bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Variants of
Vibrio cholerae
O1 Biotype El Tor with Attributes of the Classical Biotype from Hospitalized Patients with Acute Diarrhea in Bangladesh
Authors: Nair G. Balakrish , Faruque Shah M. , Bhuiyan N. A. , Kamruzzaman M. , Siddique A. K. , Sack David A. 
Published: August 2002

ABSTRACT

The sixth pandemic of cholera and, presumably, the earlier pandemics were caused by the classical biotype of
Vibrio cholerae
O1, which was progressively replaced by the El Tor biotype representing the seventh cholera pandemic. Although the classical biotype of
V. cholerae
O1 is extinct, even in southern Bangladesh, the last of the niches where this biotype prevailed, we have identified new varieties of
V. cholerae
O1, of the El Tor biotype with attributes of the classical biotype, from hospitalized patients with acute diarrhea in Bangladesh. Twenty-four strains of
V. cholerae
O1 isolated between 1991 and 1994 from hospitalized patients with acute diarrhea in Matlab, a rural area of Bangladesh, were examined for the phenotypic and genotypic traits that distinguish the two biotypes of
V. cholerae
O1. Standard reference strains of
V. cholerae
O1 belonging to the classical and El Tor biotypes were used as controls in all of the tests. The phenotypic traits commonly used to distinguish between the El Tor and classical biotypes, including polymyxin B sensitivity, chicken cell agglutination, type of
tcpA
and
rstR
genes, and restriction patterns of conserved rRNA genes (ribotypes), differentiated the 24 strains of toxigenic
V. cholerae
O1 into three types designated the Matlab types. Although all of the strains belonged to ribotypes that have been previously found among El Tor vibrios, type I strains had more traits of the classical biotype while type II and III strains appeared to be more like the El Tor biotype but had some classical biotype properties. These results suggest that, although the classical and El Tor biotypes have different lineages, there are possible naturally occurring genetic hybrids between the classical and El Tor biotypes that can cause cholera and thus provide new insight into the epidemiology of cholera in Bangladesh. Furthermore, the existence of such novel strains may have implications for the development of a cholera vaccine.
Comparative Assessment of Genotyping Methods for Epidemiologic Study of
Burkholderia cepacia
Genomovar III
Authors: Coenye Tom , Spilker Theodore , Martin Alissa , LiPuma John J. 
Published: August 2002

ABSTRACT

We analyzed a collection of 97 well-characterized
Burkholderia cepacia
genomovar III isolates to evaluate multiple genomic typing systems, including pulsed-field gel electrophoresis (PFGE), BOX-PCR fingerprinting and random amplified polymorphic DNA (RAPD) typing. The typeability, reproducibility, and discriminatory power of these techniques were evaluated, and the results were compared to each other and to data obtained in previous studies by using multilocus restriction typing (MLRT). All methods showed excellent typeability. PFGE with
Spe
I was more reproducible than RAPD and BOX-PCR fingerprinting. The discriminatory power of the methods was variable, with PFGE and RAPD typing having a higher index of discrimination than BOX-PCR fingerprinting. In general, the results obtained by PFGE, BOX-PCR fingerprinting, and MLRT were in good agreement. Our data indicate that different genomic-based methods can be used to type
B. cepacia
genomovar III isolates depending on the situation and the epidemiologic question being addressed. PFGE and RAPD fingerprinting are best suited to addressing small-scale studies (i.e., local epidemiology), whereas BOX-PCR fingerprinting is more appropriate for large-scale studies (i.e., global epidemiology). In this regard, BOX-PCR fingerprinting can be considered a rapid and easy alternative to MLRT.
Determination of NovelBorreliaGenospecies in SwedishIxodes ricinusTicks
Authors: Fraenkel Carl-Johan , Garpmo Ulf , Berglund Johan 
Published: August 2002

