bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microtiter Assay for Detecting
Campylobacter
spp. and
Helicobacter pylori
with Surface Gangliosides Which Bind Cholera Toxin
Authors: Sack David A. , Lastovica Albert J. , Chang Sunny H. , Pazzaglia Gary 
Published: December 2019

ABSTRACT

Campylobacter jejuni
with Gm1 ganglioside in the core of its lipopolysaccharide has been associated with Guillain-Barrésyndrome. Since this epitope may be of considerable pathophysiologic importance and since this ganglioside binds cholera toxin, a rapid screening assay to detect bacteria that bind cholera toxin as an indication of Gm1 on their surfaces was developed. In the assay, bacterial lawns were grown on agar plates, harvested with phosphate-buffered saline, boiled, and incubated with a standard concentration of cholera B subunit. Preparations from strains with Gm1 were observed to inhibit the binding of cholera B subunit to Gm1 in a microtiter enzyme-linked immunosorbent assay. By using this assay with two groups of strains, 37 positive strains were detected among the 197 tested. Species with positive isolates included
C. jejuni
,
Campylobacter coli
, and
Helicobacter pylori
. The assay is capable of testing large numbers of isolates and should prove useful in future clinical and epidemiological studies of bacteria with this epitope.
Clinical Importance of Identifying Coagulase-Negative Staphylococci Isolated from Blood Cultures: Evaluation of MicroScan Rapid and Dried Overnight Gram-Positive Panels versus a Conventional Reference Method
Authors: Weinstein Melvin P. , Mirrett Stanley , Van Pelt Linda , McKinnon Mary , Zimmer Barbara L. , Kloos Wesley , Reller L. Barth 
Published: December 2019

ABSTRACT

We evaluated the clinical usefulness of species identification of blood isolates of coagulase-negative staphylococci as a predictor of the clinical significance of the isolates. In addition, we compared results of species identification obtained with MicroScan Rapid Gram-Positive Identification panels and Dried Overnight (Conventional) Gram-Positive Identification panels with those obtained by a tube reference method. Two hundred eighty-five blood isolates were tested, including 92 judged to represent true bacteremia and 193 judged to represent contamination. The most common species detected were
Staphylococcus epidermidis
,
Staphylococcus hominis
, and
Staphylococcus haemolyticus
. These three species accounted for nearly 98% of the clinically significant isolates and 89% of the contaminants. The isolation of other species almost always represented contamination. However, identification of the three most common species did not help distinguish pathogens from contaminants. Both the Rapid and the Dried Overnight Gram-Positive panels identified
S. epidermidis
strains accurately, but the panels performed less well for the other species. Analysis revealed that
S. hominis
was frequently misidentified due to the presence of a previously unknown subspecies. Based on the initial results, revised investigational Dried Overnight Gram-Positive Identification panels (CPID-2) were prepared and tested. The CPID-2 panels identified 85 to 95% of
S. epidermidis
strains, 76 to 86% of
S. hominis
strains, and 88 to 92% of
S. haemolyticus
strains with high probability (>85%) and, overall, represented a significant improvement over the other panels for identification of these staphylococcal species.
Use of Fluorescent-Antibody Staining of Cytocentrifuge-Prepared Smears in Combination with Cell Culture for Direct Detection of Respiratory Viruses
Authors: Doing Kirk M. , Jerkofsky Mary Ann , Dow Elaine G. , Jellison Jo Ann 
Published: December 2019

ABSTRACT
Over a 3-year period, 1,003 respiratory samples were collected and examined for selected respiratory viruses with cytocentrifuged prepared smears stained with fluorescently labeled antibodies (IFA) in conjunction with cell culture. IFA results were compared with results obtained by cell culture. Viruses were isolated or detected by direct means in 401 samples. Agreement between culture and IFA was 90%.
Comparison of Sample Preparation Methods for Detection of
Legionella pneumophila
in Culture-Positive Bronchoalveolar Lavage Fluids by PCR
Authors: Jaulhac B. , Reyrolle M. , Sodahlon Y. K. , Jarraud S. , Kubina M. , Monteil H. , Piémont Y. , Etienne J. 
Published: December 2019

ABSTRACT

A prospective study was conducted on 25
Legionella pneumophila
culture-positive and 98 culture-negative bronchoalveolar lavage fluid samples to compare two DNA preparation methods: a rapid modified Chelex-based protocol and a proteinase K method. PCR was found to be more sensitive with the Chelex-based method (
P
= 0.03). No difference was found concerning the inhibition rate.
Isolation and Characterization of Sorbitol-Fermenting Shiga Toxin (Verocytotoxin)-Producing
Escherichia coli
O157:Hßtrains in the Czech Republic
Authors: Bielaszewska Martina , Schmidt Herbert , Karmali Mohamed A. , Khakhria Rasik , Janda Jan , Bláhová Kvĕta , Karch Helge 
Published: December 2019

