bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening of Stool Samples for Identification of Vancomycin-Resistant
Enterococcus
Isolates Should Include the Methyl-α-
d
Glucopyranoside Test To Differentiate Nonmotile
Enterococcus gallinarum
from
E. faecium
Authors: Turenne Christine Y. , Hoban Daryl J. , Karlowsky James A. , Zhanel George G. , Kabani Amin M.
Published: December 2019

The methyl-α-
d
-glucopyranoside (MDG) test has been shown to be superior to motility testing in differentiating
Enterococcus faecium
from
E. gallinarum
. In the present study, 33 vancomycin-resistant enterococcus (VRE) isolates collected as part of a stool surveillance study were compared by using motility and MDG. Motility testing identified all 33 isolates as
E. faecium
, whereas MDG identified 11 of the 33 isolates as nonmotile
E. gallinarum
. The MDG results were confirmed by sequencing the 16S rDNA V6-to-V8 region. We conclude that the MDG test is a necessary component of routine VRE screening.
Rapid Screening for Penicillin Susceptibility of Systemic Pneumococcal Isolates by Restriction Enzyme Profiling of the
pbp2B
Gene
Authors: Beall Bernard , Facklam Richard R. , Jackson Delois M. , Starling Holly H.
Published: December 2019

Restriction digest profiling of pneumococcal
pbp2b
-specific amplicons was effective for screening penicillin resistance. The
pbp2b
amplicon of all pneumococcal isolates for which the MICs of penicillin were ≤0.03 μg/ml had one of two different susceptible restriction profiles, and all 33 isolates for which MICs were 0.5 μg/ml or greater had one of seven distinct resistant profiles. Low-concentration penicillin resistance (MICs = 0.06 μg/ml to 0.25 μg/ml) was associated with sensitive
Hae
III profiles in some isolates; however,
Rsa
I profiling and
pbp2b
sequence analysis of such isolates revealed that some isolates contained low-level resistant
pbp2b
alleles, while others had susceptible
pbp2b
alleles. This data indicates that low-level penicillin resistance is sometimes conferred by determinants other than
pbp2b
.
Frequency of
vacA
Genotypes and Cytotoxin Activity in
Helicobacter pylori
Associated with Low-Grade Gastric Mucosa-Associated Lymphoid Tissue Lymphoma
Authors: Miehlke Stephan , Meining Alexander , Morgner Andrea , Bayerdörffer Ekkehard , Lehn Norbert , Stolte Manfred , Graham David Y. , Go Mae F.
Published: December 2019

The
vacA
genotypes s1,m1 and s1,m2 were detected in 44 and 30% of
Helicobacter pylori
isolates, respectively, from patients with gastric mucosa-associated lymphoid tissue lymphoma, compared to 26 and 56% of isolates, respectively, from individuals with gastritis. The
vacA
s1 genotype was significantly associated with, but not predictive of, the presence of vacuolating cytotoxin activity.
Breast Abscess Associated with
Helcococcus kunzii
Authors: Chagla Abdul H. , Borczyk Alexander A. , Facklam Richard R. , Lovgren Marguerite
Published: December 2019

Helcococcus kunzii
, a nonvirulent member of the human skin flora, has recently been implicated in causing infections in immunosuppressed patients. We report a case of breast abscess associated with
H. kunzii
in an immunocompetant patient and discuss the criteria used in its identification and our observations of susceptibility testing for this species.
Study of the Relatedness of Isolates of
Shigella flexneri
and
Shigella sonnei
Obtained in 1986 and 1987 and in 1994 and 1995 from Hong Kong
Authors: Houang E. T. S. , Chu Y.-W. , Ng T.-K. , Cheng A. F. B.
Published: December 2019

We used pulsed-field gel electrophoresis (PFGE) to study the genetic relatedness of 235 isolates of
Shigella flexneri
and
Shigella sonnei
collected in Hong Kong (97 isolates from 1986 and 1987 and 138 isolates from 1994 and 1995). Altogether, 13 gels were run with bacteriophage lambda ladder DNA (Pharmacia) as an external reference in every sixth lane, standardized reagents and methods, and isolates randomized for species and years. For quantitative illustration of the relationships within a large body of isolates, computer-generated dendrograms were used to determine the number of isolates in pulsotypes at Dice coefficients of similarity of 75% (PT
75
) and 50% (PT
50
). For
S. flexneri
, there was a significant difference in the distribution of isolates collected during the two periods in both PT
75
and PT
50
, with 68% of isolates collected in 1994 and 1995 sharing a coefficient of similarity of ≥68%. For
S. sonnei
, a significant difference was observed in PT
50
only. We also used Upholt’s formula for an approximation of the fraction of nucleotide difference between isolates and Molecular Evolutionary Genetics Analysis to determine relative genetic distances. For both species, the relative genetic distances between isolates of the earlier collection period were significantly greater (
P
< 0.0001), i.e., they were further apart and therefore more diverse than those of the later period. We conclude that it is possible for a typical clinical laboratory to analyze a large amount of PFGE information on
Shigella
isolates obtained under controlled conditions. Such data analysis should enhance surveillance capabilities and give indications of further work to be done on various aspects of bacterial pathogenicity of the species.
Evaluation of Three Commercial Enzyme-Linked Immunosorbent Assays for Diagnosis of Chagas’ Disease
Authors: Oelemann Walter M. R. , Teixeira Maria Da Glória M. , Veríssimo Da Costa Giovani C. , Borges-Pereira José , De Castro José Adail F. , Coura José Rodrigues , Peralta José Mauro
Published: December 2019

