bluuebunny/crossref_metadata_2025 huggingface dataset:
Puumala hantavirus genome in patients with nephropathia epidemica: correlation of PCR positivity with HLA haplotype and link to viral sequences in local rodents
Authors: Plyusnin A , Hörling J , Kanerva M , Mustonen J , Cheng Y , Partanen J , Vapalahti O , Kukkonen S K , Niemimaa J , Henttonen H , Niklasson B , Lundkvist A , Vaheri A
Published: January 2020

Reverse transcription-PCR was used to analyze specimens from 20 Finnish nephropathia epidemica (NE) patients hospitalized during the period from October 1994 to January 1995. Blood and/or urine sediment specimens from seven patients were found to be positive for the genome sequences of Puumala hantavirus (PUU). PCR positivity of the specimens from the patients correlated well with the HLA-DRB1*0301 and HLA B8 alleles, which previously were shown to associate with severe courses of NE. Genetic analysis of the partial M-and/or S-segment sequences obtained from three severely ill NE patients revealed three PUU strains related to but distinct from previously reported strains from Finland. The M-segment sequence of PUU from bank voles trapped near the probable site of infection for one of the patients showed 98.2% identity to that of the PUU strain obtained from the patient, suggesting a link between wild-type PUU from the natural focus and the NE case. The S-segment sequences from the patient and the bank voles, however, showed substantially lower identity (95.8%). As this difference in diversity for M and S genes (1.8 and 4.2%) is atypical for PUU genetic drift, one possibility is that the strain acquired at the putative place of infection is a reassortant one.
Characterization of urinary Escherichia coli O75 strains
Authors: Nimmich W , Voigt W , Seltmann G
Published: January 2020

Forty-four Escherichia coli O75 strains from patients with urinary tract infections were characterized by a variety of methods to obtain evidence of their clonal distribution and uropathogenic properties. By K and H antigen typing, the strains were divided into the following serotypes: O75:K5:H- (18 strains), O75:K95:H- (10 strains), O75:K95:H5 (7 strains), O75:K100:H5 (4 strains), and O75:K-:H55 (5 strains). Generally, biotyping proved to be of no discriminative value. With two exceptions the strains were found to be sensitive to the bactericidal effect of normal human serum. As shown by multilocus enzyme electrophoresis, the whole-cell protein profile (WCPP), and the patterns of the outer membrane proteins and lipopolysaccharides, all but the five O75:H55 strains were genetically closely related to each other and could be classified into one clonal group. The O75:K-:H55 strains proved to be quite different and lacked type 1 fimbriae. All 17 K95 (H-, H5) strains produced hemolysin and P fimbriae. Five of the O75:K5:H- strains were different from the other K5 strains by showing hemagglutinating properties, on the basis of the presence of the OX adhesin. The last two groups are suggested to be uropathogenic and are proposed to represent separate clonal groups or subgroups.
Species identification of Chlamydia isolates by analyzing restriction fragment length polymorphism of the 16S-23S rRNA spacer region
Authors: Meijer A , Kwakkel G J , de Vries A , Schouls L M , Ossewaarde J M
Published: January 2020

The genetic diversity of the 16S-23S rRNA spacer region of 12 Chlamydia pneumoniae isolates, 7 Chlamydia trachomatis isolates (human biovars: the trachoma serovars B and C, the urogenital serovars D, E, and F, and the lymphogranuloma venereum serovar L2; and a mouse biovar), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and one Chlamydia pecorum isolate was studied. The 16S-23S rRNA spacer region was amplified by PCR and digested with the restriction enzymes MseI, PstI, AluI, BglII, NlaIV, and BclI. All 26 isolates could be amplified by using one genus-specific primer pair, yielding an amplicon with a size of 803 bp. The analytical sensitivity of the PCR assay was < or = 100 inclusion-forming units per reaction. Digestion with MseI or AluI made it possible to differentiate the four species from each other, the C. trachomatis human biovars from the mouse biovar, and the C. psittaci avian isolates from the feline isolate. The MseI profiles were more distinct than the AluI profiles. Phylogenetic analysis of the results for all enzymes combined supported the current classification of four Chlamydia species: C. pneumoniae, C. trachomatis, C. psittaci, and C. pecorum. Phylogenetic analysis also suggested subdivision of isolates of C. trachomatis and C. psittaci into subgroups that coincide with their host range. In conclusion, we have developed an easy and rapid method for species and subspecies identification of Chlamydia based on restriction fragment length polymorphism analysis of the 16S-23S rRNA spacer region.
Isolation from diarrheal and asymptomatic kittens of three rotavirus strains that belong to the AU-1 genogroup of human rotaviruses
Authors: Mochizuki M , Nakagomi T , Nakagomi O
Published: January 2020

