bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Multilocus Variable-Number Tandem-Repeat Analysis for TypingMycobacterium aviumsubsp.paratuberculosis
Authors: Overduin Pieter , Schouls Leo , Roholl Paul , van der Zanden Adri , Mahmmod Nofel , Herrewegh Arnold , van Soolingen Dick 
Published: November 2004

ABSTRACTThe etiology of Crohn's disease in humans is largely unknown. Clinical signs of Crohn's disease partly resemble the clinical picture of Johne's disease in ruminants caused byMycobacterium aviumsubsp.paratuberculosis. Because of the high prevalence of these bacteria in (products of) ruminants and their remarkable thermostability, concern has been raised about the possible role of these bacteria in the pathogenesis of Crohn's disease. In an attempt to develop a molecular typing method to facilitate meaningful comparative DNA fingerprinting ofM. aviumsubsp.paratuberculosisisolates from the human and animal reservoirs, multilocus variable-number tandem-repeat analysis (MLVA) was explored and compared to IS900restriction fragment length polymorphism (RFLP) typing. MLVA typing subdivided the most predominant RFLP type, R01, into six subtypes and thus provides a promising molecular subtyping approach to study the diversity ofM. aviumsubsp.paratuberculosis.
Molecular Characteristics of Strains of the Cameroon Family, the Major Group of
Mycobacterium tuberculosis
in a Country with a High Prevalence of Tuberculosis
Authors: Niobe-Eyangoh Sara Ngo , Kuaban Christopher , Sorlin Philippe , Thonnon Jocelyn , Vincent Veronique , Gutierrez M. Cristina 
Published: November 2004

ABSTRACT

A preliminary investigation of the genetic biodiversity of
Mycobacterium tuberculosis
complex strains in Cameroon, a country with a high prevalence of tuberculosis, described a group of closely related
M. tuberculosis
strains (the Cameroon family) currently responsible for more than 40% of smear-positive pulmonary tuberculosis cases. Here, we used various molecular methods to study the genetic characteristics of this family of strains. Cameroon family
M. tuberculosis
strains (i) are part of the major genetic group 2 and lack the TbD1 region like other families of epidemic strains, (ii) lack spacers 23, 24, and 25 in their direct repeat (DR) region, (iii) have an identical number of repeats in 8 of 12 variable-number tandem repeats of mycobacterial interspersed repetitive unit (MIRU-VNTR) loci, (iv) have similar IS
6110
-restriction fragment length polymorphism (RFLP) multiband patterns (10 to 15 copies) with seven common IS
6110
bands, (v) do not have an IS
6110
element in their DR locus, and (vi) have four IS
6110
elements in open reading frames (adenylate cyclase, phospholipase C,
moeY
, and ATP binding genes). Analysis by spoligotyping, MIRU-VNTR, and IS
6110
-RFLP typing methods revealed differences not observed in previous studies; polymorphism as assessed by MIRU-VNTR typing was lower than suggested by spoligotyping, and in rare cases, strains with identical IS
6110
-RFLP patterns had spoligotypes differing by as much as 15 spacers. Our findings confirm the recent expansion of this family in Cameroon and indicate that the interpretation of molecular typing results has to be adapted to the characteristics of the strain population within each setting. The knowledge of this particular genotype, with its large involvement in tuberculosis in Cameroon, allows greater refinement of tuberculosis transmission studies by interpreting data in the context of this geographic area.
Longitudinal Study of Hepatitis Activity and Viral Replication before and after HBeAg Seroconversion in Chronic Hepatitis B Patients Infected with Genotypes B and C
Authors: Yuen Man-Fung , Fung Scott K. , Tanaka Yasuhito , Kato Takanobu , Mizokami Masashi , Yuen John Chi-Hang , Wong Danny Ka-Ho , Yuan He-Jun , Sum Siu-Man , Chan Annie On-On , Wong Benjamin Chun-Yu , Lai Ching-Lung 
Published: November 2004

