bluuebunny/crossref_metadata_2025 huggingface dataset:
Head-to-Head Evaluation of Five Chlamydia Tests Relative to a Quality-Assured Culture Standard
Authors: Newhall Wilbert J. , Johnson Robert E. , DeLisle Susan , Fine David , Hadgu Alula , Matsuda Bessie , Osmond Donna , Campbell Joyce , Stamm Walter E.
Published: December 2019

Nucleic acid amplification tests offer superior sensitivity for the detection of
Chlamydia trachomatis
infection, but many laboratories still use nonamplification methods because of the lower cost and ease of use. In spite of their availability for more than a decade, few studies have directly compared the nonamplification tests. Such comparisons are still needed in addition to studies that directly compare individual nonamplification and amplification tests. The purpose of this study was to evaluate and compare the performance characteristics relative to culture of five different tests for the detection of
C. trachomatis
with and without confirmation of positive results. The tests were applied to endocervical specimens from 4,980 women attending family planning clinics in the northwestern United States. The five nonculture tests included Chlamydiazyme (Abbott), MicroTrak direct fluorescent antibody (DFA) (Syva), MicroTrak enzyme immunoassay (EIA) (Syva), Pace 2 (Gen-Probe), and Pathfinder EIA (Sanofi/Kallestad). All positive results obtained with a nonculture test (except MicroTrak DFA) were confirmed by testing the original specimens with a blocking antibody test (Chlamydiazyme), a cytospin DFA (MicroTrak EIA and Pathfinder EIA), and a probe competition assay (Pace 2). The prevalence of culture-proven chlamydia was 3.9%. The sensitivities of the nonculture tests were in a range from 62 to 75%, and significant differences between tests in terms of sensitivity were observed. The positive predictive value for each test was 0.85 or higher. The specificities of the nonculture tests without performance of confirmations were greater than 99%. Performing confirmatory tests eliminated nearly all of the false positives.
Antimicrobial Susceptibility Patterns of
Aeromonas jandaei
,
A. schubertii
,
A. trota
, and
A. veronii
Biotype veronii
Authors: Overman Timothy L. , Janda J. Michael
Published: December 2019

Fifty-six isolates of four
Aeromonas
species, which have been documented as causative agents of human infections or isolated from human clinical specimens, were subjected to antimicrobial susceptibility testing using a MicroScan WalkAway conventional (overnight incubation) gram-negative panel. The four species tested and the number of isolates of each were as follows:
Aeromonas jandaei
, 17;
A. schubertii
, 12;
A. trota
, 15; and
A. veronii
biotype veronii, 12. All isolates of
A. trota
were susceptible to all antimicrobial agents tested, except cefazolin (20% of isolates were resistant) and cefoxitin (13% of isolates were resistant). All isolates of
A. schubertii
and
A. veronii
biotype veronii, as well as 88% of
A. jandaei
isolates, were resistant to ampicillin. Resistance to ampicillin-sulbactam ranged from 25% of
A. schubertii
strains to 100% of
A. veronii
biotype veronii strains. Cefazolin resistance ranged from 17% of
A. veronii
biotype veronii isolates to 59% of
A. jandaei
isolates. Imipenem resistance was detected in 65% of
A. jandaei
strains and 67% of
A. veronii
biotype veronii strains.
A. jandaei
displayed resistance to piperacillin and ticarcillin in 53 and 71% of the isolates, respectively.
A. veronii
biotype veronii strains were 100% susceptible to piperacillin and 100% resistant to ticarcillin. These antibiogram data may be useful in establishing the identification of these four species when members of the genus
Aeromonas
are isolated from human clinical sources.
Sensitivity and Specificity of Dipstick Tests for Rapid Diagnosis of Malaria in Nonimmune Travelers
Authors: Jelinek T. , Grobusch M. P. , Schwenke S. , Steidl S. , von Sonnenburg F. , Nothdurft H. D. , Klein E. , Löscher T.
Published: December 2019

Swift diagnosis of
Plasmodium falciparum
malaria in areas where the disease is not endemic is frequently complicated by the lack of experience on the side of involved laboratory personal. Diagnostic tools based on the dipstick principle for the detection of plasmodial histidine-rich protein 2 (HRP-2) and parasite-specific lactate dehydrogenase (pLDH), respectively, have become available for the qualitative detection of
P. falciparum
malaria. In order to evaluate two of the currently available assays, specimens from 231 patients were screened during a prospective multicenter study. Among the screened specimens, samples from 53 patients (22.9%) were positive for
P. falciparum
malaria by microscopy and/or PCR. While the test kit based on the detection of HRP-2 performed with a sensitivity of 92.5% and a specificity of 98.3%, the kit for the detection of pLDH showed a sensitivity of 88.5% and a specificity of 99.4%. Dipstick tests have the potential of enhancing speed and accuracy of the diagnosis of
P. falciparum
malaria, especially if nonspecialized laboratories are involved.
Multicenter Evaluation of the BACTEC MGIT 960 System for Recovery of Mycobacteria
Authors: Hanna Bruce A. , Ebrahimzadeh Adeleh , Elliott L. Bruce , Morgan Margie A. , Novak Susan M. , Rusch-Gerdes Sabine , Acio Millie , Dunbar Denise F. , Holmes T. Michele , Rexer Charles H. , Savthyakumar Chiminyan , Vannier Ann M.
Published: December 2019

