bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of rifampin resistance by single-strand conformation polymorphism analysis of cerebrospinal fluid of patients with tuberculosis of the central nervous system
Authors: Scarpellini P , Braglia S , Brambilla A M , Dalessandro M , Cichero P , Gori A , Lazzarin A
Published: January 2020

Mutations in a 69-bp region of the rpoB gene of Mycobacterium tuberculosis are associated with rifampin resistance (Rif[r]). These have been detected with mycobacterial DNA extracted from bacterial suspensions or respiratory specimens that were acid-fast smear positive. We experimented with a strategy for the rapid detection of Rif(r) in cerebrospinal fluid (CSF) samples. The strategy involves the amplification of the 69-bp region of rpoB by means of PCR and the identification of nucleotide mutations by single-strand conformation polymorphism (SSCP) analysis of the amplification products. Sixty-five CSF specimens collected from 29 patients (19 patients were coinfected with human immunodeficiency virus) with culture or autopsy-confirmed (22 patients) or highly probable (7 patients) tuberculosis of the central nervous system (CNS-TB) were processed. Amplified products suitable for evaluation by SSCP analysis were obtained from 37 CSF specimens from 25 subjects (86.2%). PCR-SSCP of CSF correctly identified the rifampin susceptibility phenotype of isolates from all 17 patients for whom the results of susceptibility tests carried out with strains cultured from CSF or respiratory samples were available. Moreover, this assay revealed the rifampin susceptibility genotype of isolates from the eight patients (three patients with culture-confirmed CNS-TB and five patients in whom CNS-TB was highly probable) for whom no susceptibility test results were available; the PCR-SSCP data obtained for these patients were concordant with the outcome after a standard antituberculosis treatment. The evolution of a mutation in the rpoB gene was documented in a patient during the course of treatment. PCR-SSCP analysis of CSF seems to be an efficacious method of predicting Rif(r) and would reduce the time required for susceptibility testing from approximately 4 to 8 weeks to a few days.
Phylogenetic analyses of Chlamydia psittaci strains from birds based on 16S rRNA gene sequence
Authors: Takahashi T , Masuda M , Tsuruno T , Mori Y , Takashima I , Hiramune T , Kikuchi N
Published: January 2020

The nucleotide sequences of 16S ribosomal DNA (rDNA) were determined for 39 strains of Chlamydia psittaci (34 from birds and 5 from mammals) and for 4 Chlamydia pecorum strains. The sequences were compared phylogenetically with the gene sequences of nine Chlamydia strains (covering four species of the genus) retrieved from nucleotide databases. In the neighbor-joining tree, C. psittaci strains were more closely related to each other than to the other Chlamydia species, although a feline pneumonitis strain was distinct (983 to 98.6% similarity to other strains) and appeared to form the deepest subline within the species of C. psittaci (bootstrap value, 99%). The other strains of C. psittaci exhibiting similarity values of more than 99% were branched into several subgroups. Two pigeon strains and one turkey strain formed a distinct clade recovered in 97% of the bootstrapped trees. The other pigeon strains seemed to be distinct from the strains from psittacine birds, with 88% of bootstrap value. In the cluster of psittacine strains, three parakeet strains and an ovine abortion strain exhibited a specific association (level of sequence similarity, 99.9% or more; bootstrap value, 95%). These suggest that at least four groups of strains exist within the species C. psittaci. The 16S rDNA sequence is a valuable phylogenetic marker for the taxonomy of chlamydiae, and its analysis is a reliable tool for identification of the organisms.
Decreased capacity for type-specific-antigen synthesis accounts for high prevalence of nontypeable strains of group B streptococci in Mexico
Authors: Palacios G C , Eskew E K , Solorzano F , Mattingly S J
Published: January 2020

The low incidence of group B streptococcal (GBS) invasive neonatal disease in Mexico has been attributed to the low prevalence of serotype III strains, a major serotype in developed countries. In addition, nontypeable strains account for 12% of the isolates in Mexico and < 1% of the isolates in the United States. In this study, 57 GBS isolates (28 nontypeable by the Lancefield procedure) from carrier and infected neonates and women from Mexico were also examined for the presence of type-specific antigen by an enzymatic procedure using N-acetylmuramidase digestion of the cell wall to release soluble type-specific antigen. Of the 28 nontypeable strains from Mexico, 23 were typeable by the enzyme extraction procedure, with serotype III being the predominant serotype in invasive disease. These results suggest that nontypeable isolates of GBS should be further examined by the enzymatic extraction procedure to determine the presence of type-specific antigen. Furthermore, these limited results suggest that serotype III is likely a major serotype in invasive disease also in Mexico.
Strains of glycopeptide-resistant Enterococcus faecium can alter their van genotypes during an outbreak
Authors: Woodford N , Chadwick P R , Morrison D , Cookson B D
Published: January 2020

Two isolates of Enterococcus faecium with VanA glycopeptide resistance were isolated during a hospital outbreak of E. faecium with plasmid-mediated VanB resistance. Both were found to be identical to the VanB outbreak strain by pulsed-field gel electrophoresis. The genotype of this strain changed from vanB to vanA through an intermediate isolate that contained both the vanA and vanB gene clusters on distinct plasmids.
Influence of endocervical specimen adequacy on PCR and direct fluorescent-antibody staining for detection of Chlamydia trachomatis infections
Authors: Welsh L E , Quinn T C , Gaydos C A
Published: January 2020

