bluuebunny/crossref_metadata_2025_split huggingface dataset:
ABC Medium, a New Chromogenic Agar for Selective Isolation of
Salmonella
spp
Authors: Perry John D. , Ford Michael , Taylor Jeffrey , Jones Amanda L. , Freeman Roger , Gould Frances K. 
Published: December 2019

ABSTRACT

We describe a new chromogenic agar medium, ABC medium (αβ-chromogenic medium), which includes two substrates, 3,4-cyclohexenoesculetin-β-
d
-galactoside and 5-bromo-4-chloro-3-indolyl-α-
d
-galactopyranoside, to facilitate the selective isolation of
Salmonella
spp. This medium exploits the fact that
Salmonella
spp. may be distinguished from other members of the family
Enterobacteriaceae
by the presence of α-galactosidase activity in the absence of β-galactosidase activity. A total of 1,022 strains of
Salmonella
spp. and 300 other gram-negative strains were inoculated onto this medium. Of these, 1,019 (99.7%) strains of
Salmonella
spp. produced a characteristic green colony, whereas only 1 strain (0.33%) of non-
Salmonella
produced a green colony. A total of 283 stool samples were cultured onto desoxycholate citrate (DC) agar and ABC medium by direct inoculation and after selective enrichment in selenite broth. Overall, the sensitivity and specificity were superior for ABC medium (100 and 90.5%, respectively) than for DC agar (88 and 26.9%, respectively). We conclude that ABC medium offers a high degree of specificity for the detection of
Salmonella
spp. in stool samples.
Comparison of Five PCR Methods for Detection of
Helicobacter pylori
DNA in Gastric Tissues
Authors: Lu Jang-Jih , Perng Cherng-Lih , Shyu Rong-Yaun , Chen Chi-Hsiang , Lou Qinyuan , Chong Sonny K. F. , Lee Chao-Hung 
Published: December 2019

ABSTRACT

Five different PCR methods for the detection of
Helicobacter pylori
were evaluated. The results of this study indicate that of the five PCR methods examined, the
ureC
(
glmM
) gene PCR is the most sensitive and specific for the detection of
H. pylori
in gastric biopsy specimens.
Streptococcus bovis
Clone Causing Two Episodes of Endocarditis 8 Years Apart
Authors: Mühlemann Kathrin , Graf Susanne , Täuber Martin G. 
Published: December 2019

ABSTRACT

A patient had endocarditis caused by
Streptococcus bovis
twice 8 years apart. According to pulsed-field gel electrophoresis (PFGE) the two isolates were identical. Seven unrelated blood isolates of
S. bovis
yielded unique PFGE patterns. Considering this heterogeneous population structure our findings demonstrate the long-term persistence of an
S. bovis
clone in a patient with recurrent endocarditis.
In Vitro Susceptibilities of
Candida dubliniensis
Isolates Tested against the New Triazole and Echinocandin Antifungal Agents
Authors: Pfaller M. A. , Messer S. A. , Gee S. , Joly S. , Pujol C. , Sullivan D. J. , Coleman D. C. , Soll D. R. 
Published: December 2019

ABSTRACT

Candida dubliniensis
is a newly recognized fungal pathogen causing mucosal disease in AIDS patients. Although preliminary studies indicate that most strains of
C. dubliniensis
are susceptible to established antifungal agents, fluconazole-resistant strains have been detected. Furthermore, fluconazole-resistant strains are easily derived in vitro, and these strains exhibit increased expression of multidrug resistance transporters, especially MDR1. Because of the potential for the development of resistant strains of
C. dubliniensis
, it is prudent to explore the in vitro activities of several of the newer triazole and echinocandin antifungals against isolates of
C. dubliniensis
. In this study we tested 71 isolates of
C. dubliniensis
against the triazoles BMS-207147, Sch 56592, and voriconazole and a representative of the echinocandin class of antifungal agents, MK-0991. We compared the activities of these agents with those of the established antifungal agents fluconazole, itraconazole, amphotericin B, and 5-fluorocytosine (5FC) by using National Committee for Clinical Laboratory Standards microdilution reference methods. Our findings indicate that the vast majority of clinical isolates of
C. dubliniensis
are highly susceptible to both new and established antifungal agents. Strains with decreased susceptibilities to fluconazole remained susceptible to the investigational agents as well as to amphotericin B and 5FC. The increased potencies of the new triazole and echinocandin antifungal agents may provide effective therapeutic options for the treatment of infections due to
C. dubliniensis.
Indirect Enzyme-Linked Immunosorbent Assay for Detection of Immunoglobulin G Reactive with a Recombinant Protein Expressed from the Gene Encoding the 116-Kilodalton Protein of
Mycoplasma pneumoniae
Authors: Duffy Michael F. , Whithear Kevin G. , Noormohammadi Amir H. , Markham Philip F. , Catton Michael , Leydon Jennie , Browning Glenn F. 
Published: December 2019