ABSTRACTA total of 301 adult questingIxodes ricinusticks were collected at 15 different locations along the south and east coasts of Sweden to determine theBorreliagenospecies diversity. Thirty-two ticks (11%) were found to be positive by nested PCR withBorrelia burgdorferisensu lato-specific primers. Species determination was based on partial sequencing of the 16S rRNA gene and the flagellin gene. Five differentBorreliaspecies were found. The nucleotide sequence of theBorreliaDNA found in two ticks differed extensively from the nucleotide sequences of theBorreliaDNA found in the other ticks, and analysis revealed that they were closely related to the relapsing fever borrelia speciesBorrelia miyamotoi. This is the first report of aB. miyamotoi-like borrelia inI. ricinusand in Europe. Moreover, theBorreliaDNA of two ticks (6%) clustered within theB. valaisianacomplex.B. valaisianahas not previously been reported in Sweden.B. afzeliiDNA was found in 14 ticks (44%), andB. gariniiDNA was found in 10 ticks (31%).B. burgdorferisensu stricto DNA was found in four ticks (13%). We conclude that all of the known human-pathogenic species (B. garinii,B. afzelii, andB. burgdorferisensu stricto) andB. valaisianafound elsewhere in Europe are also present in the Swedish host-seeking tick population and that aB. miyamotoi-likeBorreliaspecies seems to be present inI. ricinusticks in Europe.
Molecular Epidemiology of Erythromycin Resistance in
Streptococcus pneumoniae
Isolates from Blood and Noninvasive Sites
Authors: Amezaga Maria Rosario , Carter Philip E. , Cash Phillip , McKenzie Hamish 
Published: August 2002

ABSTRACT

Erythromycin-resistant isolates of
Streptococcus pneumoniae
from blood cultures and noninvasive sites were studied over a 3-year period. The prevalence of erythromycin resistance was 11.9% (19 of 160) in blood culture isolates but 4.2% (60 of 1,435) in noninvasive-site isolates. Sixty-two of the 79 resistant isolates were available for study. The M phenotype was responsible for 76% (47 of 62) of resistance, largely due to a serotype 14 clone, characterized by multilocus sequence typing as ST9, which accounted for 79% (37 of 47) of M phenotype resistance. The ST9 clone was 4.8 times more common in blood than in noninvasive sites. All M phenotype isolates were PCR positive for
mef
(A), but sequencing revealed that the ST9 clone possessed the
mef
(A) sequence commonly associated with
Streptococcus pyogenes
. All M phenotype isolates with this
mef
(A) sequence also had sequences consistent with the presence of the Tn
1207.1
genetic element inserted in the
celB
gene. In contrast, isolates with the
mef
(E) sequence normally associated with
S. pneumoniae
contained sequences consistent with the presence of the mega insertion element. All MLS
B
isolates carried
erm
(B), and two isolates carried both
erm
(B) and
mef
(E). Fourteen of the 15 MLS
B
isolates were tetracycline resistant and contained
tet
(M). However, six M phenotype isolates of serotypes 19 (two isolates) and 23 (four isolates) were also tetracycline resistant and contained
tet
(M). MICs for isolates with the
mef
(A) sequence were significantly higher than MICs for isolates with the
mef
(E) sequence (
P
< 0.001). Thus, the ST9 clone of
S. pneumoniae
is a significant cause of invasive pneumococcal disease in northeast Scotland and is the single most important contributor to M phenotype erythromycin resistance.
Rational Design of DNA Sequence-Based Strategies for Subtyping
Listeria monocytogenes
Authors: Cai Steven , Kabuki Dirce Yorika , Kuaye Arnaldo Yoshiteru , Cargioli Theresa Gina , Chung Michael S. , Nielsen Rasmus , Wiedmann Martin 
Published: August 2002

ABSTRACT

The ability to differentiate bacteria beyond the species level is essential for identifying and tracking infectious disease outbreaks and to improve our knowledge of the population genetics, epidemiology, and ecology of bacterial pathogens. Commonly used subtyping methods, such as serotyping, phage typing, ribotyping, and pulsed-field gel electrophoresis, can yield ambiguous results that are difficult to standardize and share among laboratories. DNA sequence-based subtyping strategies can reduce interpretation ambiguity. We report the development of a rational approach for designing sequence-based subtyping methods.
Listeria monocytogenes
was selected as the model organism for testing the efficacy of this approach. Two housekeeping genes (
recA
and
prs
), one stress response gene (
sigB
), two virulence genes (
actA
and
inlA
), and two intergenic regions (
hly
-
mpl
and
plcA
-
hly
) were sequenced for 15
L. monocytogenes
isolates. Isolates were chosen from a representative collection of more than 1,000
L. monocytogenes
isolates to reflect the genetic diversity of this species. DNA sequences were aligned, and sliding window analyses were performed for each gene to define 600-bp-long regions that were (i) most polymorphic (using ProSeq) or (ii) most discriminatory (using a new algorithm implemented in WINDOWMIN). Complete gene sequences for
actA
(1,929 bp) and
inlA
(2,235 bp) provided the highest discrimination (identifying 15 and 14 allelic types, respectively). WINDOWMIN allowed identification of 600-bp regions within these genes that provided similar discriminatory power (yielding 15 and 13 allelic types, respectively). The most discriminatory 600-bp fragments identified in the housekeeping and stress response genes differentiated the isolates into 8 to 10 subtypes; intergenic region sequences yielded 8 and 12 allelic types based on 335- and 242-bp sequences for
hly
-
mpl
and
plcA
-
hly
, respectively. Regions identified as most polymorphic were not necessarily most discriminatory; therefore, application of the WINDOWMIN algorithm provided a powerful tool for determining the best target regions for DNA sequence-based subtyping. Our specific results also show that inclusion of virulence gene target sequences in a DNA sequence-based subtyping scheme for
L. monocytogenes
is necessary to achieve maximum subtype differentiation.
Possible Connection between a Widely Disseminated Conjugative Gentamicin Resistance (pMG1-Like) Plasmid and the Emergence of Vancomycin Resistance in
Enterococcus faecium
Authors: Tomita Haruyoshi , Pierson Carl , Lim Suk Kyung , Clewell Don B. , Ike Yasuyoshi 
Published: August 2002