The cellular quality of the endocervical swab specimen used for the detection of Chlamydia trachomatis may dramatically impact the sensitivity of the diagnostic assay used. An evaluation of the adequacy of 319 endocervical swab specimens from women attending two inner-city sexually transmitted disease and family planning clinics, as well as five high school-based family planning clinics, was performed, and the resulting data were compared with the diagnostic results obtained by both Amplicor PCR and Microtrak direct fluorescent-antibody (DFA) staining. The swab from each patient was rolled across the open circular area of a DFA slide and then used to inoculate a transport tube for PCR (Roche), after which the swab was discarded. The slides were stained and examined by epifluorescence microscopy for the presence of C. trachomatis elementary bodies and for the presence and number of cell types to determine specimen adequacy. Cellular adequacy for a cervical swab specimen was defined as the presence of one or more columnar epithelial or metaplastic epithelial cells or the presence of more than 100 erythrocytes per high-power microscopic field. Of the 319 specimens read by DFA, 204 (63.9%) were determined to be adequate. There were 34 (10.7%) positive specimens by DFA and/or PCR. Twenty-nine (9.1%) specimens were positive by PCR, 20 (6.3%) specimens were DFA positive, and 15 (4.7%) were concordantly positive by both tests. The prevalence of chlamydia among adequate specimens was 14.2% (29/204), compared to 4.3% (5/115) for inadequate specimens (P < 0.0001). Variations in specimen quality and the sensitivity of the diagnostic assay used have a significant impact on determining the prevalence of C. trachomatis in a population.
Clinical utility of broth cultures of cerebrospinal fluid from patients at risk for shunt infections
Authors: Meredith F T , Phillips H K , Reller L B
Published: January 2020

For patients with cerebrospinal fluid (CSF) shunts, culture of the CSF remains the most valuable tool in the evaluation of suspected shunt infections. To detect anaerobic Propionibacterium sp., a well-described cause of these infections, many clinical microbiology laboratories routinely employ a broth medium as an adjunct to solid media. The use of broth, however, creates a diagnostic dilemma since many contaminants also are isolated from broth cultures. Therefore, we retrospectively reviewed the records of 59 patients with CSF shunts in whom an organism was isolated from only broth cultures to assess their utility for the diagnosis of shunt infection. We found that no single clinical or laboratory parameter, including fever, leukocytosis, pleocytosis, or CSF protein and glucose, could reliably predict or exclude a shunt infection. Isolation of coagulase-negative staphylococci only in broth, in the absence of growth on solid media in concurrent or immediately preceding cultures, virtually always represented contamination. The isolation of Propionibacterium sp. from broth only usually represented contamination; however, infection could not be excluded without a repeated CSF culture, even in the absence of pleocytosis. We recommend that specific comments be appended to laboratory reports for isolates from CSF in broth only as an aid to the physician in interpreting the clinical importance of such isolates.
Identification of pathogenic Leptospira genospecies by continuous monitoring of fluorogenic hybridization probes during rapid-cycle PCR
Authors: Woo T H , Patel B K , Smythe L D , Symonds M L , Norris M A , Dohnt M F
Published: January 2020

Partial sequences of 23S rRNA gene PCR products from 23 strains of 6 pathogenic Leptospira genospecies and from 8 strains of the saprophytic Leptospira biflexa were determined. Sequence analyses enabled Leptospira genus-specific amplification primers and pathogen-specific fluorogenic adjacent hybridization probes to be designed and synthesized. A PCR protocol was developed in which changes in fluorescence emission resulting from specific annealing of fluorogenic adjacent hybridization probes to the target DNA were continuously monitored. Nine strains of the pathogenic Leptospira genospecies could be differentiated from Leptonema illini, Escherichia coli, and eight strains of Leptospira biflexa. The PCR method was rapid, requiring 18 min for the completion of 45 cycles. It was also simple and flexible, as DNA templates prepared by four different methods, including the simple boiling method, could be used without adverse effects. Two hundred copies of target, equivalent to 100 cells, could be detected.
Specific identification of Mycobacterium tuberculosis with the luciferase reporter mycobacteriophage: use of p-nitro-alpha-acetylamino-beta-hydroxy propiophenone
Authors: Riska P F , Jacobs W R , Bloom B R , McKitrick J , Chan J
Published: January 2020

We have previously described a luciferase reporter mycobacteriophage (LRP) assay that can detect Mycobacterium tuberculosis and characterize mycobacterial drug susceptibility patterns within 24 to 48 h in positive cultures. One drawback of this LRP protocol is the ability of the recombinant mycobacteriophage phAE40 to infect a variety of Mycobacterium species, thus limiting its specificity for the detection of M. tuberculosis. In this study, we have (i) explored the host range of phAE40, (ii) developed a modified LRP assay that exploits the selective inhibitory effect of the compound p-nitro-alpha-acetylamino-beta-hydroxy propiophenone (NAP) against members of the M. tuberculosis complex to differentiate between the tubercle bacillus and other mycobacterial species, and (iii) tested over 300 samples, including primary clinical isolates and drug-resistant strains of M. tuberculosis, demonstrating the ability of the NAP-modified LRP assay to identify M. tuberculosis complex organisms with high degrees of sensitivity and specificity.
Increased levels of macrophage colony-stimulating factor, gamma interferon, and tumor necrosis factor alpha in sera of patients with Orientia tsutsugamushi infection
Authors: Iwasaki H , Takada N , Nakamura T , Ueda T
Published: January 2020

