bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of Fluconazole Resistance in a
Candida parapsilosis
Strain That Caused Infections in a Neonatal Intensive Care Unit
Authors: Sarvikivi Emmi , Lyytikäinen Outi , Soll David R. , Pujol Claude , Pfaller Michael A. , Richardson Malcolm , Koukila-Kähkölä Pirkko , Luukkainen Päivi , Saxén Harri 
Published: June 2005

ABSTRACT

Candida parapsilosis
is an increasing cause of bloodstream infections (BSIs) in neonatal intensive care units (NICUs). It has been a persistent problem in the NICU of Hospital for Children and Adolescents, Helsinki University Central Hospital, Helsinki, Finland, since 1987. Fluconazole prophylaxis has been used to control the problem. The number of new infections has, however, increased markedly since September 2000. We assessed fluconazole consumption and occurrence of all
Candida
species in the NICU from 1991 to 2002.
C. parapsilosis
bloodstream isolates obtained in the NICU from 1990 to 2002 (
n
= 26) were genotyped and their fluconazole susceptibility was defined. A low rate of
C. parapsilosis
BSIs was correlated with high rates of consumption of fluconazole. No emergence of
Candida
species with primary resistance to fluconazole was detected. However, genotyping with a complex DNA fingerprinting probe revealed that a single strain of
C. parapsilosis
with decreasing susceptibility to fluconazole was responsible for cross-infections that caused BSIs in the NICU over a 12-year period. The emergence of fluconazole resistance in that strain was observed after more than 10 years of fluconazole prophylaxis.
Characterization ofSalmonella entericaSerovar Typhimurium and MonophasicSalmonellaSerovar 1,4,[5],12:i:- Isolates in Thailand
Authors: Amavisit P. , Boonyawiwat W. , Bangtrakulnont A. 
Published: June 2005

ABSTRACTDuplex PCR was developed to screenSalmonella entericaserovar Typhimurium phage type DT104 and related strains in Thailand because a phage typing laboratory of serovar Typhimurium is not available. Of 46 isolates of serovar Typhimurium and 32 isolates ofS. entericaserovar 1,4,[5],12:i:-, 15 (33%) and 30 (94%) were duplex PCR positive, respectively. All isolates were submitted for phage typing to analyze the specificity of the PCR assay. Among serovar Typhimurium isolates that yielded positive duplex PCRs, only seven isolates were phage types DT104 or U302, and eight isolates were undefined types, whereas the negative PCR isolates were either other phage types, including DT7, DT12, DT66, DT79, DT166, DT170, DT193, and DT208 or an undefined type. The serovar Typhimurium and serovar 1,4,[5],12:i:- isolates that were duplex PCR positive were further subtyped by using XbaI PFGE to reveal their genetic relatedness. All serovar Typhimurium phage type DT104 strains had indistinguishable chromosomal patterns. The isolates of phage type U302 and most of the serovar 1,4,[5],12:i:- isolates that were duplex PCR positive yielded similar pulsed-field gel electrophoresis patterns. The patterns of PCR-negative isolates distinctly differed from the patterns of PCR-positive isolates. A total of 26% of all isolates had a dominant R-type ACSSuTG that was not found in the isolates of phage type DT104.
Central European Dobrava Hantavirus Isolate from a Striped Field Mouse (
Apodemus agrarius
)
Authors: Klempa Boris , Stanko Michal , Labuda Milan , Ulrich Rainer , Meisel Helga , Krüger Detlev H. 
Published: June 2005