ABSTRACT

The aims of this study were to compare chronic hepatitis B (CHB) patients with genotypes B and C for the probability of HBeAg seroconversion, hepatitis activity, and viral replication before and after HBeAg seroconversion and to compare the prevalence of core promoter and precore mutations. A total of 180 asymptomatic Chinese patients with CHB were monitored for a median of 53.8 months, and 38 patients with cirrhosis-related complications were studied. Hepatitis B virus (HBV) DNA levels were measured in 16 patients with HBeAg seroconversion at 3 months before, during, and 3 months after HBeAg seroconversion and in all patients at the last follow-up. Hepatitis B genotypes and core promoter and precore mutations were determined. Compared to patients with genotype C (
n
= 109), patients with subtype Ba (
n
= 69) had a higher rate of anti-HBe positivity on presentation (
P
= 0.05). HBeAg-positive patients with subtype Ba had a higher cumulative rate of HBeAg seroconversion than patients with genotype C (
P
= 0.02). However, there were no differences between the two groups with regard to the median HBV DNA levels before, during, and after HBeAg seroconversion; the probability of having persistently normal or elevated aminotransferase levels; and the median HBV DNA levels and liver biochemistry at the last follow-up. There was no difference in the prevalence of genotypes and core promoter and precore mutations between patients with and without cirrhosis-related complications. Though patients with subtype Ba had earlier HBeAg seroconversion, the liver biochemistry, HBV DNA levels in different phases of the disease, and the probability of development of cirrhosis-related complications were the same with genotypes Ba and C.
Evaluation of the BD PHOENIX Automated Microbiology System for Detection of Methicillin Resistance in Coagulase-Negative Staphylococci
Authors: Horstkotte Matthias A. , Knobloch Johannes K.-M. , Rohde Holger , Dobinsky Sabine , Mack Dietrich 
Published: November 2004

ABSTRACT

The new BD PHOENIX automated microbiology system (Becton Dickinson Diagnostic Systems, Sparks, Md.) is designed for automated rapid antimicrobial susceptibility testing and identification of clinically relevant bacteria. In our study, the accuracy and speed of the BD PHOENIX oxacillin MIC determination for detecting methicillin resistance was evaluated for 200 clinical isolates of coagulase-negative staphylococci (CoNS). Compared to
mecA
PCR, the BD PHOENIX system detected methicillin resistance with a sensitivity of 99.2%. According to the actual NCCLS oxacillin MIC breakpoint of ≥0.5 μg/ml, the specificity was only 64.9%, attributable to false-positive results in 26
mecA
-negative strains, including 16 non-
Staphylococcus epidermidis
strains. Alternative oxacillin breakpoints of ≥1, ≥2, and ≥4 μg/ml resulted in increased specificities of 83.8, 94.6, and 100% and high sensitivities of 99.2, 99.2, and 96.7%, respectively. Similarly, NCCLS broth microdilution oxacillin MICs exhibited a sensitivity of 100% but a low degree of specificity. However, the previous oxacillin MIC breakpoint of ≥4 μg/ml performed with a sensitivity of 98.4% and a specificity of 98.7%. BD PHOENIX oxacillin MIC results were available after 9 h for 40.5% of the examined CoNS strains and were completed after 17 h. Our results revealed the high reliability of the BD PHOENIX system as a phenotypic method for detection of resistance to oxacillin in
mecA
-positive CoNS. However, for the improvement of specificity, reevaluation of the optimal oxacillin MIC breakpoint for CoNS appears to be necessary.
Mycobacterium africanumGenotyping UsingNovel Spacer Oligonucleotides in the Direct RepeatLocus
Authors: Brudey Karine , Gutierrez M. Cristina , Vincent Véronique , Parsons Linda M. , Salfinger Max , Rastogi Nalin , Sola Christophe 
Published: November 2004

ABSTRACTThis study involves a first evaluation of 25 novel spacer oligonucleotides in addition to the 43 routine spacers for molecular characterization of a panel of 65 isolates of tubercle bacilli from different geographic origins that were initially classified asMycobacterium africanumbased on phenotypic characters. The 68-spacer format defined four additional patterns, and three groups were identified. The relatively homogeneous groups A1 and A2 included strains from West Africa, and A3-1 included strains from East Africa. The presence of deletion region RD9 confirmed the reclassification of theM. africanumsubtype II spoligopattern within group A3-1 asMycobacterium tuberculosis.These isolates may represent a diverging branch ofM. tuberculosisin Africa. The use of new spacers also suggested an undergoing evolution ofM. africanumsubtype I in West Africa. Our results showed that the strain differentiation within theM. tuberculosiscomplex is improved by using novel spacers, and extensive studies using new-generation spoligotyping may be helpful to better understand the evolution ofM. africanum.
Characterization of AncestralMycobacterium tuberculosisby Multiple Genetic Markers and Proposal of Genotyping Strategy
Authors: Sun Yong-Jiang , Lee Ann S. G. , Ng Sze Ta , Ravindran Sindhu , Kremer Kristin , Bellamy Richard , Wong Sin-Yew , van Soolingen Dick , Supply Philip , Paton Nicholas I. 
Published: November 2004