Chagas’ disease is a common cause of morbidity in Latin American countries. In Brazil, naturally occurring transmission of its etiologic agent,
Trypanosoma cruzi
, has been almost completely abolished through effective control programs aimed at the triatomid insect vector. Thus, transfusion of blood from infected donors has become the major route for contracting Chagas’ disease due to the socioeconomically motivated migration of residents from areas where the disease is endemic to the larger urban centers. Therefore, the employment of screening tests is mandatory for all blood banks throughout the country. We compared the diagnostic performances of three commercially available screening assays used in routine testing in Brazilian blood banks: the Abbott Chagas antibody enzyme immunoassay (Abbott Laboratórios do Brasil, São Paulo), the BIOELISACRUZI kit (Biolab-Mérieux, Rio de Janeiro, Brazil), and the BIOZIMA Chagas kit (Polychaco S.A.I.C., Buenos Aires, Argentina). The evaluation was performed with sera obtained from chagasic patients and healthy residents of four different areas in Brazil where Chagas’ disease is either endemic or emergent and where clinical manifestations of the disease and circulating parasite strains vary. The results obtained with each kit were compared to matched in-house enzyme-linked immunosorbent assay and immunofluorescence assay data obtained for each sample. Depending on the area under investigation, the three commercial kits produced specificity values between 93.3 and 100.0%, sensitivity values between 97.7 and 100%, and accuracies ranging from 93.6 to 100.0%.
Use of an Amplified-Fragment Length Polymorphism Technique To Fingerprint and Differentiate Isolates of
Helicobacter pylori
Authors: Gibson J. R. , Slater E. , Xerry J. , Tompkins D. S. , Owen R. J.
Published: December 2019

Amplified-fragment length polymorphism (AFLP) analysis is the name given to a genotypic technique in which adapter oligonucleotides are ligated to restriction enzyme fragments and then used as target sites for primers in a PCR amplification process. The amplified fragments are electrophoretically separated to give strain-specific band profiles. We have developed a single-enzyme approach that did not require costly equipment or reagents for the fingerprinting of strains of
Helicobacter pylori
. The method was assessed with 46 isolates of
H. pylori
from 28 patients, and the results were compared with those from other genotypic tests. The AFLP profiles derived from
Hin
dIII fragments differentiated strains of
H. pylori
from unrelated individuals and confirmed the common origin of strains in some family members. AFLP analysis was also applied to investigate persistent infection following antibiotic therapy. Overall, the modified technique was relatively rapid and technically simple yet gave reproducible and discriminatory results. AFLP analysis samples variation throughout the genome and is a valuable addition to the existing genotypic fingerprinting methods for
H. pylori
.
Intercontinental Spread of a Multidrug-Resistant MethicillinResistantStaphylococcus aureusClone
Authors: de Sousa M. Aires , Sanches I. Santos , Ferro M. L. , Vaz M. J. , Saraiva Z. , Tendeiro T. , Serra J. , de Lencastre H.
Published: December 2019

Two hundred ten methicillin-resistantStaphylococcus aureus(MRSA) isolates recovered between 1990 and 1997 from three Portuguese hospitals located in Lisbon and Oporto were analyzed by molecular fingerprinting techniques. The hybridization ofClaI restriction digests with themecA- and Tn554-specific DNA probes combined with pulsed-field gel electrophoresis documented the abrupt appearance and extensive intrahospital spread of the Brazilian epidemic MRSA clone in the 1995 samples of each one of the three hospitals analyzed—suggesting the intercontinental transfer of this strain from Brazil to Portugal. The appearance of this clone may challenge the dominance of another highly epidemic imported clone—the Iberian MRSA, currently the most widely spread MRSA clone in Portuguese hospitals.
Comparative Evaluation of Colorimetric Microtiter Plate Systems for Detection of Herpes Simplex Virus in Cerebrospinal Fluid
Authors: Tang Yi-Wei , Rys Paul N. , Rutledge Barbara J. , Mitchell P. Shawn , Smith Thomas F. , Persing David H.
Published: December 2019

In the past few years, application of the PCR to the detection of herpes simplex virus (HSV) DNA in the cerebrospinal fluid (CSF) from patients with encephalitis and meningitis has become standard laboratory practice. However, from an operational perspective, the true diagnostic value of PCR in this setting is yet to be realized because most laboratories subject the amplification products to lengthy probe hybridization procedures by Southern blotting. As alternatives to Southern blotting, we evaluated colorimetric microtiter plate (MTP) systems from ViroMed Laboratories, Inc. (PrimeCapture), CPG, Inc. (Quanti-PATH), and Incstar Corp. (GEN-ETI-K), in addition to a system developed at the Mayo Clinic with the PCR ELISA system (Boehringer Mannheim Corp.). We tested PCR products from 86 clinical CSF specimens submitted to our Molecular Microbiology Laboratory. The CSF specimens used had to have sufficient volume for comparative analysis. By conventional Southern blotting methods, 54 were positive and 32 were negative for HSV DNA. Compared with Southern blotting, the sensitivity and specificity were 63.0 and 100.0%, respectively, for the PrimeCapture system, 98.2 and 96.9%, respectively, for the Quanti-PATH system, 98.2 and 100.0%, respectively, for the GEN-ETI-K system, and 100.0 and 96.9%, respectively, for the Mayo system. All four MTP systems had turnaround times 12 to 24 h less than that for Southern blotting. There were no significant differences in costs or technologist time between the Mayo system and Southern blotting. Other features of the Mayo system include type-specific genotypic identification of HSV and the potential for determination of drug resistance by DNA sequencing. Overall, we found that colorimetric MTP systems were likely to improve test turnaround times and patient care at no additional cost.
Genotypic Characterization of Clarithromycin-Resistant and -Susceptible
Helicobacter pylori
Strains from the Same Patient Demonstrates Existence of Two Unrelated Isolates
Authors: Wang Ge , Jiang Qin , Taylor Diane E.
Published: December 2019