Levels of macrophage colony-stimulating factor (nine of nine patients) and gamma interferon (six of nine patients) in serum were elevated above the range of normal in the acute phase of tsutsugamushi disease. Significant increases in levels of tumor necrosis factor alpha were observed during the convalescent phase in five patients, and they exceeded the levels observed during the acute phase. Hypercytokinemia appeared to be responsible for the emergence of the symptoms of tsutsugamushi disease.
Susceptibilities of Chryseobacterium indologenes and Chryseobacterium meningosepticum to cefepime and cefpirome
Authors: Hsueh P R , Teng L J , Yang P C , Ho S W , Luh K T
Published: January 2020

In vitro activities of cefepime and cefpirome against 96 isolates of Chryseobacterium indologenes and 21 of C. meningosepticum were determined by the agar dilution method. Overall, cefepime was more active than cefpirome against C. indologenes (MIC at which 50% of the isolates were inhibited [MIC50] and MIC90, 4 and 16 microg/ml, respectively, for cefepime and 8 and 128 microg/ml, respectively, for cefpirome). Both agents had poor potency against C. meningosepticum (MIC50 and MIC90, 64 and >256 microg/ml, respectively, for cefepime and 128 and >256 microg/ml, respectively, for cefpirome).
Comparison of the Mycobacteria Growth Indicator Tube (MGIT) with radiometric and solid culture for recovery of acid-fast bacilli
Authors: Pfyffer G E , Welscher H M , Kissling P , Cieslak C , Casal M J , Gutierrez J , Rüsch-Gerdes S
Published: January 2020

In a multicenter study involving three reference centers for mycobacteria, the rate of recovery of acid-fast bacilli (AFB) and the mean time to their detection from clinical specimens was determined by using the Mycobacteria Growth Indicator Tube (MGIT). These parameters were compared to those assessed by the radiometric BACTEC 460 TB system and by cultivation on solid media. Clinical specimens (n = 1,500) were pretreated with N-acetyl-L-cysteine (NALC)-NaOH. The contamination rates for MGITs were 2.0% (center 1), 13.8% (center 2), and 6.1% (center 3). A total of 180 mycobacterial isolates were detected (M. tuberculosis complex, n = 113; nontuberculous mycobacteria [NTM], n = 67). When using a combination of liquid and solid media (the current "gold standard" for culture), MGIT plus solid media detected 156 (86.7%) of the isolates, whereas BACTEC plus solid media recovered 168 (93.3%) of all AFB. Between these two gold standards there was no statistically significant difference (P > 0.05). The combination of MGIT plus BACTEC detected 171 (95.0%) of all isolates (compared with MGIT plus solid media, P < 0.01; compared with BACTEC plus solid media, P > 0.05). Considering the efficacies of the different media separately, MGIT was superior to solid media (although not significantly; P > 0.05) in detecting AFB but was inferior to the BACTEC system (P < 0.01). The mean time to the detection of M. tuberculosis complex was 9.9 days with MGIT, 9.7 days with BACTEC, and 20.2 days with solid media. NTM needed, on average, 11.9, 13.0, and 22.2 days to appear by the three methods, respectively. In conclusion, MGIT proved to be a valuable alternative to the radiometric cultivation system.
Gordona terrae central nervous system infection in an immunocompetent patient
Authors: Drancourt M , Pelletier J , Cherif A A , Raoult D
Published: January 2020

The bacterial genus Gordona includes seven species of mycolic acid-containing actinomycetes which are cultured from environmental sources and rarely from clinical samples. They have been implicated in primary pulmonary diseases, nosocomial wound infections, and central nervous system infections in two immunocompromised patients. We isolated Gordona terrae from the cerebrospinal fluid sample of an immunocompetent patient with meningitis and multiple brain abscesses and detected Gordona terrae DNA in the abscesses. The outcome was good at the 4-year follow-up, after prolonged treatment with trimethoprim-sulfamethoxazole. Phenotypic identification of this isolate was confirmed by analysis of the 16S rRNA gene sequence, which shared 100% homology with that of G. terrae reference strains. Physicians and clinical microbiologists must be aware of the occurrence of Gordona species infection not only among immunocompromised patients but among all patients. Accurate identification of Gordona species may be accomplished by molecular techniques.
Human babesiosis in Taiwan: asymptomatic infection with a Babesia microti-like organism in a Taiwanese woman
Authors: Shih C M , Liu L P , Chung W C , Ong S J , Wang C C
Published: January 2020

An asymptomatic Babesia infection was confirmed by laboratory diagnoses. The intraerythrocytic protozoan (designed TW1) isolated from a 51-year-old Taiwanese woman appeared to be morphologically consistent with small-form piroplasm, and measurements indicated that it had a body size of 1.5 to 2.5 microm in diameter. The typical features of ring, binary, and tetrad forms were observed in Giemsa-stained thin blood smears. A persistent and low-grade parasitemia was established after hamster inoculation. Indirect immunofluorescent-antibody reactivities indicate that this strain (TW1) of Babesia was serologically related to, but not identical to, the Babesia species (B. microti) that infects rodents. Antibody titers in the patient's sera combined with the clinical symptoms suggested that the present case was a chronic and subclinical babesial infection. A neighborhood human serologic survey indicated that the infection may have been acquired accidentally from an infected rodent and localized within the same family. Indeed, rodents from areas around the neighborhood were trapped, and a high prevalence (83%) of babesial infection was observed. The possible vector responsible for the transmission remains to be identified.
A modified Elek test for detection of toxigenic corynebacteria in the diagnostic laboratory
Authors: Engler K H , Glushkevich T , Mazurova I K , George R C , Efstratiou A
Published: January 2020