ABSTRACT

Dobrava virus (DOBV) is a hantavirus that causes hemorrhagic fever with renal syndrome (HFRS) in Europe. It is hosted by at least two rodent species,
Apodemus flavicollis
and
A. agrarius
. According to their natural hosts they form the distinct genetic lineages DOBV-Af and DOBV-Aa, respectively. We have now established a DOBV isolate named Slovakia (SK/Aa) from an
A. agrarius
animal captured in Slovakia. The complete S and M and partial L segment nucleotide sequences of the new isolate were determined. Phylogenetic analyses showed that the SK/Aa isolate clustered together with the other DOBV-Aa sequences amplified from
A. agrarius
before and can be taken as the representative of this genetic lineage. SK/Aa, in comparison with a DOBV-Af isolate, was used for serotyping neutralizing antibodies of HFRS patients in Central Europe. Most patients' sera exhibited a higher endpoint titer when probed with our new isolate, suggesting that DOBV-Aa strains are responsible for most of the DOBV-caused HFRS cases in this region.
Isolation and Molecular Characterization of
Staphylococcus sciuri
in the Hospital Environment
Authors: Dakić Ivana , Morrison Donald , Vuković Dragana , Savić Branislava , Shittu Adebayo , Ježek Petr , Hauschild Tomasz , Stepanović Srdjan 
Published: June 2005

ABSTRACT

Staphylococcus sciuri
is a principally animal-associated bacterial species, but its clinical relevance for humans is increasing. Our study aimed to provide the first insight into the prevalence of this bacterium in a hospital environment. A 3-month surveillance was conducted in a hospital located in Belgrade, Serbia, and 1,028 samples taken from hands of medical personnel, medical devices, and various hospital surfaces were screened for
S. sciuri
presence. In total, 108 isolates were obtained, which resulted in a relatively high rate of colonization (10.5%). These isolates, along with 7
S. sciuri
strains previously isolated in the same hospital (
n
= 115), were phenotypically and genotypically characterized. Antimicrobial susceptibility testing revealed that 73% of the strains were resistant to one or more antibiotics, with 4.3% strains displaying multiresistance. Examination of 16S-23S ribosomal DNA intergenic spacer length polymorphism identified the strains at the subspecies level, and 74 (64.3%) strains of
S. sciuri
subsp.
sciuri
, 37 (32.2%) strains of
S. sciuri
subsp.
rodentium
, and 4 (3.5%) strains of
S. sciuri
subsp.
carnaticus
were established. Pulsed-field gel electrophoresis (PFGE) analysis showed 21 distinct pulsotypes, including 17 main types and 4 subtypes. One dominant cluster with 62 strains was found, while 19 (90.5%) of the PFGE types and subtypes identified had 5 or fewer strains. The predominance of small PFGE clusters suggests that the ubiquitous presence of
S. sciuri
in the outside environment presents the continuous source for colonization of the hospital environment. The presence of one dominant PFGE cluster of strains indicates that some
S. sciuri
strains may be capable for adaptation to hospital environment conditions and continuous existence in this environment.
Development of a Real-Time, TaqMan Reverse Transcription-PCR Assay for Detection and Differentiation of Lyssavirus Genotypes 1, 5, and 6
Authors: Wakeley P. R. , Johnson N. , McElhinney L. M. , Marston D. , Sawyer J. , Fooks A. R. 
Published: June 2005

ABSTRACT

Several reverse transcription-PCR (RT-PCR) methods have been reported for the detection of rabies and rabies-related viruses. These methods invariably involve multiple transfers of nucleic acids between different tubes, with the risk of contamination leading to the production of false-positive results. Here we describe a single, closed-tube, nonnested RT-PCR with TaqMan technology that distinguishes between classical rabies virus (genotype 1) and European bat lyssaviruses 1 and 2 (genotypes 5 and 6) in real time. The TaqMan assay is rapid, sensitive, and specific and allows for the genotyping of unknown isolates concomitant with the RT-PCR. The assay can be applied quantitatively and the use of an internal control enables the quality of the isolated template to be assessed. Despite sequence heterogeneity in the N gene between the different genotypes, a universal forward and reverse primer set has been designed, allowing for the simplification of previously described assays. We propose that within a geographically constrained area, this assay will be a useful tool for the detection and differentiation of members of the
Lyssavirus
genus.
Unique Endemicity of Cryptosporidiosis in Children in Kuwait
Authors: Sulaiman Irshad M. , Hira Parsotam R. , Zhou Ling , Al-Ali Faiza M. , Al-Shelahi Fatima A. , Shweiki Hussein M. , Iqbal Jamshaid , Khalid Nabila , Xiao Lihua 
Published: June 2005