We evaluated the BACTEC MGIT 960 system, which is a fully automated, noninvasive system for the growth and detection of mycobacteria with a capacity to incubate and continuously monitor 960 7-ml culture tubes. We studied 3,330 specimens, 2,210 respiratory and 1,120 nonrespiratory specimens, collected from 2,346 patients treated at six sites. Processed specimens were inoculated into the BACTEC MGIT 960 and BACTEC 460 TB systems, as well as onto Lowenstein-Jensen slants and Middlebrook 7H11/7H11 selective plates. From all culture systems, a total of 362 isolates of mycobacteria were recovered; these were recovered from 353 specimens collected from 247 patients. The greatest number of isolates of mycobacteria (289, or 80% of the 362 isolates) was recovered with the BACTEC MGIT 960, followed by the BACTEC 460 TB (271, or 75%) and solid media (250, or 69%). From all culture systems a total of 132 isolates of
Mycobacterium tuberculosis
complex were recovered. The greatest number of isolates of
M. tuberculosis
complex was recovered when liquid medium was combined with conventional solid media; the number recovered with BACTEC 460 TB plus solid media was 128 (97%), that recovered with BACTEC MGIT 960 plus solid media was 121 (92%), that recovered with BACTEC 460 TB was 119 (90%) and that recovered with all solid media combined was 105 (79%). The recovery with BACTEC MGIT 960 alone was 102 (77%). The mean times to detection (TTD) for
M. tuberculosis
complex were 14.4 days for BACTEC MGIT, 15.2 days for BACTEC 460 TB, and 24.1 days for solid media. The numbers of isolates of
Mycobacterium avium
complex (MAC) recovered were 172 (100%) for all systems, 147 (85%) for BACTEC MGIT 960, 123 (72%) for BACTEC 460 TB, and 106 (62%) for all solid media combined. The TTD for MAC in each system were 10.0 days for BACTEC MGIT 960, 10.4 days for BACTEC 460 TB, and 25.9 days for solid media. Breakthrough contamination rates (percentages of isolates) for each of the systems were 8.1% for BACTEC MGIT 960, 4.9% for BACTEC 460 TB, and 21.1% for all solid media combined.
Application of Dried Blood Spot Specimens for Serologic Subtyping of Human Immunodeficiency Virus Type 1 in Thailand
Authors: Chanbancherd P. , Brown A. E. , Trichavaroj R. , Tienamporn P. , Puthakird P. , Limpairojn N. , VanCott T. C. , de Souza M. S.
Published: December 2019

Dried blood spot (DBS) specimens were assessed as an alternative to plasma for human immunodeficiency virus type 1 (HIV-1) serotyping by V3 loop peptide enzyme immunoassay. Nested PCR capable of distinguishing HIV-1 subtypes B and E was used as the reference standard. Ninety-two percent of DBS samples were typeable as either HIV-1 subtype B or E. Serotype results with DBS and plasma were identical for 254 of 257 specimens. A simple DBS collection method provides a convenient alternative for conducting HIV-1 serotype surveillance while retaining sensitivity and specificity.
Analysis with a Combination of Macrorestriction Endonucleases Reveals a High Degree of Polymorphism among
Bordetella pertussis
Isolates in Eastern France
Authors: Prevost G. , Freitas F. I. S. , Stoessel P. , Meunier O. , Haubensack M. , Monteil H. , Scheftel J. M.
Published: December 2019

From 1990 to 1996, routine screening for whooping cough identified 399 patients with a calmodulin-dependent adenylate cyclase-positive test result and yielded 69
Bordetella pertussis
isolates. None of the patients were fully vaccinated, and most were less than 6 months old. Analysis of total DNA by pulsed-field gel electrophoresis (PFGE) after
Xba
I,
Spe
I, or
Dra
I macrorestriction yielded 19, 15, and 5 different patterns, respectively, whereas ribotyping failed to demonstrate any strain polymorphism. Discrimination among the isolates was improved by combining the PFGE profiles. Some patterns were more frequent, but the corresponding patients were not clearly epidemiologically related. The patterns for two strains obtained during a 3-month period from patients who were neighbors differed by the length of a single DNA fragment. These data strongly suggest that one type of isolate is widely spread throughout the world and is carried by individuals other than patients who develop a true illness.
Clinical Significance of Expression of Human Cytomegalovirus pp67 Late Transcript in Heart, Lung, and Bone Marrow Transplant Recipients as Determined by Nucleic Acid Sequence-Based Amplification
Authors: Gerna Giuseppe , Baldanti Fausto , Middeldorp Jaap M. , Furione Milena , Zavattoni Maurizio , Lilleri Daniele , Revello Maria Grazia
Published: December 2019

Human cytomegalovirus (HCMV) infection was monitored retrospectively by qualitative determination of pp67 mRNA (a late viral transcript) by nucleic acid sequence-based amplification (NASBA) in a series of 50 transplant recipients, including 26 solid-organ (11 heart and 15 lung) transplant recipients (SOTRs) and 24 bone marrow transplant recipients (BMTRs). NASBA results were compared with those obtained by prospective quantitation of HCMV viremia and antigenemia and retrospective quantitation of DNA in leukocytes (leukoDNAemia). On the whole, 29 patients were NASBA positive, whereas 10 were NASBA negative, and the blood of 11 patients remained HCMV negative. NASBA detected HCMV infection before quantitation of viremia did but after quantitation of leukoDNAemia and antigenemia did. In NASBA-positive blood samples, median levels of viremia, antigenemia, and leukoDNAemia were significantly higher than the relevant levels detected in NASBA-negative HCMV-positive blood samples. By using the quantitation of leukoDNAemia as the “gold standard,” the analytical sensitivity (47.3%), as well as the negative predictive value (68.3%), of NASBA for the diagnosis of HCMV infection intermediate between that of antigenemia quantitation (analytical sensitivity, 72.3%) and that of viremia quantitation (analytical sensitivity, 28.7%), while the specificity and the positive predictive value were high (90 to 100%). However, with respect to the clinically relevant antigenemia cutoff of ≥100 used in this study for the initiation of preemptive therapy in SOTRs with reactivated HCMV infection, the clinical sensitivity of NASBA reached 100%, with a specificity of 68.9%. Upon the initiation of antigenemia quantitation-guided treatment, the actual median antigenemia level was 158 (range, 124 to 580) in SOTRs who had reactivated infection and who presented with NASBA positivity 3.5 ± 2.6 days in advance and 13.5 (range, 1 to 270) in the group that included BMTRs and SOTRs who had primary infection (in whom treatment was initiated upon the first confirmation of detection of HCMV in blood) and who presented with NASBA positivity 2.0 ± 5.1 days later. Following antiviral treatment, the durations of the presence of antigenemia and pp67 mRNA in blood were found to be similar. In conclusion, monitoring of the expression of HCMV pp67 mRNA appears to be a promising, well-standardized tool for determination of the need for the initiation and termination of preemptive therapy. Its overall clinical impact should be analyzed in future prospective studies.
Detection of Antibody to Avian Influenza A (H5N1) Virus in Human Serum by Using a Combination of Serologic Assays
Authors: Rowe Thomas , Abernathy Robert A. , Hu-Primmer Jean , Thompson William W. , Lu Xiuhua , Lim Wilina , Fukuda Keiji , Cox Nancy J. , Katz Jacqueline M.
Published: December 2019