The detection of toxigenicity among Corynebacterium diphtheriae and Corynebacterium ulcerans strains is the most important test for the microbiological diagnosis of diphtheria. Difficulties with current methods, in particular the Elek test, are well documented. We therefore describe a modified Elek test which provides an accurate result after only 16 h of incubation, in contrast to 48 h for the conventional test.
Isolation of Bartonella (Rochalimaea) henselae: effects of methods of blood collection and handling
Authors: Brenner S A , Rooney J A , Manzewitsch P , Regnery R L
Published: January 2020

Bartonella (Rochalimaea) henselae causes cat-scratch disease, bacillary angiomatosis, peliosis hepatis, and fever in humans. B. henselae can be difficult to culture axenically, and as many as 5 weeks may be required before colonies are visible. We compared how different methods of blood collection and handling affect isolation of this pathogen. Blood specimens from B. henselae-infected cats were collected in both EDTA and Isolator blood-lysis tubes and were subsequently plated onto rabbit blood-brain heart infusion agar by using three different schedules: plating immediately, plating after 24 h at 25 degrees C, and plating after 26 days at -65 degrees C. Colonies were counted 14 and 35 days after plating. Blood collected in tubes containing EDTA, frozen at -65 degrees C, and then plated on blood agar yielded a median of 60,000 CFU/ml, compared with 25,333 CFU/ml after collection in the Isolator tubes (P < 0.01). Frozen blood yielded the largest number of B. henselae colonies for any of the schedules tested. These results support previous observations that the Isolator system is more sensitive than tubes containing EDTA for isolation of B. henselae and suggest that, for cat blood, collection in tubes containing EDTA and subsequent freezing may further improve the sensitivity of detection of B. henselae.
Emergence of a new clone of toxigenic Vibrio cholerae O1 biotype El Tor displacing V. cholerae O139 Bengal in Bangladesh
Authors: Faruque S M , Ahmed K M , Abdul Alim A R , Qadri F , Siddique A K , Albert M J
Published: January 2020

The emergence of Vibrio cholerae O139 Bengal in 1993, its rapid spread in an epidemic form, in which it replaced existing strains of V. cholerae O1 during 1992 and 1993, and the subsequent reemergence of V. cholerae O1 of the El Tor biotype in Bangladesh since 1994 have raised questions regarding the origin of the reemerged El Tor vibrios. We studied 50 El Tor vibrio strains isolated in Bangladesh and four other countries in Asia and Africa before the emergence of V. cholerae O139 and 32 strains isolated in Bangladesh during and after the epidemic caused by V. cholerae O139 and 32 strains isolated in Bangladesh during and after the epidemic caused by V. cholerae O139 to determine whether the reemerged El Tor vibrios were genetically different from the El Tor vibrios which existed before the emergence of V. cholerae O139. Analysis of restriction fragment length polymorphisms in genes for conserved rRNA, cholera toxin (ctxA), and zonula occludens toxin (zot) or in DNA sequences flanking the genes showed that the El Tor strains isolated before the emergence of V. cholerae O139 belonged to four different ribotypes and four different ctx genotypes. Of 32 El Tor strains isolated after the emergence of O139 vibrios, 30 strains (93.7%) including all the clinical isolates belonged to a single new ribotype and a distinctly different ctx genotype. These results provide evidence that the reemerged El Tor strains represent a new clone of El Tor vibrios distinctly different from the earlier clones of El Tor vibrios which were replaced by the O139 vibrios. Further analysis showed that all the strains carried the structural and regulatory genes for toxin-coregulated pilus (tcpA, tcpI, and toxR). All strains of the new clone produced cholera toxin (CT) in vitro, as assayed by the GM1-dependent enzyme-linked immunosorbent assay, and the level of CT production was comparable to that of previous epidemic isolates of El Tor vibrios. Further studies are required to assess the epidemic potential of the newly emerged clone of V. cholerae O1 and to understand the mechanism of emergence of new clones of toxigenic V. cholerae.
An aberrant variant of Histoplasma capsulatum var. capsulatum
Authors: Sutton D A , Padhye A A , Standard P G , Rinaldi M G
Published: January 2020

We studied an aberrant culture of Histoplasma capsulatum var. capsulatum isolated from synovial fluid collected from the right elbow of a patient from Kansas. Colonies on Sabouraud glucose agar and other routine mycological media were glabrous to soft, moist, heaped, deeply folded or convoluted, and orange-brown with a white, irregular margin. Microscopically, hyphae were hyaline, septate, and branched and remained totally devoid of conidiation over a period of 2 years on all mycological media. Conversion to the yeast form was achieved on Pine's medium at 37 degrees C. Colonies at early stages of growth were smooth, moist, pasty, shiny, and orange-brown but soon became wrinkled and slightly raised and produced oval, thin-walled cells measuring 2 to 3 by to 4.5 microns which multiplied by polar budding. The identity of the isolate was further confirmed by utilizing the Accuprobe DNA and the exoantigen test for H. capsulatum var. capsulatum.
Prevalence of hepatitis G viremia among healthy subjects, individuals with liver disease, and persons at risk for parenteral transmission
Authors: Feucht H H , Zöllner B , Polywka S , Knödler B , Schröter M , Nolte H , Laufs R
Published: January 2020

