bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluorescent Amplified-Fragment Length Polymorphism Genotyping of
Salmonella enterica
subsp.
enterica
Serovars and Comparison with Pulsed-Field Gel Electrophoresis Typing
Authors: Lindstedt Bjørn-Arne , Heir Even , Vardund Traute , Kapperud Georg 
Published: December 2019

ABSTRACT

We have performed the fluorescently labeled amplified-fragment length polymorphism (FAFLP) method on 97 strains of the food-borne pathogen
Salmonella enterica
subsp.
enterica
comprising seven different serovars using the restriction enzymes
Eco
RI and
Mse
I. From the total FAFLP fingerprinted strains, 81 were compared with pulsed-field gel electrophoresis (PFGE) typing of the same strains. The FAFLP method showed a discriminatory power equal to that of PFGE. We report a fast, robust, and high-resolution adaptation of the AFLP assay for fingerprinting
S. enterica
subsp.
enterica
serovars with capillary electrophoresis that can be scaled to high throughput on automated analysis instruments.
Molecular Phylogenetic Evidence for Noninvasive Zoonotic Transmission ofStaphylococcus intermediusfrom a Canine Pet to a Human
Authors: Tanner Michael A. , Everett Christine L. , Youvan Douglas C. 
Published: December 2019

ABSTRACTrRNA-based molecular phylogenetic techniques were used to identify the bacterial species present in the ear fluid from a female patient with otitis externa. We report the identification ofStaphylococcus intermediusfrom the patient and a possible route of transmission. Analysis of 16S ribosomal DNA restriction fragment length polymorphisms indicated that the dominant species present wasS. intermedius. A pet dog owned by the patient also was tested and found to harborS. intermedius. In humans, the disease is rare and considered a zoonosis. Previously,S. intermediushas been associated with dog bite wounds, catheter-related injuries, and surgery. This study represents the first reported case of a noninvasive infection withS. intermedius.
Characterization of a Recurrent Clonal Type of
Escherichia coli
O157:H7 Causing Major Outbreaks of Infection in Scotland
Authors: Allison Lesley J. , Carter Philip E. , Thomson-Carter Fiona M. 
Published: December 2019

ABSTRACT

A particular recurrent clonal type of
Escherichia coli
O157 has been isolated from multiple clinical, veterinary, food, and environmental sources throughout Scotland since 1989. Significant genotypic variation was detected among isolates from distinct outbreaks, with the presence or absence of single fragments being sufficient to delineate outbreak groups within the clonal type.
Molecular Characterization of Multidrug-Resistant
Streptococcus pneumoniae
Isolates in Korea
Authors: Song Jae-Hoon , Yang Ji-won , Jin Joung Hwa , Kim Shin Woo , Kim Choon Kwan , Lee Hyuck , Peck Kyong Ran , Kim Sungmin , Lee Nam Yong , Jacobs Michael R. , Appelbaum Peter C. ,   The Asian Network for Surveillance of Resistant Pathogens (ANSORP) Study Group
Published: December 2019

ABSTRACT
Pulsed-field gel electrophoresis, ribotyping, and fingerprinting analysis of 22 invasive isolates of multidrug-resistant (MDR) pneumococci from Korea showed that 59 to 82% were genetically related. DNA sequencing of the PBP 2B gene showed relatively uniform alterations in nucleotides (5.4 to 7.8%) and amino acids (3.0 to 4.3%), while Asn-276→Lys, Arg-285→Cys and Ser-305→Phe substitutions were unique to Korean MDR strains, suggesting the spread of a few epidemic clones of resistant pneumococci within Korea.
PCR Assay for Species-Specific Identification of
Bacteroides thetaiotaomicron
Authors: Teng Lee-Jene , Hsueh Po-Ren , Tsai Jui-Chang , Chiang Feng-Lin , Chen Ching-Yi , Ho Shen-Wu , Luh Kwen-Tay 
Published: December 2019

ABSTRACT

Bacteroides thetaiotaomicron
is the second most frequently encountered species of the anaerobes isolated from clinical specimens. We developed a PCR-based assay for the rapid identification of
B. thetaiotaomicron
. Specific primers were based on shared amplicons of about 1.2 kb generated from
B. thetaiotaomicron
by randomly amplified polymorphic DNA. This 1.2-kb fragment was sequenced and then used to design a set of PCR amplification primers. This PCR generated an amplification product of 721 bp, which was unique to all 65 isolates of
B. thetaiotaomicron
tested. There was no amplification with isolates of other bacterial species. Restriction enzyme digestion of the amplification product and dot blot hybridization further verified the specificity of the assay. These results suggest that this PCR assay targets a nucleotide sequence that is strongly conserved in
B. thetaiotaomicron
. This simple and rapid PCR assay provides a rapid and accurate method for identification of
B. thetaiotaomicron
and shows promise for the detection of
B. thetaiotaomicron
in clinical samples.
Evaluation of the PASCO Strep Plus Broth Microdilution Antimicrobial Susceptibility Panels for Testing
Streptococcus pneumoniae
and Other Streptococcal Species
Authors: Mohammed M. Jasmine , Tenover Fred C. 
Published: December 2019