Clarithromycin-susceptible and clarithromycin-resistant
Helicobacter pylori
isolates from the same patient were investigated for the mode of development and mechanism of clarithromycin resistance. The clarithromycin-resistant strain UA1182 harbors homozygous A-to-G mutations at position 2143 in both copies of the 23S rRNA gene and has a phenotype of resistance to clarithromycin and clindamycin but no significant resistance to streptogramin B. Pulsed-field gel electrophoresis patterns of
Nru
I- and
Not
I-digested genomic DNA from the Cla
s
and Cla
r
isolates demonstrated that they are genetically distinct, suggesting that the development of clarithromycin resistance is not from the mutation of the existing Cla
s
strain but from a completely new strain.
Modification of Results of Drug Susceptibility Tests by Coexistence of
Mycobacterium avium
Complex with
Mycobacterium tuberculosis
in a Sputum Sample: Case Report and Experimental Considerations
Authors: Suzuki Katsuhiro , Kimoto Terumi , Tsuyuguchi Kazunari , Matsumoto Hisako , Niimi Akio , Tanaka Eisaku , Murayama Takako , Amitani Ryoichi
Published: December 2019

We report on a patient whose sputum contained both
Mycobacterium tuberculosis
and
Mycobacterium avium
complex (MAC). The MAC failed to be detected by the PCR-based AMPLICOR test. The unrecognized coexistence of MAC in the sample modified the results of drug susceptibility tests. Experiments revealed that the presence of both
M. tuberculosis
and MAC was not detected by the AMPLICOR test under certain conditions.
Novel Method for Rapid Measurement of Growth of Mycobacteria in Detergent-Free Media
Authors: Meyers Paul R. , Bourn William R. , Steyn Lafras M. , van Helden Paul D. , Beyers Albert D. , Brown Gordon D.
Published: December 2019

We describe a novel, rapid, and inexpensive method for the measurement of growth of
Mycobacterium tuberculosis
,
Mycobacterium bovis
, and
Mycobacterium smegmatis
in the presence or absence of detergent. The method, which employs hot NaOH treatment of mycobacterial cells to release total cellular protein, compares favorably with other methods for monitoring mycobacterial growth but is particularly useful for heavily clumped cultures grown in defined minimal medium.
Molecular Epidemiology of Extended-Spectrum β-Lactamase-Producing
Klebsiella pneumoniae
Isolates in a District Hospital in Taiwan
Authors: Liu Peter Yuk-Fong , Tung Jai-Chin , Ke Se-Chin , Chen Shun-Liang
Published: December 2019

Thirty-one of 104 clinical isolates of
Klebsiella pneumoniae
collected over a period of 8 months were found to be putative extended-spectrum β-lactamase (ESBL) producers. Isoelectric focusing and an iodine overlay agar method were used for preliminary identification of the ESBLs. They were further identified by DNA sequencing. Seventy-one percent of the isolates were found to produce SHV-5. The variation in the ESBL patterns of these isolates was slight, with only five patterns being identified. The strains were typed by pulsed-field gel electrophoresis (PFGE), and 16 different genotypes were identified. When the PFGE patterns were analyzed by the algorithmic clustering method called the unweighted-pair group method using arithmetic averages, five clusters were found. However, significant genetic variations were found among 11 isolates and between each cluster. A plasmid of 36 kb was found in all clinical isolates and in the transconjugants. Our results indicate that the increase in the number of ESBL-producing
K. pneumoniae
isolates in this hospital is due mainly to the dissemination of a resistance plasmid rather than to the clonal spread of a few epidemic strains.
Clinical Evaluation of the BDProbeTec Strand Displacement Amplification Assay for Rapid Diagnosis of Tuberculosis
Authors: Bergmann John S. , Woods Gail L.
Published: December 2019

The reliability of the BDProbeTec MTB Test (Becton Dickinson, Sparks, Md.) for direct detection of
Mycobacterium tuberculosis
in respiratory specimens was evaluated by comparing results to those of conventional mycobacterial culture, with the BACTEC TB 460 and Middlebrook 7H11 biplates. Patients known to have tuberculosis were excluded from analysis. Of 523 specimens from 277 patients, 53 grew a mycobacterium: 24 specimens of
M. tuberculosis
and 29 specimens of nontuberculous mycobacteria. After initial testing, 42 specimens were positive by the BDProbeTec, for overall sensitivity, specificity, and positive and negative predictive values of 95.8, 96.2, 54.8, and 99.8%, respectively. After resolution of discrepancies, 28 specimens were positive by the BDProbeTec, for overall sensitivity, specificity, and positive and negative predictive values of 100, 99.2, 85.7, and 100%, respectively. These same values were 100, 80.8, 93.4, and 100%, respectively, for smear-positive samples and 100, 99.4, 75.0, and 100%, respectively, for smear-negative specimens.
Isolation of
Francisella tularensis
by Centrifugation of Shell Vial Cell Culture from an Inoculation Eschar
Authors: Fournier Pierre-Edouard , Bernabeu Lionel , Schubert Bernard , Mutillod Maryse , Roux Veronique , Raoult Didier
Published: December 2019

A 52-year-old man was admitted to the hospital following the development of an inoculation eschar and fever six days after being bitten by a tick. He was clinically diagnosed as suffering from rickettsiosis. Eschar biopsy cultures on standard bacteriological media remained sterile. However, inoculation of cells with the homogenized specimen by the centrifugation-shell vial technique (M. Marrero and D. Raoult, Am. J. Trop. Med. Hyg. 40:197–199, 1989) resulted in the recovery of a bacterium. Determination of the sequence of the 16S rRNA gene amplified from the organism and comparison of the sequence to other sequences identified it as a strain of
Francisella tularensis
, whereas the specific serology was still negative. Our findings demonstrate that the centrifugation-cell culture, which is a tool for investigation of tick-transmitted diseases, may have the potential to serve as a method for the cultural isolation of
F. tularensis
.
Antimicrobial Susceptibility of
Helicobacter pylori
Determined by the E Test Using Tetrazolium Egg Yolk Agar
Authors: Valdez Yanet , Velapatiño Billie , Gilman Robert H. , Gutierrez Vilma , León Carlos
Published: December 2019