A survey of 143 stool specimens collected during a 17-month period in Japan from diarrheal and asymptomatic kittens identified three rotavirus strains that were similar in their genomic RNA constellation to human rotavirus AU-1 (G3P3[9]), lending strong support to the view that rotaviruses belonging to the same genogroup are circulating in both the human and the feline population.
Variability in susceptibilities of Haemophilus influenzae to clarithromycin and azithromycin due to medium pH
Authors: Nilius A M , Beyer J M , Flamm R K , Tanaka S K
Published: January 2020

The National Committee for Clinical Laboratory Standards (NCCLS) methods for susceptibility testing of Haemophilus influenzae in Haemophilus test medium allow a pH range of 7.2 to 7.4. However, it is known that bacteria may appear to be less susceptible to macrolides at lower pHs. Forty-four strains of H. influenzae were tested for their susceptibilities to clarithromycin and azithromycin by the disk diffusion and broth microdilution methods. The isolates appeared to be less susceptible at pH 7.2 than at pH 7.4 by both methods. Clarithromycin was less active at pH 7.2 against 43% of the isolates by the disk diffusion method and against 52% of the isolates by the broth microdilution method. Similarly, azithromycin was less active at pH 7.2 against 41 and 45% of the isolates by the disk diffusion and broth microdilution methods, respectively. Forty-two isolates were classified as clarithromycin susceptible and all isolates were classified as azithromycin susceptible by the disk diffusion method, regardless of the medium pH. However, only 21 isolates were clarithromycin susceptible at pH 7.2 and 34 isolates were susceptible at pH 7.4 by the broth microdilution method, even though quality control results indicated valid testing at both pHs. This study indicated that the results of tests of the susceptibility of H. influenzae with clarithromycin and azithromycin are highly dependent on the pH of the medium. Test results and their interpretations varied even when the medium pH was within the NCCLS-approved range and, coupled with the current NCCLS breakpoint of 8 microg/ml in the case of clarithromycin, may explain some of the observed discordances between the disk diffusion and broth microdilution methods.
Detection of Treponema pallidum by a sensitive reverse transcriptase PCR
Authors: Centurion-Lara A , Castro C , Shaffer J M , Van Voorhis W C , Marra C M , Lukehart S A
Published: January 2020

Syphilis is diagnosed by serologic testing or by identification of the causative agent, Treponema pallidum. The bacterium has historically been detected in clinical specimens by dark-field microscopy, immunostaining with polyclonal or monoclonal antibodies, or the rabbit inoculation test (RIT). RIT is considered to be very sensitive and specific, although it is available only in research settings and is not clinically useful due to the length of time required to obtain a result. In recent years, several PCR methods have been developed for the detection of T. pallidum, but none of these has shown a clear advantage in sensitivity over RIT. We have developed a specific and highly sensitive reverse transcriptase PCR (RT-PCR) that targets a 366 bp region of the 16S rRNA of T. pallidum. This RT-PCR can detect a single organism by Southern analysis when whole organisms are diluted and 10(-2) to 10(-3) T. pallidum organisms when RNA equivalents are used to make cDNA. The test was demonstrated to detect 10(-2) T. pallidum RNA equivalents in cerebrospinal fluid. Twenty different strains of T. pallidum, isolated from cerebrospinal fluids, aqueous humor, blood, and chancres, were shown to be detectable by this test. This efficient and sensitive technique could be more useful than existing methods for detecting very low numbers of organisms in clinical samples.
Detection and identification of fungal pathogens in blood by using molecular probes
Authors: Einsele H , Hebart H , Roller G , Löffler J , Rothenhofer I , Müller C A , Bowden R A , van Burik J , Engelhard D , Kanz L , Schumacher U
Published: January 2020