ABSTRACT

Serology remains the method of choice for laboratory diagnosis of
Mycoplasma pneumoniae
infection. Currently available serological tests employ complex cellular fractions of
M. pneumoniae
as antigen. To improve the specificity of
M. pneumoniae
diagnosis, a recombinant protein was assessed as a serodiagnostic reagent. A panel of recombinant proteins were expressed from a cloned
M. pneumoniae
gene that encodes a 116-kDa surface protein antigen. The recombinant proteins were assessed for reactivity with patient sera and the most antigenic was further assessed for its serodiagnostic potential by indirect enzyme-linked immunosorbent assay (ELISA). The ELISA based on the recombinant protein was equivalent in sensitivity to the commercial test (Serodia Myco II; Fujirebio Inc.) to which it was compared. Southern and Western blotting data suggested that the recombinant protein derived from the 116-kDa protein of
M. pneumoniae
could provide a species-specific diagnostic tool, although further assessment is required.
Rapid and Sensitive Detection of Immunoglobulin M (IgM) and IgG Antibodies against Canine Distemper Virus by a New Recombinant Nucleocapsid Protein-Based Enzyme-Linked Immunosorbent Assay
Authors: von Messling Veronika , Harder Timm C. , Moennig Volker , Rautenberg Peter , Nolte Ingo , Haas Ludwig 
Published: December 2019

ABSTRACT

Canine distemper morbillivirus (CDV) infection causes a frequently fatal systemic disease in a broad range of carnivore species, including domestic dogs. In CDV infection, classical serology provides data of diagnostic and prognostic values (kinetics of seroconversion) and is also used to predict the optimal vaccination age of pups. Routine CDV serology is still based on time- and cost-intensive virus neutralization assays (V-NA). Here, we describe a new capture-sandwich enzyme-linked immunosorbent assay (ELISA) that uses recombinant baculovirus-expressed nucleocapsid (N) protein of a recent CDV wild-type isolate (2544/Han95) for the detection of CDV-specific antibodies in canine sera. Recombinant antigen was produced with high efficacy in
Heliothis virescens
larvae. The capture-sandwich ELISA enabled a clear-cut qualitative evaluation of the CDV-specific immunoglobulin G (IgG) and IgM serostatuses of 196 and 35 dog sera, respectively. Inter-rater agreement analysis (κ = 0.988) indicated that the ELISA can be used unrestrictedly as a substitute for the V-NA for the qualitative determination of CDV-specific IgG serostatus. In an attempt to semiquantify N-specific antibodies, a one-step-dilution (alpha method) IgG-specific ELISA was implemented. Alpha values of ≥50% showed very good inter-rater agreement (κ = 0.968) with V-NA titers of ≥1/100 50% neutralizing dose (ND
50
) as measured against the central European CDV wild-type isolate 2544/Han95 in canine sera originating from northern Germany. An ND
50
titer of 1/100 is considered a threshold, and titers of ≥1/100 indicate a resilient, protective immunity. CDV N-specific antibodies of the IgM class were detected by the newly developed ELISA in 9 of 15 sera obtained from dogs with symptoms of acute distemper. In leucocytes of 5 of the 15 dogs (all of which were also IgM positive) CDV RNA was detected by reverse transcription (RT)-PCR. The recombinant capture-sandwich ELISA detecting N-specific antibodies of the IgG class provided superior sensitivity and specificity and thus represents a rapid and cost-effective alternative to classical CDV V-NA. By detection of specific IgM antibodies, the ELISA will be complementary to RT-PCR and V-NA in the diagnosis of acute distemper infections.
Characterization of a Culturable “
Gastrospirillum hominis
” (
Helicobacter heilmannii
) Strain Isolated from Human Gastric Mucosa
Authors: Andersen L. P. , Boye K. , Blom J. , Holck S. , Nørgaard A. , Elsborg L. 
Published: December 2019