ABSTRACT

To understand the transmission of
Cryptosporidium
infection in children, fecal specimens from 62 Kuwaiti children with gastrointestinal symptoms found to be positive by microscopy were genotyped and subtyped with a small subunit rRNA-based PCR-restriction fragment length polymorphism analysis and a 60-kDa glycoprotein-based DNA sequencing tool. The median age of infected children was 4.5 years, and 77% of infections occurred during the cool season of November to April. Fifty-eight of the children (94%) had
Cryptosporidium parvum
, three (5%) had
Cryptosporidium hominis
, and one (1%) had both
C. parvum
and
C. hominis
. Altogether, 13 subtypes of
C. parvum
(belonging to four subtype allele families) and
C. hominis
(belonging to three subtype allele families) were observed, with 92% of specimens belonging to the common allele family IIa and the unusual allele family IId. Thus, the transmission of cryptosporidiosis in Kuwaiti children differed significantly from other tropical countries.
Matrix-Assisted Laser Desorption Ionization-Time of Flight (Mass Spectrometry) for Hepatitis C Virus Genotyping
Authors: Ilina Elena N. , Malakhova Maja V. , Generozov Edward V. , Nikolaev Eugene N. , Govorun Vadim M. 
Published: June 2005

ABSTRACT
Determination of the hepatitis C virus (HCV) genotype has become accepted as the standard procedure in laboratory practice. Genotype assignment helps in disease prognosis and assists in establishing the appropriate duration of treatment. More than 10 types and 70 subtypes of HCV have been described. In Russia the most common subtypes are 1a, 1b, 2a, and 3a, and the types 4 and 5 are relatively rare. The “gold standard” for testing is gene sequencing. However, a variety of other assays had been developed to provide more rapid and cheaper forms of testing. The aim of this study was to determine the HCV genotype by minisequencing followed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Fragments of 5′ untranslated region of the HCV genome were amplified. Three oligonucleotide primers were designed to detect two sets of genotype-specific single nucleotide polymorphisms. The primer extension reaction was performed using modified thermostable DNA polymerase and in the presence of dideoxynucleosides. The molecular weights of the reaction products were analyzed with MALDI-TOF mass spectrometer. The HCV genotype was determined by registering the particles of the expected molecular weights. The method was used to genotype HCV from HCV-positive blood sera or plasma. The 1a, 1b, 2a, 3a, and 4 genotype HCVs were determined in the samples examined. The data were confirmed by direct sequencing. Thus, we propose a new accurate and efficient method for HCV genotyping based on minisequencing followed by mass spectrometry.
Analysis of
Bordetella pertussis
Populations in European Countries with Different Vaccination Policies
Authors: van Amersfoorth S. C. M. , Schouls L. M. , van der Heide H. G. J. , Advani A. , Hallander H. O. , Bondeson K. , von König C. H. W. , Riffelmann M. , Vahrenholz C. , Guiso N. , Caro V. , Njamkepo E. , He Q. , Mertsola J. , Mooi F. R. 
Published: June 2005

ABSTRACT

Despite the widespread use of pertussis vaccines during the last decades, pertussis has remained an endemic disease with frequent epidemic outbreaks. Currently two types of vaccines are used: whole-cell vaccines (WCVs) and recently developed acellular vaccines (ACVs). The long-term aim of our studies is to assess the effect of different vaccination policies on the population structure of
Bordetella pertussis
and ultimately on the disease burden in Europe. In the present study, a total of 102
B. pertussis
isolates from the period 1998 to 2001 from five European countries (Finland, Sweden, Germany, The Netherlands, and France) were characterized. The isolates were analyzed by typing based on variable number of tandem repeats (VNTR); by sequencing of polymorphic genes encoding the surface proteins pertussis toxin S1 and S3 subunits (
ptxA
and
ptxC
), pertactin (
prn
), and tracheal colonization factor (
tcfA
); and by fimbrial serotyping. The results reveal a relationship between geographic location and VNTR types, the frequency of the
ptxC
alleles, and serotypes. We have not observed a relationship between the strain characteristics we studied and vaccination programs. Our results provide a baseline which can be used to reveal changes in the
B. pertussis
population in Europe in the coming years.
Community-Wide Outbreaks of Clonally Related CTX-M-14 β-Lactamase-Producing
Escherichia coli
Strains in the Calgary Health Region
Authors: Pitout Johann D. D. , Gregson Daniel B. , Church Deirdre L. , Elsayed Sameer , Laupland Kevin B. 
Published: June 2005