A PCR assay was developed for the detection and identification of Candida and Aspergillus species. The design of the oligonucleotide primer pair as well as the species-specific probes used for species identification was derived from a comparison of the sequences of the 18S rRNA genes of various fungal pathogens. The primers targeted a consensus sequence for a variety of fungal pathogens. The assay was tested for sensitivity and specificity with 134 fungal and 85 nonfungal isolates. To assess clinical applicability, 601 blood samples from four defined groups were tested: group A (n = 35), controls; groups B to D (n = 86), patients with febrile neutropenia, without fungal colonization (group B; n = 29) and with fungal colonization (group C; n = 36); and patients with documented invasive fungal infection (IFI) (group D; n = 21). The assay detected and, by species-specific hybridization, identified most of the clinically relevant Candida and Aspergillus species at 1 CFU/ml of blood. Amplification was 100% sensitive for all molds and yeasts tested, with Histoplasma capsulatum being the only non-Aspergillus species hybridizing with the Aspergillus spp. probe. None of 35 group A patients and only 3 of 65 group B and C patients were PCR positive. The sensitivity of the assay for specimens from patients with IFI (21 patients in group D) was 100% if two specimens were tested. For specificity, 3 of 189 specimens from patients at risk but with negative cultures were positive by the assay, for a specificity of 98%. PCR preceded radiological signs by a median of 4 days (range, 4 to 7 days) for 12 of 17 patients with hepatosplenic candidiasis or pulmonary aspergillosis. For the 10 patients with IFI responding to antifungal therapy, PCR assays became persistently negative after 14 days of treatment, in contrast to the case for 11 patients, who remained PCR positive while not responding to antifungal therapy. Thus, the described PCR assay allows for the highly sensitive and specific detection and identification of fungal pathogens in vitro and in vivo. Preliminary data from the screening of a selected group of patients revealed some value in the early diagnosis and monitoring of antifungal therapy.
A new PCR-based seroneutralization assay in cell culture for diagnosis of hepatitis E
Authors: Meng J , Dubreuil P , Pillot J
Published: January 2020

A new method for the serological diagnosis of hepatitis E virus (HEV) infection based on neutralization of the virus in cell culture was developed. The test involves a short incubation of the virus in the presence of the serum sample to be tested and permissive cells. With viral replication being limited and without a cytopathic effect, viral growth in cells is evaluated by reverse transcription and PCR. The specificity of the test was established by studying sera from healthy individuals and patients with hepatitis living in France, where autochthonous hepatitis E is unknown. The kinetics and sensitivity of antibody detection were evaluated during the experimental infection of monkeys. Neutralizing antibodies were found in 79% of patients during an outbreak of hepatitis E and in 43% of patients with sporadic, acute non-A, non-B (without anti-hepatitic C virus antibodies) hepatitis. This neutralization assay is proposed as a confirmatory test for the available enzyme-linked immunosorbent assay (ELISA), which is now recognized as giving many false-positive reactions, and to improve identification of new hepatitis viruses since false-negative reactions with HEV ELISA are also encountered.
Characterization of Bacteroides forsythus isolates
Authors: Takemoto T , Kurihara H , Dahlen G
Published: January 2020

Fifteen Bacteroides forsythus strains freshly isolated from patients with periodontitis were used together with three collection strains and one type strain for characterization of growth on various media; determination of enzymatic profiles, antibiotic susceptibility profiles, 16S rRNA ribotypes, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) outer membrane protein profiles, and pathogenicity; and gas chromatography analysis by using a wound chamber model in rabbits. All strains were stimulated by N-acetylmuramic acid, while one strain needed a further supplement such as yeast extract for optimal growth. All strains showed trypsin-like activity. While 10 different ribotypes were found, the SDS-PAGE profiles revealed similar patterns for all strains. All strains were sensitive to penicillin G (MICs, <0.5 microg/ml), ampicillin (MICs, <1.0 microg/ml), amoxicillin (MICs, <0.38 microg/ml), metronidazole (MICs, <0.005 microg/ml), tetracycline (MICs, <0.19 microg/ml), doxycycline (MICs, 0.05 microg/ml), erythromycin (MICs, <0.4 microg/ml), and clindamycin (MICs, <0.016 microg/ml), while they were less sensitive to ciprofloxacin (MICs, <4 microg/ml). B. forsythus did not cause abscess formation by monoinoculation. B. forsythus coinoculated with Fusobacterium nucleatum ATCC 10953 caused abscess formation in 75% of rabbits, while it caused abscess formation in 100% of rabbits when it was coinoculated with Porphyromonas gingivalis FDC 381. In the case of the latter combination, four of six rabbits died of sepsis after 6 to 7 days, and P. gingivalis and B. forsythus were recovered from the heart blood at a proportion of 10:1. B. forsythus strains were highly virulent and invasive in combination with P. gingivalis.
Clinical comparison of BACTEC 9240 plus aerobic/F resin bottles and the isolator aerobic culture system for detection of bloodstream infections
Authors: Cockerill F R , Reed G S , Hughes J G , Torgerson C A , Vetter E A , Harmsen W S , Dale J C , Roberts G D , Ilstrup D M , Henry N K
Published: January 2020