ABSTRACTSixty-eight ancestralMycobacterium tuberculosisisolates were previously identified by using the tuberculosis-specific deletion 1 (TbD1) PCR and mycobacterial interspersed-repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing (Y. J. Sun, R. Bellamy, A. S. G. Lee, S. T. Ng, S. Ravindran, S.-Y. Wong, C. Locht, P. Supply, and N. I. Paton, J. Clin. Microbiol.42:1986-1993, 2004). These TbD1+ancestral isolates were further characterized and typed in this study by IS6110restriction fragment length polymorphism (RFLP) typing, VNTR typing using exact tandem repeats (VNTR-ETR), and spoligotyping of the direct-repeat region. To our knowledge, this is the first characterization of this genogroup by multiple genetic markers based on a fairly large sample size. In this genogroup, all spoligotypes were characterized by the absence of spacers 29 to 32 and 34. In addition, VNTR-ETR typing could add further resolution to the clustered isolates identified by MIRU-VNTR, and the combination of MIRU-VNTR and VNTR-ETR, called MIRU-ETR, showed the highest discriminatory power for these strains compared to IS6110RFLP typing and spoligotyping alone. However, MIRU-ETR appeared to still cluster some probably epidemiologically unrelated strains, as judged by IS6110RFLP divergence. Therefore, a typing strategy based on stepwise combination of MIRU-ETR and IS6110RFLP is proposed to achieve maximal discrimination for unrelated TbD1+strains. This typing strategy may be useful in areas where TbD1+ancestral strains are prevalent.
Multilocus Microsatellite Typing System for
Penicillium marneffei
Reveals Spatially Structured Populations
Authors: Fisher Matthew C. , Aanensen David , de Hoog Sybren , Vanittanakom Nongnuch 
Published: November 2004

ABSTRACT

For eukaryotic pathogens that have low levels of genetic variation, multilocus microsatellite typing (MLMT) offers an accurate and reproducible method of characterizing genetic diversity. Here, we describe the application of an MLMT system to the emerging pathogenic fungus
Penicillium marneffei
. Isolates used for this study were those held in the culture collections of the Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands, and the Chiang Mai University Department of Microbiology, Chang Mai, Thailand. High genetic diversity and extensive spatial structure were observed among clinical isolates, with the geographical area of origin for each isolate strongly correlating with the occurrence of two deeply divided clades. Within each clade, multilocus linkage associations were highly significant and could be explained by genetically differentiated populations or by an exclusively clonal reproductive mode, or both. Our results show that southeast Asian penicilliosis is caused by a fungus with a complex population genetic structure. Furthermore, this MLMT system generates digital data that can be easily queried against a centrally held database via the internet (
http://pmarneffei.multilocus.net/
); this provides a powerful epidemiological tool for analyzing the underlying parameters that are responsible for the emergence of
P. marneffei
in human immunodeficiency virus-positive populations.
Role of
Cannomys badius
as a Natural Animal Host of
Penicillium marneffei
in India
Authors: Gugnani Harish , Fisher Matthew C. , Paliwal-Johsi Anubha , Vanittanakom Nongnuch , Singh Irabanta , Yadav Pratap Singh 
Published: November 2004

ABSTRACT

Infection by
Penicillium marneffei
in human immunodeficiency virus-positive patients in India has recently been described; the aim of our study was to survey wild rodents and their associated environment in order to identify the natural populations of this fungus. Surveys recovered
P. marneffei
from the internal organs of 10 (9.1%) of 110 bamboo rats (
Cannomys badius
) examined from Manipur state, India, an area endemic for penicilliosis marneffei. Identification of the isolates was based on a detailed study of their morphological characteristics, in vitro conversion to fission yeast form, and exoantigen tests. Multilocus microsatellite typing (MLMT) of the isolates revealed five genotypes. No genotypes were shared between sample sites, and all bamboo rats were infected with a single genotype within sample sites, demonstrating spatial genetic heterogeneity. One MLMT genotype was identical to that seen in a human isolate, suggesting that either coinfection from a common source or host-to-host transmission had occurred. This demonstrates the utility of an MLMT-based approach to elucidating the epidemiology of
P. marneffei
.
Borrelia
Species in Host-Seeking Ticks and Small Mammals in Northern Florida
Authors: Clark Kerry 
Published: November 2004