ABSTRACT

Two sorbitol-fermenting (SF) Shiga toxin-producing
Escherichia coli
(STEC) O157:H− strains were isolated from patients with hemolytic-uremic syndrome in the Czech Republic in 1995. Their phenotypic and genotypic characteristics and genomic DNA fingerprints were identical or closely related to those of SF STEC O157:H− strains isolated in Germany in 1988 to 1997. This indicates that the Czech isolates belong to the SF STEC O157 clone which is widespread in Germany. It is the first finding of the clone outside Germany.
Molecular Epidemiology of Reemergent
Vibrio cholerae
O139 Bengal in India
Authors: Mukhopadhyay Asish Kumar , Basu Arnab , Garg Pallavi , Bag Prasanta K. , Ghosh Amit , Bhattacharya S. K. , Takeda Yoshifumi , Nair G. Balakrish 
Published: December 2019

ABSTRACT

We report the prevalence of the O139 serogroup in Calcutta, India, after its reemergence in August 1996 and the spread of the reemerged clone to other parts of the country by using previously established molecular markers. Phenotypically, the reemerged
Vibrio cholerae
O139 displayed a difference compared to those that appeared in late 1992 and 1993 in that the current O139 strains are sensitive to co-trimoxazole. Ribotyping with the enzyme
Bgl
I produced two rRNA restriction patterns in the O139 strains isolated after August 1996, and these patterns were identical to those exhibited by strains of O139 isolated in 1992. Three clones of
V. cholerae
O139 are currently prevailing in the country, with strains exhibiting three bands after
Hin
dIII digestion and hybridization with a
ctxA
probe being dominant. The reemergence of
V. cholerae
O139 in Calcutta after a 32-month quiescent period reestablishes the O139 serogroup as an entity which is likely to play a crucial role in the temporal antigenic variations among the serogroups of
V. cholerae
causing cholera.
Fatal
Hormonema dematioides
Peritonitis in a Patient on Continuous Ambulatory Peritoneal Dialysis: Criteria for Organism Identification and Review of Other Known Fungal Etiologic Agents
Authors: Shin Jong Hee , Lee Sang Ku , Suh Soon Pal , Ryang Dong Wook , Kim Nam Ho , Rinaldi Michael G. , Sutton Deanna A. 
Published: December 2019

ABSTRACT

We report a fatal case a fungal peritonitis caused by the yeast-like dematiaceous mould
Hormonema dematioides
in a 45-year-old woman. The woman had a 13-year history of insulin-dependent diabetes mellitus and had been on continuous ambulatory peritoneal dialysis for chronic renal failure.
H. dematioides
was repeatedly isolated from the dialysate culture specimens collected on days 3, 9, 16, and 20 of her hospital stay. Preliminary culture reports on day 7 of the growth of a yeast-like fungus, a probable
Candida
species, prompted the administration of fluconazole (FLU). Intraperitoneal and intravenous FLU failed to eliminate the mould, and the patient expired on day 21 of her hospital stay. We use this case to present what appears to be the first report of fungal peritonitis due to
H. dematioides
, to provide laboratorians with criteria for differentiating this organism from the similar mould
Aureobasidium pullulans
and from various yeast genera, and to provide a review of known fungal taxa inciting peritonitis.
Streptococcus iniae
, a Human and Animal Pathogen: Specific Identification by the Chaperonin 60 Gene Identification Method
Authors: Goh Swee Han , Driedger David , Gillett Sandra , Low Donald E. , Hemmingsen Sean M. , Amos Mayben , Chan David , Lovgren Marguerite , Willey Barbara M. , Shaw Carol , Smith John A. 
Published: December 2019

ABSTRACT

It was recently reported that
Streptococcus iniae
, a bacterial pathogen of aquatic animals, can cause serious disease in humans. Using the chaperonin 60 (Cpn60) gene identification method with reverse checkerboard hybridization and chemiluminescent detection, we identified correctly each of 12
S. iniae
samples among 34 aerobic gram-positive isolates from animal and clinical human sources.
Molecular Epidemiology of Two Consecutive Outbreaks of Parainfluenza 3 in a Bone Marrow Transplant Unit
Authors: Zambon Maria , Bull Tim , Sadler Carol J. , Goldman John M. , Ward Katherine N. 
Published: December 2019