The prevalence of hepatitis G virus (HGV) and hepatitis C virus (HCV) infection was determined by reverse transcription-PCR in 777 individuals with and without risk factors for viral transmission via blood. From our results we conclude that transmission of HGV and that of HCV are favored by similar risk factors.
The Honduran human immunodeficiency virus type 1 (HIV-1) epidemic is dominated by HIV-1 subtype B as determined by V3 domain sero- and genotyping
Authors: Lara C , Sällberg M , Johansson B , de Rivera I L , Sönnerborg A
Published: January 2020

The distribution of subtypes A through F of human immunodeficiency virus type 1 (HIV-1) in Honduras was analyzed in 120 HIV-1 positive serum samples by V3 peptide serotyping and HIV-1 cDNA sequencing. In the Honduran HIV-1 epidemic, subtype B was detected in 98 of 99 subtyped samples.
Evaluation of a quantitative plasma PCR plate assay for detecting cytomegalovirus infection in marrow transplant recipients
Authors: Gallez-Hawkins G M , Tegtmeier B R , ter Veer A , Niland J C , Forman S J , Zaia J A
Published: January 2020

A plasma PCR test, using a nonradioactive PCR plate assay, was evaluated for detection of human cytomegalovirus reactivation. This assay was compared to Southern blotting and found to perform well. As a noncompetitive method of quantitation, it was similar to a competitive method for detecting the number of genome copies per milliliter of plasma in marrow transplant recipients. This is a technically simplified assay with potential for adaptation to automation.
Identification and characterization of a novel DNA marker associated with epidemic Burkholderia cepacia strains recovered from patients with cystic fibrosis
Authors: Mahenthiralingam E , Simpson D A , Speert D P
Published: January 2020

Burkholderia cepacia is a problematic pathogen that may spread among patients with cystic fibrosis (CF). One highly infectious CF strain that causes epidemics in both the United Kingdom and eastern Canada has been shown to possess both the cable pilin subunit gene (cblA) and a unique combination of insertion sequences. However, no genetic markers linking this strain type with other types epidemic at various centers have been identified. Using a randomly amplified polymorphic DNA (RAPD) typing scheme, we identified an apparently conserved 1.4-kb fragment in the DNA fingerprint of epidemic B. cepacia strains. Conservation of the DNA marker among epidemic strains was demonstrated by Southern hybridization, and its prevalence was assessed in a collection of chromosomal DNAs extracted from 627 isolates representative of 132 RAPD-defined B. cepacia strain types. The marker was specifically associated with seven epidemic CF strains, was absent among nonepidemic strains infecting individual patients with CF, and rare among strains recovered from the natural environment. Only one of the seven epidemic CF strain types possessed DNA homologous to cblA. The RAPD marker was designated the "B. cepacia epidemic strain marker" (BCESM). Sequence analysis of chromosomal DNA corresponding to the 1.4-kb RAPD marker revealed the presence of a putative open reading frame (ORF) with significant homology to several negative transcriptional regulators; the ORF was designated the "epidemic strain marker regulator," or esmR. The BCESM DNA is the first genetic marker that has been identified to be specifically associated with and conserved among several epidemic B. cepacia strains which infect multiple patients with CF.
Infected abdominal aortic aneurysm due to penicillin-, ceftriaxone-, and cefotaxime-resistant Streptococcus pneumoniae
Authors: Albrecht W E , Papasian C J , Bamberger D M , Fiorella R , Riddell S W
Published: January 2020

The clinical course for a patient hospitalized with pneumonia and meningitis due to penicillin-, ceftriaxone-, and cefotaxime-resistant Streptococcus pneumoniae is described. The pneumonia and meningitis responded to antimicrobial therapy, but the patient died following rupture of an infected abdominal aortic aneurysm; gram-positive cocci resembling S. pneumoniae were detected within the aneurysm.
Detection of Francisella tularensis in ulcers of patients with tularemia by PCR
Authors: Sjöstedt A , Eriksson U , Berglund L , Tärnvik A
Published: January 2020

The diagnosis of human cases of tularemia is usually confirmed by the demonstration of an antibody response to Francisella tularensis, which occurs about 2 weeks after the onset of disease. Due to a high risk of infection in the laboratory, cultivation of the causative agent tends to be avoided. During an outbreak in Sweden, the use of PCR for diagnosing the ulceroglandular form of tularemia was evaluated. Extraction and preparation of F. tularensis DNA from swab samples from the wounds of patients with tularemia involved the use of the nuclease inhibitor guanidine thiocyanate. The DNA was detected by multiplex PCR targeting the 16S rRNA gene and a 17-kDa lipoprotein gene of F. tularensis. In 29 of 40 (73%) patients with serologically confirmed tularemia, F. tularensis DNA was successfully amplified. Considering the limitations of current diagnostic procedures, PCR may become useful for the early diagnosis of tularemia.
Hepatitis C virus replicative levels and efficiency of genotyping by specific PCR and antibody assay
Authors: Yuki N , Hayashi N , Mita E , Hagiwara H , Ohkawa K , Katayama K , Sasaki Y , Kasahara A , Fusamoto H , Kamada T
Published: January 2020