From May to December 1997, 18 cases of mild to severe respiratory illness caused by avian influenza A (H5N1) viruses were identified in Hong Kong. The emergence of an avian virus in the human population prompted an epidemiological investigation to determine the extent of human-to-human transmission of the virus and risk factors associated with infection. The hemagglutination inhibition (HI) assay, the standard method for serologic detection of influenza virus infection in humans, has been shown to be less sensitive for the detection of antibodies induced by avian influenza viruses. Therefore, we developed a more sensitive microneutralization assay to detect antibodies to avian influenza in humans. Direct comparison of an HI assay and the microneutralization assay demonstrated that the latter was substantially more sensitive in detecting human antibodies to H5N1 virus in infected individuals. An H5-specific indirect enzyme-linked immunosorbent assay (ELISA) was also established to test children’s sera. The sensitivity and specificity of the microneutralization assay were compared with those of an H5-specific indirect ELISA. When combined with a confirmatory H5-specific Western blot test, the specificities of both assays were improved. Maximum sensitivity (80%) and specificity (96%) for the detection of anti-H5 antibody in adults aged 18 to 59 years were achieved by using the microneutralization assay combined with Western blotting. Maximum sensitivity (100%) and specificity (100%) in detecting anti-H5 antibody in sera obtained from children less than 15 years of age were achieved by using ELISA combined with Western blotting. This new test algorithm is being used for the seroepidemiologic investigations of the avian H5N1 influenza outbreak.
Comparison of the Mycobacteria Growth Indicator Tube with MB Redox, Löwenstein-Jensen, and Middlebrook 7H11 Media for Recovery of Mycobacteria in Clinical Specimens
Authors: Somoskövi Ákos , Magyar Pál
Published: December 2019

The rate of recovery and the mean time to detection of mycobacteria in clinical specimens were evaluated with two nonradiometric broth-based systems, the Mycobacteria Growth Indicator Tube (MGIT) and MB Redox systems. The data obtained for each system were compared with each other and with those obtained with the Löwenstein-Jensen (LJ) and Middlebrook 7H11 reference media. A total of 117 mycobacterial isolates (
Mycobacterium tuberculosis
,
n
= 112; nontuberculous mycobacteria,
n
= 5) were detected in 486 clinical specimens. The recovery rates for
M. tuberculosis
were 91 of 112 (81.3%) isolates with MGIT and 81 of 112 (72.3%) isolates with MB Redox. The combination of MGIT plus MB Redox recovered 104 of the 112 (92.9%)
M. tuberculosis
isolates. MGIT plus LJ plus Middlebrook 7H11 recovered 106 of the 112 (94.6%) isolates, MB Redox plus LJ plus Middlebrook 7H11 recovered 99 of the 112 (88.4%) isolates, and LJ plus Middlebrook 7H11 recovered 84 of the 112 (75.0%) isolates. The mean time to detection of
M. tuberculosis
in smear-positive specimens was 7.2 days with MGIT, 6.9 days with MB Redox, 20.4 days with LJ, and 17.6 days with Middlebrook 7H11. The mean time to detection of
M. tuberculosis
in smear-negative specimens was 19.1 days with MGIT, 15.5 days with MB Redox, 25.8 days with LJ, and 21.6 days with Middlebrook 7H11. The contamination rates were 4.4, 3.8, 2.1, and 2.7% for MGIT, MB Redox, LJ, and Middlebrook 7H11, respectively. In conclusion, MGIT and MB Redox can be viable tools in the routine mycobacteriology laboratory.
Characterization of Nonenterotoxigenic
Escherichia coli
Strains Producing F17 Fimbriae Isolated from Diarrheic Lambs and Goat Kids
Authors: Cid D. , Sanz R. , Marín I. , de Greve H. , Ruiz-Santa-Quiteria J. A. , Amils R. , de la Fuente R.
Published: December 2019