ABSTRACT

Antimicrobial resistance continues to increase worldwide among isolates of
Streptococcus pneumoniae
and other species of streptococci. Increasing rates of penicillin resistance, particularly in viridans group streptococci, and resistance to multiple classes of antimicrobial agents, including β-lactams, macrolides, and fluoroquinolones, in pneumococci have increased the importance of having accurate antimicrobial susceptibility testing results for guiding therapy. One commercial method of assessing resistance in streptococci is the PASCO Strep Plus panel. This broth microdilution-based method has recently been expanded to include a variety of newer antimicrobial agents. Therefore, we compared the results of the new PASCO Strep Plus panels for 26 antimicrobial agents against the results generated using the National Committee for Clinical Laboratory Standards (NCCLS) broth microdilution reference method for 75 pneumococci and 68 other streptococcal isolates. Only 4 (0.2%) very major errors (all with pneumococci and each with a different antimicrobial agent) were observed. There were 5 (0.3%) major errors observed with pneumococci (each with a different antimicrobial agent), but only 1 major error with nonpneumococcal streptococci. All of the very major and major errors resolved on retesting. Of the 65 (3.9%) and 17 (1.6%) minor errors observed with pneumococci and other streptococci, respectively, all were within 1 dilution of the broth microdilution reference MIC result. Thus, the PASCO Strep Plus panel has comparable accuracy to the NCCLS broth microdilution reference method.
Use of Clindamycin Disks To Detect Macrolide Resistance Mediated by
ermB
and
mefE
in
Streptococcus pneumoniae
Isolates from Adults and Children
Authors: Waites Ken , Johnson Crystal , Gray Barry , Edwards Kathryn , Crain Marilyn , Benjamin William 
Published: December 2019

ABSTRACT

We studied 198 macrolide-resistant
S. pneumoniae
isolates obtained from adults and children to evaluate whether 2-μg clindamycin disks can distinguish between isolates manifesting
ermB
- versus
mefE
-mediated resistance to clarithromycin and to determine the relative frequency with which each resistance mechanism occurred in these populations. The
mefE
gene was predominant among 109 isolates from children, occurring in 73.4% versus 50.6% of 89 isolates from adults. Three isolates (1.5%) did not amplify either gene. Among 125
mefE
+
isolates, the MIC of clarithromycin at which 90% of the isolates tested were inhibited, determined by Etest, was 32 μg/ml versus >256 μg/ml in 70
ermB
+
isolates. All
ermB
+
isolates were highly resistant to clindamycin (MICs >256 μg/ml), whereas all
mefE
+
isolates were susceptible to clindamycin using the 2-μg disk. Testing
S. pneumoniae
from the respiratory tract for susceptibility to clindamycin by agar disk diffusion is an easy and inexpensive method to estimate the frequency of resistance mediated by
ermB
in specific patient populations. Macrolide resistance mediated by
ermB
is usually of greater magnitude than that due to
mefE
. Clinical studies are needed to determine the significance of high- versus low-level macrolide resistance in
S. pneumoniae
.
Distribution of Genes Encoding Putative Transmissibility Factors among Epidemic and Nonepidemic Strains of
Burkholderia cepacia
from Cystic Fibrosis Patients in the United Kingdom
Authors: Clode Fiona E. , Kaufmann Mary E. , Malnick Henry , Pitt Tyrone L. 
Published: December 2019