We studied factors which influence the detection of hepatitis C virus genotypes by the group-specific PCR of the sequence within the core region gene and by the newly developed genotype-specific NS4 antibody assay. Genotyping was performed on 75 hepatitis C virus carriers in Japan, where patients with hepatitis C viremia are exclusively infected with genotype 1b, 2a, and 2b. PCR failed to identify genotypes in 8 (11%) patients, whereas 12 (16%) patients, including the 8 patients mentioned above, could not be genotyped by the serological assay. Serological genotypes showed almost complete agreement with those found by the PCR except that double infection was revealed in only two of the eight patients serologically judged to be coinfected with genotypes 1 and 2. In each assay, disease activity and levels of viremia assessed by a competitive reverse transcription PCR assay were significantly lower in patients infected with untypeable isolates than in those infected with typeable ones (P < 0.01). The PCR could identify the genotypes of isolates from all 64 patients with levels of viremia of > or = 10(6) copies/ml, and the genotype-specific antibody responses were found in 60 (94%) patients. In contrast, isolates from only 3 (27%) of 11 patients with low levels of viremia (< 10(6) copies/ml) could be genotyped by the PCR (P < 0.00001), and these patients showed the genotype-specific antibody responses (P < 0.00001). These findings suggest that low levels of hepatitis C virus replication may reduce the efficiency of genotyping by serological assay as well as by PCR.
Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5' end of the large-subunit (26S) ribosomal DNA gene
Authors: Kurtzman C P , Robnett C J
Published: January 2020

Clinically important species of Candida and related organisms were compared for extent of nucleotide divergence in the 5' end of the large-subunit (26S) ribosomal DNA (rDNA) gene. This rDNA region is sufficiently variable to allow reliable separation of all known clinically significant yeast species. Of the 204 described species examined, 21 appeared to be synonyms of previously described organisms. Phylogenetic relationships among the species are presented.
Seroreactivity to hepatitis E virus in areas where the disease is not endemic
Authors: Thomas D L , Yarbough P O , Vlahov D , Tsarev S A , Nelson K E , Saah A J , Purcell R H
Published: January 2020

If the occurrence of hepatitis E virus antibody (anti-HEV) in regions where the disease is not endemic represents infection, rates may be greater in high-risk populations and behavioral correlates may reflect recognized transmission modes. Serum samples from 300 homosexual males, 300 injection drug users (IDUs), and 300 blood donors from Baltimore, Md., were tested for anti-HEV by enzyme immunoassay. Anti-HEV was found in an unexpectedly high percentage of homosexual men (15.9%) and IDUs (23.0%). However, anti-HEV was present in a similar proportion of blood donors (21.3%) (P > 0.05), while hepatitis A, B, and C virus antibodies were more prevalent in the high-risk groups (P < 0.001). Among homosexual men, anti-HEV was not significantly correlated with a history of hepatitis, high-risk sexual practices, or sexually transmitted infections, in contrast to hepatitis A and B antibodies. Among IDUs, anti-HEV was not significantly associated with a history of hepatitis or high-risk drug-using practices, as was found with hepatitis C antibodies. In a setting without endemic hepatitis E disease, there was no evidence that anti-HEV reflected subclinical infection. Until the basis for HEV seroreactivity in such areas is elucidated, anti-HEV results should be interpreted with caution.
A PCR assay for identification of Enterococcus faecium
Authors: Cheng S , McCleskey F K , Gress M J , Petroziello J M , Liu R , Namdari H , Beninga K , Salmen A , DelVecchio V G
Published: January 2020

Enterococcus faecium has recently emerged as a serious nosocomial pathogen. The prevalence and severity of enterococcal infections, the mortality rate from such infections, and the antibiotic resistance of enterococci are often species dependent. Since conventional biochemical methods fail to differentiate E. faecium from certain newly described enterococcal species, a PCR-based assay was developed for the rapid identification of E. faecium.
Evaluation of bichro-latex albicans, a new method for rapid identification of Candida albicans
Authors: Quindos G , San Millan R , Robert R , Bernard C , Ponton J
Published: January 2020

A method for identification of Candida albicans within 5 min was evaluated by using 4,643 yeast isolates. Six false-positive and three false-negative reactions were observed. The specificity (99.87%) and sensitivity (99.74%) obtained indicate that the Bichro-latex albicans test is a useful method for the rapid identification of C. albicans colonies.
Direct detection and identification of Pseudomonas aeruginosa in clinical samples such as skin biopsy specimens and expectorations by multiplex PCR based on two outer membrane lipoprotein genes, oprI and oprL
Authors: De Vos D , Lim A , Pirnay J P , Struelens M , Vandenvelde C , Duinslaeger L , Vanderkelen A , Cornelis P
Published: January 2020

A multiplex PCR test based on the simultaneous amplification of two lipoprotein genes, oprI and oprL, was designed and evaluated for its ability to directly detect fluorescent pseudomonads (amplification of oprI open reading frame, 249 bp) and Pseudomonas aeruginosa (amplification of oprL open reading frame, 504 bp) in clinical material. A collection of reference strains including 20 different species of fluorescent pseudomonads was tested. Positive PCR results for both genes were observed only for P. aeruginosa isolates (n = 150), including strains of clinical and environmental origin, while only one gene, oprI, was amplified from the other fluorescent pseudomonads. All other bacteria tested (n = 15) were negative by the amplification test. The lower detection level for P. aeruginosa was estimated to be 10(2) cells/ml. Preliminary evaluation on testing skin biopsy specimens from patients with burns (n = 14) and sputum samples from cystic fibrosis patients (n = 49) and other patients (n = 19) showed 100% sensitivity and 74% specificity in comparison with culture. This multiplex PCR assay appears promising for the rapid and sensitive detection of P. aeruginosa in clinical specimens. Further evaluation of its specificity in longitudinal clinical studies is warranted.
Prevalence of Bartonella henselae and Bartonella clarridgeiae in stray cats
Authors: Heller R , Artois M , Xemar V , De Briel D , Gehin H , Jaulhac B , Monteil H , Piemont Y
Published: January 2020