ABSTRACT

Spiral organisms were isolated from an antral gastric mucosal biopsy specimen from a dyspeptic patient with gastritis. Only corkscrew-shaped organisms resembling “
Gastrospirillum hominis
” (“
Helicobacter heilmannii
”) but no
Helicobacter pylori
-like organisms were seen in histological sections.
H. pylori
was not cultured from specimens from this patient. On the basis of biochemical reactions, morphology, ultrastructure, and 16S DNA sequencing, the isolated “
G. hominis
” was shown to be a true
Helicobacter
sp. very similar to
Helicobacter felis
and the “
Gastrospirillum
” but was separate from
H. pylori
. “
G. hominis
” is a pleomorphic gram-negative cork-screw-shaped, motile rod with 3 to 8 coils and a wavelength of about 1 μm. In contrast to
H. pylori
, it has up to 14 sheathed flagellar uni- or bipolar fibrils but no periplasmic fibrils. “
G. hominis
” grows under microaerobic conditions at 36 and 41°C on 7% lysed, defibrinated horse blood agar plates within 3 to 7 days and can be subcultured under microaerobic but not under anaerobic conditions on media similar to those used for
H. pylori
and
H. felis
. The small translucent colonies were, in contrast to those of
H. felis
, indistinguishable from those of
H. pylori
. “
G. hominis
” is, like
H. pylori
and
H. felis
, motile, is oxidase, catalase, nitrite, nitrate, and urease positive, and produces alkaline phosphatase and arginine arylamidase. Like
H. pylori
and
H. felis
, it is sensitive to cephalothin (30-μg disc), resistant to nalidixic acid (30-μg disc), and sensitive to most other antibiotics. The 16S DNA sequence clusters “
G. hominis
” together with “
Gastrospirillum
,”
H. felis
,
Helicobacter bizzozeronii
,
Helicobacter salmonii, Helicobacter nemestrinae
,
Helicobacter acinonychis
, and
H. pylori
.
DNA Banding Pattern Polymorphism in Vancomycin-Resistant
Enterococcus faecium
and Criteria for Defining Strains
Authors: Morrison D. , Woodford N. , Barrett S. P. , Sisson P. , Cookson B. D. 
Published: December 2019

ABSTRACT

The degree of DNA banding pattern polymorphism exhibited by vancomycin-resistant
Enterococcus faecium
(VREM) strains isolated on a renal unit over an 11-month period was investigated. Thirty VREM strains from different patients were analyzed by pulsed-field gel electrophoresis (PFGE; with extended run and optimal pulse times), ribotyping, plasmid profile analysis, biotyping, pyrolysis mass spectrometry, and antibiogram analysis. PFGE resolved 17 banding patterns which formed four distinct clusters at the 82% similarity level. Intercluster band differences ranged from 14 to 31 bands. The strains in one cluster, which contained seven patterns that differed from each other by one to seven bands and from the common pattern by five bands, were confirmed to be a single strain by four of the five other typing methods. The strains in a second cluster with eight patterns, which differed from each other by 1 to 12 bands, contained two subclusters. This subdivision was supported by ribotyping and biotyping. However, it was unclear whether these subclusters represented distinct strains. In one strain, marked polymorphism (patterns that differed from each other by up to four bands) was observed in the ribotype pattern. This study demonstrates the high degree of DNA banding pattern polymorphism found for some strains of VREM and illustrates the complexity involved in defining such strains.
Allelic Diversity of the
Helicobacter pylori
Vacuolating Cytotoxin Gene in South Africa: Rarity of the
vacA
s1a Genotype and Natural Occurrence of an s2/m1 Allele
Authors: Letley D. P. , Lastovica A. , Louw J. A. , Hawkey C. J. , Atherton J. C. 
Published: December 2019