Forty-five ovine and caprine nonenterotoxigenic
Escherichia coli
strains producing F17-related fimbriae were characterized with respect to the fimbrial structural subunit and adhesin subtypes produced. In addition, several characteristics related to the virulence of strains producing F17 fimbriae were studied. Most of the strains (73%) possessed the
f17cA
structural subunit gene, whereas the
f17aA
and
f17dA
genes were detected only on three (6%) and two (4%) strains, respectively. The
f17bA
gene was not detected. All but one of these strains possessed the
f17G
genes of the adhesin subfamily II. The only strain having the
f17G
gene of subfamily I possessed the structural subunit gene
f17dA
. Sequencing of the
f17A
and
f17G
genes of four selected strains confirmed the association of
f17cA
and
f17dA
structural subunit genes with the
f17G
genes of the adhesin subfamily II. These results indicated that adhesins of the subfamily II are prominent among ovine and caprine isolates and that they are indistinctly associated with the F17 structural subunit subtypes on these field strains. CS31A- and CNF2-related genes were not detected. Most of the strains adhered in vitro to ovine intestinal brush borders (36 of 45) and agglutinated the erythrocytes of different species in the presence of
d
-mannose (39 of 45). F17-positive strains produced colicin V (57%) and were resistant to the bactericidal effect of serum (91%) in significantly higher percentages than F17-negative strains (34% produced colicin V, and 66% were serum resistant). Thus, most of the studied ovine and caprine strains showed phenotypic characteristics of septicemic strains.
Detection by Enzyme Immunoassay of Serum Immunoglobulin G Antibodies That Recognize Specific
Cryptosporidium parvum
Antigens
Authors: Priest Jeffrey W. , Kwon James P. , Moss Delynn M. , Roberts Jacquelin M. , Arrowood Michael J. , Dworkin Mark S. , Juranek Dennis D. , Lammie Patrick J.
Published: December 2019

Human infection with
Cryptosporidium parvum
usually elicits characteristic immunoglobulin G (IgG), IgA, and IgM antibody responses against two sporozoite surface antigens with apparent molecular masses of approximately 27 and 17 kDa. We have determined that these two antigens are actually complex families of related antigens. We have developed two new enzyme-linked immunosorbent assays (ELISAs) for the detection and quantitation of serum IgG antibodies against both antigens. The assays utilize a recombinant form of the 27-kDa antigen and a partially purified native fraction isolated from sonicated whole oocysts that contains 17-kDa antigen. An immunoblot assay previously developed in our laboratory served as the reference, or “gold standard,” seroassay for the assessment of the new ELISAs. Positive responses with the recombinant-27-kDa-antigen ELISA were correlated with the immunoblot results for the 27-kDa antigen, with a sensitivity and specificity of 90 and 92%, respectively. Similarly, positive responses with the partially purified native-17-kDa-antigen ELISA correlated with the immunoblot results for the 17-kDa antigen, with a sensitivity and specificity of 90 and 94%, respectively. For both ELISAs the median IgG antibody levels for serum sets collected during outbreaks of waterborne
C. parvum
infection were at least 2.5-fold higher than the levels determined for a nonoutbreak set. Using the immunoblot as the “gold standard,” the new ELISAs were more specific and, in the case of the 27-kDa-antigen ELISA, more sensitive than the crude oocyst antigen ELISA currently in use. These assays will be useful in future epidemiologic studies.
Abiotrophia
Species as a Cause of Endophthalmitis Following Cataract Extraction
Authors: Namdari Hassan , Kintner Kathleen , Jackson Barbara A. , Namdari Surena , Hughes Joan L. , Peairs Randall R. , Savage Donald J.
Published: December 2019

Microorganisms of the genus
Abiotrophia
, members of the oral flora, are known as important causes of bacterial endocarditis. In this study, we report two individual cases of acute vitreous infection caused by
Abiotrophia adiacens
and
Abiotrophia defectiva
approximately a week after cataract extraction.
Abiotrophia
isolates were recovered by cultivation of vitreous humor on chocolate agar and identified via conventional and API 20 Strep identification systems. An 83-year-old male patient (A) and an 80-year-old female patient (B) demonstrated almost identical symptoms of infectious endophthalmitis manifested as hypopyon and opaque media. The vision of both patients was reduced to detection of hand motion in the left and the right eyes, respectively. An emergency pars plana core vitrectomy was performed, and intraocular antibiotics were administered to each patient, who presented 8 months apart in two different institutions. Patients A and B were treated with an intravitreal injection of vancomycin-amikacin and vancomycin-ceftazidime, respectively, which resulted in complete recovery.
Simultaneous Detection of
Bacteroides forsythus
and
Prevotella intermedia
by 16S rRNA Gene-Directed Multiplex PCR
Authors: Conrads Georg , Flemmig Thomas F. , Seyfarth Ilse , Lampert Friedrich , Lütticken Rudolf
Published: December 2019

In a 16S rRNA gene-directed multiplex PCR,
Prevotella intermedia
- and
Bacteroides forsythus
-specific reverse primers were combined with a single conserved forward primer. A 660-bp fragment and an 840-bp fragment that were specific for both species could be amplified simultaneously. A total of 152 clinical samples, subgingival plaque and swabs of three different oral mucosae, from 38 periodontitis patients were used for the evaluation.
Assessment of Metronidazole Susceptibility in
Helicobacter pylori
: Statistical Validation and Error Rate Analysis of Breakpoints Determined by the Disk Diffusion Test
Authors: Chaves Sandra , Gadanho Mário , Tenreiro Rogério , Cabrita José
Published: December 2019

Metronidazole susceptibility of 100
Helicobacter pylori
strains was assessed by determining the inhibition zone diameters by disk diffusion test and the MICs by agar dilution and PDM Epsilometer test (E test). Linear regression analysis was performed, allowing the definition of significant linear relations, and revealed correlations of disk diffusion results with both E-test and agar dilution results (
r
2
= 0.88 and 0.81, respectively). No significant differences (
P
= 0.84) were found between MICs defined by E test and those defined by agar dilution, taken as a standard. Reproducibility comparison between E-test and disk diffusion tests showed that they are equivalent and with good precision. Two interpretative susceptibility schemes (with or without an intermediate class) were compared by an interpretative error rate analysis method. The susceptibility classification scheme that included the intermediate category was retained, and breakpoints were assessed for diffusion assay with 5-μg metronidazole disks. Strains with inhibition zone diameters less than 16 mm were defined as resistant (MIC > 8 μg/ml), those with zone diameters equal to or greater than 16 mm but less than 21 mm were considered intermediate (4 μg/ml < MIC ≤ 8 μg/ml), and those with zone diameters of 21 mm or greater were regarded as susceptible (MIC ≤ 4 μg/ml). Error rate analysis applied to this classification scheme showed occurrence frequencies of 1% for major errors and 7% for minor errors, when the results were compared to those obtained by agar dilution. No very major errors were detected, suggesting that disk diffusion might be a good alternative for determining the metronidazole sensitivity of
H. pylori
strains.
Improved Mg2+-Based Reverse Transcriptase Assay for Detection of Primate Retroviruses
Authors: Sears Johnna F. , Repaske Roy , Khan Arifa S.
Published: December 2019

