bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Comparison of Nonvented Aerobic BacT/Alert Blood Culture Bottle and Standard Aerobic Bottle for Detection of Microorganisms in Blood
Authors: Snyder James W. , Benzing Karen S. , Munier Gina K. , Bostic Grace D. , Bozigar Pamela S. , Hanna Rami , Zervos Marcus J.
Published: December 2019

The current BacT/Alert standard aerobic (VA) blood culture bottle was redesigned and designated a nonvented aerobic (NVA) culture bottle; this bottle does not require venting. A total of 3,873 sets of blood samples for culture were obtained from adult patients with suspected bacteremia or fungemia. The NVA bottle showed performance equivalent to that of the VA bottle for recovery and speed of detection of microorganisms from blood without the need for venting the bottle.
Molecular Analysis of Methicillin-Resistant
Staphylococcus aureus
as a Causative Agent of Bronchopulmonary Infection: Relation to Colonization in the Upper Respiratory Tract
Authors: Watanabe Hiroshi , Masaki Hironori , Asoh Norichika , Watanabe Kiwao , Oishi Kazunori , Kobayashi Shinobu , Sato Akiyoshi , Nagatake Tsuyoshi
Published: December 2019

Using five diagnostic markers, we compared the types of 72 strains of methicillin-resistant
Staphylococcus aureus
(MRSA) isolated simultaneously from the nasal cavity, pharynx, and sputum from 24 patients. Almost identical MRSA types had colonized the nasal cavity and sputum from the same patient for 21 (88%) of the patients. We speculate that most MRSA organisms isolated in sputum are derived from the nasal cavity, while a few are derived from the pharynx.
Diagnostic Value of Immunoglobulin G (IgG) and IgM Anti-Hepatitis E Virus (HEV) Tests Based on HEV RNA in an Area Where Hepatitis E Is Not Endemic
Authors: Lin Chen-Chun , Wu Jaw-Ching , Chang Ting-Tsung , Chang Wen-Yu , Yu Ming-Lung , Tam Albert W. , Wang Shen-Chin , Huang Yi-Hsiang , Chang Full-Young , Lee Shou-Dong
Published: December 2019

Acute hepatitis E (AHE) has rarely been reported in industrialized countries, but the rate of seroprevalence of hepatitis E virus (HEV) antibodies (anti-HEV) is inappropriately high. The sensitivity and specificity of the assay used to test for immunoglobulin G (IgG) and IgM anti-HEV have not been well established in areas where hepatitis E is not endemic (hereafter referred to as “nonendemic areas”). We collected serum samples from 13 AHE patients, 271 healthy subjects, and 160 other liver disease patients in Taiwan to test for HEV RNA by reverse transcription (RT)-PCR and for IgG and IgM anti-HEV by enzyme-linked immunosorbent assays. The sensitivities of IgG and IgM anti-HEV (relative to RT-PCR) were 86.7 and 53.3%, respectively. The specificities of IgG and IgM anti-HEV assays for diagnosing AHE were 92.1 and 98.6%, respectively. The rate of seroprevalence of IgG anti-HEV was 11% among healthy subjects in this nonendemic area, and it increased with age. In summary, IgG anti-HEV is a good diagnostic test for screening for AHE in nonendemic areas. The high rate of prevalence of anti-HEV in healthy subjects indicates that subclinical infection may exist.
Genetic Diversity of Protease and Reverse Transcriptase Sequences in Non-Subtype-B Human Immunodeficiency Virus Type 1 Strains: Evidence of Many Minor Drug Resistance Mutations in Treatment-Naive Patients
Authors: Vergne Laurence , Peeters Martine , Mpoudi-Ngole Eitel , Bourgeois Anke , Liegeois Florian , Toure-Kane Coumba , Mboup Souleymane , Mulanga-Kabeya Claire , Saman Eric , Jourdan Jacques , Reynes Jacques , Delaporte Eric
Published: December 2019

Most human immunodeficiency virus (HIV) drug susceptibility studies have involved subtype B strains. Little information on the impact of viral diversity on natural susceptibility to antiretroviral drugs has been reported. However, the prevalence of non-subtype-B (non-B) HIV type 1 (HIV-1) strains continues to increase in industrialized countries, and antiretroviral treatments have recently become available in certain developing countries where non-B subtypes predominate. We sequenced the protease and reverse transcriptase (RT) genes of 142 HIV-1 isolates from antiretroviral-naive patients: 4 belonged to group O and 138 belonged to group M (9 subtype A, 13 subtype B, 2 subtype C, 5 subtype D, 2 subtype F1, 9 subtype F2, 4 subtype G, 5 subtype J, 2 subtype K, 3 subtype CRF01-AE, 67 subtype CRF02-AG, and 17 unclassified isolates). No major mutations associated with resistance to nucleoside reverse transcriptase inhibitors (NRTIs) or protease inhibitors were detected. Major mutations linked to resistance to non-NRTI agents were detected in all group O isolates (A98G and Y181C) and in one subtype J virus (V108I). In contrast, many accessory mutations were found, especially in the protease gene. Only 5.6% of the 142 strains, all belonging to subtype B or D, had no mutations in the protease gene. Sixty percent had one mutation, 22.5% had two mutations, 9.8% had three mutations, and 2.1% (all group O strains) had four mutations. In order of decreasing frequency, the following mutations were identified in the protease gene: M36I (86.6%), L10I/V (26%), L63P (12.6%), K20M/R (11.2%), V77I (5.6%), A71V (2.8%), L33F (0.7%), and M46I (0.7%). R211K, an accessory mutation associated with NRTI resistance, was also observed in 43.6% of the samples. Phenotypic and clinical studies are now required to determine whether multidrug-resistant viruses emerge more rapidly during antiretroviral therapy when minor resistance-conferring mutations are present before treatment initiation.
Development of a Highly Sensitive and Specific Enzyme-Linked Immunosorbent Assay Based on Recombinant Matrix Protein for Detection of Avian Pneumovirus Antibodies
Authors: Gulati Baldev R. , Cameron Kjerstin T. , Seal Bruce S. , Goyal Sagar M. , Halvorson David A. , Njenga M. Kariuki
Published: December 2019

