bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salmonella
Enteritidis Phage Types 1 and 4: Pheno- and Genotypic Epidemiology of Recent Outbreaks in Finland
Authors: Lukinmaa Susanna , Schildt Raili , Rinttilä Teemu , Siitonen Anja 
Published: December 2019

ABSTRACT

In the 1990s,
Salmonella enterica
subsp.
enterica
serovar Enteritidis has caused 15 outbreaks in Finland; 12 of them were caused by phage type 1 (PT1) and PT4. Thus far, there has been no clear evidence as to the source of these
Salmonella
Enteritidis PT1 and PT4 strains, so it was necessary to try to characterize them further.
Salmonella
Enteritidis PT1 (
n
= 57) and PT4 (
n
= 43) isolates from different sources were analyzed by genomic pulsed-field gel electrophoresis (PFGE), plasmid profiling, and antimicrobial resistance testing to investigate the distribution of their subtypes in Finland. It was also hoped that this investigation would help in identifying the sources of the infections, especially the sources of the outbreaks caused by PT1 and PT4 in the 1990s. The results showed that both PFGE and plasmid profiling, but not antimicrobial susceptibility testing, were capable of differentiating isolates of
Salmonella
Enteritidis PT1 and PT4. By genotypic methods, it was possible to divide both PT1 and PT4 isolates into 12 subtypes. It could also be shown that all PT1 outbreak isolates were identical and, at least with this collection of isolates, that the outbreaks did not originate from the Baltic countries or from Russia, where this phage type predominates. It was also established that the outbreaks caused by PT4 all had different origins. Valuable information for future investigations was gained on the distribution of molecular subtypes of strains that originated from the tourist resorts that are popular among Finns and of strains that were isolated from livestock.
Nocardia
Thyroiditis: Unusual Location of Infection
Authors: Carriere Christian , Marchandin Helene , Andrieu Jean Michel , Vandome Anne , Perez Colette 
Published: December 2019

ABSTRACT

Nocardia asteroides
complex is an important opportunistic agent in immunocompromised hosts. Usually, primary pulmonary infection occurs and is followed by dissemination of the pathogen to the central nervous system and soft tissues. As described in the literature, almost every organ can be infected, but to our knowledge,
Nocardia
has been described as a pathogen responsible for thyroid abscess in only one report, which was published in 1993. The present report is the second case report of
Nocardia
thyroiditis. The patient was under immunosuppressor treatment following a combined liver-kidney transplant and presented with a preexisting nodular goiter which was probably a predisposing factor to the start and development of the thyroid infection.
Prenatal Diagnosis of Parvovirus B19-Induced Hydrops Fetalis by Chemiluminescence In Situ Hybridization
Authors: Musiani M. , Pasini P. , Zerbini M. , Gentilomi G. , Roda A. , Gallinella G. , Manaresi E. , Venturoli S. 
Published: December 2019

ABSTRACT
Parvovirus B19 can be transmitted transplacentally from the infected mother to the fetus during pregnancy, and hydrops fetalis, abortion, or stillbirth can result. In our study we explored the use of chemiluminescence in situ hybridization to detect B19 DNA on cord blood cells, amniotic fluid cells, and pleuric fluid cells from several cases of hydrops fetalis. B19 DNA was detected by using digoxigenin-labeled probes immunoenzymatically visualized with the chemiluminescent adamantil-1,2-dioxetane phenyl phosphate substrate for alkaline phosphatase. The luminescent signal emitted from the hybridized probes was detected, analyzed, and measured with a high-performance, low-light-level imaging luminograph connected to an optical microscope and to a personal computer for the quantification and localization of the chemiluminescent emission inside individual cells.
Clonal Diversity among Recently Emerged Strains of
Vibrio parahaemolyticus
O3:K6 Associated With Pandemic Spread
Authors: Bag Prasanta K. , Nandi Suvobroto , Bhadra Rupak K. , Ramamurthy T. , Bhattacharya S. K. , Nishibuchi M. , Hamabata T. , Yamasaki Shinji , Takeda Yoshifumi , Nair G. Balakrish 
Published: December 2019