ABSTRACT
Two consecutive nosocomial outbreaks of parainfluenza 3, in which 5 of 15 infected patients died, occurred in an adult bone marrow transplant unit. Parainfluenza 3 strain variation was assessed by reverse transcription-PCR sequencing of part of the parainfluenza 3 F gene, including the noncoding region, directly from clinical samples. Sequence data from the outbreaks were compared with those from 15 other parainfluenza 3 isolates circulating concurrently in the community; altogether, 13 strains which fell into three lineages were identified. Four immunosuppressed patients shed virus persistently for between 1 and 4 months without change in sequence. The first outbreak lasted 4 months and involved three parainfluenza 3 strains, and one persistently infected patient was implicated as the source of infection for three others. The second outbreak lasted for 1 month but involved only one strain. These data indicate that introduction of community parainfluenza 3 strains to the bone marrow transplant unit was followed by person-to-person transmission within the unit rather than reintroduction of virus from the community.
Direct Detection of
eae
-Positive Bacteria in Human and Veterinary Colorectal Specimens by PCR
Authors: Hubbard A. L. , Harrison D. J. , Moyes C. , McOrist S. 
Published: December 2019

ABSTRACT

A PCR test based on the amplification of an
eae
-specific sequence was designed and evaluated for its ability to directly detect homologous sequences in enteropathogenic
Escherichia coli
and
Citrobacter
spp. (amplification of
eae
open reading frame, 178 bp) in sections of the intestines of humans and animals with colonic lesions. Positive PCR results were observed with
eae
-positive reference strains of
E. coli
and
Citrobacter rodentium
(
Citrobacter freundii
biotype 4280). Known
eae
-negative reference strains of
E. coli
and other laboratory strains of enteric bacteria were negative by the amplification test. The sensitivity of the PCR for detection of
eae
-positive
E. coli
and
C. rodentium
was between 1 and 2 CFU. To detect these sequences directly from sections of fixed colon from human and veterinary sources, PCR conditions were modified by the addition of 0.1 mM 8-methoxypsoralen to eliminate extraneous bacterial DNA from the PCR amplification cocktail without added template. Sections of colon from three pigs experimentally affected with colon lesions due to enteropathogenic (attaching and effacing)
E. coli
were PCR positive for bacterial
eae
genome. Sections from control animals were negative. Sections of colon from one of 18 biopsies from confirmed AIDS patients and from 22 of 35 colorectal cancer patients were PCR positive for bacterial
eae
genome. The PCR test was a simple and quick method of detecting bacterial
eae
genome in human and veterinary clinical specimens. This method may remove the need for initial culture and detection of the gene by DNA probing from potential associated lesions. The clear relationship of bacteria containing the
eae
gene with colonic lesions in the pigs and mice indicates that a similar relationship is possible for human patients having similar lesions.
Rapid and Specific Molecular Identification of Methicillin-Resistant
Staphylococcus aureus
in Endotracheal Aspirates from Mechanically Ventilated Patients
Authors: Vannuffel Pascal , Laterre Pierre-François , Bouyer Michele , Gigi Jacques , Vandercam Bernard , Reynaert Marc , Gala Jean-Luc 
Published: December 2019

ABSTRACT

Multiplex amplification of
femA
and
mecA
genetic determinants allowed an early and rapid identification of methicillin-resistant
Staphylococcus aureus
(MRSA) in endotracheal aspirates of mechanically ventilated patients.
femA
and/or
mecA
amplification and bacteriological results were concordant in 57 of 60 samples. In all three discrepant cases, complementary bacteriological tests confirmed the presence of MRSA first identified by molecular analysis. These results underline the value and rapidity of this molecular diagnosis for MRSA infection and control surveillance in intensive care units. Rapid MRSA detection is expected to have a significant clinical impact not only on patient outcome but also on the costs for isolation and treatment.
Prevalence of and Factors Associated with Visceral Leishmaniasis in Human Immunodeficiency Virus Type 1-Infected Patients in Southern Spain
Authors: Pineda Juan A. , Gallardo José A. , Macías Juan , Delgado Juan , Regordán Carmen , Morillas Francisco , Relimpio Federico , Martín-Sánchez Joaquina , Sánchez-Quijano Armando , Leal Manuel , Lissen Eduardo 
Published: December 2019

