bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Coryneform Bacterial Isolates by Ribosomal DNA Sequence Analysis
Authors: Tang Yi-Wei , Von Graevenitz Alexander , Waddington Michael G. , Hopkins Marlene K. , Smith Douglas H. , Li Haijing , Kolbert Christopher P. , Montgomery Stacy O. , Persing David H. 
Published: December 2019

ABSTRACT

Identification of coryneform bacteria to the species level is important in certain circumstances for differentiating contamination and/or colonization from infection, which influences decisions regarding clinical intervention. However, methods currently used in clinical microbiology laboratories for the species identification of coryneform bacteria are often inadequate. We evaluated the MicroSeq 500 16S bacterial sequencing kit (Perkin-Elmer Biosystems, Foster City, Calif.), which is designed to sequence the first 527 bp of the 16S rRNA gene for bacterial identification, by using 52 coryneform gram-positive bacilli from clinical specimens isolated from January through June 1993 at the Mayo Clinic. Compared to conventional and supplemented phenotypic methods, MicroSeq provided concordant results for identification to the genus level for all isolates. At the species level, MicroSeq provided concordant results for 27 of 42 (64.3%)
Corynebacterium
isolates and 5 of 6 (83.3%)
Corynebacterium
-related isolates, respectively. Within the
Corynebacterium
genus, MicroSeq gave identical species-level identifications for the clinically significant
Corynebacterium diphtheriae
(4 of 4) and
Corynebacterium jeikeium
(8 of 8), but it identified only 50.0% (15 of 30) of other species (
P
< 0.01). Four isolates from the genera
Arthrobacter
,
Brevibacterium
, and
Microbacterium
, which could not be identified to the species level by conventional methods, were assigned a species-level identification by MicroSeq. The total elapsed time for running a MicroSeq identification was 15.5 to 18.5 h. These data demonstrate that the MicroSeq 500 16S bacterial sequencing kit provides a potentially powerful method for the definitive identification of clinical coryneform bacterium isolates.
Selective Isolation ofeae-Positive Strains of Shiga Toxin-ProducingEscherichia coli
Authors: Fukushima Hiroshi , Hoshina Ken , Gomyoda Manabu 
Published: December 2019

ABSTRACTCulture on cefixime, tellurite, and sorbitol-MacConkey agar after HCl treatment facilitated the growth of 410 (94%) of 436eae-positive Shiga toxin-producingEscherichia coli(STEC) strains and 17 (16%) of 107eae-negative STEC strains. This selectivity was closely related to acid resistance inE. coliand tellurite resistance ineae-positive STEC strains.
Pseudomembranous Colitis Caused by a Toxin A
−
B
+
Strain of
Clostridium difficile
Authors: Limaye Ajit P. , Turgeon David K. , Cookson Brad T. , Fritsche Thomas R. 
Published: December 2019

ABSTRACT

We report a case of severe pseudomembranous colitis due to a toxin A
−
B
+
strain of
Clostridium difficile
in an immunosuppressed patient and discuss the implications for diagnostic testing in suspected
C. difficile
-associated diarrhea.
Aerococcus urinae
in Urinary Tract Infections
Authors: Zhang Qing , Kwoh Christopher , Attorri Silvia , Clarridge Jill E. 
Published: December 2019

ABSTRACT

Aerococcus urinae
is a rarely reported pathogen, possibly due to difficulties in the identification of the organism.
A. urinae
is a gram-positive coccus that grows in pairs and clusters, produces alpha-hemolysis on blood agar, and is negative for catalase and pyrrolidonyl aminopeptidase. Some of these characteristics and its being absent from the databases of most commercial identification systems could allow
A. urinae
to be misidentified as a streptococcus, enterococcus, or staphylococcus. We report two cases of urinary tract infection (UTI) caused by
A. urinae
and characterize these isolates by morphology, biochemical testing, whole-cell fatty acid analysis, 16S rRNA gene sequencing, and antibiotic susceptibilities. Most patients infected with
A. urinae
are elderly males with predisposing conditions who present initially with UTI. Because
A. urinae
is resistant to sulfonamides, treatment could be inappropriate, with infections resulting in serious complications, including death. It is important for the clinician and the microbiologist to consider
A. urinae
a potential pathogen and proceed with thorough microbiological identification.
Distribution of Rotavirus VP4 Genotypes and VP7 Serotypes among Nonhospitalized and Hospitalized Patients with Gastroenteritis and Patients with Nosocomially Acquired Gastroenteritis in Austria
Authors: Frühwirth M. , Brösl S. , Ellemunter H. , Moll-Schüler I. , Rohwedder A. , Mutz I. 
Published: December 2019