ABSTRACT

We describe the rarity of
Helicobacter pylori
strains of vacuolating cytotoxin type s1a (the type most commonly associated with peptic ulceration in the United States) among black and mixed-race South Africans. We also provide the first description of a naturally occurring strain with the
vacA
allelic structure s2/m1.
Comparison of the MB/BacT and BACTEC 460 TB Systems for Recovery of Mycobacteria from Various Clinical Specimens
Authors: Brunello Francesca , Favari Flavio , Fontana Roberta 
Published: December 2019

ABSTRACT

A total of 1,830 specimens (75.7% respiratory and 24.3% nonrespiratory) were cultured in parallel with the MB/BacT and BACTEC 460 TB systems and on Lowenstein-Jensen (LJ) medium. Mycobacteria were identified from 173 (6.5%) specimens. The most common species recovered were
Mycobacterium tuberculosis
complex (65.9%),
Mycobacterium avium
complex (22.5%), and
Mycobacterium chelonae
(9.2%). The recovery rates by individual systems were 96.5, 99.4, and 95.9% for MB/BacT, BACTEC 460 TB, and LJ medium, respectively, for all mycobacteria; the recovery rates were 99.1, 100, and 98.2%, respectively, for
M. tuberculosis
complex alone. The difference among the recovery rates for all mycobacteria and those for individual species was not significant. The BACTEC 460 TB system detected
M. tuberculosis
isolates more rapidly than the MB/BacT system (8 versus 11.8 days for smear-positive specimens [
P
< 0.01] and 18 versus 21 days for smear-negative specimens [
P
< 0.05]), whereas the MB/BacT system more rapidly detected the nontuberculous mycobacteria (17.1 versus 12.7 days [
P
< 0.01]). These results indicate that the nonradiometric MB/BacT system is a rapid, sensitive, and efficient method for the recovery of
M. tuberculosis
and nontuberculous mycobacteria from both pulmonary and extrapulmonary clinical specimens.
Extremely High Incidence of Macrolide and Trimethoprim-Sulfamethoxazole Resistance among Clinical Isolates of
Streptococcus pneumoniae
in Taiwan
Authors: Hsueh Po-Ren , Teng Lee-Jene , Lee Li-Na , Yang Pan-Chyr , Ho Shen-Wu , Luh Kwen-Tay 
Published: December 2019

ABSTRACT

From January 1996 to December 1997, 200 isolates of
Streptococcus pneumoniae
recovered from 200 patients treated at National Taiwan University Hospital were serotyped and their susceptibilities to 16 antimicrobial agents were determined by the agar dilution method. Sixty-one percent of the isolates were nonsusceptible to penicillin, exhibiting either intermediate resistance (28%) or high-level resistance (33%). About two-fifths of the isolates displayed intermediate or high-level resistance to cefotaxime, ceftriaxone, cefepime, imipenem, and meropenem. Extremely high proportions of the isolates were resistant to erythromycin (82%), clarithromycin (90%), and trimethoprim-sulfamethoxazole (TMP-SMZ) (87%). Among the isolates nonsusceptible to penicillin, 23.8% were resistant to imipenem; more than 60% displayed resistance to cefotaxime, ceftriaxone, cefepime, and carbapenems; 96.7% were resistant to erythromycin; and 100% were resistant to TMP-SMZ. All isolates were susceptible to rifampin and vancomycin. The MICs at which 50% and 90% of the isolates were inhibited were 0.12 and 1 μg/ml, respectively, for cefpirome, and 0.12 and 0.25 μg/ml, respectively, for moxifloxacin. Six serogroups or serotypes (23F, 19F, 6B, 14, 3, and 9) accounted for 77.5% of all isolates. Overall, 92.5% of the isolates were included in the serogroups or serotypes represented in the 23-valent pneumococcal vaccine. The incidence of macrolide and TMP-SMZ resistance for
S. pneumoniae
isolates in Taiwan in this study is among the highest in the world published to date.
Species Identification and Strain Differentiation of Dermatophyte Fungi by Analysis of Ribosomal-DNA Intergenic Spacer Regions
Authors: Jackson Colin J. , Barton Richard C. , Evans E. Glyn V. 
Published: December 2019