ABSTRACT

The genomes of the O3:K6 strains of
Vibrio parahaemolyticus
which abruptly emerged in Calcutta, India, in February 1996 and which demonstrated an unusual potential to spread and an enhanced propensity to cause infections were examined by different molecular techniques to determine clonality. No restriction fragment length polymorphism (RFLP) in the gene encoding the thermostable direct hemolysin was observed among the O3:K6 isolates of
V. parahaemolyticus
. Clonal diversity among the O3:K6 strains became evident by examining the RFLPs of the
rrn
operons and by the use of pulsed-field gel electrophoresis. Five ribotypes were distinguished among the O3:K6 strains examined, with ribotype R4 constituting the major type. Strains of O3:K6 isolated between June and August 1996 showed different pulsotypes compared to the pulsotypes of strains isolated before and after this period, indicating genetic reassortment among these strains, but those isolated between August 1996 and March 1998 showed identical or nearly similar pulsotypes. It is clear that there is a certain degree of genomic reassortment among the O3:K6 clones but that these strains are predominantly one clone.
Level of Human Immunodeficiency Virus DNA in Peripheral Blood Mononuclear Cells Correlates with Efficacy of Antiretroviral Therapy
Authors: McDermott Jennifer L. , Giri Adriana A. , Martini Isabella , Bono Maria , Giacomini Mauro , Campelli Antonio , Tagliaferro Luigi , Cara Andrea , Varnier Oliviero E. 
Published: December 2019

ABSTRACT
A novel colorimetric assay was developed and validated for accurate quantitation of human immunodeficiency virus (HIV) DNA in peripheral blood mononuclear cells (PBMCs). We tested 318 sequential samples from 56 subjects, 53 of whom were undergoing dual or triple therapy. Patients were considered responders when viremia levels were below 5,000 HIV RNA copies/ml. The mean DNA copy numbers for untreated and responder subjects were similar (72 and 75, respectively), while it was 4.54-fold higher for nonresponders (339). This report provides strong evidence that HIV DNA levels in PBMCs correlate with therapeutic efficacy and suggests that DNA quantitation is a useful tool to monitor the decay of the HIV reservoir toward disease remission, especially when viremia is undetectable.
Evaluation of an Epstein-Barr Virus (EBV) Immunoglobulin M Enzyme-Linked Immunosorbent Assay Using a Synthetic Convergent Peptide Library, or Mixotope, for Diagnosis of Primary EBV Infection
Authors: Tranchand-Bunel D. , Gras-Masse H. , Bourez B. , Dedecker L. , Auriault C. 
Published: December 2019

ABSTRACT
An immunoglobulin M (IgM) enzyme-linked immunosorbent assay (ELISA) was developed by using a 24-amino-acid peptide of the 18-kDa Epstein-Barr virus (EBV) viral capsid antigen (VCAp18). IgM detection was increased by 23% by using this antigen. Detection of IgM antibodies to the EBV proteins in the new ELISA was 100% specific and 95% sensitive.
Molecular Analysis of
Mycobacterium avium
Isolates by Using Pulsed-Field Gel Electrophoresis and PCR
Authors: Pestel-Caron Martine , Graff Gabriel , Berthelot Gilles , Pons Jean-Louis , Lemeland Jean-François 
Published: December 2019

ABSTRACT

Genetic relationships among 46 isolates of
Mycobacterium avium
recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS
1245
and IS
1311
. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of
M. avium
strains is high in a given community. Furthermore, this retrospective analysis of sporadic isolates allowed us (i) to suggest the existence of two remanent strains in our region, (ii) to raise the question of the possibility of nosocomial acquisition of
M. avium
strains, and (iii) to document laboratory contamination. The methods applied in the present study were found to be useful for the typing of
M. avium
isolates. In general, both methods yielded similar results for both related and unrelated isolates. However, the isolates in five of the six PCR clusters were distributed among two to three PFGE patterns, suggesting that this PCR-based method may have limitations for the analysis of strains with low insertion sequence copy numbers or for resolution of extended epidemiologic relationships.
TT Virus Infection in French Hemodialysis Patients: Study of Prevalence and Risk Factors
Authors: Gallian Pierre , Berland Yvon , Olmer Michel , Raccah Denis , de Micco Philippe , Biagini Philippe , Simon Sophie , Bouchouareb Dammar , Mourey Catherine , Roubicek Christa , Touinssi M’hammed , Cantaloube Jean-François , Dussol Bertrand , de Lamballerie Xavier 
Published: December 2019