ABSTRACT

A total of 640 vancomycin-resistant
Enterococcus faecium
(VRE) isolates, which were obtained between 1994 and 1999 from the Medical School Hospital of the University of Michigan, Ann Arbor, were used in this study. Of the 640 strains, 611 and 29 were VanA and VanB VRE, respectively, based on PCR analysis. Four hundred ninety-two (77%) of the strains exhibited resistance to concentrations of gentamicin from 64 μg/ml (MIC) to more than 1,024 μg/ml (MIC). The gentamicin resistance of each of 261 (53%) of the 492 gentamicin-resistant strains was transferred to
E. faecium
at a frequency of about 10
−5
to 10
−6
per donor cell in broth mating. More than 90% of vancomycin resistances of the 261 strains cotransferred with the gentamicin resistances to
E. faecium
strains by filter mating. The conjugative gentamicin resistance plasmids were identified and were classified into five types (A through E) with respect to their
Eco
RI restriction profiles. The transfer frequencies of each type of plasmid between
E. faecium
strains or
Enterococcus faecalis
strains were around 10
−3
to 10
−5
per donor cell or around 10
−6
to 10
−7
per donor cell, respectively, in broth mating. Type A and type B were the most frequently isolated, at an isolation frequency of about 40% per VRE isolate harboring the gentamicin resistance conjugative plasmid. The plasmids did not show any homology in Southern hybridization with the pheromone-responsive plasmids and broad-host-range plasmids pAMβ1 and pIP501. The
Eco
RI or
Nde
I restriction fragments of each type of plasmids hybridized to the conjugative gentamicin resistance plasmid pMG1 (65.1 kb), which was originally isolated from an
E. faecium
clinical isolate, and transfer efficiently in broth mating.
Detection and Quantification of Oral Treponemes in Subgingival Plaque by Real-Time PCR
Authors: Asai Yasuyuki , Jinno Takayoshi , Igarashi Hajime , Ohyama Yoshinori , Ogawa Tomohiko 
Published: August 2002

ABSTRACT

Oral treponemes have been associated with periodontal diseases. We developed a highly sensitive and specific method to detect and quantify cultivable oral treponemes (
Treponema denticola
,
Treponema vincentii
, and
Treponema medium
) in 50 subgingival plaque samples from 13 healthy subjects as well as 37 patients with periodontal diseases using real-time PCR assays with specific primers and a TaqMan probe for each 16S rRNA sequence. The specificity for each assay was examined by using DNA specimens from various treponemal and other bacterial species. The TaqMan real-time PCR was able to detect from 10
3
to 10
8
cells of the oral treponemes, with correlation coefficients as follows:
T. denticola
, 0.984;
T. vincentii
, 0.991; and
T. medium
, 0.984. The frequencies of occurrence of these three oral treponemes in subgingival plaque samples were as follows:
T. denticola
, 68.0%;
T. vincentii
, 36.0%; and
T. medium
, 48.0%. In addition, the number of
T. denticola
,
T. vincentii
, and
T. medium
cells in plaque samples detected by real-time PCR ranged from 3 to 15,184, 1 to 447, and 1 to 7,301 cells/pg of plaque DNA, respectively. Increased numbers of
T. denticola
cells were detected in plaque samples from deep periodontal pockets, and
T. medium
was also detected in deep pockets. On the other hand,
T. vincentii
was mainly found in shallow pockets. These results suggest that various oral treponemes are associated with the formation of each stage of periodontal disease.
High Prevalence of Human Papillomavirus (HPV) Infections and High Frequency of Multiple HPV Genotypes in Human Immunodeficiency Virus-Infected Women in Brazil
Authors: Levi José E. , Kleter Bernhard , Quint Wim G. V. , Fink Maria C. S. , Canto Cynthia L. M. , Matsubara Regina , Linhares Iara , Segurado Aluísio , Vanderborght Bart , Neto José Eluf , van Doorn Leen-Jan 
Published: August 2002

