rifampin Resistance in Clinical Specimens from Tuberculosis Patients by Line Probe Assay
Authors: Traore Hamidou , van Deun Armand , Shamputa Isdore Chola , Rigouts Leen , Portaels Françoise 
Published: December 2006

ABSTRACT

The INNO-LiPA.Rif TB test (LiPA) has only been applied to a limited number of clinical specimens. To assess the utility of this test for detecting
Mycobacterium tuberculosis
complex DNA and rifampin (RMP) resistance, 420 sputum samples comprising specimens from untreated (
n
= 160) and previously treated (
n
= 260) patients from 11 countries in Asia, Africa, Europe, and Latin America were tested. DNA was extracted from sputum samples by using a modification of the Boom's method, while the
rpoB
core region was amplified by nested PCR. The results were analyzed in conjunction with those obtained by Ziehl-Neelsen (ZN) microscopy and by culture on solid media. The LiPA test was positive for
M. tuberculosis
complex DNA in 389 (92.9%) specimens, including 92.0% (286 of 311) ZN-positive and 94.5% (103 of 109) ZN-negative specimens. Of these, 30.6% were RMP resistant. In contrast, 74.3% of the specimens were positive for
M. tuberculosis
by culture, and 30.8% of them were RMP resistant. LiPA detected
M. tuberculosis
complex DNA in 92.4% (110 of 119) of the culture-positive and 100.0% (41 of 41) of the culture-negative specimens from untreated patients. There was a 99.6% concordance between the RMP resistance as determined by culture and by the LiPA test. With an optimal DNA extraction method, LiPA allows rapid detection of
M. tuberculosis
complex DNA and RMP resistance directly from sputum specimens. LiPA can still provide useful information when culture fails for various reasons. The rapid availability of this information is necessary to adjust patient treatment and avoid the risk of amplification of drug resistance.
Application of SmartGene IDNS Software to Partial 16S rRNA Gene Sequences for a Diverse Group of Bacteria in a Clinical Laboratory
Authors: Simmon Keith E. , Croft Ann C. , Petti Cathy A. 
Published: December 2006

ABSTRACT
Laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. With the emergence of 16S rRNA gene sequencing as an identification tool, we evaluated the usefulness of SmartGene IDNS, a 16S rRNA sequence database and software program for microbial identification. Identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the SmartGene and MicroSeq databases. Of 300 isolates, SmartGene identified 295 (98%) to the genus level and 262 (87%) to the species level, with 5 (2%) being inconclusive. MicroSeq identified 271 (90%) to the genus level and 223 (74%) to the species level, with 29 (10%) being inconclusive. SmartGene and MicroSeq agreed on the genus for 233 (78%) isolates and the species for 212 (71%) isolates. Conventional methods identified 291 (97%) isolates to the genus level and 208 (69%) to the species level, with 9 (3%) being inconclusive. SmartGene, MicroSeq, and conventional identifications agreed for 193 (64%) of the results. Twenty-seven microorganisms were not represented in MicroSeq, compared to only 2 not represented in SmartGene. Overall, SmartGene IDNS provides comprehensive and accurate identification of a diverse group of bacteria and has the added benefit of being a user-friendly program that can be modified to meet the unique needs of clinical laboratories.
Simultaneous Quantification and Genotyping of Hepatitis B Virus for Genotypes A to G by Real-Time PCR and Two-Step Melting Curve Analysis
Authors: Liu Wen-Chun , Mizokami Masashi , Buti Maria , Lindh Magnus , Young Kung-Chia , Sun Koun-Tem , Chi Yun-Chan , Li Hsi-Hsien , Chang Ting-Tsung 
Published: December 2006

ABSTRACT

Both the viral titer and the genotype significantly determine clinical outcomes and responses to antiviral treatment in chronic hepatitis B virus (HBV) infection. A method was developed for large-scale A-to-G genotyping with simultaneous viral quantification. The assay was run on a LightCycler instrument using hybridization probes. The genotype was determined from the melting points of the probes in a two-step manner. Set 1 amplicons differentiated genotypes B, E, and F from A, C, D, and G and simultaneously quantified viremia by real-time PCR. Melting curve analysis using the set 2-1 amplicon or the set 2-2 amplicon reaction mixture was then used to differentiate these genotype groups into single genotypes. HBV DNA quantification was consistent with that of the Amplicor assay and linear in a range from 10
2
to 10
13
copies/ml. By comparison with the restriction fragment length polymorphism method, 92.3% of 441 samples were accurately genotyped by the current assay. The method should be useful for genotyping and quantification of HBV DNA in areas where all genotypes exist.