ABSTRACT
The TT virus (TTV) is a recently discovered DNA virus which was first identified in patients with non-A to -G hepatitis following blood transfusion. In this study, we tested 150 attendees of two hemodialysis (HD) units of the public hospitals of Marseilles, France, for the presence of TTV genome by using a PCR-based methodology. The overall prevalence of TTV viremia was 28% (compared to 5.3% in blood donors from the same region). We demonstrated the existence of chronic infections and superinfections by strains belonging to different genotypes. The prevalence of infection was higher in patients originating from Africa, in patients with previous blood transfusion or organ transplantation, in patients with antibody to hepatitis B core antigen, and in those with diabetes mellitus. A high prevalence of TTV infection (50%) was also observed in a population of patients with diabetes mellitus but without renal disease. No significant relationship was found between TTV viremia and hepatitis C virus or GB virus C, transaminases, age, sex, and duration of HD treatment. The PCR amplification products (located in open reading frame 1 of the TTV genome) were sequenced. These genomic sequences were submitted to phylogenetic analysis by using the Jukes-Cantor algorithm for distance determination and the neighbor-joining method for tree building. In several instances, sequences from viruses isolated in a HD unit were grouped in the same phylogenetic cluster. These results together with the different distribution of cases in the two HD units suggest there is viral transmission within each.
Comparison of
Ehrlichia chaffeensis
Recombinant Proteins for Serologic Diagnosis of Human Monocytotropic Ehrlichiosis
Authors: Yu Xue-Jie , Crocquet-Valdes Patricia A. , Cullman Louis C. , Popov Vsevolod L. , Walker David H. 
Published: December 2019

ABSTRACT

Diagnosis of human monocytotropic ehrlichiosis (HME) generally depends on serology that detects the antibody response to immunodominant proteins of
Ehrlichia chaffeensis
. Protein immunoblotting was used to evaluate the reaction of the antibodies in patients’ sera with the recombinant
E. chaffeensis
120- and 28-kDa proteins as well as the 106- and the 37-kDa proteins. The cloning of the genes encoding the latter two proteins is described in this report. Immunoelectron microscopy demonstrated that the 106-kDa protein is located at the surfaces of ehrlichiae and on the intramorular fibrillar structures associated with
E. chaffeensis
. The 37-kDa protein is homologous to the iron-binding protein of gram-negative bacteria. Forty-two serum samples from patients who were suspected to have HME were tested by immunofluorescence (IFA) using
E. chaffeensis
antigen and by protein immunoblotting using recombinant
E. chaffeensis
proteins expressed in
Escherichia coli
. Thirty-two serum samples contained IFA antibodies at a titer of 1:64 or greater. The correlation of IFA and recombinant protein immunoblotting was 100% for the 120-kDa protein, 41% for the 28-kDa protein, 9.4% for the 106-kDa protein, and 0% for the 37-kDa protein. None of the recombinant antigens yielded false-positive results. All the sera reactive with the recombinant 28- or the 106-kDa proteins also reacted with the recombinant 120-kDa protein.
Evaluation of the PrimeCapture CMV DNA Detection Plate System for Detection of Cytomegalovirus in Clinical Specimens
Authors: Davoli Eugene H. , Lipson Steven M. , Match Mark E. , Shepp David H. , Morin Joseph W. , Curley Dennis M. 
Published: December 2019

ABSTRACT
With the availability of anticytomegalovirus (CMV) therapeutic agents, rapid detection of CMV is important in the care and management of the immunosuppressed patient. The PrimeCapture CMV DNA Detection Plate System (PC-PCR) was evaluated for the detection of CMV in blood and cerebrospinal fluid (CSF). The resolution of discordant results was performed by consensus testing utilizing a combination of conventional cell culture (TC-CPE), the CMV-antigenemia (CMV-Ag) assay, one or more in-house CMV nested PCR assays, and/or patient evaluation and follow-up. Of 51 blood specimens from 34 patients, 23 (45%) were identified as true positives. PC-PCR was significantly more sensitive than the CMV-Ag assay, TC-CPE, or a combination of both tests. The sensitivities, specificities, positive predictive values (PPV), and negative predictive values (NPV) for PC-PCR, the CMV-Ag assay, TC-CPE, and a combination of CMV-Ag and TC-CPE were 78, 75, 72, 81%; 46, 100, 100, 70%; 39, 100, 100, 67%; and 58, 100, 100, 73%, respectively. CMV was not detected or isolated in CSF, resulting in a combined PC-PCR sensitivity, specificity, PPV, and NPV of 77, 90, 68, and 93%, respectively. Among those laboratorians considering the incorporation of molecular CMV diagnostics into their clinical microbiology or virology laboratories, the CMV PC-PCR offers a relatively simple-to-perform and sensitive assay system.
Comparison of Methods Based on Different Molecular Epidemiological Markers for Typing of
Mycobacterium tuberculosis
Complex Strains: Interlaboratory Study of Discriminatory Power and Reproducibility
Authors: Kremer K. , van Soolingen D. , Frothingham R. , Haas W. H. , Hermans P. W. M. , Martín C. , Palittapongarnpim P. , Plikaytis B. B. , Riley L. W. , Yakrus M. A. , Musser J. M. , van Embden J. D. A. 
Published: December 2019