The Plus Aerobic/F resin bottle of the BACTEC 9240 automated blood culture system (Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.) was compared with aerobic culture of the Isolator system (Wampole Laboratories, Cranbury, N.J.) for the detection of bloodstream microorganisms from 6,145 blood cultures collected from adult patients with suspected septicemia. The BACTEC resin bottles were incubated for 7 days, and the sediment from the Isolator tube was inoculated to sheep blood and chocolate agars which were incubated for 72 h and to inhibitory mold, brain heart infusion, and Sabouraud agars which were incubated for 21 days. A total of 622 microorganisms were recovered from 583 blood cultures. The BACTEC resin bottle recovered statistically significantly more pathogens overall than the Isolator system (P = 0.0006). When individual pathogens isolated from either system for a 7-day study period were assessed, it was determined that the BACTEC resin bottle detected statistically significantly more isolates of Staphylococcus aureus (P = 0.0113) and coagulase-negative Staphylococcus spp. (P = 0.0029) than the Isolator system. The BACTEC resin bottle also detected statistically significantly more bloodstream infections (septic episodes) caused by coagulase-negative Staphylococcus spp. (P = 0.0146). The Isolator system recovered statistically significantly more contaminants overall (P < 0.0001), and among this group of microorganisms, recovered statistically significantly more Bacillus spp. (P < 0.0001), coagulase-negative Staphylococcus spp. (P < 0.0001), and viridans group Streptococcus spp. (P = 0.0156). The Isolator system detected statistically significantly more isolates of Histoplasma capsulatum (P = 0.004), but all of these isolates were detected at > or = 7 days of incubation of fungal plates, i.e., after the system to system comparison study period (7 days). In blood culture sets which produced growth of the same pathogen in both systems, there was a statistically significant difference in median time to detection for all pathogens combined favoring the BACTEC resin bottle over the Isolator tube (P < 0.05). When assessing individual microorganisms, the median times for detection of S. aureus, Enterococcus spp., and Pseudomonas spp. were all statistically significantly less for the BACTEC system (P < 0.05). The BACTEC instrument had 79 (1.3%) false positive signals. The BACTEC system required less processing time than the Isolator system and eliminates the hands-on time for detection of positive cultures required with the Isolator system.
Evaluation of a rapid enzyme immunoassay for diagnosis of hepatic amoebiasis
Authors: Kraoul L , Adjmi H , Lavarde V , Pays J F , Tourte-Schaefer C , Hennequin C
Published: January 2020

We compared the capability of rapid enzyme immunoassay (EIA) to detect antiamoebic antibodies during hepatic amoebiasis with those of indirect hemagglutination and latex agglutination. EIA is simple to perform and rapid (20 min) and does not require any special equipment (optical reading is sufficient). EIA of 143 sera (including 43 from patients with proven hepatic amoebic abscess, 33 from patients with other hepatic disorders and/or parasitic infections, and 67 from healthy individuals) yielded a specificity, a sensitivity, and positive and negative predictive values of 100, 93, 100, and 97.1, respectively. This test could thus be considered another valuable tool for the diagnosis of hepatic amoebiasis.
Emergence and dissemination of a highly vancomycin-resistant vanA strain of Enterococcus faecium at a large teaching hospital
Authors: Pegues D A , Pegues C F , Hibberd P L , Ford D S , Hooper D C
Published: January 2020