The reverse transcriptase (RT) assay is a simple, relatively inexpensive, widely used assay that can detect all retroviruses (known and novel retroviruses as well as infectious and defective retroviruses) on the basis of the divalent cation requirement of their RT enzyme, i.e., Mg2+or Mn2+. Descriptions of various RT assays have been published; however, they cannot be directly applied to the analysis of biological products or clinical samples without further standardization to determine the lower limit of virus detection (sensitivity), assay variability (reproducibility), or ability to detect different retroviruses (specificity). We describe the detection of type E and type D primate retroviruses, which may be pathogenic for humans, by a new32P-based, Mg2+-containing RT assay. The results show that the sensitivity of detection is <3.2 50% tissue culture infective doses (TCID50s) for human immunodeficiency virus type 1 (HIV-1) and <1 TCID50for simian immunodeficiency virus isolated from a rhesus macaque (SIVmac). Analysis of recombinant HIV-1 RT enzyme indicated that 10−5U, which is equivalent to 4.25 × 104virions, could be detected. Additionally, genetically distinct type D retroviruses such as simian AIDS retrovirus and squirrel monkey retrovirus were also detected in the assay with similar sensitivities. Thus, the improved RT assay can be used to detect genetically divergent Mg2+-dependent retroviruses of human and simian origin that can infect human cells and that therefore pose a potential health risk to humans.
Characterization of Antimicrobial Resistance in
Streptococcus pyogenes
Isolates from the San Francisco Bay Area of Northern California
Authors: York Mary K. , Gibbs Laurel , Perdreau-Remington Francoise , Brooks G. F.
Published: December 2019

During 1994 and 1995, 157 isolates of
Streptococcus pyogenes
from patients with invasive disease were consecutively collected in the San Francisco Bay area to determine the frequency of antimicrobial resistance. Susceptibility testing was performed according to the guidelines of the National Committee for Clinical Laboratory Standards by the disk method and by broth microdilution. For comparison of susceptibility patterns, an additional 149 strains were randomly collected from patients with pharyngitis. For San Francisco County, 32% of the isolates from invasive-disease-related specimens but only 9% of the isolates from throat cultures from the same period were resistant to erythromycin (
P
= 0.0007). Alameda County and Contra Costa County had rates of resistance of ≤10% from isolates from all cultures. When the data were analyzed by hospital, the San Francisco County Hospital had a statistically higher rate of erythromycin resistance (39%) among the strains from serious infections compared to those from other counties (P = <0.0003). For tetracycline, high rates of resistance were observed in San Francisco County for both isolates from patients with invasive disease (34%) and pharyngitis (21%) in the same period. Using pulsed-field gel electrophoresis, two clones, one at the San Francisco County Hospital and a second in the entire area, were identified. The latter clone exhibited resistance to bacitracin. Of 146 strains that were tested by microdilution, all were susceptible to penicillin. Clindamycin resistance was not seen among the erythromycin-susceptible strains, but two of the 39 erythromycin-resistant strains were also resistant to clindamycin. An additional 34 strains showed resistance to clindamycin when exposed to an erythromycin disk in the double-disk diffusion test, suggesting that the mechanism of erythromycin resistance is due to an
erm
gene. This study demonstrates a high rate of resistance to macrolides and tetracycline among
S. pyogenes
isolates in San Francisco County and shows that macrolide resistance is more common in strains from patients with invasive disease than in strains from those with pharyngitis.
Rapid Identification of Fungi by Using the ITS2 Genetic Region and an Automated Fluorescent Capillary Electrophoresis System
Authors: Turenne Christine Y. , Sanche Steven E. , Hoban Daryl J. , Karlowsky James A. , Kabani Amin M.
Published: December 2019

Invasive fungal disease often plays an important role in the morbidity and mortality of immunocompromised patients. The poor sensitivity of current fungal blood culture and histological practices has led to the development of highly sensitive and specific molecular techniques, such as the PCR. Sequence variability of the internal transcribed spacer 2 (ITS2) region of fungi is potentially useful in rapid and accurate diagnosis of clinical fungal isolates. PCR with fungus-specific primers targeted toward conserved sequences of the 5.8S and 28S ribosomal DNA (rDNA) results in amplification of the species-specific ITS2 regions, which are variable in amplicon length. We have made use of the ABI PRISM 310 genetic analyzer and the ABI PRISM 310 GeneScan analysis software for the determination of variable size differences of the ITS2 region of clinically important fungi, including
Candida
and non-
Candida
yeasts,
Aspergillus
species, and a variety of dermatophytes. No cross-reaction occurred when samples were tested against human and bacterial genomic DNA. We have found that most clinically significant fungal isolates can be differentiated by this method, and it therefore serves to be a promising tool for the rapid (<7 h) diagnosis of fungemia and other invasive fungal infections.
Molecular Relationships and Antimicrobial Susceptibilities of Viridans Group Streptococci Isolated from Blood of Neutropenic Cancer Patients
Authors: Wisplinghoff H. , Reinert R. R. , Cornely O. , Seifert H.
Published: December 2019