ABSTRACT

The aim of this study was to improve understanding of several factors related to the ecology and environmental risk of
Borrelia
infection in northern Florida. Small mammals and host-seeking adult ticks were collected at several sites, and specimens were tested for the presence of
Borrelia
species, primarily by PCR amplification. Tissues from some vertebrates and ticks were initially cultured in BSK-H medium to isolate spirochetes, but none were recovered. However, comparison of partial flagellin (
flaB
), 66-kDa protein (
p66
), and outer surface protein A (
ospA
) gene sequences from DNAs amplified from small mammals and ticks confirmed the presence of several
Borrelia
species.
Borrelia lonestari
DNA was detected among lone star ticks (
Amblyomma americanum
) at four sites.
Borrelia burgdorferi
sensu stricto strains were detected in all small mammal species tested and in
A. americanum
,
Ixodes affinis
, and
Ixodes scapularis
ticks.
Borrelia bissettii
was found in a cotton mouse and cotton rats and in
I. affinis
ticks. The study findings extend the known geographic distributions of
B. lonestari
in
A. americanum
and of
B. burgdorferi
sensu lato in
A. americanum
,
I. affinis
,
I. scapularis
, and small mammals to new sites in Florida. The presence of
B. burgdorferi
sensu stricto strains in host-seeking lone star ticks at two sites in Florida suggests that
A. americanum
should still be considered a possible vector of
B. burgdorferi
sensu lato.
Genetic Diversity of Human Pathogenic Members of the
Fusarium oxysporum
Complex Inferred from Multilocus DNA Sequence Data and Amplified Fragment Length Polymorphism Analyses: Evidence for the Recent Dispersion of a Geographically Widespread Clonal Lineage and Nosocomial Origin
Authors: O'Donnell Kerry , Sutton Deanna A. , Rinaldi Michael G. , Magnon Karen C. , Cox Patricia A. , Revankar Sanjay G. , Sanche Stephen , Geiser David M. , Juba Jean H. , van Burik Jo-Anne H. , Padhye Arvind , Anaissie Elias J. , Francesconi Andrea , Walsh Thomas J. , Robinson Jody S. 
Published: November 2004

ABSTRACT

Fusarium oxysporum
is a phylogenetically diverse monophyletic complex of filamentous ascomycetous fungi that are responsible for localized and disseminated life-threatening opportunistic infections in immunocompetent and severely neutropenic patients, respectively. Although members of this complex were isolated from patients during a pseudoepidemic in San Antonio, Tex., and from patients and the water system in a Houston, Tex., hospital during the 1990s, little is known about their genetic relatedness and population structure. This study was conducted to investigate the global genetic diversity and population biology of a comprehensive set of clinically important members of the
F. oxysporum
complex, focusing on the 33 isolates from patients at the San Antonio hospital and on strains isolated in the United States from the water systems of geographically distant hospitals in Texas, Maryland, and Washington, which were suspected as reservoirs of nosocomial fusariosis. In all, 18 environmental isolates and 88 isolates from patients spanning four continents were genotyped. The major finding of this study, based on concordant results from phylogenetic analyses of multilocus DNA sequence data and amplified fragment length polymorphisms, is that a recently dispersed, geographically widespread clonal lineage is responsible for over 70% of all clinical isolates investigated, including all of those associated with the pseudoepidemic in San Antonio. Moreover, strains of the clonal lineage recovered from patients were conclusively shown to genetically match those isolated from the hospital water systems of three U.S. hospitals, providing support for the hypothesis that hospitals may serve as a reservoir for nosocomial fusarial infections.
Diagnostic Relevance of Immunoglobulin G Avidity for Hepatitis A Virus
Authors: Roque-Afonso Anne-Marie , Grangeot-Keros Liliane , Roquebert Bénédicte , Desbois Delphine , Poveda Jean-Dominique , Mackiewicz Vincent , Dussaix Elisabeth 
Published: November 2004