We prospectively identified patients at the Massachusetts General Hospital from whom vancomycin-resistant enterococci (VRE) were isolated from a clinical specimen from 1 January 1991 through 31 December 1995. VRE strains were available from 139 (82%) of the 169 patients with clinical cases. Of these, 39 (28%) were identical or closely related by pulsed-field gel electrophoresis (i.e., VRE type A strain), including 38 (43%) of 89 VRE strains in 1995. By multivariate analysis, acquisition of the VRE type A strain was associated with receipt of clindamycin (odds ratio [OR] = 10.5), 15 or more days of hospitalization before the first isolation of VRE (OR = 2.9), and residence on one of the general medical floors (OR = 7.8). The VRE type A strain was a vanA strain of Enterococcus faecium and was highly resistant to all antimicrobial agents tested except chloramphenicol. These findings document the rapid dissemination of a highly resistant strain of E. faecium among patients and among other extant VRE strains at the Massachusetts General Hospital in 1995.
Evaluation of the COBAS AMPLICOR MTB system
Authors: Bodmer T , Gurtner A , Scholkmann M , Matter L
Published: January 2020

A panel of 1,012 respiratory sediments was retrospectively tested by PCR amplification to detect Mycobacterium tuberculosis with the COBAS AMPLICOR MTB system. The sensitivities and specificities of COBAS and fluorescence microscopy compared to culture were 92.6 versus 95.6% and 99.6 versus 95.3%, respectively. Inhibition occurred in 48 (4.7%) specimens.
Use of quantitative competitive PCR to measure Epstein-Barr virus genome load in the peripheral blood of pediatric transplant patients with lymphoproliferative disorders
Authors: Rowe D T , Qu L , Reyes J , Jabbour N , Yunis E , Putnam P , Todo S , Green M
Published: January 2020

A quantitative competitive PCR (QC-PCR) assay for Epstein-Barr virus (EBV) has been developed to provide accurate measurement of EBV genome load in pediatric transplant recipients at risk for developing posttransplant lymphoproliferative disorder (PTLD). The assay quantifies between 8 and 5,000 copies of the EBV genome in 10(5) lymphocytes after a 30-cycle amplification reaction. For 14 pediatric patients diagnosed with PTLD, the median EBV genome load was 4,000, and 13 of the 14 patients had values of >500 copies per 10(5) lymphocytes. Only 3 of 12 control transplant recipients not diagnosed with PTLD had detectable viral genome loads (median value, 40). This median was calculated by using the highest value obtained by PCR testing on each of these patients posttransplantation. PCR values of >500 copies per 10(5) lymphocytes appear to correlate with a diagnosis of PTLD. By a modified protocol, the EBV genome copy number in latently infected adults was estimated to be <0.1 copy per 10(5) lymphocytes.
Fecal PCR assay for diagnosis of Helicobacter infection in laboratory rodents
Authors: Beckwith C S , Franklin C L , Hook R R , Besch-Williford C L , Riley L K
Published: January 2020

A fecal PCR assay for detection of Helicobacter infections in laboratory rodents was developed. DNA was isolated from murine fecal pellets, and a region of the 16S rRNA gene conserved among murine Helicobacter species was amplified. The fecal PCR was sensitive and specific. This assay does not require euthanasia of rodents, which is especially important for valuable rodents, such as transgenic mice.
A reverse-type sandwich enzyme-linked immunosorbent assay for detecting antibodies to Borna disease virus
Authors: Horimoto T , Takahashi H , Sakaguchi M , Horikoshi K , Iritani S , Kazamatsuri H , Ikeda K , Tashiro M
Published: January 2020