ABSTRACT

In the last 15 years,
Burkholderia cepacia
has emerged as a significant pathogen in cystic fibrosis (CF) patients, mainly due to the severity of infection observed in a subset of patients and the fear of transmission of the organism to noncolonized patients. Although patients who deteriorate rapidly cannot be predicted by microbiological characteristics, three genetic markers have been described for strains that spread between patients. These are the
cblA
gene, encoding giant cable pili; a hybrid of two insertion sequences, IS
1356
and IS
402
; and a 1.4-kb open reading frame known as the
B. cepacia
epidemic strain marker (BCESM). The latter two are of unknown function. An epidemic strain lineage was previously identified among CF patients in the United Kingdom that apparently had spread from North America and that was characterized by a specific random amplified polymorphic DNA (RAPD) pattern. We searched for the described genetic markers using specific PCR assays with 117 patient isolates of
B. cepacia
from 40 United Kingdom hospitals. Isolates were grouped according to genomovar and epidemic strain lineage RAPD pattern with a 10-base primer, P272. A total of 41 isolates from patients in 12 hospitals were classified as the epidemic strain, and 40 of these were distributed in genomovars IIIa (11 isolates), IIIb (1 isolate), and IIIc (28 isolates). All isolates of the epidemic strain were positive for the
cblA
gene and BCESM, but two lacked the insertion sequence hybrid. None of the 76 sporadic isolates contained
cblA
or the insertion sequence hybrid, but 11 of them were positive for BCESM. Nonepidemic isolates were distributed among genomovars I or IV (9), II (49), IIIa (11), IIIb (3), and IIIc (4). There were three clusters of cross-infection (one involving two patients and two involving three patients) with isolates of genomovar II. We conclude that in the United Kingdom, a single clonal lineage has spread between and within some hospitals providing care for CF patients. The presence of the
cblA
gene is the most specific marker for the epidemic strain. We recommend that all isolates of
B. cepacia
from CF patients should be screened by PCR to influence segregation and infection control strategies.
Occurrence and Detection of AmpC Beta-Lactamases among
Escherichia coli
,
Klebsiella pneumoniae
, and
Proteus mirabilis
Isolates at a Veterans Medical Center
Authors: Coudron Philip E. , Moland Ellen S. , Thomson Kenneth S. 
Published: December 2019

ABSTRACT

AmpC beta-lactamases are cephalosporinases that confer resistance to a wide variety of β-lactam drugs and that may thereby create serious therapeutic problems. Although reported with increasing frequency, the true rate of occurrence of AmpC beta-lactamases in
Escherichia coli
,
Klebsiella pneumoniae
, and
Proteus mirabilis
remains unknown. We tested a total of 1,286 consecutive, nonrepeat isolates of these three species and found that, overall, 45 (3.5%) yielded a cefoxitin zone diameter less than 18 mm (screen positive) and that 16 (1.2%) demonstrated AmpC bands by isoelectric focusing. Based on the species, of 683
E. coli
, 371
K. pneumoniae
, and 232
P. mirabilis
isolates tested, 13 (1.9%), 28 (7.6%), and 4 (1.7%), respectively, demonstrated decreased zone diameters and 11 (1.6%), 4 (1.1%), and 1 (0.4%), respectively, demonstrated AmpC bands. Cefoxitin resistance was transferred for all but 8 (
E. coli
) of the 16 AmpC producers. We also describe a three-dimensional extract test, which was used to detect phenotypically isolates that harbor AmpC beta-lactamase. Of the 45 cefoxitin-resistant isolates, the three-dimensional extract test accurately identified all 16 AmpC producers and 28 of 29 (97%) isolates as non-AmpC producers. Interestingly, most (86%) isolates in the latter group were
K. pneumoniae
isolates. These data confirm that, at our institution,
E. coli
,
K. pneumoniae
, and
P. mirabilis
harbor plasmid-mediated AmpC enzymes.
Human Cytomegalovirus Immediate-Early mRNA Detection by Nucleic Acid Sequence-Based Amplification as a New Parameter for Preemptive Therapy in Bone Marrow Transplant Recipients
Authors: Gerna Giuseppe , Baldanti Fausto , Lilleri Daniele , Parea Maurizio , Alessandrino Emilio , Pagani Ambrogio , Locatelli Franco , Middeldorp Jaap , Revello M. Grazia 
Published: December 2019