The matrix (M) protein of avian pneumovirus (APV) was evaluated for its antigenicity and reliability in an enzyme-linked immunosorbent assay (ELISA) for diagnosis of APV infection, a newly emergent disease of turkeys in United States. Sera from APV-infected turkeys consistently contained antibodies to a 30-kDa protein (M protein). An ELISA based on recombinant M protein generated in
Escherichia coli
was compared with the routine APV ELISA that utilizes inactivated virus as antigen. Of 34 experimentally infected turkeys, 33 (97.1%) were positive by M protein ELISA whereas only 18 (52.9%) were positive by routine APV ELISA 28 days after infection. None of the serum samples from 41 uninfected experimental turkeys were positive by M protein ELISA. Of 184 field sera from turkey flocks suspected of having APV infection, 133 (72.3%) were positive by M protein ELISA whereas only 99 (53.8%) were positive by routine APV ELISA. Twelve serum samples, which were negative by M protein ELISA but positive by routine APV ELISA, were not reactive with either recombinant M protein or denatured purified APV proteins by Western analysis. This indicates that the samples had given false-positive results by routine APV ELISA. The M protein ELISA was over six times more sensitive than virus isolation (11.5%) in detecting infections from samples obtained from birds showing clinical signs of APV infection. Taken together, these results show that ELISA based on recombinant M protein is a highly sensitive and specific test for detecting antibodies to APV.
Quality of Human Immunodeficiency Virus Viral Load Testing in Australia
Authors: Best Susan J. , Gust Anthony P. , Johnson Elizabeth I. M. , McGavin Catherine H. , Dax Elizabeth M.
Published: December 2019

This study determined the proficiencies of laboratories measuring human immunodeficiency virus type 1 (HIV-1) viral loads and the accuracies of two assays used for HIV-1 viral load measurement in Australia and investigated the variability of the new versions of these assays. Quality assessment program panels containing (i) dilutions of HIV-1 subtype B, (ii) replicates of identical samples of HIV-1 subtype B, and (iii) samples of subtype E and B were tested by laboratories. Total variability (within and between laboratories) was tested with quality control samples. The coefficients of variation (CVs) for the Roche AMPLICOR HIV-1 MONITOR version (v) 1.0 and Chiron Quantiplex bDNA 2.0 assays ranged from 53 to 87% and 22 to 31%, respectively. The widespread occurrence of invalid runs with the AMPLICOR HIV-1 MONITOR 1.0 assay was identified. The CVs of the new versions of the assays were 82 to 86% for the AMPLICOR HIV-1 MONITOR v 1.5 assay and 16 to 23% for the Quantiplex bDNA 3.0 assay. For virus dilution samples, all but 5 of 19 laboratories obtained results within 2 standard deviations of the mean. The Quantiplex bDNA 2.0 assay reported values lower than those reported by the AMPLICOR HIV-1 MONITOR version 1.0 assay for samples containing HIV-1 subtype B, whereas the reverse was true for subtype E. Identification and resolution of the problem of invalid runs markedly improved the quality of HIV-1 viral load testing. The variability observed between laboratories and between assays, even the most recent versions, dictates that monitoring of viral load in an individual should always be by the same laboratory and by the same assay. Results for an individual which differ by less than 0.5 log
10
HIV-1 RNA copy number/ml should not be considered clinically significant.
Human T-Cell Lymphotropic Virus Type 1 Gag Indeterminate Western Blot Patterns in Central Africa: Relationship toPlasmodium falciparumInfection
Authors: Mahieux Renaud , Horal Peter , Mauclère Philippe , Mercereau-Puijalon Odile , Guillotte Micheline , Meertens Laurent , Murphy Edward , Gessain Antoine
Published: December 2019

To gain insight on the significance of human T-cell lymphotropic virus type 1 (HTLV-1) indeterminate serological reactivities, we studied villagers of South Cameroon, focusing on a frequent and specific HTLV-1 Gag indeterminate profile (HGIP) pattern (gagp19, p26, p28, and p30 without p24 or Env gp21 and gp46). Among the 102 sera studied, 29 from all age groups had a stable HGIP pattern over a period of 4 years. There was no epidemiological evidence for sexual or vertical transmission of HGIP. Seventy-five percent of HGIP sera reacted positively on MT2 HTLV-1-infected cells by immunofluorescence assay. However, we could not isolate any HTLV-1 virus or detect the presence of p19 Gag protein in cultures of peripheral blood mononuclear cells obtained from individuals with strong HGIP reactivity. PCR experiments conducted with primers for HTLV-1 and HTLV-2 (HTLV-1/2 primers) encompassing different regions of the virus did not yield HTLV-1/2 proviral sequences from individuals with HGIP. Using 11 peptides corresponding to HTLV-1 or HTLV-2 immunodominant B epitopes in an enzyme-linked immunosorbent assay, one epitope corresponding to the Gag p19 carboxyl terminus was identified in 75% of HGIP sera, while it was recognized by only 41% of confirmed HTLV-1-positive sera. A positive correlation between HTLV-1 optical density values and titers of antibody toPlasmodium falciparumwas also demonstrated. Finally, passage of sera through aP. falciparum-infected erythrocyte-coupled column was shown to specifically abrogate HGIP reactivity but not the HTLV-1 pattern, suggesting the existence of cross-reactivity between HTLV-1 Gag proteins and malaria-derived antigens. These data suggest that in Central Africa, this frequent and specific Western blot is not caused by HTLV-1 infection but could instead be associated withP. falciparuminfection.
Evaluation of PCR-Based Methods for Discrimination of
Francisella
Species and Subspecies and Development of a Specific PCR That Distinguishes the Two Major Subspecies of
Francisella tularensis
Authors: Johansson Anders , Ibrahim Ashraf , Göransson Ingela , Eriksson Ulla , Gurycova D. , Clarridge Jill E. , Sjöstedt Anders
Published: December 2019