ABSTRACT

Enterobacteriaceae
producing extended-spectrum β-lactamases (ESBLs) typically cause nosocomial infections. Previous surveillance in the Calgary Health Region showed that
Escherichia coli
strains producing ESBLs were common among community patients. During the period (2000 to 2002): 23 of 157 (15%) of the strains were positive for
bla
CTX-M
genes from the CTX-M-I group (CTX-M-1-like) and 87 of 157 (55%) of the strains were positive for
bla
CTX-M
genes from the CTX-M-III group (CTX-M-14-like). The objective of this study was to investigate the molecular epidemiology of these strains. The β-lactamases were characterized, and the genetic relatedness of the isolates was analyzed by digesting genomic DNA with the restriction endonuclease XbaI and by performing pulse-field gel electrophoresis (PFGE). PFGE revealed two closely related restriction patterns (clusters CTXM14A and CTXM14AR) among 67 (77%) CTX-M-14 producers. These strains from CTXM14A had nearly identical susceptibility patterns and were isolated most often from urine samples obtained at community sites during 2000 and 2001. Strains from the CTX-M-1-like and CTX-M-negative groups were unrelated to clusters CTXM14, CTXM14AR, and CTXM14NR. We conclude that clonally related strains of
E. coli
producing CTX-M-14 β-lactamases were responsible for a predominantly community-wide outbreak. Further studies are warranted to investigate whether community-onset diseases caused by ESBL-producing
E. coli
are related to a point source or transmission within the community.
Genomic Analysis of Vaccine-Derived Poliovirus Strains in Stool Specimens by Combination of Full-Length PCR and Oligonucleotide Microarray Hybridization
Authors: Laassri Majid , Dragunsky Eugenia , Enterline Joan , Eremeeva Tatiana , Ivanova Olga , Lottenbach Kathleen , Belshe Robert , Chumakov Konstantin 
Published: June 2005

ABSTRACT
Sabin strains of poliovirus used in the manufacture of oral poliovirus vaccine (OPV) are prone to genetic variations that occur during growth in cell cultures and the organisms of vaccine recipients. Such derivative viruses often have increased neurovirulence and transmissibility, and in some cases they can reestablish chains of transmission in human populations. Monitoring for vaccine-derived polioviruses is an important part of the worldwide campaign to eradicate poliomyelitis. Analysis of vaccine-derived polioviruses requires, as a first step, their isolation in cell cultures, which takes significant time and may yield viral stocks that are not fully representative of the strains present in the original sample. Here we demonstrate that full-length viral cDNA can be PCR amplified directly from stool samples and immediately subjected to genomic analysis by oligonucleotide microarray hybridization and nucleotide sequencing. Most fecal samples from healthy children who received OPV were found to contain variants of Sabin vaccine viruses. Sequence changes in the 5′ untranslated region were common, as were changes in the VP1-coding region, including changes in a major antigenic site. Analysis of stool samples taken from cases of acute flaccid paralysis revealed the presence of mixtures of recombinant polioviruses, in addition to the emergence of new sequence variants. Avoiding the need for cell culture isolation dramatically shortened the time needed for identification and analysis of vaccine-derived polioviruses and could be useful for preliminary screening of clinical samples. The amplified full-length viral cDNA can be archived and used to recover live virus for further virological studies.
Comparison of Immunohistochemistry and Virus Isolation for Diagnosis of West Nile Virus
Authors: Ellis Angela E. , Mead Daniel G. , Allison Andrew B. , Gibbs Samantha E. J. , Gottdenker Nicole L. , Stallknecht David E. , Howerth Elizabeth W. 
Published: June 2005