To investigate whether there is an epidemiological correlation between Borna disease virus (BDV) infection and human neuropsychiatric diseases, we established a reverse-type sandwich enzyme-linked immunosorbent assay (RS-ELISA) for detecting specific antibodies to BDV. In this assay, microplate wells were coated dispersely with BDV p40 antigen, followed by the addition of test samples at a low dilution and then the biotinylated p40. A preformed complex of streptavidin and horseradish peroxidase-conjugated biotin and an enzyme substrate were used to measure the captured biotinylated p40. Theoretically, RS-ELISA should specifically detect anti-BDV antibodies without nonspecific signals; such signals possibly occur in conventional serological assays. Additionally, the RS-ELISA could be applied under the same protocols to test samples from a variety of animals. By using anti-BDV rat and rabbit sera, the assay was standardized so that it had high specificity and sensitivity. When we used the RS-ELISA to determine the presence of anti-BDV antibodies in plasma from 70 patients with chronic schizophrenia as well as 40 healthy individuals in the Tokyo area of Japan, no plasma sample was found to possess specific antibodies to BDV p40, indicating no association between BDV infection and the disease in our testing population. A negative reaction was also shown for the sera that had previously been judged to be seropositive for BDV by an immunofluorescence or immunoblot test. These findings suggested that false-positive cases of infection due to nonspecific reactions may be included in previous seroepidemiological information with regard to BDV.
Detection of Mycoplasma pulmonis in cilia-associated respiratory bacillus isolates and in respiratory tracts of rats by nested PCR
Authors: Schoeb T R , Dybvig K , Keisling K F , Davidson M K , Davis J K
Published: January 2020

To improve the detection of Mycoplasma pulmonis contamination of isolates of cilia-associated respiratory (CAR) bacillus, we developed a nested PCR method using primers for 16S rRNA gene sequences. Of 140 samples of 16 different CAR bacillus isolates, 73 (52%) were inhibitory in the first PCR, as indicated by the absence of amplicons of the internal control, but only 11 of 140 (7.9%) were inhibitory in the second PCR. Of 27 samples known to contain M. pulmonis, only 12 (44%) were positive in the first PCR, but 25 of 27 (93%) were positive in the second PCR. Nested PCR also detected M. pulmonis in 21 of 61 (34%) CAR bacillus samples from which M. pulmonis could not be cultured and identified 2 additional M. pulmonis-contaminated CAR bacillus isolates. Of 359 respiratory and reproductive tract lavage samples from rats and mice, 35 (9.8%) were inhibitory in the first PCR, but only 15 (4.2%) were inhibitory in the second PCR. Of 72 lavage specimens from rats inoculated with an avirulent, poorly infective M. pulmonis strain, 14 (19%) were positive by nested PCR, but only 2 of 72 (2.8%) were positive by culture. Nested PCR also detected M. pulmonis in 14 of 20 (70%) paraffin sections of lung and trachea from rats and mice inoculated with CAR bacillus isolates known to contain M. pulmonis, whereas single PCR gave no positive results. We conclude that nested PCR is superior to single PCR or culture for detecting M. pulmonis, and that M. pulmonis is present in all but four CAR bacillus isolates in our collection that were from naturally infected rats; the four isolates that were exceptions were obtained from rats from a single colony.
Identification of Aeromonas clinical isolates by restriction fragment length polymorphism of PCR-amplified 16S rRNA genes
Authors: Borrell N , Acinas S G , Figueras M J , Martínez-Murcia A J
Published: January 2020

Identification of Aeromonas species, emergent pathogens for humans, has long been controversial due to their phenotypic and genomic heterogeneities. Computer analysis of the published 16S rRNA gene sequences revealed that restriction fragment length polymorphism of the PCR-amplified 16S rRNA gene is a good and rapid way of assessing the identities of all known species of Aeromonas. The method was evaluated with the reference strains of all species (or DNA homology groups) and 76 clinical isolates of diverse origin. Most results from the two approaches were in agreement, but some discrepancies were discerned. Advantages over previous phenotypic and genetic methods are discussed.
Molecular typing of enterohemorrhagic Escherichia coli O157:H7 isolates in Japan by using pulsed-field gel electrophoresis
Authors: Izumiya H , Terajima J , Wada A , Inagaki Y , Itoh K I , Tamura K , Watanabe H
Published: January 2020