Previous studies have demonstrated that the four subspecies of the human pathogen
Francisella tularensis
, despite showing marked variations in their virulence for mammals and originating from different regions in the Northern Hemisphere, display a very close phylogenetic relationship. This property has hampered the development of generally applicable typing methods. To overcome this problem, we evaluated the use of PCR for discrimination of the subspecies using various forms of long arbitrary primers or primers specific for repetitive extragenic palindromic sequences (REP) or enterobacterial repetitive intragenic consensus (ERIC) sequences. Patterns generated by use of REP, ERIC, or long arbitrary primers allowed differentiation at the species level and of the four subspecies of
F. tularensis
. With each of these three methods, similar or identical clustering of strains was found, and groups of strains of different geographical origins or differing in virulence showed distinct patterns. The discriminatory indices of the methods varied from 0.57 to 0.65; thus, the patterns were not sufficiently discriminatory to distinguish individual strains. The sequence of a fragment generated by amplification with an arbitrary primer was determined, and a region showing interstrain heterogeneity was identified. Specific primers were designed, and a PCR was developed that distinguished strains of
F. tularensis
subsp.
holarctica
from strains of other
F. tularensis
subspecies, including strains of the highly virulent
F. tularensis
subsp.
tularensis
. Notably, one European isolate showed the genetic pattern typical of the highly virulent
F. tularensis
subsp.
tularensis
, generally believed to exist only in North America. It is proposed that a combination of the specific PCR together with one method generating subspecies-specific patterns is suitable as a rapid and relatively simple strategy for discrimination of
Francisella
species and subspecies.
Emergence of
Vibrio cholerae
O1 Biotype El Tor Serotype Inaba from the Prevailing O1 Ogawa Serotype Strains in India
Authors: Garg Pallavi , Nandy Ranjan K. , Chaudhury Papiya , Chowdhury Nandini Roy , De Keya , Ramamurthy T. , Yamasaki Shinji , Bhattacharya S. K. , Takeda Yoshifumi , Nair G. Balakrish
Published: December 2019

The toxigenic Inaba serotype of
Vibrio cholerae
O1 biotype El Tor reappeared in India in 1998 and 1999, almost 10 years after its last dominance in Calcutta in 1989. Extensive molecular characterization by ribotyping, restriction fragment length polymorphism, and pulsed-field gel electrophoresis indicated that recent Inaba strains are remarkably different from the earlier Inaba strains but are very similar to the prevailing
V. cholerae
O1 Ogawa El Tor biotype strains. The antibiograms of the Inaba strains were also similar to those of the recent
V. cholerae
Ogawa strains. These
V. cholerae
O1 Inaba strains appear to have evolved from the currently prevailing Ogawa strains and are likely to dominate in the coming years.
Evaluation of a Commercial DNA Enzyme Immunoassay for Detection of Enterovirus Reverse Transcription-PCR Products Amplified from Cerebrospinal Fluid Specimens
Authors: Young Pampee P. , Buller Richard S. , Storch Gregory A.
Published: December 2019

We evaluated the DiaSorin DNA enzyme immunoassay (DEIA) kit for detection of enteroviral reverse transcription-PCR (RT-PCR) products amplified from cerebrospinal fluid. By use of an optical density of 0.05 as the absorbance cutoff, 35% of 198 specimens were PCR positive, whereas 16% were culture positive. DEIA was rapid and sensitive and can help implement enterovirus RT-PCR in clinical laboratories.
Detection of Hepatitis G Virus (HGV) RNA and Antibodies to the HGV Envelope Protein E2 in a Cohort of Hemodialysis Patients
Authors: Pérez-Gracia T. , Galán F. , Girón-González J. A. , Lozano A. , Benavides B. , Fernández E. , Rodríguez-Iglesias M.
Published: December 2019

An analysis of the evolution of hepatitis G virus (HGV) infection markers was performed for a cohort of 58 hemodialyzed patients. During follow-up (4.88 ± 0.42 years), a group of these patients cleared their antibodies against the envelope protein E2 with (4 of 29 cases; 13.8%) or without (9 of 29 cases; 31%) the reappearance of viremia. This finding implies a temporally limited protection in patients previously infected with HGV.
Value of Examining Three Acid-Fast Bacillus Sputum Smears for Removal of Patients Suspected of Having Tuberculosis from the “Airborne Precautions” Category
Authors: Craft David W. , Jones Melissa C. , Blanchet Cherie N. , Hopfer Roy L.
Published: December 2019

We examined the potential risk of tuberculosis transmission if we modified our policy for release of patients from the “airborne precautions” category from three negative acid-fast bacillus (AFB) smears to two, or even one. Over a 4-year period, respiratory cultures from 42 patients grew
Mycobacterium tuberculosis
. Of these, 36 patients (81%) had a positive AFB smear result on the first submitted specimen. One additional patient (2%) had a first smear-positive finding on the second submitted specimen, and no patients had a first smear-positive result on the third submitted specimen. Respiratory cultures from five patients (12%) grew
M. tuberculosis
without ever having a positive AFB smear result. These data indicate that in our institution, reducing the number of negative smears required before removal of patients from the airborne precautions category would pose little, if any, increase in the risk of spreading tuberculosis.
White Grain Mycetoma Caused by a
Cylindrocarpon
sp. in India
Authors: Hemashettar B. M. , Siddaramappa B. , Padhye A. A. , Sigler L. , Chandler F. W.
Published: December 2019