ABSTRACT

The actual prevalence of visceral leishmaniasis among human immunodeficiency type 1 (HIV-1)-infected patients in the Mediterranean basin remains unknown. There is also controversy about the risk factors for
Leishmania infantum
and HIV-1 coinfection. To appraise the prevalence of visceral leishmaniasis in patients infected with HIV-1 in southern Spain and to identify factors associated with this disease, 291 HIV-1 carriers underwent a bone marrow aspiration, regardless of their symptoms. Giemsa-stained samples were searched for
Leishmania
amastigotes. Thirty-two (11%) patients showed visceral leishmaniasis. Thirteen (41%) patients had subclinical cases of infection. Centers for Disease Control and Prevention (CDC) clinical category C was the factor most strongly associated with this disease (adjusted odds ratio [OR], 1.88 [95% confidence interval, 1.22 to 2.88]), but patients with subclinical cases of infection were found in all CDC categories. Female sex was negatively associated with visceral leishmaniasis (adjusted OR, 0.42 [95% confidence interval, 0.18 to 0.97]). Intravenous drug users showed a higher prevalence than the remaining patients (13.3 versus 4.9%;
P
= 0.04), but such an association was not independent. These results show that visceral leishmaniasis is a very prevalent disease among HIV-1-infected patients in southern Spain, with a high proportion of cases being subclinical. Like other opportunistic infections, subclinical visceral leishmaniasis can be found at any stage of HIV-1 infection, but symptomatic cases of infection appear mainly when a deep immunosuppression is present. There is also an association of this disease with male sex and intravenous drug use.
Evaluation of the AMPLICOR Cytomegalovirus Test with Specimens from Human Immunodeficiency Virus-Infected Subjects
Authors: Boivin Guy , Handfield Julie , Toma Emil , Murray Gilles , Lalonde Richard , Tevere Vincent J. , Sun Rita , Bergeron Michel G. 
Published: December 2019

ABSTRACT

The AMPLICOR cytomegalovirus (CMV) test, a new qualitative assay for the detection of CMV DNA in plasma, was compared to conventional methods and quantitative PCR (Q-PCR) assays by using leukocytes and plasma from 179 blood samples from subjects with AIDS. For the diagnosis of CMV disease, cell-based assays such as a Q-PCR with polymorphonuclear leukocytes (Q-PCR-PMNL) and a pp65 antigenemia assay had the highest sensitivities but suffered from a lack of specificity. The best agreement between the results of the Q-PCR-PMNL assay and those of the AMPLICOR test was found when a threshold diagnostic value of 690 copies per 10
5
cells was selected for the Q-PCR-PMNL assay. In that context, the AMPLICOR CMV test had a sensitivity of 96.4% and a specificity of 95.3% when results were compared to results of the cell-based PCR assay. This threshold was close to the one described as associated with the best sensitivity and specificity for the diagnosis of CMV disease in a recently published study (4). Blood samples that tested positive by the Q-PCR-PMNL assay but negative by the AMPLICOR CMV test were associated with viral loads (mean, 785 copies, median, 96 copies per 10
5
leukocytes) lower than the viral loads of blood samples that tested positive by both assays (mean, 21,452 copies; median, 9,784 copies per 10
5
leukocytes) (
P
= 0.003). The AMPLICOR CMV test gave positive results at least 48 days before the development of symptomatic CMV disease in a longitudinal analysis of a limited subset of patients (
n
= 6) from whom sequential specimens were available for testing. In conclusion, the AMPLICOR CMV test is a very convenient assay combining rapidity, simplicity, and the possibility of batch testing. A positive result by this test seems particularly important since this implies, in most instances, the presence or the imminence of CMV disease, although a negative test result does not rule out disease.
Microaerophilic Conditions Promote Growth of
Mycobacterium genavense
Authors: Realini L. , De Ridder K. , Palomino J.-C. , Hirschel B. , Portaels F. 
Published: December 2019

ABSTRACT

Our studies show that microaerophilic conditions promote the growth of
Mycobacterium genavense
in semisolid medium. The growth of
M. genavense
at 2.5 or 5% oxygen was superior to that obtained at 21% oxygen in BACTEC primary cultures (Middlebrook 7H12, pH 6.0, without additives). By using nondecontaminated specimens, it was possible to detect growth with very small inocula (25 bacilli/ml) of 12 different
M. genavense
strains (from nude mice) within 6 weeks of incubation under low oxygen tension; conversely, with 21% oxygen, no growth of 8 of 12 (66.7%)
M. genavense
strains was detected (growth index, <10). The same beneficial effect of 2.5 or 5% oxygen was observed in primary cultures of a decontaminated clinical specimen. Low oxygen tension (2.5 or 5%) is recommended for the primary isolation of
M. genavense
. Microaerophilic cultivation of other atypical mycobacteria, especially slow-growing (e.g.,
Mycobacterium avium
) and difficult-to-grow (e.g.,
Mycobacterium ulcerans
) species, is discussed.
Performance of Transcription-Mediated Amplification and Ligase Chain Reaction Assays for Detection of Chlamydial Infection in Urogenital Samples Obtained by Invasive and Noninvasive Methods
Authors: Stary Angelika , Schuh Elisabeth , Kerschbaumer Martina , Götz Birgit , Lee Helen 
Published: December 2019