ABSTRACT

A group of 208 human immunodeficiency virus (HIV)-infected women in Brazil were studied for the presence of human papillomavirus with the general SPF
10
PCR primer set. Virtually all (98%) women were found positive for human papillomavirus (HPV) DNA. Genotyping by the reverse hybridization line probe assay (HPV-LiPA) revealed a high prevalence of multiple genotypes (78.9% of the cases), with an average of 3.1 genotypes per patient (range, 1 to 10 genotypes). HPV 6 was the most prevalent genotype and was observed in 80 (39.2%) patients, followed by types 51 (31.9%), 11 (26.0%), 18 (24.0%), and 16 (22.5%). Of the genotypes detected, 40.9% were low-risk genotypes. Twenty-two (10.5%) patients showed normal (Pap I) cytology, 149 (71.6%) patients had inflammation (Pap II), and 28 patients (13.4%) had a Pap III score. The prevalence of high-risk genotypes increased with the cytological classification. There were no significant associations between the number of HPV genotypes detected and the cytological classification, HIV viral load, and CD4 count in these patients. In conclusion, the highly sensitive SPF
10
LiPA system shows that a very high proportion of HIV-infected women in Brazil are infected with HPV and often carry multiple HPV genotypes.
Leptotrichia amnionii
sp. nov., a Novel Bacterium Isolated from the Amniotic Fluid of a Woman after Intrauterine Fetal Demise
Authors: Shukla Sanjay K. , Meier Paul R. , Mitchell Paul D. , Frank Daniel N. , Reed Kurt D. 
Published: August 2002

ABSTRACT

A novel bacterium was isolated and characterized from the amniotic fluid of a woman who experienced intrauterine fetal demise in the second trimester of pregnancy. The bacterium was a slow-growing, gram-negative anaerobic coccobacillus belonging to the genus
Leptotrichia
. Unlike
Leptotrichia sanguinegens
, the isolate did not grow in chopped-meat glucose broth or on sheep blood agar upon subculturing. The isolate was characterized by sequencing and analyzing its 16S rRNA gene. The 1,493-bp 16S ribosomal DNA sequence had only 96% homology with
L. sanguinegens.
Several phylogenetic analyses indicated that
L. amnionii
is a distinct species and most closely related to
L. sanguiegens
.
Fast, Noninvasive Method for Molecular Detection and Differentiation of
Malassezia
Yeast Species on Human Skin and Application of the Method to Dandruff Microbiology
Authors: Gemmer Christina M. , DeAngelis Yvonne M. , Theelen Bart , Boekhout Teun , Dawson, Thomas L. 
Published: August 2002

ABSTRACT

Malassezia
fungi have been the suspected cause of dandruff for more than a century. Previously referred to as
Pityrosporum ovale
,
Pityrosporum orbiculare
, or
Malassezia
, these fungi are now known to consist of at least seven
Malassezia
species. Each species has a specific ecological niche, as well as specific biochemical and genetic characteristics.
Malassezia
yeasts have fastidious culture conditions and exceedingly different growth rates. Therefore, the results of surveys of
Malassezia
based on culture methods can be difficult to interpret. We developed a molecular technique, terminal fragment length polymorphism analysis, to more accurately survey the ecology of
Malassezia
yeasts without bias from culture. This technique involves fluorescent nested PCR of the intergenic transcribed spacer (ITS) ITS I and ITS II region ribosomal gene clusters. All known
Malassezia
species can be differentiated by unique ITS fragment lengths. We have used this technique to directly analyze scalp samples from subjects enrolled in a demographic scalp health study. Results for subjects assigned composite adherent scalp flaking scores (ASFS) <10 were compared to those for subjects assigned composite ASFS >24.
Malassezia restricta
and
M. globosa
were found to be the predominant
Malassezia
species present in both groups. Importantly, we found no evidence of
M. furfur
in either group, indicating that
M. furfur
can be eliminated as the causal organism for dandruff. Both groups also showed the presence of non-
Malassezia
fungi. This method, particularly when it is used in combination with existing fungal ITS databases, is expected to be useful in the diagnosis of multiple other fungal infections.
Detection ofRickettsia prowazekiiin Body Lice and Their Feces by Using Monoclonal Antibodies
Authors: Fang Rong , Houhamdi Linda , Raoult Didier 
Published: August 2002