We describe a case of white grain eumycetoma of the foot of an Indian male caused by a slow-growing, poorly sporulating fungus that does not match any known agent of this infection. Histologic examination of a biopsy tissue specimen showed oval, lobular, white granules composed of hyaline, septate hyphae, and thick-walled chlamydospores. Culture of granules from a draining sinus yielded compact, very-slow-growing, poorly sporulating colonies producing a strong reddish brown pigment that diffused into the medium. The fungus was identified as a
Cylindrocarpon
sp. based on the development of rare cylindrical conidia borne from solitary phialides lacking collarettes, in addition to chlamydospores formed singly or in short chains.
Use of Whole Blood Specimens for Routine Clinical Quantitation of Hepatitis C Virus RNA Does Not Increase Assay Sensitivity
Authors: Cook Linda , Ross Angela M. , Knight Glenn B. , Agnello Vincent
Published: December 2019

The measurement of hepatitis C virus (HCV) RNA levels in the blood has, in the last few years, become a critical component in the therapy of patients with HCV infections. Initially, extraction methods for serum and plasma were used, but a newer method that uses Catrimox-14 as the extraction agent for whole blood has been reported. Because the whole blood extraction method may yield higher virus levels if significant levels of virus are present in the white blood cells (WBC), the method was evaluated for use in our clinical diagnostic laboratory despite its higher reagent costs and more time-consuming methodology. RNA was simultaneously extracted from 39 clinical samples by four different methods: Catrimox-14–Trizol extraction from whole blood, Trizol extraction from whole blood, Trizol extraction from serum, and a commercial serum extraction method, the EZNA total RNA kit. In addition, in an effort to quantitate the amount of HCV RNA virus in the WBC, Trizol extraction from isolated WBC was also performed. Quantitative results for samples from which RNA was extracted by all four methods were essentially the same; the Catrimox-14–Trizol method did not yield increased virus levels. Insignificant levels of virus were found in the WBC. The results did not demonstrate a clinical usefulness for the Catrimox-14–Trizol method.
Molecular Epidemiology of Penicillin-Nonsusceptible
Streptococcus pneumoniae
among Children in Greece
Authors: Bogaert Debby , Syrogiannopoulos George A. , Grivea Ioanna N. , de Groot Ronald , Beratis Nicholas G. , Hermans Peter W. M.
Published: December 2019

A total of 145 penicillin-nonsusceptible
Streptococcus pneumoniae
strains were isolated from young carriers in Greece and analyzed by antibiotic susceptibility testing, serotyping, restriction fragment end labeling (RFEL), and penicillin-binding protein (PBP) genotyping. The serotypes 23A and 23F (54%), 19A and 19F (25%), 9V (5%), 15A, 15B, and 15C (4%), 6A and 6B (4%), and 21 (4%) were most prevalent in this collection. Fifty-three distinct RFEL types were identified. Sixteen different RFEL clusters, harboring 2 to 32 strains each, accounted for 82% of all strains. Eight of these genetic clusters representing 60% of the strains were previously identified in other countries. A predominant lineage of 66 strains (46%) harboring five RFEL types and the serotypes 19F and 23F was closely related to the pandemic clone Spain
23F
-1 (genetic relatedness of ≥85%). Another lineage, representing 11 strains, showed close genetic relatedness to the pandemic clone France
9V
-3. Another lineage of 8 serotype 21 strains was Greece specific since the RFEL types were not observed in an international collection of 193 genotypes from 16 different countries. Characterization of the PBP genes
pbp1a
,
pbp2b
, and
pbp2x
revealed 20 distinct PBP genotypes of which PBP type 1-1-1, initially observed in the pandemic clones 23F and 9V, was predominantly present in 11 RFEL types in this Greek collection of penicillin-nonsusceptible strains (55%). Sixteen PBP types covering 52 strains (36%) were Greece specific. This study underlines the strong contribution of penicillin-resistant international clones to the prevalence and spread of penicillin-nonsusceptible pneumococci among young children in Greece.
Clonal Groups of Penicillin-Nonsusceptible
Streptococcus pneumoniae
in Baltimore, Maryland: a Population-Based, Molecular Epidemiologic Study
Authors: McEllistrem M. Catherine , Pass Margaret , Elliott John A. , Whitney Cynthia G. , Harrison Lee H.
Published: December 2019

Few data are available on the molecular subtypes of all penicillin-nonsusceptible
Streptococcus pneumoniae
(PNSP) from a defined population base. Pulsed-field gel electrophoresis (PFGE), serotyping, and antibiotic susceptibility testing were performed for all available invasive PNSP isolates for which the penicillin (MIC) was ≥0.1 μg/ml from Baltimore, Md., during 1995–1996 (
n
= 143). The dendrogram analysis of PFGE patterns included 32 distinct clonal groups. Six major clonal groups included two-thirds of the PNSP strains. Major clonal groups 2, 3, 4, and 6 strains were genetically related to four previously described international clones and were all multidrug resistant. Major clonal group 3 was genetically related to the Tennessee
23F
-4 clone and contained all four strains for which the penicillin MIC was 8 μg/ml. Most of the clonal group 1 and 5 strains had intermediate susceptibility to penicillin and were rarely multidrug resistant. The latter clonal groups represent two previously undescribed penicillin-intermediate pneumococcal clones. Clonal group homogeneity was greater for serotype 9V, 19A, and 23F strains than for serotype 6A, 6B, 14, and 19F strains. The classification of PNSP strains into clonal groups is essential for future population-based epidemiologic studies of PNSP.
Restriction Endonuclease Analysis Discriminates
Bordetella bronchiseptica
Isolates
Authors: Sacco Randy E. , Register Karen B. , Nordholm Gwen E.
Published: December 2019