The aim of the present work was to determine by blood culture the prevalence of blood infection with Bartonella species in a well-defined, European, urban stray cat population. Therefore, 94 stray cats were trapped from 10 cat colonies. Blood samples of these cats were cultured on both blood agar and liquid medium in order to raise the likelihood of bacterial detection. Fifty blood samples (53%) gave a positive culture result for Bartonella species. Isolate identification was performed by sequencing the first 430 bases of the 16S ribosomal DNA. Three types of sequences were thus obtained. The first type (17 isolates; 34%) was identical to that of B. henselae Houston-1 and the corresponding strains were referred as B. henselae type I. The second sequence type (18 isolates; 36%) was identical to that initially described as "BA-TF," and the corresponding strains were referred to as B. henselae type II. The third sequence type (15 isolates; 30%) was identical to that of the Bartonella clarridgeiae type strain (ATCC 51734). Our study points out the major role of stray cats as a reservoir of Bartonella spp. which can be transmitted to pet cats and, consequently, to humans. The study also highlights the high prevalence of B. clarridgeiae (16%) in the blood of stray cats.
Genetic characterization of multidrug-resistant Mycobacterium bovis strains from a hospital outbreak involving human immunodeficiency virus-positive patients
Authors: Blázquez J , Espinosa de Los Monteros L E , Samper S , Martín C , Guerrero A , Cobo J , Van Embden J , Baquero F , Gómez-Mampaso E
Published: January 2020

Nineteen multidrug-resistant (MDR) Mycobacterium complex strains isolated in a nosocomial outbreak were characterized at the molecular level. The strains were microbiologically characterized as Mycobacterium bovis. The mpt40 sequence was not present in chromosomal DNA from these strains, supporting the fact that they were M. bovis. All of the isolates were resistant to isoniazid, rifampin, pyrazinamide, ethambutol, streptomycin, para-aminosalicylic acid, clarithromycin, cycloserine, ethionamide, ofloxacin, capreomycin, and amikacin. By performing the standardized IS6110 fingerprinting by restriction fragment length polymorphism (RFLP) analysis, we were able to differentiate two groups (groups A and B) containing two (16 isolates) and three (3 isolates) IS6110 copies, respectively. These strains were typed by spoligotyping, developed to distinguish M. bovis strains and also to distinguish them from M. tuberculosis strains (J. Kamerbeek et al., J. Clin. Microbiol. 35:907-914, 1997). All the strains were confirmed to be M. bovis. In addition, spoligotyping showed a difference in only 1 of 43 spacers between RFLP groups A and B. The rpo beta region of several strains representative of each identified group was cloned and sequenced, and identical mutations (Ser-531 to Leu) responsible for the rifampin resistance phenotype were found. To our knowledge, this is the first characterization at the molecular level of an MDR M. bovis strain responsible for a nosocomial outbreak.
Performance of an automated Q-beta replicase amplification assay for Mycobacterium tuberculosis in a clinical trial
Authors: Smith J H , Radcliffe G , Rigby S , Mahan D , Lane D J , Klinger J D
Published: January 2020

We present data from a clinical trial study in which an automated version (Galileo) of a previously described Q-Beta replicase-amplified probe assay (J. S. Shah et al., J. Clin. Microbiol. 33:1435-1441, 1995) was used for the direct detection of Mycobacterium tuberculosis complex in sputum. The assay was designed to target specific regions of 23S rRNA found in M. tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium microti and had a sensitivity ranging from approximately <10 to 300 CFU. The assay was tested for cross-hybridization by using large numbers (e.g., 10(5)to 10(10) CFU/assay) of 133 other organisms commonly found in respiratory tract samples, including non-M. tuberculosis Mycobacterium spp., other bacteria, fungi, and viruses. All of these competitors tested negative by the assay. Automated assay results for 780 respiratory tract samples (sputum or bronchoalveolar lavage specimens) collected and tested at three trial sites in the United States) were compared with the results of culture and acid-fast microscopy. Aliquots of conventionally digested and decontaminated sputum pellets were heated at 100 degrees C and mechanically disrupted prior to hybridization and background reduction, amplification, and detection in a closed disposable test pack. Pertinent elements of individual patient histories relating to tuberculosis exposure, previous active disease, antituberculosis therapy status, etc., were considered in the resolution of discrepant results for 48 (assay false-positive) samples. Seventy-one of 90 (78.9%) culture-positive samples were positive when tested in the Galileo assay, while 7% of culture-negative samples were assay positive, corresponding to a sensitivity of 79% and a specificity of 93%. Following resolution of discrepant results by chart review, the sensitivity and specificity for the Q-Beta replicase amplification assay with the Galileo analyzer were 84 and 97%, respectively. A total of 69.2% of smear-negative (culture positive) samples were detected by the assay. Ten test packs at a time were automatically processed by the Galileo analyzer without operator intervention following loading of samples. The first result was reported in approximately 3 h, and the last result was available in 6.5 h. To our knowledge, this is the first report of a clinical study with a fully automated amplification probe hybridization assay for the detection of pathogens directly from a clinical specimen.
Use of pulsed-field gel electrophoresis to investigate a pseudo-outbreak of Bacillus cereus in a pediatric unit
Authors: Liu P Y , Ke S C , Chen S L
Published: January 2020