ABSTRACTIn order to identifyRickettsia prowazekiiin lice, we developed a panel of 29 representative monoclonal antibodies selected from 187 positive hybridomas made by fusing splenocytes of immunized mice with SP2/0-Ag14 myeloma cells. Immunoblotting revealed that 15 monoclonal antibodies reacted with the lipopolysaccharide-like (LPS-L) antigen and 14 reacted with the epitopes of a 120-kDa protein. Only typhus group rickettsiae reacted with the monoclonal antibodies against LPS-L.R. felis, a recently identified rickettsial species, did not react with these monoclonal antibodies, confirming that it is not antigenically related to the typhus group. Monoclonal antibodies against the 120-kDa protein were highly specific forR. prowazekii.We successfully applied a selected monoclonal antibody against the 120-kDa protein to detect by immunofluorescence assayR. prowazekiiin smears from 56 wild and laboratory lice, as well as in 10 samples of louse feces infected or not infected with the organism. We have developed a simple, practical, and specific diagnostic assay for clinical specimens and large-scale epidemiological surveys with a sensitivity of 91%. These monoclonal antibodies could be added to the rickettsial diagnostic panel and be used to differentiateR. prowazekiifrom other rickettsial species.
Rapid-Cycle PCR and Fluorimetry for Detection of Mycobacteria
Authors: Lachnik Jacqueline , Ackermann Birgit , Bohrssen Antje , Maass Silvia , Diephaus Catharina , Puncken Axel , Stermann Marion , Bange Franz-Christoph 
Published: August 2002

ABSTRACT

In this study we used LightCycler PCR amplification and product detection by fluorescence resonance energy transfer probes to identify mycobacteria and differentiate between
Mycobacterium tuberculosis
complex,
Mycobacterium avium,
and other nontuberculous mycobacteria. Targeting the 16S rRNA gene, three different probes specific for mycobacteria,
M
.
tuberculosis
complex, and
M
.
avium
were constructed. As few as five genome copies of target nucleic acid were detected by the probes, illustrating the high sensitivity of the system. All 33 mycobacterial species tested but none of the closely related actinomycetes and other bacteria produced a specific fluorescence signal. A specificity of 100% was also demonstrated for the
M
.
tuberculosis
complex-specific probe and the
M
.
avium
-specific probe. Within 45 min, the LightCycler method correctly detected mycobacteria and specifically identified
M
.
tuberculosis
complex and
M
.
avium
without any post-PCR sample manipulation. In view of future clinical studies, we also constructed and tested an internal control which could be used to assure successful amplification and detection of mycobacteria. Monitoring of PCR inhibition will be essential for evaluation of this system for direct detection of mycobacteria in clinical specimens. Finally, we tested our system on sputum seeded with mycobacteria and were able to detect as few as 10 organisms. At present, this system is the fastest available method for identification and differentiation of mycobacteria from culture-positive specimens and offers an excellent alternative to previously established nucleic acid amplification-based techniques for the diagnostic mycobacterial laboratory.
Clinical and Epidemiological Correlates of Genotypes within the
Mycobacterium avium
Complex Defined by Restriction and Sequence Analysis of
hsp65
Authors: Smole Sandra C. , McAleese Fionnuala , Ngampasutadol Jutamas , von Reyn C. Fordham , Arbeit Robert D. 
Published: August 2002

ABSTRACT

Species identification of isolates of the
Mycobacterium avium
complex (MAC) remains a difficult task. Although
M
.
avium
and
Mycobacterium intracellulare
can be identified with expensive, commercially available probes, many MAC isolates remain unresolved, including those representing
Mycobacterium lentiflavum
as well as other potentially undefined species. PCR restriction analysis (PRA) of the
hsp65
gene has been proposed as a rapid and inexpensive approach. We applied PRA to 278 MAC isolates, including 126 from blood of human immunodeficiency virus (HIV)-infected patients, 59 from sputum of HIV-negative patients with chronic obstructive pulmonary disease, 88 from environmental sources, and 5 pulmonary isolates from a different study. A total of 15 different PRA patterns were observed. For 27 representative isolates, a 441-bp fragment of the
hsp65
gene was sequenced; based on 54 polymorphic sites, 18 different alleles were defined, including 12 alleles not previously reported. Species and phylogenetic relationships were more accurately defined by sequencing than by PRA or commercial probe. The distribution of PRA types and, by implication, phylogenetic lineages among blood isolates was significantly different from that for pulmonary and environmental isolates, suggesting that particular lineages have appreciably greater virulence and invasive potential.