One hundred ninety-five
Bordetella bronchiseptica
isolates from 12 different host species worldwide were characterized by restriction enzyme analysis (REA). These isolates had previously been categorized into 19
Pvu
II ribotypes. Twenty restriction endonucleases were evaluated for use in REA. Digestion of chromosomal DNA with
Hin
fI, followed by submarine electrophoresis in agarose gels and staining with ethidium bromide, produced DNA fragments in the 4.0- to 10-kb range, which readily discriminated
B. bronchiseptica
isolates, resulting in 48 fingerprint patterns. Moreover,
Alu
I digestion of chromosomal DNA produced 39 distinct fingerprint profiles with DNA fragments ranging from 6.0 to 20.0 kb. While REA frequently provided more discriminatory power than ribotyping, there were examples where the use of ribotyping was more discriminatory than REA. Passage of selected isolates up to passage 25 did not change the REA profile. Moreover, the Bvg phase did not alter the fingerprint profile of chromosomal DNA from
B. bronchiseptica
strains digested with
Hin
fI or
Alu
I. Based on the results presented herein, the combination of REA and ribotyping should provide valuable information in understanding the molecular epidemiology of
B. bronchiseptica
infections.
Tween 80 Opacity Test Responses of Various
Candida
Species
Authors: Slifkin Malcolm
Published: December 2019

A total of 111
Candida
isolates representing 11 species were examined for their respective responses to a Tween 80 opacity test. The strains of
Candida albicans
and
C. tropicalis
that were examined produced an opacity response around their colonies at 2 to 3 days postinoculation. A second group of
Candida
species yielded a halo around their colonies at 8 to 10 days postinoculation. The remaining
Candida
species did not produce a positive test response through 10 days postinoculation. The strains of
C. dubliniensis
were easily differentiated from strains of
C. albicans
by this test. The Tween 80 opacity test is simple and economical to prepare and is easy to interpret.
Comparison of Human Immunodeficiency Virus Type 1 RNA Sequence Heterogeneity in Cerebrospinal Fluid and Plasma
Authors: Tang Yi-Wei , Huong Joe T.-J. , Lloyd Robert M. , Spearman Paul , Haas David W.
Published: December 2019

The source of human immunodeficiency virus type 1 (HIV-1) RNA in cerebrospinal fluid (CSF) during HIV-1 infection is uncertain. The sequence heterogeneity of HIV-1 RNA in simultaneous CSF and plasma samples was characterized for five patients at the baseline and during the first week of antiretroviral therapy by two commercial genotyping methodologies. In individual subjects, the sequences in CSF samples differed significantly from those in plasma. In contrast, the viral sequences in CSF at the baseline did not differ from the sequences in CSF during treatment. Similarly, viral sequences in plasma did not vary over this interval. This study provides evidence that HIV-1 RNA in CSF and plasma arise from distinct compartments.
Evaluation of R-Mix FreshCells in Shell Vials for Detection of Respiratory Viruses
Authors: Fong Caroline K. Y. , Lee Mi Kyung , Griffith Brigitte P.
Published: December 2019

The performance of a mixture of mink lung and A549 cell lines in shell vials (MSVs) for the detection of respiratory viruses in 159 specimens was evaluated. MSVs, conventional culture, and direct immunofluorescence assay identified 96, 85, and 67% of the influenza A virus-positive specimens, respectively. MSVs provided both a high degree of sensitivity and rapid turnaround times for the detection of influenza A virus.
Acute Echinococcosis: a Case Report
Authors: Di Comite Gabriele , Dognini Giuseppina , Gaiera Giovanni , Ieri Rossella , Praderio Luisa
Published: December 2019

We report the case of a 69-year-old man with acute pulmonary echinococcosis. A computed tomographic scan of the thorax revealed the presence of multiple nodules in both lungs, and laboratory tests showed eosinophilia and the presence of antibodies against
Echinococcus granulosus
. Therapy with albendazole led to resolution of the pulmonary nodules and a normalization of the white cell count. To our knowledge this is the first described case of acute echinococcosis, as the diagnosis of this disease is usually delayed to chronic phases. Therefore, finding unexplained eosinophilia, especially in association with pulmonary nodules, should lead one to suspect acute hydatid disease.
Value of Different Assays for Detection of Human Cytomegalovirus (HCMV) in Predicting the Development of HCMV Disease in Human Immunodeficiency Virus-Infected Patients
Authors: Blank Brian S. N. , Meenhorst Pieter L. , Mulder Jan Willem , Weverling Gerrit Jan , Putter Hein , Pauw Wouter , van Dijk Willemien C. , Smits Paul , Lie-A-Ling Sonja , Reiss Peter , Lange Joep M. A.
Published: December 2019