Bacillus cereus is a well-known cause of food poisoning. It also causes rare systemic infections, usually in immunocompromised patients. Dissemination of this species in hospitals had been reported. Most of these episodes were pseudo-outbreaks and were usually secondary to equipment or environmental contamination. We report here on the use of pulsed-field gel electrophoresis (PFGE) to analyze a pseudo-outbreak of B. cereus in a pediatric unit. Different restriction endonucleases had been tested, and SmaI was found to give the best result for PFGE. Among the 26 clinical isolates of B. cereus and the type strain of the species, 15 distinct PFGE patterns were distinguished. PFGE after DNA macrorestriction with SmaI could clearly differentiate between the epidemiologically related isolates and the unrelated isolates. Because the same epidemic strain of B. cereus was isolated from the settle plates which were exposed near the outlet of the ventilation system, the source of this pseudo-outbreak was suspected to be the unit's air filtration system. This is one of the first reports of the application of PFGE to the study of B. cereus, and this method is useful for epidemiological investigation.
Development of a PCR assay for rapid diagnosis of Mycobacterium ulcerans infection
Authors: Ross B C , Marino L , Oppedisano F , Edwards R , Robins-Browne R M , Johnson P D
Published: January 2020

The diagnosis of Mycobacterium ulcerans infection is hampered by the slow growth of the bacterium in culture, resulting in a delay of several months before a specific diagnosis can be obtained. In addition, M. ulcerans cannot be isolated from water even when there is convincing epidemiological evidence implicating this as the source of infection. The aim of the present study was to develop a PCR assay to circumvent the problems of delayed diagnosis and insensitivity of standard bacterial culture for M. ulcerans. For the PCR, we isolated an M. ulcerans-specific DNA fragment, 1,109 bp long, which is repeated at least 50 times throughout the genome. Use of this sequence as a target for PCR allowed us to detect as few as 2 molecules of genomic DNA in vitro. The PCR was used to detect M. ulcerans DNA in fresh tissue and paraffin-embedded sections from all seven patients with culture-confirmed cases of infection.
Potential for gene transfer among enterococci from a single patient and the possibility of confounding typing results
Authors: Petts D N , Noble W C , Howell S A
Published: January 2020

The results of typing methods used in a study of the epidemiology of enterococci in burn patients showed inconsistencies. The possibility that these inconsistencies were the result of gene acquisition or loss was investigated by using 12 isolates of Enterococcus faecalis from a single patient. In vivo and in vitro exchange and loss of genes were observed. The study showed that the typing results for isolates from this patient can be modified by known and demonstrated genetic elements; as a result, the isolates could be divided into between three and seven strains. In the present study, the SmaI digestion patterns gave the most consistent results, correctly identifying the transconjugants as indistinguishable from recipient strain 196R.
Identification of enteroinvasive Escherichia coli and Shigella strains in pediatric patients by an IpaC-specific enzyme-linked immunosorbent assay
Authors: Pal T , Al-Sweih N A , Herpay M , Chugh T D
Published: January 2020

A new method, a monoclonal antibody-based enzyme-linked immunosorbent assay (ELISA) recognizing a secreted, invasion plasmid-coded protein antigen (IpaC), was used to identify enteroinvasive Escherichia coli and Shigella strains among colonies from 859 cultures of fecal samples from children in Kuwait. A total of 33.8% of the samples were diarrheal. By the immunoassay, enteroinvasive E. coli strains were identified from two diarrheal samples but from none of the samples from children without diarrhea. These strains were fully virulent and belonged to serogroup O28ac. In addition, 26 Shigella strains were also recognized by the ELISA, while only 23 were isolated by routine biotyping and serotyping. For two diarrheal patients, Shigella was identified by culture only. The study showed that the IpaC-specific immunoassay is a simple and useful tool for identifying enteroinvasive strains. Furthermore, by reporting the first enteroinvasive E. coli isolates from Kuwait, the study indicates the presence of this group of pathogens as a potential source of diarrhea in the region.
IS6110 homologs are present in multiple copies in mycobacteria other than tuberculosis-causing mycobacteria
Authors: McHugh T D , Newport L E , Gillespie S H
Published: January 2020

We have previously demonstrated homology between a 181-bp fragment of IS6110 and DNA from mycobacteria other than tuberculosis-causing mycobacteria (MOTT). Genomic DNA from 14 strains of MOTT was digested with PvuII and was hybridized with a probe derived from the 181-bp fragment and the INS1/INS2 international standard probe at high stringency. Multiple banding patterns were obtained from isolates of M. avium-M. intracellulare, M. fortuitum, M. kansasii, and M. malmoense. Differences in the banding patterns between and within species were obtained. This suggests that mycobacteria possess a family of IS3-like elements. The species of isolates suspected of being M. tuberculosis must be carefully determined before IS6110 restriction fragment length polymorphism analysis, and caution must be used in designing and evaluating diagnostic PCR tests based on this element.