ABSTRACT
Immunohistochemistry and virus isolation were performed on 1,057 birds. Immunohistochemistry, virus isolation, or both found 325 birds to be West Nile virus positive. Of these, 271 were positive by both methods. These results indicate that virus isolation and immunohistochemistry are approximately equal in their ability to detect West Nile virus.
Multicenter Evaluation of a
Candida albicans
Peptide Nucleic Acid Fluorescent In Situ Hybridization Probe for Characterization of Yeast Isolates from Blood Cultures
Authors: Wilson D. A. , Joyce M. J. , Hall L. S. , Reller L. B. , Roberts G. D. , Hall G. S. , Alexander B. D. , Procop G. W. 
Published: June 2005

ABSTRACT

We evaluated aliquots from 244 clinical blood culture bottles that demonstrated yeasts on Gram stain using a
Candida albicans
peptide nucleic acid (PNA) fluorescent in situ hybridization (FISH) probe. The sensitivity, specificity, positive predictive value, and negative predictive value of the
C. albicans
PNA FISH test in this study were 99%, 100%, 100%, and 99.3%, respectively.
Clinical Relevance of the
vacA
,
iceA
,
cagA
, and
flaA
Genes of
Helicobacter pylori
Strains Isolated in Eastern Taiwan
Authors: Wu Chao-Chuan , Chou Pai-Yu , Hu Chi-Tan , Liu Zuo-Chai , Lin Chih-Yung , Tseng Yi-Hsiung , Lin Nien-Tsung 
Published: June 2005

ABSTRACT

The genotypes of
Helicobacter pylori flaA
,
cagA
,
vacA
, and
iceA
were determined for DNA isolated from patients with chronic gastritis or peptic ulcer in eastern Taiwan. The
vacA
gene encoding the s1a subtype was found to predominate in peptic ulcer patients, and the
iceA1
genotype was associated with chronic gastritis.
cagA
and
flaA
genes were not found to be associated with these types of disease.
Surveillance ofStaphylococcus aureusin Veterinary Teaching Hospitals
Authors: Middleton John R. , Fales William H. , Luby Christopher D. , Oaks J. Lindsay , Sanchez Susan , Kinyon Joann M. , Wu Ching Ching , Maddox Carol W. , Welsh Ronald D. , Hartmann Faye 
Published: June 2005

ABSTRACTStaphylococcus aureusisolates (n= 70) from 65 patients (36 canine, 18 equine, 7 bovine, 2 avian, and 2 feline) at seven veterinary teaching hospitals in the United States were studied. The majority of patients (83%) with anS. aureusinfection were canine and equine, but this may have reflected a sample bias based on clinic case loads and diagnostic lab submissions at the participating institutions. Fourteen percent of patients with anS. aureusinfection were infected with a methicillin-resistantS. aureus(MRSA) isolate. Six of seven institutions had at least one MRSA infection during the study. Pulsed-field gel electrophoresis on 63 of the 70 isolates yielded 58 unique strains ofS. aureus. None of the strain types of the MRSA isolates matched each other or the type of any otherS. aureusisolate. The proportions of patients infected with an MRSA isolate were not significantly different between institutions or animal species (P≥ 0.222). Methicillin-resistantS. aureusisolates in this study seemed to be community acquired rather than hospital acquired.
Evaluation of a New Molecular System for Simultaneous Identification of Four
Enterococcus
Species and Their Glycopeptide Resistance Genotypes
Authors: Eigner U. , Fahr A. , Weizenegger M. , Witte W. 
Published: June 2005