ABSTRACT
Human cytomegalovirus (HCMV) infection was monitored retrospectively by qualitative determination of immediate-early (IE) mRNA by nucleic acid sequence-based amplification (NASBA) in a series of 51 bone marrow transplant (BMT) recipients. The qualitative results for IE mRNA obtained by NASBA were compared with those obtained by prospective quantitation of HCMV viremia and antigenemia and retrospective quantitation of DNA in blood (DNAemia) by PCR as well as by qualitative determination of late pp67 mRNA by NASBA. On the whole, of the 39 HCMV-positive patients (all asymptomatic), HCMV was detected in 14 (35.9%) by quantitation of viremia, 15 (38.5%) by detection of pp67 mRNA by NASBA, 32 (82.1%) by quantitation of DNAemia, and 33 (84.6%) by quantitation of antigenemia, while HCMV was detected in 38 (97.4%) patients by detection of IE mRNA by NASBA. In the immunocompetent host, IE mRNA was not detected by NASBA in 100 blood donors or during reactivated infections in 30 breast-feeding mothers. Likewise, NASBA did not detect IE mRNA in 56 solid-organ transplant recipients in the first 21 days after transplantation. By using NASBA for detection of IE mRNA as the reference standard for detection of HCMV infection in blood samples, the diagnostic sensitivities were 67.7% for quantitation of DNAemia, 59.0% for quantitation of antigenemia, 18.3% for detection of pp67 mRNA by NASBA, and 16.0% for quantitation of viremia. Specificities and negative and positive predictive values were >90.0, >70.0, and >80.0%, respectively, for all four assays. The mean times to first HCMV detection after bone marrow transplantation were 37.7 ± 15.4 days for detection of IE mRNA by NASBA, 39.6 ± 15.6 days for quantitation of antigenemia, 40.9 ± 15.2 days for quantitation of DNAemia, and 43.7 ± 16.3 or 43.7 ± 17.5 days for quantitation of viremia and detection of pp67 mRNA by NASBA, respectively. On the whole, 31 BMT recipients received preemptive therapy by using confirmed antigenemia positivity as a cutoff, while 35 patients could have been treated by using NASBA positivity as a cutoff and 31 could have been treated by using quantitation of DNAemia as a cutoff. In single patients, IE mRNA was detected in every episode of active HCMV infection, mostly preceding and sometimes accompanying antigenemia and DNAemia, whereas pp67 mRNA was detected only concomitantly with the highest peaks of infection. HCMV IE mRNA detection may represent a useful parameter for initiation of preemptive therapy in BMT recipients.
Direct Molecular Typing of
Borrelia burgdorferi
Sensu Lato Species in Synovial Samples from Patients with Lyme Arthritis
Authors: Jaulhac B. , Heller R. , Limbach F. X. , Hansmann Y. , Lipsker D. , Monteil H. , Sibilia J. , Piémont Y. 
Published: December 2019

ABSTRACT

Since Lyme arthritis was first described in the United States, it has now been reported in many countries of Europe. However, very few strains of the causative bacterium,
Borrelia burgdorferi
, have been isolated from synovial samples. For this reason, different molecular direct typing methods were developed recently to assess which species could be involved in Lyme arthritis in Europe. We developed a simple oligonucleotide typing method with PCR fragments from the flagellin gene of
B. burgdorferi
sensu lato, which is able to differentiate seven different
Borrelia
species. Among 10 consecutive PCR-positive patients with Lyme arthritis from the northeastern France, two species were identified in synovial samples:
B. burgdorferi
sensu stricto in 9 cases and
B. garinii
in 1 case. Conversely, all
B. burgdorferi
sensu lato species detected in 10 consecutive PCR-positive biopsies from a second set of patients with erythema migrans from the same geographical area were identified as either
B. afzelii
or
B. garinii
(
P
< 0.001). These results indicate that
B. burgdorferi
sensu stricto is the principal but not the only
Borrelia
species involved in Lyme arthritis in northeastern France.
Technical Assessment of the Affymetrix Yeast Expression GeneChip YE6100 Platform in a Heterologous Model of Genes That Confer Resistance to Antimalarial Drugs in Yeast
Authors: Nau Martin E. , Emerson Lyndal R. , Martin Rodger K. , Kyle Dennis E. , Wirth Dyann F. , Vahey Maryanne 
Published: December 2019

ABSTRACT
The advent of high-density gene array technology has revolutionized approaches to drug design, development, and characterization. At the laboratory level, the efficient, consistent, and dependable exploitation of this complex technology requires the stringent standardization of protocols and data analysis platforms. The Affymetrix YE6100 expression GeneChip platform was evaluated for its performance in the analysis of both global (6,000 yeast genes) and targeted (three pleiotropic multidrug resistance genes of the ATP binding cassette transporter family) gene expression in a heterologous yeast model system in the presence and absence of the antimalarial drug chloroquine. Critical to the generation of consistent data from this platform are issues involving the preparation of the specimen, use of appropriate controls, accurate assessment of experiment variance, strict adherence to optimized enzymatic and hybridization protocols, and use of sophisticated bioinformatics tools for data analysis.
Coinfection with Multiple TT Virus Strains Belonging to Different Genotypes Is a Common Event in Healthy Brazilian Adults
Authors: Niel Christian , Saback Felipe L. , Lampe Elisabeth 
Published: December 2019