From January 1995 to May 1998, 57 episodes of bacteremia due to viridans group streptococci were identified in 50 febrile neutropenic patients with hematologic malignancies. Four patients experienced two separate episodes of streptococcal bacteremia, and one patient had four separate episodes of streptococcal bacteremia. Strains were identified to species level as
Streptococcus mitis
(
n
= 37),
Streptococcus oralis
(
n
= 19), and
Streptococcus salivarius
(
n
= 1). Epidemiologic relatedness of these strains was studied by using PCR-based fingerprinting with M13 and ERIC-2 primers and pulsed-field gel electrophoresis with restriction enzyme
Sma
I. All strains that were isolated from different patients exhibited unique fingerprint patterns, thus suggesting that viridans group streptococcal bacteremia usually derives from an endogenous source. Cross-transmission of strains between patients could not be established. Four
S. mitis
isolates recovered during four separate bacteremic episodes in a single patient had identical fingerprint patterns. Susceptibility testing was carried out by broth microdilution technique according to National Committee for Clinical Laboratory Standards guidelines. The MICs at which 90% of the isolates are inhibited were (in milligrams per liter) as follows: 0.5 (penicillin), 0.5 (amoxicillin), 0.25 (cefotaxime), 2 (chloramphenicol), 4 (erythromycin), 0.5 (clindamycin), ≥32 (tetracycline), ≥32 (trimethoprim-sulfamethoxazole), 4 (ciprofloxacin), 0.5 (sparfloxacin), 0.5 (vancomycin), 0.25 (teicoplanin), and 1 (quinupristin-dalfopristin). High-level penicillin resistance (MIC, ≥4 mg/liter) was found in one isolate only, but intermediate penicillin resistance was noted in 11 isolates (19%). Resistance rates to other drugs were as follows: 7% (amoxicillin), 4% (cefotaxime), 4% (chloramphenicol), 32% (erythromycin), 9% (clindamycin), 39% (tetracycline), 68% (trimethoprim-sulfamethoxazole), 23% (ciprofloxacin), 0% (sparfloxacin), 0% (vancomycin), 0% (teicoplanin), and 0% (quinupristin-dalfopristin).
High-Resolution Genotyping of
Streptococcus pyogenes
Serotype M1 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis
Authors: Desai Meeta , Efstratiou Androulla , George Robert , Stanley John
Published: December 2019

We have used fluorescent amplified-fragment length polymorphism (FAFLP) analysis to subtype clinical isolates of
Streptococcus pyogenes
serotype M1. Established typing methods define most M1 isolates as members of a clone that has a worldwide distribution and that is strongly associated with invasive diseases. FAFLP analysis simultaneously sampled 90 to 120 loci throughout the M1 genome. Its discriminatory power, precision, and reproducibility were compared with those of other molecular typing methods. Irrespective of disease symptomatology or geographic origin, the majority of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestriction profile, and
emm
1 gene sequence. Nonetheless, among these isolates, FAFLP analysis could differentiate 17 distinct profiles, including seven multi-isolate groups. The FAFLP profiles of M1 isolates reproducibly exhibited between 1 and more than 20 amplified fragment differences. The high discriminatory power of genotyping by FAFLP analysis revealed genetic microheterogeneity and differentiated otherwise “identical” M1 isolates as members of a clone complex.
Lacazia loboi
gen. nov., comb. nov., the Etiologic Agent of Lobomycosis
Authors: Taborda Paulo R. , Taborda Valeria A. , McGinnis Michael R.
Published: December 2019

The new genus
Lacazia
P. Taborda, V. Taborda, et McGinnis is proposed to accommodate
Lacazia loboi
(O. M. Fonseca et Lacaz) P. Taborda, V. Taborda, et McGinnis, the obligate pathogen that causes lobomycosis in mammals. The continued placement of that fungus in the genus
Paracoccidioides
Almeida as
Paracoccidioides loboi
is taxonomically inappropriate.
Loboa loboi
Ciferri et al. is a synonym of
Paracoccidioides brasiliensis
.
Epidemiological Study of an
Acinetobacter baumannii
Outbreak by Using a Combination of Antibiotyping and Ribotyping
Authors: Biendo M. , Laurans G. , Lefebvre J. F. , Daoudi F. , Eb F.
Published: December 2019

From June to November 1994 (period 1) and from February to June 1995 (period 2), multiresistant
Acinetobacter baumannii
strains were isolated in intensive care units and surgical wards of the Amiens Teaching Hospital Center (Amiens, France). Eighteen isolates were obtained from 17 (1%) of 1,706 patients admitted during both of these periods, giving an incidence rate of nosocomial infection per 1,000 patient days of 0.6%. Of 17 infected patients, 9 had pneumonia, 3 had urinary tract infection, 2 had peritonitis, 1 had septicemia, 1 had a catheter infection, and 1 had pneumonia and urinary tract infection. According to typing results, four antibiotic resistance profiles were detected: a, b, c, and d; seven ribotypes were distinguished by both restriction enzymes
Eco
RI and
Sal
I (A, B, C, D, E, F, and G). By combining antibiotyping and ribotyping, we obtained eight groups of strains (groups I to VIII). Group I contained five strains (strains 4, 5, 7, 8, and 9) which had antibiogram pattern a and ribopattern A and constituted the outbreak strains. The strains of group II (strains 3, 10, 11, 13, and 14) were closely related to outbreak strain A and appeared to be variants of ribotype A (A2 [strain 3]; A4 [strain 10]; A5 [strains 11, 13, and 14]). Groups III, IV, V, VI, VII, and VIII included strains which were epidemiologically unrelated to the strains of group I and were considered nonoutbreak strains.
Nosocomial Pseudoepidemic Caused by
Bacillus cereus
Traced to Contaminated Ethyl Alcohol from a Liquor Factory
Authors: Hsueh Po-Ren , Teng Lee-Jene , Yang Pan-Chyr , Pan Hui-Lu , Ho Shen-Wu , Luh Kwen-Tay
Published: December 2019