In the present prospective study, five blood tests for detection of human cytomegalovirus (HCMV), nucleic acid sequence-based amplification (NASBA) for detection of early (immediate-early antigen) and late (pp67) mRNA, PCR for detection of HCMV DNA (DNA PCR), culture, and pp65 antigenemia assay, and culture and DNA PCR of urine and throat swab specimens were compared for their abilities to predict the development of disease caused by HCMV (HCMV disease). Of 101 human immunodeficiency virus (HIV)-infected patients with ≤100 CD4
+
lymphocytes per mm
3
, 25 patients developed HCMV disease. The pp65 antigenemia assay (sensitivity, 50%; specificity, 89%) and DNA PCR of blood (sensitivity, 69%; specificity, 75%) were most accurate in predicting the development of HCMV disease within the next 12 months. Both blood culture and late pp67 mRNA NASBA had high specificities (91 and 90%, respectively) but low sensitivities (25 and 13%, respectively). The sensitivities of urine culture, DNA PCR, throat swab specimen culture, DNA PCR, and NASBA of blood for detection of the immediate-early antigen were 73, 87, 53, 67, and 63%, respectively, and the specificities were 58, 46, 76, 60, and 72%, respectively. The positive predictive values of all tests however, were low and did not exceed 50%. In conclusion, virological screening by these qualitative assays for detection of HCMV is of limited value for prediction of the development of HCMV disease in HIV-infected patients.
Pulsed-Field Gel Electrophoresis Analysis of Nasopharyngeal Flora in Children Attending a Day Care Center
Authors: Yano Hisakazu , Suetake Mitsuko , Kuga Akio , Irinoda Kazuhiko , Okamoto Ryoichi , Kobayashi Toshimitsu , Inoue Matsuhisa
Published: December 2019

To investigate how bacterial pathogens spread from child to child in a day care center, we monitored six children, two boys and four girls, born between August 1995 and November 1997, attending a day care center and analyzed nasopharyngeal samples from them using pulsed-field gel electrophoresis (PFGE). We obtained nasopharyngeal cultures from all of the affected children and almost all of the unaffected children between September 1998 and March 1999 after some children presented simultaneously with purulent rhinorrhea. Moreover, when a child was found to have acute otitis media, nasopharyngeal secretions from the child were independently cultured during treatment. During this period, 28 isolates of
Moraxella catarrhalis
, 13 of
Streptococcus pneumoniae
, and 4 of
Haemophilus influenzae
were recovered. PFGE gave 8 patterns for
M. catarrhalis
, 10 for
S. pneumoniae
, and 1 for
H. influenzae
. PFGE patterns demonstrated spread of
M. catarrhalis
between children. However, each occurrence of clusters of infection with
M. catarrhalis
lasted 2 to 6 weeks, with a change in PFGE pattern between occurrences of clusters. The
M. catarrhalis
strain infecting each child also changed. Similarly, the
S. pneumoniae
strain in each child also changed. In contrast, infection with
H. influenzae
persisted for about 3 months in an affected child.
Performance of a Multiplex Qualitative PCR LCx Assay for Detection of Human Immunodeficiency Virus Type 1 (HIV-1) Group M Subtypes, Group O, and HIV-2
Authors: Abravaya Klara , Esping Claudia , Hoenle Robert , Gorzowski Jacek , Perry Robert , Kroeger Paul , Robinson John , Flanders Richard
Published: December 2019

Early detection of human immunodeficiency virus (HIV) in blood and blood products can be achieved by a sensitive nucleic acid amplification-based assay. We report on the performance of a PCR-based qualitative assay that detects both HIV type 1 (HIV-1) and HIV-2 with a sensitivity of 20 to 50 copies/ml. The assay has a specificity of 99.6% and an inhibition rate of 1.7%. One milliliter of sample is processed with a manifold system and Qiagen columns, and one-third of the extracted sample is used for PCR amplification. An internal control sequence, which is processed and amplified with each sample, monitors for amplification inhibition. Samples are reverse transcribed and are then amplified by reverse transcription-coupled PCR, after which HIV-1- and HIV-2-specific probes are hybridized to the amplified products. Following hybridization, samples are detected in the LCx instrument by microparticle enzyme immunoassay techniques. The detection system has an automated inactivation step that controls for PCR contamination. The HIV-1/2 qualitative RNA assay detects HIV-1 group M subtypes A, B, C, D, E, F, and G and group O. Testing of several HIV-1 seroconversion panels has demonstrated that the HIV-1/2 qualitative RNA assay detects HIV infection on the average of 6 days before p24 antigen can be detected and 11 days before antibodies can be detected.
Resistance of
Trichomonas vaginalis
to Metronidazole: Report of the First Three Cases from Finland and Optimization of In Vitro Susceptibility Testing under Various Oxygen Concentrations
Authors: Meri Taru , Jokiranta T. Sakari , Suhonen Lauri , Meri Seppo
Published: December 2019

Trichomonas vaginalis
is a globally common sexually transmitted human parasite. Many strains of
T. vaginalis
from around the world have been described to be resistant to the current drug of choice, metronidazole. However, only a few cases of metronidazole resistance have been reported from Europe. The resistant strains cause prolonged infections which are difficult to treat.
T. vaginalis
infection also increases the risk for human immunodeficiency virus transmission. We present a practical method for determining the resistance of
T. vaginalis
to 5-nitroimidazoles. The suggested method was developed by determining the MICs and minimal lethal concentrations (MLCs) of metronidazole and ornidazole for
T. vaginalis
under various aerobic and anaerobic conditions. Using this assay we have found the first three metronidazole-resistant strains from Finland, although the origin of at least one of the strains seems to be Russia. Analysis of the patient-derived and previously characterized isolates showed that metronidazole-resistant strains were also resistant to ornidazole, and MLCs for all strains tested correlated well with the MICs. The suggested MICs of metronidazole for differentiation of sensitive and resistant isolates are >75 μg/ml in an aerobic 24-h assay and >15 μg/ml in an anaerobic 48-h assay.
Diagnosis of Herpes Simplex Virus Infections in the Clinical Laboratory by LightCycler PCR
Authors: Espy Mark J. , Uhl James R. , Mitchell P. Shawn , Thorvilson Jill N. , Svien Kathleen A. , Wold Arlo D. , Smith Thomas F.
Published: December 2019