ABSTRACT

In this study, the currently known typing methods for
Mycobacterium tuberculosis
isolates were evaluated with regard to reproducibility, discrimination, and specificity. Therefore, 90
M. tuberculosis
complex strains, originating from 38 countries, were tested in five restriction fragment length polymorphism (RFLP) typing methods and in seven PCR-based assays. In all methods, one or more repetitive DNA elements were targeted. The strain typing and the DNA fingerprint analysis were performed in the laboratory most experienced in the respective method. To examine intralaboratory reproducibility, blinded duplicate samples were included. The specificities of the various methods were tested by inclusion of 10 non-
M. tuberculosis
complex strains. All five RFLP typing methods were highly reproducible. The reliability of the PCR-based methods was highest for the mixed-linker PCR, followed by variable numbers of tandem repeat (VNTR) typing and spoligotyping. In contrast, the double repetitive element PCR (DRE-PCR), IS
6110
inverse PCR, IS
6110
ampliprinting, and arbitrarily primed PCR (APPCR) typing were found to be poorly reproducible. The 90 strains were best discriminated by IS
6110
RFLP typing, yielding 84 different banding patterns, followed by mixed-linker PCR (81 patterns), APPCR (71 patterns), RFLP using the polymorphic GC-rich sequence as a probe (70 patterns), DRE-PCR (63 patterns), spoligotyping (61 patterns), and VNTR typing (56 patterns). We conclude that for epidemiological investigations, strain differentiation by IS
6110
RFLP or mixed-linker PCR are the methods of choice. A strong association was found between the results of different genetic markers, indicating a clonal population structure of
M. tuberculosis
strains. Several separate genotype families within the
M. tuberculosis
complex could be recognized on the basis of the genetic markers used.
Determination of Hepatitis C Virus Genotype by Direct Sequence Analysis of Products Generated with the Amplicor HCV Test
Authors: Germer Jeff J. , Rys Paul N. , Thorvilson Jill N. , Persing David H. 
Published: December 2019

ABSTRACT

Consistent with other members of the family
Flaviviridae
, hepatitis C virus (HCV) demonstrates a high degree of sequence variation throughout the coding regions of its genome. However, there is a high degree of sequence conservation found within the 5′ untranslated region (UTR) of the genome, making this region a target of choice for most nucleic acid amplification-based detection assays. In this study, the Amplicor HCV test, a commercially available assay which detects the 5′UTR, was used for the detection of HCV RNA in 669 serum samples obtained from a cohort of liver transplantation patients. Amplification products obtained from the HCV-positive cases were subjected to direct sequencing and genotyping based upon seven phylogenetically informative regions within the 5′UTR. Of the 669 specimens, 416 (62.2%) tested positive for the presence of HCV RNA. Of these, 372 (89.4%) specimens were successfully classified into 11 HCV genotypes and subtypes after computer-assisted analysis of the sequence data. Forty-four (10.6%) of the HCV RNA-positive specimens were not classifiable, the majority corresponding to low-titer specimens as determined by the Chiron Quantiplex HCV RNA 2.0 assay. Additional comparative studies targeting the NS-5 region of the viral genome generally confirmed the accuracy and sensitivity of the 5′UTR-based classifications, with the exception of the misclassification of a small number of type 1a cases as type 1b. We conclude that although the high sequence conservation within the 5′UTR results in the misclassification of a small number of HCV subtypes, the overall gains of efficiency, the shorter turnaround time, the inclusion of contamination control measures, and the low rate of test failure compared to that of methods based on the NS-5 gene together constitute significant advantages over other techniques.
Destructive Knee Joint Infection Caused by
Peptostreptococcus micros
: Importance of Early Microbiological Diagnosis
Authors: Riesbeck Kristian , Sanzén Lennart 
Published: December 2019