ABSTRACT

Restriction fragment length polymorphisms (RFLPs) identified in the ribosomal-DNA (rDNA) repeat were used for molecular strain differentiation of the dermatophyte fungus
Trichophyton rubrum
. The polymorphisms were detected by hybridization of
Eco
RI-digested
T. rubrum
genomic DNAs with a probe amplified from the small-subunit (18S) rDNA and adjacent internal transcribed spacer (ITS) regions. The rDNA RFLPs mapped to the nontranscribed spacer (NTS) region of the rDNA repeat and appeared similar to those caused by short repetitive sequences in the intergenic spacers of other fungi. Fourteen individual RFLP patterns (DNA types A to N) were recognized among 50 random clinical isolates of
T. rubrum
. A majority of strains (19 of 50 [38%]) were characterized by one RFLP pattern (DNA type A), and four types (DNA types A to D) accounted for 78% (39 of 50) of all strains. The remaining types (DNA types E to N) were represented by one or two isolates only. A rapid and simple method was also developed for molecular species identification of dermatophyte fungi. The contiguous ITS and 5.8S rDNA regions were amplified from 17 common dermatophyte species by using the universal primers ITS 1 and ITS 4. Digestion of the amplified ITS products with the restriction endonuclease
Mva
I produced unique and easily identifiable fragment patterns for a majority of species. However, some closely related taxon pairs, such as
T. rubrum-T. soudanense
and
T. quinkeanum-T. schoenlenii
could not be distinguished. We conclude that RFLP analysis of the NTS and ITS intergenic regions of the rDNA repeat is a valuable technique both for molecular strain differentiation of
T. rubrum
and for species identification of common dermatophyte fungi.
Mailed, Home-Obtained Urine Specimens: a Reliable Screening Approach for Detecting Asymptomatic
Chlamydia trachomatis
Infections
Authors: Morré Servaas A. , van Valkengoed Irene G. M. , de Jong Afke , Boeke A. Joan P. , van Eijk Jacques T. M. , Meijer Chris J. L. M. , van den Brule Adriaan J. C. 
Published: December 2019

ABSTRACT

The use of mailed, home-obtained urine specimens could facilitate screening programs for the detection of asymptomatic
Chlamydia trachomatis
infections. Since transport time could have an adverse effect on the sensitivity of
C. trachomatis
detection by PCR, the influence of DNA degradation on amplification was monitored over the course of 1 week. Therefore, urine specimens were aliquoted on the day of collection or arrival. Two groups of urine specimens were investigated. Group I contains first-void
C. trachomatis
-positive and -negative urine samples. DNA degradation was monitored in group I samples for 7 days at room temperature (RT) and at 4°C by amplifying different lengths of the human β-globin gene and the
C. trachomatis
plasmid target. DNA degradation was observed only for the larger human β-globin fragments at days 5 to 7 at RT. In contrast, at 4°C all targets could be amplified. Urine specimens were also frozen and thawed before aliquoting to mimic freezing during transport. This resulted in a lower sensitivity for the detection of
C. trachomatis
after thawing and 3 to 4 days at RT. In addition, mailed, home-obtained
C. trachomatis
-positive urine specimens (group II) were analyzed for 7 days after arrival by two commercially available
C. trachomatis
detection systems (PCR and ligase chain reaction [LCR]). The
C. trachomatis
plasmid target in mailed, home-obtained urine specimens could be amplified by both PCR and LCR after 1 week of storage and/or transport at RT. In conclusion, our findings indicate that mailed, home-obtained urine specimens are suitable for the sensitive detection of asymptomatic
C. trachomatis
infections by amplification methods, even if the transport time is up to 1 week at RT. These findings support the feasibility and validity of screening programs based on mailed, home-obtained urine specimens. Larger studies should be initiated to confirm our results.
Rapid and Sensitive Quantification of
Borrelia burgdorferi
-Infected Mouse Tissues by Continuous Fluorescent Monitoring of PCR
Authors: Morrison Tom B. , Ma Ying , Weis John H. , Weis Janis J. 
Published: December 2019