From September 1990 to October 1990, 15 patients who were admitted to four different departments of the National Taiwan University Hospital, including nine patients in the emergency department, three in the hematology/oncology ward, two in the surgical intensive care unit, and one in a pediatric ward, were found to have positive blood (14 patients) or pleural effusion (1 patient) cultures for
Bacillus cereus
. After extensive surveillance cultures, 19 additional isolates of
B. cereus
were recovered from 70% ethyl alcohol that had been used as a skin disinfectant (14 isolates from different locations in the hospital) and from 95% ethyl alcohol (5 isolates from five alcohol tanks in the pharmacy department), and 10 isolates were recovered from 95% ethyl alcohol from the factory which supplied the alcohol to the hospital. In addition to these 44 isolates of
B. cereus
, 12 epidemiologically unrelated
B. cereus
isolates, one
Bacillus sphaericus
isolate from a blood specimen from a patient seen in May 1990, and two
B. sphaericus
isolates from 95% alcohol in the liquor factory were also studied for their microbiological relatedness. Among these isolates, antibiotypes were determined by using the disk diffusion method and the E test, biotypes were created with the results of the Vitek
Bacillus
Biochemical Card test, and random amplified polymorphic DNA (RAPD) patterns were generated by arbitrarily primed PCR. Two clones of the 15
B. cereus
isolates recovered from patients were identified (clone A from 2 patients and clone B from 13 patients), and all 29 isolates of
B. cereus
recovered from 70 or 95% ethyl alcohol in the hospital or in the factory belonged to clone B. The antibiotype and RAPD pattern of the
B. sphaericus
isolate from the patient were different from those of isolates from the factory. Our data show that the pseudoepidemic was caused by a clone (clone B) of
B. cereus
from contaminated 70% ethyl alcohol used in the hospital, which we successfully traced to preexisting contaminated 95% ethyl alcohol from the supplier, and by another clone (clone A) without an identifiable source.
Worldwide Evaluation of DNA Sequencing Approaches for Identification of Drug Resistance Mutations in the Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Authors: Schuurman Rob , Demeter Lisa , Reichelderfer Patricia , Tijnagel Jolanda , de Groot Tom , Boucher Charles
Published: December 2019

A panel (ENVA-1) of well-defined blinded samples containing wild-type and mutant human immunodeficiency virus type 1 (HIV-1) reverse transcriptase was analyzed by automated DNA sequencing in 23 laboratories worldwide. Drug resistance mutations at codons 41, 215, and 184 were present in the panel samples at different ratios to the wild type. The presence of mutant genotypes was determined qualitatively and quantitatively. All laboratories reported the presence of sequence heterogeneities at codons 41, 215, and 184 in one or more of the panel samples, though not all reported the correct codon genotypes. Two laboratories reported a mutant genotype in samples containing only the wild type, whereas two and three laboratories failed to detect the mutant genotypes at codons 41 and 215, respectively, in a completely mutant DNA population. Mutations present at relative concentrations of 25% of the total DNA population were successfully identified by 13 of 23, 10 of 23, and 16 of 23 labs for codons 41, 215, and 184Val, respectively. For more than 80% of those laboratories that qualitatively detected the presence of a mutation correctly, the estimated wild type/mutant ratio was less than 25% different from the input ratio in those samples containing 25 to 50% or 75% mutant input. This first multicenter study on the quality of DNA sequencing approaches for identifying HIV-1 drug resistance mutations revealed large interlaboratory differences in the quality of the results. The application of these procedures in their current state would in several cases lead to inaccurate or even incorrect diagnostic results. Therefore, proper quality control and standardization are urgently needed.
Detection by an Immunofluorescence Test of
Encephalitozoon intestinalis
Spores in Routinely Formalin-Fixed Stool Samples Stored at Room Temperature
Authors: Moura H. , Sodre F. C. , Bornay-Llinares F. J. , Leitch G. J. , Navin T. , Wahlquist S. , Bryan R. , Meseguer I. , Visvesvara G. S.
Published: December 2019

Of the several microsporidia that infect humans,
Enterocytozoon bieneusi
is known to cause a gastrointestinal disease whereas
Encephalitozoon intestinalis
causes both a disseminated and an intestinal disease. Although several different staining techniques, including the chromotrope technique and its modifications, Uvitex 2B, and the quick-hot Gram-chromotrope procedure, detect microsporidian spores in fecal smears and other clinical samples, they do not identify the species of microsporidia. A need for an easily performed test therefore exists. We reevaluated 120 stool samples that had been found positive for microsporidia previously, using the quick-hot Gram-chromotrope technique, and segregated them into two groups on the basis of spore size. We also screened the smears by immunofluorescence microscopy, using a polyclonal rabbit anti-
E. intestinalis
serum at a dilution of 1:400. Spores in 29 (24.1%) of the 120 samples fluoresced brightly, indicating that they were
E. intestinalis
spores. No intense background or cross-reactivity with bacteria, yeasts, or other structures in the stool samples was seen. Additionally, the numbers of spores that fluoresced in seven of these samples were substantially smaller than the numbers of spores that were present in the stained smears, indicating that these samples were probably derived from patients with mixed infections of
Enterocytozoon bieneusi
and
E. intestinalis
. Because a 1:400 dilution of this serum does not react with culture-grown
Encephalitozoon hellem
,
Encephalitozoon cuniculi
, or
Vittaforma corneae
or with
Enterocytozoon bieneusi
spores in feces, we concluded that an immunofluorescence test using this serum is a good alternative for the specific identification of
E. intestinalis
infections.
Molecular Evidence of Mother-to-Infant Transmission of Hepatitis G Virus among Women without Known Risk Factors for Parenteral Infections
Authors: Menéndez Clara , Sánchez-Tapias José-María , Alonso Pedro-Luis , Giménez-Barcons Mireia , Kahigwa Elizeus , Aponte John-Jairo , Mshinda Hassan , Navia Margarita-María , Jiménez de Anta María-Teresa , Rodés Juan , Saiz Juan-Carlos
Published: December 2019