ABSTRACT

We compared the performances of a new DNA-based strip assay and the VITEK 2 system for identification of 105 enterococcal strains and differentiation of their
van
gene-associated resistance levels. Both methods provided excellent results. The molecular assay showed advantages in time to result for identification of
van
-associated genes.
Dissemination of Multisusceptible Methicillin-Resistant
Staphylococcus aureus
in Singapore
Authors: Hsu Li-Yang , Koh Tse-Hsien , Singh Kamaljit , Kang Mei-Ling , Kurup Asok , Tan Ban-Hock 
Published: June 2005

ABSTRACT

Analysis of hospital-acquired methicillin-resistant
Staphylococcus aureus
strains isolated from a tertiary public hospital in Singapore revealed that multisusceptible strains had gradually started to replace the endemic multiresistant strain (ST239-MRSA-III) since 2002. Molecular typing showed that this was a predominantly clonal outbreak of a UK-EMRSA-15 strain (ST22-MRSA-IV).
Distribution of
Burkholderia cepacia
Complex Species among Isolates Recovered from Persons with or without Cystic Fibrosis
Authors: Reik Rebecca , Spilker Theodore , LiPuma John J. 
Published: June 2005

ABSTRACT

We analyzed
Burkholderia cepacia
complex isolates recovered from 1,218 cystic fibrosis (CF) patients and 90 patients without CF. Although all
B. cepacia
complex species were found, some were rarely identified. The distribution of species differed between the CF and non-CF populations and appears to be changing over time among CF patients.
Molecular Detection of a New
Anaplasma
Species Closely Related to
Anaplasma phagocytophilum
in Canine Blood from South Africa
Authors: Inokuma Hisashi , Oyamada Maremichi , Kelly Patrick J. , Jacobson Linda A. , Fournier Pierre-Edouard , Itamoto Kazuhito , Okuda Masaru , Brouqui Philippe 
Published: June 2005

ABSTRACT

Canine DNA samples from South Africa were found to contain 16S rRNA gene nucleotide and citrate synthase gene nucleotide and deduced amino acid sequences that were most similar to
Anaplasma phagocytophilum
: 98%, 66%, and 69% similarity, respectively. This suggests that a new
Anaplasma
species closely related to
A. phagocytophilum
occurs in Africa.
Four Laboratory-Associated Cases of Infection with
Escherichia coli
O157:H7
Authors: Spina Nancy , Zansky Shelley , Dumas Nellie , Kondracki Stan 
Published: June 2005

ABSTRACT

An investigation of four cases of infection with
Escherichia coli
O157:H7 among laboratorians from different clinical laboratories revealed that the DNA fingerprint pattern of each case isolate was indistinguishable from that of an isolate handled in the laboratory prior to illness. These data suggest that the infections were laboratory acquired, and they demonstrate the importance of laboratorians strictly adhering to biosafety practices recommended for the handling of infectious materials.
Molecular Epidemiology Investigation of Outbreaks of Fowl Cholera in Geographically Related Poultry Flocks
Authors: Kardos G. , Kiss I. 
Published: June 2005

ABSTRACTThe present work describes two cases of consecutive fowl cholera outbreak series occurring in goose and turkey flocks. Most strains isolated from epidemiologically related outbreaks showed genetic relatedness, as revealed by enterobacterial repetitive intergenic consensus-PCR and pulsed-field gel electrophoresis, suggesting that the consecutive outbreaks were due to recurrences rather than reinfections.
Prevalence ofHelicobacter pullorumamong Patients with Gastrointestinal Disease and Clinically Healthy Persons
Authors: Ceelen Liesbeth , Decostere Annemie , Verschraegen Gerda , Ducatelle Richard , Haesebrouck Freddy 
Published: June 2005

ABSTRACTFeces from 531 patients with gastroenteritis and from 100 clinically healthy individuals were tested forHelicobacter pullorumby use of PCR. Samples positive by PCR were qualified for isolation.H. pullorumDNA was demonstrated to be present in feces from 4.3% of patients with gastrointestinal disease but also in feces from 4.0% of clinically healthy persons. One strain was isolated from one patient with gastrointestinal disease.