ABSTRACT
To assess the potential benefits of a reassortant tetravalent rotavirus vaccine, we investigated stool specimens from children in three different groups by reverse transcription-PCR (RT-PCR) for rotavirus G and P types: (i) children not hospitalized with community-acquired rotavirus-acute gastroenteritis (RV-AGE), (ii) children hospitalized for RV-AGE, and (iii) children with nosocomially acquired RV-AGE. From a total of 553 samples investigated, 335 were positive by enzyme-linked immunosorbent assay, of which 294 (88%) were positive by RT-PCR. Among the RT-PCR-positive samples, the predominant types were G1P[8] (84%), followed by G4P[8] (9%) and G3P[8] (2%). No differences between the three groups were observed, suggesting that community vaccination will diminish the most cost-relevant cases of hospitalizations and nosocomial infections.
Helicobacter mesocricetorum
sp. nov., a Novel Helicobacter Isolated from the Feces of Syrian Hamsters
Authors: Simmons J. H. , Riley L. K. , Besch-Williford C. L. , Franklin C. L. 
Published: December 2019

ABSTRACT

A spiral-shaped bacterium with bipolar, single, nonsheathed flagella was isolated from the feces of Syrian hamsters. The bacterium grew as a thin spreading film at 37°C under microaerobic conditions, did not hydrolyze urea, was positive for catalase and alkaline phosphatase, reduced nitrate to nitrite, did not hydrolyze hippurate, and was sensitive to nalidixic acid but resistant to cephalothin. Sequence analysis of the 16S rRNA gene and biochemical and phenotypic criteria indicate that the novel bacterium is a helicobacter. The novel bacterium is most closely related to the recently described mouse enteric helicobacter,
Helicobacter rodentium
. This is the first urease-negative
Helicobacter
species with nonsheathed flagella isolated from feces of asymptomatic Syrian hamsters. We propose to name this novel helicobacter
Helicobacter mesocricetorum
. The type strain is MU 97-1514 (GenBank accession number
AF072471
).
Comparison of Agar Diffusion Methodologies for Antimicrobial Susceptibility Testing of
Pseudomonas aeruginosa
Isolates from Cystic Fibrosis Patients
Authors: Burns Jane L. , Saiman Lisa , Whittier Susan , Larone Davise , Krzewinski Jay , Liu Zhenling , Marshall Steven A. , Jones Ronald N. 
Published: December 2019

ABSTRACT

Pseudomonas aeruginosa
is the most common pathogen infecting the lungs of patients with cystic fibrosis (CF). Improved antimicrobial chemotherapy has significantly increased the life expectancy of these patients. However, accurate susceptibility testing of
P. aeruginosa
isolates from CF sputum may be difficult because the organisms are often mucoid and slow growing. This study of 597 CF isolates of
P. aeruginosa
examined the correlation of disk diffusion and Etest (AB BIODISK, Solna, Sweden) results with a reference broth microdilution method. The rates of interpretive errors for 12 commonly used antipseudomonal antimicrobials were determined. The disk diffusion method correlated well (zone diameter versus MIC) for all of the agents tested. However, for mucoid isolates, correlation coefficients (
r
values) for piperacillin, piperacillin-tazobactam, and meropenem were <0.80. The Etest correlation with reference broth microdilution results (MIC versus MIC) was acceptable for all of the agents tested, for both mucoid and nonmucoid isolates. Category interpretation errors were similar for the disk diffusion and Etest methods with 0.4 and 0.1%, respectively, very major errors (false susceptibility) and 1.1 and 2.2% major errors (false resistance). Overall, both agar diffusion methods appear to be broadly acceptable for routine clinical use in susceptibility testing of CF isolates of
P. aeruginosa
.
Standardization of Immunoglobulin M Capture Enzyme-Linked Immunosorbent Assays for Routine Diagnosis of Arboviral Infections
Authors: Martin Denise A. , Muth David A. , Brown Teresa , Johnson Alison J. , Karabatsos Nick , Roehrig John T. 
Published: December 2019