Hepatitis G virus (HGV) RNA was detected in 18 of 133 pregnant women from Tanzania without known risk factors for HGV infection and in 7 of 18 children born to HGV RNA-positive mothers. Molecular evidence of mother-to-infant transmission was obtained only for three of seven children. HGV RNA was also detected in 4 of 42 children born to non-HGV-infected women. Thus, mechanisms other than materno-filial may play an important role in HGV transmission during early childhood.
In Vitro Amphotericin B Resistance in Clinical Isolates of
Aspergillus terreus
, with a Head-to-Head Comparison to Voriconazole
Authors: Sutton Deanna A. , Sanche Stephen E. , Revankar Sanjay G. , Fothergill Annette W. , Rinaldi Michael G.
Published: December 2019

Amphotericin B therapy continues to be the “gold standard” in the treatment of invasive aspergillosis in the immunocompromised host. Although
Aspergillus fumigatus
and
Aspergillus flavus
constitute the major species, several reports have described invasive pulmonary or disseminated disease due to the less common
Aspergillus terreus
and dismal clinical outcomes with high-dose amphotericin B. We therefore evaluated 101 clinical isolates of
A. terreus
for their susceptibility to amphotericin B and the investigational triazole voriconazole by using the National Committee for Clinical Laboratory Standards M27-A method modified for mould testing. Forty-eight-hour MICs indicated 98 and 0% resistance to amphotericin B and voriconazole, respectively. We conclude that
A. terreus
should be added to the list of etiologic agents refractory to conventional amphotericin B therapy and suggest the potential clinical utility of voriconazole in aspergillosis due to this species.
Molecular Epidemiology of Hepatitis C Virus Infection in an Area of Hyperendemicity in Southern Italy: a Population-Based Study
Authors: Osella Alberto R. , Sonzogni Laura , Cavallini Aldo , Foti Luciana , Guerra Vito , Di Leo Alfredo , Mondelli Mario U. , Misciagna Giovanni , Silini Enrico M.
Published: December 2019

In a cohort of subjects from Italy, anti-hepatitis C virus (HCV) and HCV RNA [HCV(+) subgroup] prevalences were 24.6 and 79.6%, respectively. HCV types 1b and 2a/c accounted for 95% of infections. Adjusted alanine aminotransferase levels were higher in males than in females and in RNA-positive subjects than in RNA-negative subjects regardless of HCV type. Genotype distribution was unrelated to demographic variables.
Evaluation of the AnaeroPack Campylo System for Growth of Microaerophilic Bacteria
Authors: Van Horn Kenneth , Tóth Clara
Published: December 2019

Growth of microaerophilic bacteria in the AnaeroPack Campylo (Mitsubishi Gas Chemical America, Inc., New York, N.Y.) atmosphere generation system was compared to growth in the CampyPak Plus jar and CampyPak pouch (Becton-Dickinson Microbiology Systems [BDMS], Cockeysville, Md.). Growth in the AnaeroPack Campylo system was considered equivalent to or better than growth obtained in the CampyPak Plus and CampyPak pouch systems for 48 of the 50
Helicobacter pylori
strains and for all 28
Campylobacter
species tested. All of the 78 organisms tested were recovered in each system in equivalent colony counts. Two strains of
H. pylori
grown in the AnaeroPack Campylo system were observed to have colony morphology growth discrepancies when compared to growth in the two BDMS systems. Atmosphere failure with the AnaeroPack Campylo was not detected with
Campylobacter jejuni
ATCC 33291 used as a growth control. The AnaeroPack Campylo system is easy to use and supports the growth of campylobacters and
H. pylori
.
Field Evaluation of the ICT Malaria P.f/P.v Immunochromatographic Test for Detection of
Plasmodium falciparum
and
Plasmodium vivax
in Patients with a Presumptive Clinical Diagnosis of Malaria in Eastern Indonesia
Authors: Tjitra Emiliana , Suprianto Sri , Dyer Mary , Currie Bart J. , Anstey Nicholas M.
Published: December 2019

In areas such as eastern Indonesia where both
Plasmodium falciparum
and
Plasmodium vivax
occur, rapid antigen detection tests for malaria need to be able to detect both species. We evaluated the new combined
P. falciparum-P. vivax
immunochromatographic test (ICT Malaria P.f/P.v.) in Radamata Primary Health Centre, Sumba, Indonesia, from February to May 1998 with 560 symptomatic adults and children with a presumptive clinical diagnosis of malaria. Blinded microscopy was used as the “gold standard,” with all discordant and 20% of concordant results cross-checked blindly. Only 50% of those with a presumptive clinical diagnosis of malaria were parasitemic. The ICT Malaria P.f/P.v immunochromatographic test was sensitive (95.5%) and specific (89.8%) for the diagnosis of falciparum malaria, with a positive predictive value (PPV) and a negative predictive value (NPV) of 88.1 and 96.2%, respectively. HRP2 and panmalarial antigen line intensities were associated with parasitemia density for both species. Although the specificity and NPV for the diagnosis of vivax malaria were 94.8 and 98.2%, respectively, the overall sensitivity (75%) and PPV (50%) for the diagnosis of vivax malaria were less than the desirable levels. The sensitivity for the diagnosis of
P. vivax
malaria was 96% with parasitemias of >500/μl but only 29% with parasitemias of <500/μl. Nevertheless, compared with the test with HRP2 alone, use of the combined antigen detection test would reduce the rate of undertreatment from 14.7 to 3.6% for microscopy-positive patients, and this would be at the expense of only a modest increase in the rate of overtreatment of microscopy-negative patients from 7.1 to 15.4%. Cost remains a major obstacle to widespread use in areas of endemicity.