ABSTRACT

Diagnosis of acute hepatitis A virus (HAV) infection is based on the detection of HAV immunoglobulin M (IgM). However, IgM could be detected due to nonspecific polyclonal activation of the immune system. An avidity test for anti-HAV IgG was developed to distinguish acute infection, where low-avidity antibodies are detected, from immune reactivation. The assay was tested on 104 samples, including 11 sera from patients with past infection, 15 sera from patients with acute infection and 4 collected after recovery, 10 sera from vaccinated subjects, 4 sera from patients with suspected immune reactivation, and 60 unselected HAV-IgM positive sera, collected over 1 year in a routine laboratory. The avidity index (AI) was expressed as percentage. The results were provided as the mean ± one standard deviation. Patients with a history of prior infection had AIs of >70% (mean, 86% ± 10), whereas the mean AI was 36% ± 16 during acute HAV infection (
P
< 0.001). Within the first month after the onset of hepatitis, avidity was either noncalculable due to a very low IgG titer or <50%. In patients with immune reactivation, avidity was >70% (88% ± 10%), a finding consistent with a prior infection. Among the 60 unselected sera, 35 (58%) had a noncalculable or <50% avidity, and most of them had a detectable HAV RNA, confirming HAV infection. In contrast, 16 (27%) had an avidity of >70%, and none was reverse transcription-PCR positive, suggesting immune reactivation. These 16 patients were significantly older than the others (50 ± 16 years versus 26 ± 14 years). The new anti-HAV IgG avidity assay we developed could improve HAV infection diagnosis, particularly in elderly patients.
Detection of
Campylobacter
spp. in ChickenFecal Samples by Real-TimePCR
Authors: Lund Marianne , Nordentoft Steen , Pedersen Karl , Madsen Mogens 
Published: November 2004

ABSTRACT

A
real-time PCR assay for detecting thermophilic
Campylobacter
spp. directly in chicken feces has been developed. DNA was isolated
from fecal material by using magnetic beads followed by PCR with a
prealiquoted PCR mixture, which had been stored at−
18°C.
Campylobacter
could be detected in less
than 4 h, with a detection limit of 100 to 150 CFU/ml, in a
fecal suspension. A bacterial internal control was added before DNA
extraction to control both DNA isolation and the presence of PCR
inhibitors in the samples. The assay was performed on 111 swab samples
from a Danish surveillance program and compared to conventional
culturing using selective enrichment. There was no statistically
significant difference in performance between real-time PCR and culture
by selective enrichment, and the diagnostic specificity was 0.96 with
an agreement of 0.92. Therefore, the assay should be useful for
screening poultry flocks for the presence of
Campylobacter
.
Nocardia kruczakiae
sp. nov., a Pathogen in Immunocompromised Patients and a Member of the “
N. nova
Complex”
Authors: Conville Patricia S. , Brown June M. , Steigerwalt Arnold G. , Lee Judy W. , Anderson Victoria L. , Fishbain Joel T. , Holland Steven M. , Witebsky Frank G. 
Published: November 2004

ABSTRACT

Molecular methodologies have become useful techniques for the identification of pathogenic
Nocardia
species and for the recognition of novel species that are capable of causing human disease. Two isolates recovered from immunocompromised patients were characterized as
Nocardia nova
by biochemical and susceptibility testing results. The restriction fragment length polymorphism (RFLP) patterns obtained by restriction endonuclease analysis (REA) of an amplified portion of the heat shock protein gene were identical to those obtained with the type strain of
N. nova
. REA of an amplified portion of the 16S rRNA gene showed RFLP patterns that were unlike those obtained for the type strain of
N. nova
but that were similar to those obtained for the type strains of
N. africana
and
N. veterana
. Subsequent sequencing of a portion of the 16S rRNA gene produced identical results for the two patient isolates. Sequence analysis of 1,352-bp portions of the 16S rRNA gene indicated that these isolates were 99.8% similar to the recently described species
N. veterana
but were only 99.3, 98.1, and 98.1% similar to the type strains of
N. africana
,
N. nova
, and
N. vaccinii
, respectively. DNA-DNA hybridization studies confirmed that the two patient isolates belonged to the same species but were not closely related to
N. africana
,
N. nova
,
N. vaccinii
, or
N. veterana
. The patient isolates have been designated
N. kruczakiae
sp. nov. Because
N. africana
,
N. veterana
, and the new species are not readily differentiated from
N. nova
by phenotypic methods alone, the designation “
N. nova
complex” can be used to designate isolates such as these that phenotypically resemble
N. nova
but that have not been definitively characterized by 16S rRNA gene sequencing or DNA-DNA hybridization.