ABSTRACTImmunoglobulin M antibody-capture enzyme-linked immunosorbent assay (MAC-ELISA) is a rapid and versatile diagnostic method that readily permits the combination of multiple assays. Test consolidation is especially important for arthropod-borne viruses (arboviruses) which belong to at least three virus families: theTogaviridae,Flaviviridae, andBunyaviridae. Using prototype viruses from each of these families and a panel of well-characterized human sera, we have evaluated and standardized a combined MAC-ELISA capable of identifying virus infections caused by members of each virus family. Furthermore, by grouping antigens geographically and utilizing known serological cross-reactivities, we have reduced the number of antigens necessary for testing, while maintaining adequate detection sensitivity. We have determined that a 1:400 serum dilution is most appropriate for screening antiviral antibody, using a positive-to-negative ratio of ≥2.0 as a positive cutoff value. With a blind-coded human serum panel, this combined MAC-ELISA was shown to have test sensitivity and specificity that correlated well with those of other serological techniques.
Distinguishing Species of the
Burkholderia cepacia
Complex and
Burkholderia gladioli
by Automated Ribotyping
Authors: Brisse Sylvain , Verduin Cees M. , Milatovic Dana , Fluit Ad , Verhoef Jan , Laevens Severine , Vandamme Peter , Tümmler Burkhard , Verbrugh Henri A. , van Belkum Alex 
Published: December 2019

ABSTRACT

Several species belonging to the genus
Burkholderia
are clinically relevant, opportunistic pathogens that inhabit major environmental reservoirs. Consequently, the availability of means for adequate identification and epidemiological characterization of individual environmental or clinical isolates is mandatory. In the present communication we describe the use of the Riboprinter microbial characterization system (Qualicon, Warwick, United Kingdom) for automated ribotyping of 104 strains of
Burkholderia
species from diverse sources, including several publicly accessible collections. The main outcome of this analysis was that all strains were typeable and that strains of
Burkholderia gladioli
and of each species of the
B. cepacia
complex, including
B. multivorans
,
B. stabilis
, and
B. vietnamiensis
, were effectively discriminated. Furthermore, different ribotypes were discerned within each species. Ribotyping results were in general agreement with strain classification based on restriction fragment analysis of 16S ribosomal amplicons, but the resolution of ribotyping was much higher. This enabled automated molecular typing below the species level. Cluster analysis of the patterns obtained by ribotyping (riboprints) showed that within
B. gladioli
,
B. multivorans
, and
B. cepacia
genomovar VI, the different riboprints identified always clustered together. Riboprints of
B. cepacia
genomovars I and III,
B. stabilis
, and
B. vietnamiensis
did not show distinct clustering but rather exhibited the formation of loose assemblages within which several smaller, genomovar-specific clusters were delineated. Therefore, ribotyping proved useful for genomovar identification. Analysis of serial isolates from individual patients demonstrated that infection with a single ribotype had occurred, despite minor genetic differences that were detected by pulsed-field gel electrophoresis of DNA macrorestriction fragments. The automated approach allows very rapid and reliable identification and epidemiological characterization of strains and generates an easily manageable database suited for expansion with information on additional bacterial isolates.
Distribution and Molecular Characterization of
Porphyromonas gingivalis
Carrying a New Type of
fimA
Gene
Authors: Nakagawa Ichiro , Amano Atsuo , Kimura Richard K. , Nakamura Takayuki , Kawabata Shigetada , Hamada Shigeyuki 
Published: December 2019

ABSTRACT

Fimbriae of
Porphyromonas gingivalis
are filamentous appendages on the cell surface and are thought to be one of the virulence factors. The
fimA
gene encoding the subunit protein of fimbriae, fimbrillin (FimA), was classified into four typeable variants (types I to IV). We previously examined the distribution of
P. gingivalis
in terms of
fimA
genotypes in periodontitis patients using a
fimA
type-specific PCR assay. However, some patients harbored
P. gingivalis
with untypeable
fimA
. In this study, we have cloned a new type (type V) of
fimA
from dental plaque samples.
P. gingivalis
with type V
fimA
was isolated from dental plaque of a periodontitis patient, and the isolate was named HNA-99. The deduced amino acid sequences were compared with those of type I
P. gingivalis
ATCC 33277, type II strain HW24D1, type III strain 6/26, and type IV strain HG564, and the homologies were found to be 45, 44, 43, and 55%, respectively. Southern blot analysis showed that the clinical isolate HNA-99 possessed
P. gingivalis
-specific genes
sod
and
kgp
. However, in terms of serological specificities, type V FimA showed a difference from other types of FimA. In addition, type V
P. gingivalis
bacteria were detected in 16.4% (12 of 73) of the
P. gingivalis
-positive patients with periodontitis by PCR assay using specific primers. Thus, a new type of
fimA
gene is now established, and the
fimA
genotyping could be useful in determining the disease-associated genotypes of
P. gingivalis
involved in the development of adult periodontitis.
Evaluation of the LiPA MYCOBACTERIA Assay for Identification of Mycobacterial Species from BACTEC 12B Bottles
Authors: Miller Nancimae , Infante Susanna , Cleary Tim 
Published: December 2019