Herpes simplex virus (HSV) causes several clinical manifestations in both normal and immunocompromised hosts; this agent is the most frequently detected virus in diagnostic laboratories. Recovery of the virus in cell culture is considered the “gold standard” for detection of this virus from sources other than cerebrospinal fluid. LightCycler is a newly developed, commercially available system designed to rapidly perform PCR, with real-time detection of PCR products by a fluorescence resonance energy transfer assay. We compared the detection of HSV for 200 specimens (number of genital specimens, 160; number of dermal specimens, 38; number of ocular specimens, 2) by shell vial cell cultures (MRC-5) and by LightCycler PCR. Of a total of 88 (44%) HSV strains detected, 69 (78%) were detected by both shell vial cell cultures and LightCycler PCR (DNA polymerase target). A total of 19 (22%) specimens were detected exclusively by LightCycler PCR. No specimens were positive by the shell vial assay only. All 19 discrepant samples had HSV DNA detected by an independent PCR directed to the thymidine kinase gene of the virus. The melting curve analysis feature of the LightCycler instrument identified identical genotype results for HSV type 1 (HSV-1) and HSV-2 from 84 of 88 (96%) positive samples. Specimens can be extracted, target HSV DNA can be amplified, and HSV PCR products can be identified by genotype within 2 h after receipt of specimen into the laboratory. The increased level of accurate identification (all 88 positive samples) compared with that of shell vial cell culture (69 of 88 samples identified as positive) and the agreement of LightCycler PCR results with all shell vial positive results indicate the potential for routine implementation of this technology for laboratory diagnosis of HSV infections.
Effect of a
Mycoplasma hominis
-Like Mycoplasma on the Infection of HEp-2 Cells by the TW-183 Strain of
Chlamydia pneumoniae
Authors: Castilla Elias A. , Wadowsky Robert M.
Published: December 2019

We isolated a
Mycoplasma hominis
-like mycoplasma from a stock culture of
Chlamydia pneumoniae
TW-183 obtained from the American Type Culture Collection and eradicated the contaminant by treating the stock suspension with a nonionic detergent, Igepal CA-630. The
M. hominis
-like mycoplasma neither inhibits nor enhances the infectivity of
C. pneumoniae
for HEp-2 cells.
Trends in Antifungal Susceptibility among
Candida
sp. Urinary Isolates from 1994 and 1998
Authors: Baran Joseph , Klauber Enid , Barczak Jeffrey , Riederer Kathleen , Khatib Riad
Published: December 2019

Antifungal susceptibilities were determined from 80 urinary isolates of
Candida
species collected in 1994 and 1998. Our findings demonstrate increasing geometric means of fluconazole MICs and fluconazole resistance in
Candida albicans
and
Candida tropicalis
(those for
Candida glabrata
were unchanged) within the 4-year span. Amphotericin B and voriconazole MICs remained constant.
Diversity within the VP4 Gene of Rotavirus P[8] Strains: Implications for Reverse Transcription-PCR Genotyping
Authors: Iturriza-Gómara Miren , Green Jon , Brown David W. G. , Desselberger Ulrich , Gray James J.
Published: December 2019

A degenerate version (1T1-D) of the rotavirus P[8]-specific primer (1T-1) allowed strains previously untypeable due to the accumulation of point mutations at the primer binding site to be P typed by reverse transcription-PCR. Sequencing of the cDNA followed by sequence alignment and phylogenetic analysis identified lineages and sublineages within the rotavirus P[8] types, while the use of 1T-1 or 1T-1D primers did not yield viral clusters in any particular lineage.
Evaluation of the Discriminatory Powers of the Dienes Test and Ribotyping as Typing Methods for
Proteus mirabilis
Authors: Pfaller M. A. , Mujeeb I. , Hollis R. J. , Jones R. N. , Doern G. V.
Published: December 2019

A total of 63 clinical isolates of
Proteus mirabilis
collected over a 19-month period were typed by the Dienes test and ribotyping. Ribotyping was performed using the fully automated RiboPrinter Microbial Characterization System (Qualicon, Wilmington, Del.). Isolates that were indistinguishable by the Dienes test and/or ribotyping were characterized further by pulsed-field gel electrophoresis (PFGE). Most of the isolates represented unique strains as judged by the Dienes test and ribotyping. Forty isolates represented 40 different ribotypes and Dienes types. The remaining 23 isolates were grouped into 13 Dienes types, 12 ribotypes, and 14 PFGE types. The index of discrimination was 0.980 for the Dienes test, 0.979 for ribotyping, and 0.992 for PFGE. Both the Dienes test and ribotyping are useful methods for identifying individual strains of
P. mirabilis
. The Dienes test is simple, inexpensive, and easy to perform. It can be performed in virtually any laboratory and should be used in the initial epidemiologic characterization of
P. mirabilis
isolates.
Genome-Sequence-Based Fluorescent Amplified-Fragment Length Polymorphism Analysis of
Mycobacterium tuberculosis
Authors: Goulding Jonathan N. , Stanley John , Saunders Nick , Arnold Catherine
Published: December 2019

The whole-genome fingerprinting technique, fluorescent amplified-fragment length polymorphism (FAFLP) analysis, was applied to
Mycobacterium tuberculosis
. Sixty-five clinical isolates were analyzed to determine the value of FAFLP as a stand-alone genotyping technique and to compare it with the well-established IS
6110
typing system. The genome sequence of
M. tuberculosis
strain H37Rv (S. T. Cole et al., Nature 393:537–544, 1998) was used to model computer-generated informative primer combination(s), and the precision and reproducibility of FAFLP were evaluated by comparing the results of in vitro and computer-generated experiments. Multiplex FAFLP was used to increase resolving power in a predictable and systematic fashion. FAFLP analysis was broadly congruent with IS
6110
typing for those strains with multiple IS
6110
copies. It was also able to resolve an epidemiologically unlinked group of strains with only one copy of IS
6110
; up to 10% of clinical isolates may fall into this category. For certain epidemiological investigations, it was concluded that a combination of FAFLP and IS
6110
typing would give higher resolution than would either alone. FAFLP data were digital, precise, reproducible, and suitable for rapid electronic dissemination, manipulation, interlaboratory comparison, and storage in national or international epidemiological databases. Because FAFLP samples and analyzes base substitution across the genome as a whole, FAFLP could generate new information about the microevolution of the
M. tuberculosis
complex.
Evaluation of autoSCAN-W/A and the Vitek GNI+ AutoMicrobic System for Identification of Non-Glucose-Fermenting Gram-Negative Bacilli
Authors: Sung Ling Ling , Yang Dine Ie , Hung Chia Chien , Ho Hsin Tsung
Published: December 2019