Metronidazole and tetracycline E tests were compared to an agar dilution method for the antimicrobial susceptibility testing of
Helicobacter pylori
. Sixteen strains were tested by using tetrazolium egg yolk (TEY) agar. The characteristic E test inhibition ellipse was clearer on TEY agar than on standard blood agar and gave results comparable to those of the agar dilution test. The use of TEY medium is preferable to that of blood agar medium in E test MIC determinations for
H. pylori.
Rapid Identification of
Candida glabrata
by Using a Dipstick To Detect Trehalase-Generated Glucose
Authors: Peltroche-Llacsahuanga Heidrun , Schnitzler Norbert , Lütticken Rudolf , Haase Gerhard
Published: December 2019

Candida glabrata
is a yeast frequently isolated from human specimens. Based upon its well-known ability to rapidly hydrolyze trehalose, we have developed a novel and cost-effective test incubating one yeast colony emulsified in 50 μl of citrate buffer (0.1 M [pH 5.0]) containing 4% (wt/vol) trehalose for 3 h at 37°C. Trehalase-generated glucose is detected with a commercially available dipstick (range, 1.0 to 50 g/liter). For evaluation, consecutive clinical isolates and several reference strains of
C. glabrata
(
n
= 160),
C. albicans
(
n
= 120), and other yeast species with potential ability for utilization of trehalose (
C. dubliniensis
,
n
= 11;
C. famata
,
n
= 15;
C. guilliermondii
,
n
= 5;
C. lusitaniae
,
n
= 16;
C. parapsilosis
,
n
= 20;
C. tropicalis
,
n
= 34;
C. viswanathii
,
n
= 5;
Pichia angusta
,
n
= 2;
C. zeylanoides
,
n
= 2;
Saccharomyces cerevisiae
,
n
= 16;
C. neoformans
,
n
= 7) were tested. Identification of
C. glabrata
is achieved within 3 h, with a specificity of 99.1% and a sensitivity of 98.8% when grown on Sabouraud dextrose agar supplemented with 4% glucose.
Evaluation of the Abbott LCx
Mycobacterium tuberculosis
Assay for Direct Detection of
Mycobacterium tuberculosis
Complex in Human Samples
Authors: Garrino Maria Grazia , Glupczynski Youri , Degraux Josiane , Nizet Henri , Delmée Michel
Published: December 2019

Seven hundred thirty-seven clinical samples from 460 patients were processed for direct detection of
Mycobacterium tuberculosis
complex by a semiautomated ligase chain reaction commercial assay, the LCx
Mycobacterium tuberculosis
Assay (LCx assay) from Abbott Laboratories. Results were compared to those of direct microscopy and standard microbiological culture. Of 26 patients (5.7%) with a culture positive for
M. tuberculosis
, 22 (84.6%) were found positive by the LCx assay. The sensitivity of the LCx assay was 98% for smear-positive samples and 27% for smear-negative samples. With an overall culture positivity rate for
M. tuberculosis
of 8.3% (61 of 737 samples) and after resolution of discrepant results according to clinical data, the sensitivity, specificity, and positive and negative predictive values of the LCx assay were 78, 100, 95, and 98%, respectively, compared to 85, 100, 100, and 98%, respectively, for culture and 67, 99, 87, and 97%, respectively, for acid-fast staining. In conclusion, the LCx assay proved satisfactory and appears to be an easy-to-use 1-day test which must be used with standard culture methods but can considerably reduce diagnosis time versus culture. However, its clinical interest appears to be limited in our population with low mycobacterial prevalence because of its cost considering the small gain in sensitivity versus direct microscopy.
Analysis of
Legionella pneumophila
Serogroup 1 Isolates by Pulsed-Field Gel Electrophoresis
Authors: Marrie Thomas J. , Tyler Shaun , Bezanson Gregory , Dendy Charles , Johnson Wendy
Published: December 2019

At a hospital in Halifax, Nova Scotia, Canada, three strains of
Legionella pneumophila
were detectable based on plasmid content, while the isolates collected at another hospital in Halifax had no plasmids. Genomic DNA was digested with
Bss
HII,
Sal
I, and
Spe
I and subjected to pulsed-field gel electrophoresis (PFGE). We found no relationship between plasmid profile and PFGE pattern.
Case of Onychomycosis Caused by
Microsporum racemosum
Authors: García-Martos Pedro , Gené Josepa , Solé María , Mira José , Ruíz-Henestrosa Ricardo , Guarro Josep
Published: December 2019

We report the case of a Spanish 60-year-old female who presented in 1997 with onychomycosis of the left thumbnail following an injury caused by a fresh fish bone.
Microsporum racemosum
was repeatedly cultured from nail scrapings, and its identity was confirmed by sequencing the isolate’s ITS1/ITS2 and 5.8S rRNA regions. The patient was successfully treated with itraconazole, which was administered for 12 weeks. This represents the first case of onychomycosis due to
M. racemosum
and the first time that this species has been isolated from a human in Europe.
Development of a
Plasmodium
PCR for Monitoring Efficacy of Antimalarial Treatment
Authors: Ciceron Liliane , Jaureguiberry Ginette , Gay Frederick , Danis Martin
Published: December 2019