ABSTRACT

The LiPA MYCOBACTERIA (Innogenetics NV, Ghent, Belgium) assay was used to identify mycobacterial isolates using culture fluid from positive BACTEC 12B bottles. The LiPA method involves reverse hybridization of a biotinylated mycobacterial PCR fragment, a 16 to 23S rRNA spacer region, to oligonucleotide probes arranged in lines on a membrane strip, with detection via biotin-streptavidin coupling by a colorimetric system. This system identifies
Mycobacterium
species and differentiates
M. tuberculosis
complex,
M. avium-M. intracellulare
complex, and the following mycobacterial species:
M. avium
,
M. intracellulare
,
M. kansasii
,
M. chelonae
group,
M. gordonae
,
M. xenopi
, and
M. scrofulaceum
. The mycobacteria were identified in the laboratory by a series of tests, including the Roche AMPLICOR
Mycobacterium tuberculosis
(MTB) test, the Gen-Probe ACCUPROBE, and a PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 65-kDa heat shock protein gene. The LiPA MYCOBACTERIA assay detected 60 mycobacterium isolates from 59 patients. There was complete agreement between LiPA and the laboratory identification tests for 26
M. tuberculosis
complex, 9
M. avium
, 3
M. intracellulare
complex, 3
M. kansasii
, 4
M. gordonae
, and 5
M. chelonae
group (all were
M. abscessus
) isolates. Three patient samples were LiPA positive for
M. avium-M. intracellulare
complex, and all were identified as
M. intracellulare
by the PCR-RFLP analysis. Seven additional mycobacterial species were LiPA positive for
Mycobacterium
spp. (six were
M. fortuitum
, and one was
M. szulgai
). The LiPA MYCOBACTERIA assay was easy to perform, and the interpretation of the positive bands was clear-cut. Following PCR amplification and gel electrophoresis, the LiPA assay was completed within 3 h.
Evaluation of Commercially Available Preservatives for Laboratory Detection of Helminths and Protozoa in Human Fecal Specimens
Authors: Pietrzak-Johnston S. M. , Bishop H. , Wahlquist S. , Moura H. , Da Silva N. De Oliveira , Da Silva S. Pereira , Nguyen-Dinh P. 
Published: December 2019

ABSTRACT

Formalin and mercuric chloride-based low-viscosity polyvinyl alcohol (LV-PVA) are widely used by most diagnostic parasitology laboratories for preservation of helminth eggs and protozoan cysts and trophozoites in fecal specimens. Concerns about the toxicity of formalin and the difficulty of disposal of LV-PVA are powerful incentives to use alternate preservatives. Such alternatives have been marketed by several companies and are often presented as one-vial, non-mercuric chloride fixatives that aim at performing the same role as formalin and PVA combined. We compared five, one-vial commercial preservatives, two from Meridian Diagnostics, Inc. (Ecofix and sodium acetate-acetic acid-formalin), and one each from Scientific Device Laboratories, Inc. (Parasafe), Alpha Tec Systems, Inc. (Proto-fix), and Streck Laboratories, Inc. (STF), with 10% formalin and LV-PVA. Fecal specimens obtained from patients in a Brazilian hospital were aliquoted within 12 h of collection into the seven preservatives mentioned above and were processed after 1 month at the Centers for Disease Control and Prevention. Direct and concentrated permanent smears as well as concentrates for 20 positive specimens (a total of 259 processed samples) were prepared, stained according to the manufacturers' instructions, examined, and graded. Positive specimens contained one or more parasites with stages consisting of eggs, larvae, cysts, and a few trophozoites of
Giardia intestinalis
. Criteria for assessment of the preservatives included the quality of the diagnostic characteristics of helminth eggs, protozoan cysts, and trophozoites, ease of use, and cost. Acceptable alternatives to formalin for wet preparations were found. Ecofix was found to be comparable to the traditional “gold standard” LV-PVA for the visualization of protozoa in permanent stained smears. This study suggests that more acceptable alternatives to the traditional formalin and LV-PVA exist.
Macrorestriction Fragment Profiles Reveal Genetic Variation of
Cowdria ruminantium
Isolates
Authors: de Villiers E. P. , Brayton K. A. , Zweygarth E. , Allsopp B. A. 
Published: December 2019