ABSTRACT
Testing of the DNA of TT virus (TTV) was done with serum samples obtained from 191 persons working in a public hospital of the city of Rio de Janeiro, Brazil. TTV DNA was detected by PCR in the sera of 125 (65.4%) individuals. PCR products were cloned, and sequences with a length of 159 bases surrounding the TATA signal region were determined for 100 clones derived from 31 individuals. One clone from each of 23 subjects was sequenced, while 7 to 19 clones from eight individuals were sequenced. None of the sera contained a viral sequence identical to that of any other individual. Phylogenetic analysis revealed the existence of a divergent TTV genotype possessing a single-base deletion at position 140. Among the eight persons for whom various sequences were analyzed, six were coinfected with between two and seven TTV strains belonging to different genotypes. The results suggest that coinfection with multiple TTV strains belonging to different genotypes is a common event in healthy Brazilian adults.
Acute Cerebral Phaeohyphomycosis due to
Wangiella dermatitidis
Accompanied by Cerebrospinal Fluid Eosinophilia
Authors: Chang Chulhun Ludgerus , Kim Dae-Seong , Park Dong June , Kim Hak Jin , Lee Chang Hun , Shin Jong Hee 
Published: December 2019

ABSTRACT

We report a case of cerebral phaeohyphomycosis due to
Wangiella dermaitidis
in an immunocompetent adult man. His cerebrospinal fluid (CSF) showed pleocytosis with a high eosinophil count but without peripheral blood eosinophilia. The present case suggested that this black yeast-like fungus should be included when the causes of CSF eosinophilia are considered, even though it is an extremely rare pathogen.
Evidence from a Nine-Year Birth Cohort Study in Japan of Transmission Pathways of
Helicobacter pylori
Infection
Authors: Malaty Hoda M. , Kumagai Toshiko , Tanaka Eiji , Ota Hiroyoshi , Kiyosawa Kendo , Graham David Y. , Katsuyama Tsutomu 
Published: December 2019

ABSTRACT

We examined the longitudinal changes of
Helicobacter pylori
infection within 46 families with children and 48 couples without children living in Japan. The study cohort was monitored from 1986 to 1994.
H. pylori
status was assessed by the presence of anti-
H. pylori
immunoglobulin G antibodies. At study entry,
H. pylori
prevalence in children with positive mothers was 23% versus 5% in children with negative mothers (odds ratio = 5.3; 95% confidence interval = 0.6 to 42.8). Seroconversion (rate of 1.5%/year) was evident only among children living with positive mothers and did not differ among adults living with or without children. These data strongly support the cluster phenomenon of
H. pylori
infection among families, the key role of the infected mothers in the transmission within families, and the importance of adult-child transmission and not vice versa.
Evaluation of the MB/BacT Mycobacterium Detection System for Susceptibility Testing of
Mycobacterium tuberculosis
Authors: Díaz-Infantes María S. , Ruiz-Serrano María J. , Martínez-Sánchez Lucía , Ortega Arturo , Bouza Emilio 
Published: December 2019

ABSTRACT

The MB/BacT mycobacterium detection system was evaluated for its performance in the susceptibility testing of
Mycobacterium tuberculosis
. Eighty-three
M. tuberculosis
isolates were processed. Results for all isoniazid-, rifampin- and streptomycin-susceptible, isoniazid-resistant, and rifampin-resistant
M. tuberculosis
isolates with the MB/BacT system agreed 100% with those obtained by the agar proportion method. The agreements between the two methods for streptomycin- and ethambutol-resistant isolates were 96.4 and 90.4%, respectively. The susceptibility test results were obtained in 7 days, on average. These data demonstrate that the MB/BacT system is an accurate, nonradiometric method for rapid susceptibility testing of
M. tuberculosis
.
Bartonella henselae
Infection as a Cause of Fever of Unknown Origin
Authors: Tsukahara Masato , Tsuneoka Hidehiro , Iino Hidechika , Murano Ichiro , Takahashi Hirohiko , Uchida Masashi 
Published: December 2019

ABSTRACT

Fourteen of 41 patients (34%) with a serological diagnosis of
Bartonella henselae
infection were found to have prolonged fever or fever of unknown origin, suggesting that generalized systemic
B. henselae
infection is not rare in immunocompetent healthy individuals.
Multiplex PCRs for Identification of
Escherichia coli
Virulence Genes
Authors: Pass M. A. , Odedra R. , Batt R. M. 
Published: December 2019

ABSTRACT

PCRs were developed to detect 11
Escherichia coli
virulence genes. Primers amplified the respective genes without cross-reaction with other genes. Specificity was maintained in multiplex reactions; excellent amplification of target genes was possible with a minimum of four multiplex reactions. These reactions successfully identified genes in
E. coli
from the feces of four dogs.