We report in this work a highly sensitive and nonradioactive PCR method for the detection of the four species of parasite causing human malaria.
Plasmodium
-specific primers corresponding to the small-subunit rRNA genes of the malaria parasite were used, and a 291-bp fragment was amplified. Our results showed a high specificity for the four human
Plasmodium
species, and we were able to detect one parasite in 50 μl of whole blood. The responses of 12 patients infected with
Plasmodium falciparum
to antimalarial therapy were monitored by PCR diagnosis and examination of thick blood film for at least 20 min by an experienced microscopist. For one patient this study allowed early diagnosis of therapeutic failure, confirmed 7 days later by examination of the thick blood film. A total of 134 samples were examined; 94 were positive by PCR, and among these 68 were positive by thick blood film examination. The sensitivity of the thick blood film was 72.3% compared to PCR and 60.7% compared to dot blot hybridization.
Multicenter Evaluation of the Mycobacteria Growth Indicator Tube for Testing Susceptibility of
Mycobacterium tuberculosis
to First-Line Drugs
Authors: Rüsch-Gerdes Sabine , Domehl Cornelia , Nardi Giampietro , Gismondo Maria Rita , Welscher Hans-Martin , Pfyffer Gaby E.
Published: December 2019

In a multicenter study involving three reference centers for mycobacteria, the reliability of the Mycobacteria Growth Indicator Tube (MGIT) for rapid antimicrobial susceptibility testing (AST) of
Mycobacterium tuberculosis
was evaluated and compared to the radiometric method (BACTEC 460TB). Test cultures for which the results of the MGIT and BACTEC 460TB tests were discordant were checked by the conventional proportion method on solid medium. Four hundred forty-one isolates have been tested for susceptibility to isoniazid (INH), rifampin (RMP), ethambutol (EMB), and streptomycin (SM). Discrepant results were obtained for three isolates (0.7%) with INH (susceptible by MGIT, resistant by BACTEC 460TB), for four isolates (0.9%) with RMP (susceptible by MGIT, resistant by BACTEC 460TB), for six isolates (1.9%) with EMB (four susceptible by MGIT, resistant by BACTEC 460TB; two resistant by MGIT, susceptible by BACTEC 460TB), and for four isolates (0.9%) with SM (two susceptible by MGIT, resistant by BACTEC 460TB; two resistant by MGIT, susceptible by BACTEC 460TB). When cultures with discordant results were tested by the conventional proportion method, about half of the cultures yielded results similar to the BACTEC 460TB results, while the other half yielded results similar to the MGIT results. Turnaround times were 3 to 14 days (median, 8.8 days) for MGIT and 3 to 15 days (median, 7.8 days) for BACTEC 460TB. There was no statistically significant difference between the susceptibility testing results of the two methods (
P
> 0.05). These data demonstrate that the MGIT system is an accurate, nonradiometric alternative to the BACTEC 460TB method for rapid susceptibility testing of
M. tuberculosis
.
Evaluation of a Novel Dry Latex Preparation for Demonstration of Infectious Mononucleosis Heterophile Antibody in Comparison with Three Established Tests
Authors: Rogers Richard , Windust Alison , Gregory Josie
Published: December 2019

A new, dried antigen-coated latex preparation for the demonstration of infectious mononucleosis (IM) heterophile antibody (Dryspot IM kit; Oxoid, Ltd., Basingstoke, Hampshire, United Kingdom) was compared with the IM kit (a liquid latex reagent from the same source), an immunoassay (ImmunoCard Mono; Meridian Diagnostics), and an absorption test (Monospot; Meridian Diagnostics). The latter was used as a standard for initial statistical comparisons. Discrepancies were resolved by using Epstein-Barr virus serology. Of the 328 routine samples tested, 77 were positive and 222 were negative by all IM heterophile antibody-based kits. Twenty-nine samples gave discrepant results. Following resolution of discrepant results, the sensitivity and specificity values for the IM Dryspot kit were 87.0 and 98.7%, those for the Oxoid liquid latex IM kit were 83.0 and 99.6%, and those for the ImmunoCard Mono immunoassay were 85.0 and 100.0%, respectively. The evaluation shows that the Dryspot kit, which is uniquely straightforward to use and may be stored at room temperature, is comparable in performance to other rapid heterophile tests for the confirmation of IM.
Determination of
Chlamydia trachomatis
Prevalence in an Asymptomatic Screening Population: Performances of the LCx and COBAS Amplicor Tests with Urine Specimens
Authors: Morré Servaas A. , Van Valkengoed Irene G. M. , Moes Robert M. , Boeke A. Joan P. , Meijer Chris J. L. M. , Van den Brule Adriaan J. C.
Published: December 2019

This study determined the performances of the LCx (Abbott) and COBAS Amplicor (Roche) tests with urine specimens for the detection of
Chlamydia trachomatis
in an asymptomatic screening population. Randomly selected women and men (age range, 15 to 40 years) registered in 20 general practices in Amsterdam, The Netherlands, were invited to participate in this study. Urine specimens (
n
= 2,906; 1,138 specimens from men and 1,717 specimens from women) were tested for
C. trachomatis
by the COBAS Amplicor (Roche) and LCx (Abbott) tests. Samples which were positive by only one assay were subjected to discrepant analyses by a third assay (in-house plasmid PCR). By the LCx assay
C. trachomatis
DNA was detected in urine specimens from 46 of 1,717 women and 29 of 1,138 men, while the COBAS Amplicor detected
C. trachomatis
DNA in 52 and 35 specimens, respectively. When comparing the LCx and COBAS Amplicor tests, 32 test results (20 for women and 12 for men) were discrepant. After discrepant analyses the following sensitivities, specificities, and positive predictive values were found for the LCx and COBAS Amplicor tests: 78.6 versus 98.8%, 99.7 versus 99.9%, and 88.0 versus 95.4%, respectively. No prominent differences were found between men and women with regard to the test performances. After discrepant analyses the overall prevalences of
C. trachomatis
in women and men were 3.0 and 2.8%, respectively. For both women and men the prevalence in the younger age groups was higher than that in the older age groups. In conclusion, the COBAS Amplicor tests shows better diagnostic characteristics than the LCx assay for the detection of
C. trachomatis
in urine specimens from an asymptomatic screening population. In this asymptomatic population the overall prevalence of
C. trachomatis
was 2.9%.
Development of rRNA-Based PCR Assays for Identification of
Burkholderia cepacia
Complex Isolates Recovered from Cystic Fibrosis Patients
Authors: LiPuma John J. , Dulaney Betty Jo , McMenamin Jennifer D. , Whitby Paul W. , Stull Terrence L. , Coenye Tom , Vandamme Peter
Published: December 2019