ABSTRACT

The quantity of
Borrelia burgdorferi
organisms in tissue samples is an important determinant for infection studies in the mouse model of Lyme disease. This report presents the development of a rapid and sensitive external-standard-based PCR assay for the absolute quantification of
B. burgdorferi
in mouse tissue samples. The assay uses a double-stranded DNA dye to continuously monitor product formation and in less than an hour was able to quantify samples ranging up to 6 log units in concentration. The PCR efficiencies of the sample and the standard were matched by using a standard composed of purified
B. burgdorferi
chromosome mixed with tissue-matched mouse genome lacking bacterial DNA. Normalization of
B. burgdorferi
quantities to the mouse
nidogen
gene allowed comparison of
B. burgdorferi
numbers in samples isolated from different tissues and strains. PCR analysis of the chromosomal gene
recA
in cultured
B. burgdorferi
was consistent with a single
recA
per bacterium. The parameters defined in this assay should be applicable to quantification of other organisms, even infectious agents for which no ready source of DNA standard is available. In summary, this report presents a rapid external-standard-based PCR method for the quantification of
B. burgdorferi
in mouse DNA samples.
Prevalence ofMycobacterium aviumin Slaughter Pigs in The Netherlands and Comparison of IS1245Restriction Fragment Length Polymorphism Patterns of Porcine and Human Isolates
Authors: Komijn Ruud E. , de Haas Petra E. W. , Schneider Margriet M. E. , Eger Tony , Nieuwenhuijs Jan H. M. , van den Hoek Remco J. , Bakker Douwe , van Zijderveld Fred G. , van Soolingen Dick 
Published: December 2019

ABSTRACTA significant increase in the incidence of caseous lesions in the lymph nodes of slaughter pigs prompted a large-scale investigation in five slaughterhouses in The Netherlands. In total, 158,763 pigs from 2,899 groups underwent gross examination. At least one pig with caseous lesions in the submaxillary and/or mesenteric lymph nodes was observed in each of 154 of the 2,899 groups examined (5%). In total, 856 pigs (0.5%) were affected. As many as five pigs in each of 141 of the 154 positive groups (91.5%) had lymph node lesions. Greater numbers of pigs with affected lymph nodes were found in 13 groups (8.5%). Four pigs had lesions in the kidneys, liver, or spleen. Acid-fast bacteria were detected by microscopic examination of 121 of 292 Ziehl-Neelsen-stained smears of caseous lesions (41%). In a follow-up study,Mycobacterium aviumcomplex (MAC) bacteria were isolated from 219 of 402 affected lymph nodes (54.2%). Ninety-one of the isolated strains were analyzed by restriction fragment length polymorphism (RFLP) typing with insertion sequence IS1245as a probe. All but 1 of these 91 strains contained IS1245DNA, indicating that pigs in The Netherlands carried almost exclusivelyM. aviumbacteria and no other bacteria of MAC. Only one pig isolate exhibited the bird-type RFLP pattern. MAC isolates from 191 human patients in The Netherlands in 1996 were also typed by RFLP analysis. Computer-assisted analysis showed that the RFLP patterns of 61% of the human isolates and 59% of the porcine isolates were at least 75% similar to the RFLP patterns of the other group of strains. This indicates that pigs may be an important vehicle forM. aviuminfections in humans or that pigs and humans share common sources of infection.