ABSTRACT

Peptostreptococcus micros
is a commensal of the oral cavity and the genitourinary tract that rarely causes serious infections. A case of a destructive knee joint infection with rapid progress caused by
P. micros
is presented. The significance of the microbiological findings was initially not acknowledged, which contributed to a nonsuccessful clinical outcome.
PCR-Based Methods for Genotyping Viridans Group Streptococci
Authors: Alam Sharmin , Brailsford Susan R. , Whiley Robert A. , Beighton David 
Published: December 2019

ABSTRACT

Standard repetitive extragenic palindromic (REP)-PCR, enterobacterial repetitive intergenic consensus-PCR, and
Salmonella enteritidis
repetitive element-PCR methods for bacterial strain typing were performed with DNA extracted by boiling members of each of the currently recognized species of human viridans group streptococci. Each of the methods was reproducible. The unique isolates (
n
= 72) from 15 species of viridans group streptococci were readily distinguishable, with no two isolates showing greater than 90% per cent similarity. The majority of strains exhibited much less than 90% similarity. Isolates identical by REP-PCR were also identical by the other two methods. These PCR-based typing methods, although they do not permit determination of the species of the isolates, are simple to perform and are suitable for clinical and ecological investigations of viridans group streptococci.
Impact of Reference Standard Sensitivity on Accuracy of Rapid Antigen Detection Assays and a Leukocyte Esterase Dipstick for Diagnosis of
Chlamydia trachomatis
Infection in First-Void Urine Specimens from Men
Authors: Chernesky M. , Jang D. , Krepel J. , Sellors J. , Mahony J. 
Published: December 2019

ABSTRACT

A total of 128 previously frozen first-void urine (FVU) specimens from selected asymptomatic men were centrifuged and tested by three
Chlamydia trachomatis
rapid antigen detection tests and with a leukocyte esterase (LE) dipstick. When the results were compared to those of a reference standard of positivity determined by the Chlamydiazyme enzyme immunoassay as confirmed by a blocking assay, the sensitivities of the Testpack Chlamydia (Abbott), Clearview Chlamydia (Unipath), and Surecell Chlamydia (Kodak) tests and the LE dipstick test were 76.4, 76.4, 67.3, and 88.6%, respectively. Use of the ligase chain reaction (LCR), whose results were confirmed by direct fluorescent-antibody staining of elementary bodies, as the reference standard reduced the sensitivities to 70.9, 67.7, 62.9, and 87.5%, respectively. The specificities by use of LCR as the reference standard were 95.5, 95.5, 100, and 92.4%, respectively. These rapid chlamydial antigen tests performed reasonably well with FVU specimens, but the simple LE dipstick test, which had the highest sensitivity, would have enabled treatment of the greatest number of infected male patients.
Methicillin-Resistant
Staphylococcus aureus
Clonal Types in the Czech Republic
Authors: Melter O. , Santos Sanches I. , Schindler J. , Aires de Sousa M. , Mato R. , Kovárova V. , Zemlicková H. , de Lencastre H. 
Published: December 2019

ABSTRACT

Molecular surveillance studies have documented the extensive spread of methicillin-resistant
Staphylococcus aureus
(MRSA) clones. Studies carried out by Centro de Epidemiologia Molecular-Network for Tracking Gram-Positive Pathogenic Bacteria (CEM/NET) led to the identification of two international multidrug-resistant strains, which were designated as the Iberian and Brazilian MRSA clones and which were defined by multiple genomic typing methods; these included
Cla
I restriction digests hybridized with
mecA
- and Tn
554
-specific DNA probes and pulsed-field gel electrophoresis (PFGE). The genotypic characteristics of these clones are distinct: the Iberian clone is defined as
mecA
type I, Tn
554
type E (or its variants), and PFGE pattern A (I:E:A), whereas the Brazilian clone is defined as
mecA
type XI (or its variants), Tn
554
type B, and PFGE pattern B (XI:B:B). In this study, we characterized 59 single-patient isolates of MRSA collected during 1996 and 1997 at seven hospitals located in Prague and five other cities in the Czech Republic by using the methodologies mentioned above and by using ribotyping of
Eco
RI and
Hin
dIII digests hybridized with a 16S-23S DNA probe. The Brazilian MRSA clone (XI:B:B) was the major clone (80%) spread in two hospitals located in Prague and one located in Brno; the Iberian MRSA clone (I:E:A or its variant I:DD:A), although less representative (12%), was detected in two hospitals, one in Prague and the other in Plzen. Almost all the strains belonging to clone XI:B:B (45 of 47) corresponded to a unique ribotype, E1H1, whereas most strains of the I:E:A and I:DD:A clonal types (6 of 7) corresponded to ribotype E2H2.