PCR assays targeting rRNA genes were developed to identify species (genomovars) within the
Burkholderia cepacia
complex. Each assay was tested with 177 bacterial isolates that also underwent taxonomic analysis by whole-cell protein profile. These isolates were from clinical and environmental sources and included 107
B. cepacia
complex strains, 23
Burkholderia gladioli
strains, 20
Ralstonia pickettii
strains, 10
Pseudomonas aeruginosa
strains, 8
Stenotrophomonas maltophilia
strains, and 9 isolates belonging to nine other species. The sensitivity and specificity of the 16S rRNA-based assay for
Burkholderia multivorans
(genomovar II) were 100 and 99%, respectively; for
Burkholderia vietnamiensis
(genomovar V), sensitivity and specificity were 87 and 92%, respectively. An assay based on 16S and 23S rRNA gene analysis of
B. cepacia
ATCC 25416 (genomovar I) was useful in identifying genomovars I, III, and IV as a group (sensitivity, 100%, and specificity, 99%). Another assay, designed to be specific at the genus level, identified all but one of the
Burkholderia
and
Ralstonia
isolates tested (sensitivity, 99%, and specificity, 96%). The combined use of these assays offers a significant improvement over previously published PCR assays for
B. cepacia
.
Diverse Restriction Fragment Length Polymorphism Patterns of the PCR-Amplified 16S rRNA Genes in
Aeromonas veronii
Strains and Possible Misidentification of
Aeromonas
Species
Authors: Graf Joerg
Published: December 2019

Restriction fragment length polymorphism analysis after PCR amplification (RFLP-PCR) of the 16S rRNA gene has been previously proposed as a rapid method to identify
Aeromonas
species. In the present study, the precision of RFLP-PCR was evaluated with 62
Aeromonas
reference strains. The analysis revealed that
Aeromonas veronii
biovar sobria strains produce various patterns, possibly leading to its misidentification as an environmental species. For most other
Aeromonas
species little variation was noted. This study supports the usefulness of RFLP-PCR analysis to separate three clinically important species but also reveals possible misidentifications that necessitate further biochemical tests to validate the preliminary identification.
Direct Detection of Shiga Toxigenic
Escherichia coli
Strains Belonging to Serogroups O111, O157, and O113 by Multiplex PCR
Authors: Paton Adrienne W. , Paton James C.
Published: December 2019

Shiga toxigenic
Escherichia coli
(STEC) strains are a diverse group of organisms associated with severe gastrointestinal and systemic diseases in humans. Within the STEC family,
eae
-positive STEC strains, particularly those belonging to serogroups O157 and O111, appear to have greater virulence for humans. However, in spite of being
eae
negative, STEC strains belonging to serogroup O113 have frequently been associated with cases of severe STEC disease, including hemolytic-uremic syndrome (HUS). We have developed a modified multiplex PCR assay for detection of STEC strains belonging to these three serogroups in cultures of feces by using primers specific for portions of the genetic loci (
rfb
) encoding biosynthesis of the respective O antigen. These primers direct amplification of PCR products of 259, 406, and 593 bp for serogroups O157, O111, and O113, respectively. The assay was validated by testing 40 previously characterized STEC strains, with 100% agreement. It also detected STEC strains of the appropriate genotype in primary fecal cultures from 13 patients with HUS or bloody diarrhea. Thirty other primary fecal cultures from patients without evidence of STEC infection were negative.
Molecular Identification of a
Nocardiopsis dassonvillei
Blood Isolate
Authors: Beau Frédéric , Bollet Claude , Coton Thierry , Garnotel Eric , Drancourt Michel
Published: December 2019

Nocardiopsis dassonvillei
is an environmental aerobic actinomycete seldom isolated in cutaneous and pulmonary infections. We herein report the first
N. dassonvillei
blood isolate in a patient hospitalized for cholangitis. Although morphological characteristics and biochemical tests allowed a presumptive identification of this isolate, cell wall fatty acid chromatographic analysis confirmed identification at the genus level, and 16S rRNA gene sequencing achieved definite identification. This study illustrates the usefulness of 16S rRNA gene sequencing as a routine method for the identification of actinomycetes.
Cloning and Expression of a 48-KilodaltonBabesia caballiMerozoite Rhoptry Protein and Potential Use of the Recombinant Antigen in an Enzyme-Linked Immunosorbent Assay
Authors: Ikadai Hiromi , Xuan Xuenan , Igarashi Ikuo , Tanaka Shigeyasu , Kanemaru Takumi , Nagasawa Hideyuki , Fujisaki Kozo , Suzuki Naoyoshi , Mikami Takeshi
Published: December 2019