ABSTRACT

Macrorestriction profile analysis by pulsed-field gel electrophoresis (PFGE) was used to distinguish between seven isolates of
Cowdria ruminantium
from geographically different areas. Characteristic profiles were generated for each isolate by using the restriction endonucleases
Ksp
I,
Sal
I, and
Sma
I with chromosomal sizes ranging between 1,546 and 1,692 kb. Statistical analysis of the macrorestriction profiles indicated that all the isolates were distinct from each other; these data contribute to a better understanding of the epidemiology of this pathogen and may be exploited for the identification of genotype-specific DNA probes.
Evaluation of Quantitative PCR and Branched-Chain DNA Assay for Detection of Hepatitis B Virus DNA in Sera from Hepatocellular Carcinoma and Liver Transplant Patients
Authors: Chen Tao , Luk John M. , Cheung Siu-Tim , Yu Wan-Ching , Fan Sheung-Tat 
Published: December 2019

ABSTRACT
This study evaluated the applicability of quantitative PCR (Q-PCR) and branched-chain DNA assays for detection of hepatitis B virus (HBV) DNA in sera. For 42 samples, the detection rates were 81 and 41%, respectively, with a correlation coefficient of 0.633. The Q-PCR is useful for early monitoring of HBV load in high-risk patients.
Comparison of PCR-Ribotyping, Arbitrarily Primed PCR, and Pulsed-Field Gel Electrophoresis for Typing
Clostridium difficile
Authors: Bidet Philippe , Lalande Valérie , Salauze Béatrice , Burghoffer Béatrice , Avesani Véronique , Delmée Michel , Rossier Anne , Barbut Frédéric , Petit Jean-Claude 
Published: December 2019

ABSTRACT

Clostridium difficile
is now recognized as the major agent responsible for nosocomial diarrhea in adults. Among the genotyping methods available, arbitrarily primed PCR (AP-PCR), PCR-ribotyping, and pulsed-field gel electrophoresis (PFGE) have been widely used for investigating outbreaks of
C. difficile
infections. However, the comparative typing ability, reproducibility, discriminatory power, and efficiency of these methods have not been fully investigated. We compared the results of three methods—AP-PCR with three different primers (AP3, AP4, and AP5), PCR-ribotyping, and PFGE (with
Sma
I endonuclease)—to differentiate 99 strains of
C. difficile
that had been previously serogrouped. Typing abilities were 100% for PCR-ribotyping and AP-PCR with AP3 and 90% for PFGE, due to early DNA degradation in strains from serogroup G. Reproducibilities were 100% for PCR-ribotyping and PFGE but only 88% for AP-PCR with AP3, 67% for AP-PCR with AP4, and 33% for AP-PCR with AP5. Discriminatory power for unrelated strains was >0.95 for all the methods but was lower for PCR-ribotyping among serogroups D and C. PCR-based methods were easier and quicker to perform, but their fingerprints were more difficult to interpret than those of PFGE. We conclude that PCR-ribotyping offers the best combination of advantages as an initial typing tool for
C. difficile
.
Performance of Phenotypic and Genotypic Methods To Determine the Clinical Relevance of Serial Blood Isolates of
Staphylococcus epidermidis
in Patients with Septicemia
Authors: Sloos J. H. , Dijkshoorn L. , Vogel L. , van Boven C. P. A. 
Published: December 2019

ABSTRACT

Five typing methods, including biotyping (API ID32; BioMérieux, Marcy l'Etoile, France), quantitative antibiogram typing based on actual zone sizes, plasmid typing, randomly amplified polymorphic DNA (RAPD) analysis (with primer M13 and primer set ERIC-2–1026), and pulsed-field gel electrophoresis (PFGE), were compared with a previously performed method of DNA fingerprinting by AFLP (amplified fragment length polymorphism analysis) for their performance in the typing of blood isolates of
Staphylococcus epidermidis
. Sixteen epidemiologically unrelated strains and 11 sets of four blood culture isolates from 11 patients with septicemia were used. The stabilities and reproducibilities of the patterns, the discriminatory capacities of the methods, and the ability to apply the methods to blood culture isolates were used as performance criteria. All strains tested were typeable by each method, and the patterns were stable and reproducible. The numbers of different types within the collection of 16 epidemiologically different isolates were 5 by biotyping, 14 by antibiogram typing, 4 by plasmid typing, 9 by the RAPD assay (combination of results with primer M13 and primer set ERIC-2–1026), and 16 by PFGE. Within the 11 sets of four blood culture isolates the types found by quantitative antibiogram typing, plasmid typing, and PFGE were unique for each set, whereas by biotyping and RAPD analysis some types were observed in more than one set. The results of biotyping did not correspond with the results of the other methods or the results of AFLP. For 6 of the 11 sets, the results of all methods except those of biotyping corresponded completely. Quantitative antibiogram typing, PFGE, and AFLP proved to be the most accurate of the six typing methods tested.