The autoSCAN-W/A (W/A; Dade Behring Microscan Inc., West Sacramento, Calif.) and Vitek AutoMicrobic System (Vitek AMS; bioMérieux Vitek Systems, Inc., Hazelwood, Mo.) are both fully automated microbiology systems. We evaluated the accuracy of these two systems in identifying nonglucose-fermenting gram-negative bacilli. We used the W/A with conventional-panel Neg Combo type 12 and Vitek GNI+ identification systems. A total of 301 isolates from 25 different species were tested. Of these, 299 isolates were identified in the databases of both systems. The conventional biochemical methods were used for reference. The W/A correctly identified 215 isolates (71.4%) to the species level at initial testing with a high probability of ≥85%. The Vitek GNI+ correctly identified 216 isolates (71.8%) to the species level at initial testing with a high probability of ≥90%. After additional testing that was recommended by the manufacturer's protocol, the correct identifications of the W/A and Vitek GNI+ improved to 96.0 and 92.3%, respectively. The major misidentified species were
Sphingomonas paucimobilis
and
Agrobacterium radiobacter
in the W/A system and
Acinetobacter lwoffii
,
Chryseobacterium indologenes
, and
Comamonas acidovorans
in the Vitek GNI+ system. The error rates were 4.0 and 7.6%, respectively. The overall accuracy for both systems was above 90% if the supplemental tests were applied. There was no significant difference in accuracy (
P
> 0.05) between the two systems.
Molecular Characterization of
Staphylococcus sciuri
Strains Isolated from Humans
Authors: Couto Isabel , Sanches Ilda Santos , Sá-Leão Raquel , de Lencastre Hermínia
Published: December 2019

We previously characterized over 100
Staphylococcus sciuri
isolates, mainly of animal origin, and found that they all carried a genetic element (
S. sciuri mecA
) closely related to the
mecA
gene of methicillin-resistant
Staphylococcus aureus
(MRSA) strains. We also found a few isolates that carried a second copy of the gene, identical to MRSA
mecA
. In this work, we analyzed a collection of 28
S. sciuri
strains isolated from both healthy and hospitalized individuals. This was a relatively heterogeneous group, as inferred from the different sources, places, and dates of isolation and as confirmed by pulsed-field gel electrophoresis analysis. All strains carried the
S. sciuri mecA
copy, sustaining our previous proposal that this element belongs to the genetic background of
S. sciuri
. Moreover, 46% of the strains also carried the MRSA
mecA
copy. Only these strains showed significant levels of resistance to beta-lactams. Strikingly, the majority of the strains carrying the additional MRSA
mecA
copy were obtained from healthy individuals in an antibiotic-free environment. Most of the 28 strains were resistant to penicillin, intermediately resistant to clindamycin, and susceptible to tetracycline, erythromycin, and gentamicin. Resistance to these last three antibiotics was found in some strains only. The findings reported in this work confirmed the role of
S. sciuri
in the evolution of the mechanism of resistance to methicillin in staphylococci and suggested that this species (like the pathogenic staphylococci) may accumulate resistance markers for several classes of antibiotics.
A Simplified Method for Testing
Bordetella pertussis
for Resistance to Erythromycin and Other Antimicrobial Agents
Authors: Hill Bertha C. , Baker Carolyn N. , Tenover Fred C.
Published: December 2019

Present methods of antimicrobial susceptibility testing of
Bordetella pertussis
are time consuming and require specialized media that are not commercially available. We tested 52 isolates of
B. pertussis
for resistance to erythromycin, trimethoprim-sulfamethoxazole, chloramphenicol, and rifampin by agar dilution with Bordet-Gengou agar (BGA) containing 20% horse blood (reference method), Etest using BGA and Regan-Lowe agar without cephalexin (RL−C), and disk diffusion using BGA and RL−C. The organisms tested included four erythromycin-resistant isolates of
B. pertussis
from a single patient, a second erythromycin-resistant strain of
B. pertussis
from an unrelated patient in another state, and 47 nasopharyngeal surveillance isolates of
B. pertussis
from children in the western United States. The results of agar dilution testing using direct inoculation of the organisms suspended in Mueller-Hinton broth were within ±1 dilution of those obtained after overnight passage of the inoculum in Stainer-Scholte medium, which is the traditional method of testing
B. pertussis
. The Etest method produced MICs similar to those of the agar dilution reference method for three of the four antimicrobial agents tested; the trimethoprim-sulfamethoxazole results were lower with Etest, particularly when the direct suspension method was used. Most of the Etest MICs, except for that of erythromycin, were on scale. Disk diffusion testing using RL−C medium was helpful in identifying the erythromycin-resistant strains, which produced no zone of inhibition around the disk; susceptible isolates produced zones of at least 42 mm. Thus, the antimicrobial susceptibility testing of
B. pertussis
can be simplified by using the Etest or disk diffusion on RL−C to screen for erythromycin-resistant isolates of
B. pertussis
.