A cDNA expression library prepared fromBabesia caballimerozoite mRNA was screened with a monoclonal antibody BC11D against the rhoptry protein ofB. caballimerozoite. A cDNA encoding a 48-kDa protein ofB. caballiwas cloned and designated BC48. The complete nucleotide sequence of the BC48 gene had 1,828 bp and was shown to contain no intron. Southern blotting analysis indicated that the BC48 gene contained more than two copies in theB. caballigenome. Computer analysis suggested that this sequence contained an open reading frame of 1,374 bp with a coding capacity of approximately 52 kDa. The recombinant protein expressed by the vaccinia virus vector in horse cells had an apparent molecular mass of 48 kDa, which was the same as that of the nativeB. caballi48-kDa protein. Moreover, recombinant proteins expressed by the pGEX4T expression vector inEscherichia colias glutathioneS-transferase fusion proteins were used for antigen in an enzyme-linked immunosorbent assay (ELISA). The ELISA was able to differentiate very clearly betweenB. caballi-infected horse sera andB. equi-infected horse sera or noninfected normal horse sera. These results suggest that this simple and highly sensitive test might be applicable to the detection ofB. caballi-infected horses in the field.
Comparison of Direct and Concentrated Acid-Fast Smears To Identify Specimens Culture Positive for
Mycobacterium
spp
Authors: Peterson Ellena M. , Nakasone Audrey , Platon-DeLeon J. M. , Jang Y. , de la Maza Luis M. , Desmond Edward
Published: December 2019

Microscopic examination of respiratory specimens for acid-fast bacilli (AFB) plays a key role in the initial diagnosis of tuberculosis, monitoring of treatment, and determination of eligibility for release from isolation. The objective of this study was to compare the sensitivity obtained with smears for detection of AFB (AFB smears) made directly from respiratory specimens (direct AFB smears) to that obtained with parallel smears made from concentrates of the specimens (concentrated AFB smears). A total of 2,693 specimens were evaluated; 1,806 were from the University of California Irvine Medical Center Medical Microbiology Laboratory (UCIMC), which serves a tertiary-care hospital with outpatient clinics, and 887 were from the Microbial Disease Laboratory at the California Department of Public Health (MDL), which receives specimens from outpatient facilities and clinics on Pacific islands. Of the 353 AFB culture-positive specimens at UCIMC, there was a statistically significant difference in the sensitivity of the direct AFB smear (34%) and that of the smear made from the concentrated specimen (58%) (
P
< 0.05). This was also true for the 208 specimens positive for
Mycobacterium tuberculosis
, for which the sensitivity of the direct smear was 42% (87 of 208) and that for the smear made from the concentrated specimen was 74% (154 of 208). At MDL, where all but 1 of the 45 culture-positive specimens grew
M. tuberculosis
, the sensitivity of the smear made from the concentrated specimen was 93% (42 of 45) and was not significantly higher than the sensitivity of the direct smear, which was 82% (37 of 45). By combining the results from both laboratories, 42 patients from whom at least three specimens were received were culture positive for
M. tuberculosis
. The cumulative results for the initial three specimens from these patients showed that the direct smear detected
M. tuberculosis
in 81% of these patients, whereas the smear made from the concentrate detected
M. tuberculosis
in 91% of these patients. In summary, when all culture-positive specimens are considered, the sensitivity of the direct smear compared to that of a smear made from the concentrated specimen was significantly different overall in the two different laboratory settings. However, this difference was reduced only if the cumulative results for the initial three specimens received from patients who were culture positive for
M. tuberculosis
were evaluated.
Evaluation of the Prototype Roche DNA Amplification Kit Incorporating the New SSK145 and SKCC1B Primers in Detection of Human Immunodeficiency Virus Type 1 DNA in Zimbabwe
Authors: Zijenah Lynn S. , Humphrey Jean , Nathoo Kussum , Malaba Lucie , Zvandasara Parteson , Mahomva Agnes , Iliff Peter , Mbizvo Michael T.
Published: December 2019

We assessed the sensitivity and specificity of a newly developed DNA PCR kit (Roche Diagnostic Corporation, Indianapolis, Ind.) that incorporates primers for all the group M viruses for the detection of human immunodeficiency virus (HIV) type 1 (HIV-1) infection in Zimbabwe. A total of 202 whole-blood samples from adults whose HIV status was known were studied. This included 100 HIV-1-positive and 102 HIV-1-negative samples selected on the basis of concordant results obtained with two enzyme-linked immunosorbent assay kits. The prototype Roche DNA PCR assay had a 100% sensitivity for the detection of HIV-1 DNA and a specificity of 100%. We conclude that the new Roche DNA PCR kit is accurate for the detection of HIV DNA in Zimbabwean samples, in which HIV-1 subtype C dominates.
Comparison of Direct Inoculation and Copan Transport Systems for Isolation of
Neisseria gonorrhoeae
from Endocervical Specimens
Authors: Olsen C. C. , Schwebke J. R. , Benjamin W. H. , Beverly A. , Waites K. B.
Published: December 2019

Two commercial swab transport systems, Copan Amies gel agar with and without charcoal (Copan Diagnostics, Corona, Calif.), were compared to direct inoculation onto modified Thayer-Martin medium for detection of
Neisseria gonorrhoeae
in 1,490 endocervical specimens obtained from women attending a sexually transmitted disease clinic. Copan swabs were held in the transport system for 24 h at room temperature prior to inoculation onto modified Thayer-Martin medium. All cultures were incubated at 35°C in 5% CO
2
, and bacteria were identified on the basis of Gram stain, oxidase, and biochemical reactions. Copan Amies gel agar transport system without charcoal detected 77 of 81 (95%) direct inoculation culture-positive specimens, and Copan Amies gel agar transport system with charcoal detected 53 of 56 (95%) directly inoculated culture-positive specimens. Copan Amies gel agar without charcoal inoculated after 6 h supported growth of 56 (98%) positive cultures out of only 55 directly inoculated culture-positive specimens. This study demonstrates that Copan swabs represent a reasonable alternative, providing convenience, low cost, and ease of use while still maintaining a satisfactory recovery rate of
N. gonorrhoeae
from clinical specimens, if specimens can be inoculated onto selective media within a relatively short time period not involving overnight shipment.
Isolation, Identification, and Molecular Characterization of Strains of
Photorhabdus luminescens
from Infected Humans in Australia
Authors: Peel Margaret M. , Alfredson David A. , Gerrard John G. , Davis Jennifer M. , Robson Jennifer M. , McDougall Rodney J. , Scullie Barry L. , Akhurst Raymond J.
Published: December 2019