ABSTRACT

Based on the amplification of chlamydia-specific rRNA sequences and the ligase chain reaction (LCR), the performance characteristics of the Gen-Probe
Chlamydia trachomatis
transcription-mediated amplification (TMA) assay were evaluated with endocervical, urine, and vulval specimens from women and urethral and urine specimens from men and were compared with those for cultures on endocervical, vulval, and urethral swabs. Of the 308 women and 240 men tested, 25 (8.1%) and 44 (18.3%), respectively, were shown to be infected. By using the infected individual as the expanded “gold standard” for calculations, the TMA assay and LCR gave similar performances for the sensitivity of male urethral (93.2%) and urine (88.6 and 86.4%) samples, while culture detected only half of the 44 infected men. In women, the sensitivities of the TMA assay for endocervical and vulval samples were 88 and 92%, respectively, compared to values of 92% for the LCR on both sample types and of 52 and 8%, respectively, for culture. By using first-void urine for chlamydial diagnosis in women, LCR detected 24 (96%) and TMA assay detected 19 (76%) infected individuals, showing a significantly lower sensitivity for urine in women (
P
= 0.0253). The results indicate a high overall agreement for both amplifying techniques for all examined specimen types, except for female urine. Furthermore, they confirm the previous observation that vulval swabs are an effective alternative noninvasive sample type for the detection of
C. trachomatis
infection in women by nucleic acid-based amplification technologies.
Clonal Expansion of
Staphylococcus epidermidis
Strains Causing Hickman Catheter-Related Infections in a Hemato-Oncologic Department
Authors: Nouwen Jan L. , van Belkum Alex , de Marie Siem , Sluijs Jacqueline , Wielenga Jenne J. , Kluytmans Jan A. J. W. , Verbrugh Henri A. 
Published: December 2019

ABSTRACT

The detailed analysis of 411 strains of coagulase-negative staphylococci (CoNS) obtained from 40 neutropenic hemato-oncologic patients (61 Hickman catheter episodes) on intensive chemotherapy is described. By random amplification of polymorphic DNA (RAPD) analysis, a total of 88 different genotypes were detected: 51 in air samples and 30 in skin cultures prior to insertion, 12 in blood cultures after insertion, and only 5 involved in catheter-related infections (CRI). Two RAPD genotypes of
Staphylococcus epidermidis
predominated, and their prevalence increased during patient hospitalization. At insertion, these clones constituted 11 of 86 (13%) CoNS isolated from air samples and 33 of 75 (44%) CoNS isolated from skin cultures. After insertion, their combined prevalence increased to 33 of 62 (53%) in catheters not associated with CRI and 139 of 188 (74%) in catheters associated with CRI (
P
= 0.0041). These two predominant
S. epidermidis
clones gave rise to a very high incidence of CRI (6.0 per 1,000 catheter days) and a very high catheter removal rate for CRI, 70%, despite prompt treatment with vancomycin. A likely source of
S. epidermidis
strains involved in CRI appeared to be the skin flora in 75% of cases. The validity of these observations was confirmed by pulsed-field gel electrophoresis (PFGE) of
Sma
I DNA macrorestriction fragments of blood culture CoNS isolates. Again, two predominant CoNS genotypes were found (combined prevalence, 60%). RAPD and PFGE yielded concordant results in 75% of cases. Retrospectively, the same two predominant CoNS clones were also found among blood culture CoNS isolates from the same hematology department in the period 1991 to 1993 (combined prevalence, 42%) but not in the period 1978 to 1982. These observations underscore the pathogenic potential of clonal CoNS types that have successfully and persistently colonized patients in this hemato-oncology department.
Molecular Procedure for Rapid Detection of
Burkholderia mallei
and
Burkholderia pseudomallei
Authors: Bauernfeind Adolf , Roller Carsten , Meyer Detlef , Jungwirth Renate , Schneider Ines 
Published: December 2019

ABSTRACT

A PCR procedure for the discrimination of
Burkholderia mallei
and
Burkholderia pseudomallei
was developed. It is based on the nucleotide difference T 2143 C (T versus C at position 2143) between
B. mallei
and
B. pseudomallei
detected in the 23S rDNA sequences. In comparison with conventional methods the procedure allows more rapid identification at reduced risk for infection of laboratory personnel.