We describe the isolation of
Photorhabdus
(
Xenorhabdus
)
luminescens
from four Australian patients: two with multiple skin lesions, one with bacteremia only, and one with disseminated infection. One of the patients had multiple skin lesions following the bite of a spider, while the lesions in the other patient were possibly associated with a spider bite. The source of infection for the remaining two patients is unknown. As a member of the family
Enterobacteriaceae
,
P. luminescens
is unusual in that it fails to reduce nitrate and ferments only glucose and mannose. It gives negative reactions for lysine decarboxylase, arginine dihydrolase, and ornithine decarboxylase (Moeller). The species is motile, utilizes citrate, hydrolyzes urea, and usually produces a unique type of annular hemolysis on sheep blood agar plates incubated at 25°C. A weak bioluminescence is the defining characteristic.
P. luminescens
is an insect pathogen and is symbiotically associated with entomopathogenic nematodes. Its isolation from human clinical specimens has been reported previously from the United States. Restriction fragment length polymorphism-PCR analysis of the 16S rRNA gene demonstrated a high level of similarity among the Australian clinical strains and significant differences between the Australian clinical strains and the U.S. clinical strains. However, numerical analyses of the data suggest that the two groups of clinical strains are more similar to each other than they are to the symbiotic strains found in nematodes. This is the first report of the isolation of
P. luminescens
from infected humans in Australia and the second report of the isolation of this species from infected humans worldwide.
Application of Different Genotyping Methods for
Pseudomonas aeruginosa
in a Setting of Endemicity in an Intensive Care Unit
Authors: Speijer Han , Savelkoul Paul H. M. , Bonten Marc J. , Stobberingh Ellen E. , Tjhie Jeroen H. T.
Published: December 2019

Colonization with
Pseudomonas aeruginosa
was studied by taking serial swab specimens from the oropharynges and anuses and tracheal and gastric aspirates from patients in an intensive care unit during a 10-month period in a setting of endemicity. Nineteen (10%) of the 192 patients included in the study were colonized on admission, while another 30 (16%) patients acquired
P. aeruginosa
while in the hospital. Typing of 353 isolates was performed by random amplified polymorphic DNA (RAPD) analysis, and 56 strains were selected for further typing by RAPD analysis, pulsed-field gel electrophoresis (PFGE), and amplified fragment length polymorphism (AFLP) analysis. By these methods, 42, 44, and 44 genotypes were found, respectively. Computer-aided cluster analysis indicated that similar groups of related isolates were obtained by each method. By taking admission periods into account, analysis of the typing results suggested cross-acquisition of
P. aeruginosa
for five patient pairs. The small number of transfers and the large number of genotypes found indicate that most
P. aeruginosa
strains were derived from the patients themselves. The numbers of observed typing patterns and band differences between related isolates were counted for each typing method. AFLP analysis with primers without a selective base proved to be the most discriminatory method, followed by PFGE, AFLP analysis (with one selective base), and RAPD analysis. On the basis of a comparison with established strain differentiation criteria for PFGE, the criteria for differentiation of
P. aeruginosa
by AFLP analysis are presented.
Candida
Isolates from Neonates: Frequency of Misidentification and Reduced Fluconazole Susceptibility
Authors: Rowen Judith L. , Tate Judy M. , Nordoff Nicole , Passarell Lester , McGinnis Michael R.
Published: December 2019

Systemic candidiasis affects 1.6 to 4.5% of very low birth weight (≤1,500 g) infants. A specimen archive of
Candida
strains from intensive care nurseries was created; it currently houses 98 isolates from 17 institutions. Eight isolates (8.2%) were misidentified at the referring institution. The MICs of fluconazole for seven isolates (7.1%, all non-
C. albicans
species, one misidentified initially) were >8 μg/ml.
Novel Method for Rapid Determination of Clarithromycin Sensitivity in
Helicobacter pylori
Authors: Gibson J. R. , Saunders N. A. , Burke B. , Owen R. J.
Published: December 2019

A novel PCR-hybridization assay, performed in single closed capillaries, was developed to detect clarithromycin resistance-associated gene mutations in
Helicobacter pylori
. Mutations were detected by thermal analysis in 33 of 34 (97%) resistant isolates but not in 66 isolates determined to be sensitive by conventional antibiotic assays. The method was rapid and reproducible, and it reduced PCR product contamination risk.
Evaluation of the Revised MicroScan Dried Overnight Gram-Positive Identification Panel To Identify
Enterococcus
Species
Authors: Iwen Peter C. , Rupp Mark E. , Schreckenberger Paul C. , Hinrichs Steven H.
Published: December 2019

The revised MicroScan Dried Overnight Gram-Positive Identification panel was evaluated for its efficacy at identifying
Enterococcus
species in comparison with conventional biochemical tests. Supplemental testing of ampicillin-susceptible
Enterococcus faecium
for motility and the ability to acidify methyl-α-
d
-glucopyranoside helped recognize
E. gallinarum
and increased the accuracy of the panel for identifying
Enterococcus
species to 98.5%.