Pulsed-field gel electrophoresis (PFGE) was applied for molecular typing of 825 enterohemorrhagic Escherichia coli (EHEC) O157:H7 isolates, most of which were from 19 outbreaks and 608 sporadic cases in Japan, mainly in May to August 1996. By PFGE, the EHEC O157:H7 isolates were classified into six types (type I to V and ND [nondescript]) and UT untypeable isolates. Fifty isolates from seven outbreaks in May to June and 60 isolates from patients with sporadic cases of infection showed almost identical PFGE patterns which differed in only 1 of 22 DNA fragments. They were classified into type I. Ninety-nine isolates from 10 other outbreaks and 156 isolates from patients in the Kinki area with sporadic cases of infection obtained in the early summer of 1996 showed identical PFGE patterns, suggesting that they were derived from one huge outbreak. They were classified into type II. Type IV EHEC isolates, which had only the stx2 gene, caused another outbreak in a primary school in June. EHEC isolates of two other types, types III and V, were not related to the outbreak but were isolated in several parts of Japan. ND EHEC isolates included a variety of patterns which could not be classified into either of the types mentioned above. Twenty-five isolates could not be analyzed due to degradation of their genomic DNAs and were represented as UT. These results indicate that EHEC O157:H7 strains with various PFGE types have already spread to Japan and caused the multiple outbreaks and sporadic infections in Japan in the summer of 1996.
Isolation of Ehrlichia chaffeensis from wild white-tailed deer (Odocoileus virginianus) confirms their role as natural reservoir hosts
Authors: Lockhart J M , Davidson W R , Stallknecht D E , Dawson J E , Howerth E W
Published: January 2020

Field and experimental studies have implicated white-tailed deer (Odocoileus virginianus) as probable reservoir hosts for Ehrlichia chaffeensis, the causative agent of human monocytic ehrlichiosis, but natural infection in deer has not been confirmed through isolation of E. chaffeensis. Thirty-five white-tailed deer collected from three Amblyomma americanum-infested populations in Georgia were examined for evidence of E. chaffeensis infection by serologic, molecular, cell culture, and xenodiagnostic methods. Twenty-seven deer (77%) had E. chaffeensis-reactive indirect fluorescent-antibody assay titers of > or = 1:64; and the blood, spleens, or lymph nodes of seven (20%) deer were positive in a nested PCR assay with E. chaffeensis-specific primers. E. chaffeensis was isolated in DH82 cell cultures from the blood of five (14%) deer, including two deer that were PCR negative. Combination of culture and PCR results indicated that six (17%) deer were probably rickettsemic and that nine (26%) were probably infected. Restriction digestion of PCR products amplified from deer tissues and cell culture isolates resulted in a banding pattern consistent with the E. chaffeensis 16S rRNA gene sequence. The sequences of all PCR products from deer tissues or cell culture isolates were identical to the sequence of the Arkansas type strain of E. chaffeensis. Xenodiagnosis with C3H mice inoculated intraperitoneally with deer blood, spleen, or lymph node suspensions was unsuccessful. When viewed in the context of previous studies, these findings provide strong evidence that E. chaffeensis is maintained in nature primarily by a tick vector-vertebrate reservoir system consisting of lone star ticks and white-tailed deer.
Simple differential detection of Entamoeba histolytica and Entamoeba dispar in fresh stool specimens by sodium acetate-acetic acid-formalin concentration and PCR
Authors: Troll H , Marti H , Weiss N
Published: January 2020

Amoebiasis is caused by two distinct species, a pathogenic form (Entamoeba histolytica) and a nonpathogenic form (Entamoeba dispar), which are morphologically identical. Although the distinction between these two species is of great clinical importance, the methods developed for this purpose either are very time-consuming or involve laborious procedures for isolation of the DNA. We report here a simple PCR method starting with fresh stool specimen that allows for the sensitive and reliable distinction between E. histolytica and E. dispar. After initial concentration by the sodium acetate-acetic acid-formalin (SAF) method and digestion with proteinase K, a 0.88-kb sequence of the multicopy 16S rRNA gene served as a target for PCR amplification. The method starting with unpreserved specimens proved to be very sensitive and was not influenced by the quick exposure to SAF fixative during the initial concentration step. However, storage in SAF fixative prior to testing resulted in a decreased sensitivity within 2 days. The detection limit of the method was as low as one copy of the 16S rRNA gene. No cross-reactivity was observed with other common intestinal protozoa. Mixed infections involving both E. histolytica and E. dispar could easily be detected at a ratio of 1:10,000 by agarose gel electrophoresis or a DNA hybridization immunoassay.
Emergence of rifampin-resistant Rhodococcus equi in an infected foal
Authors: Takai S , Takeda K , Nakano Y , Karasawa T , Furugoori J , Sasaki Y , Tsubaki S , Higuchi T , Anzai T , Wada R , Kamada M
Published: January 2020

To investigate the emergence of rifampin resistance in Rhodococcus equi strains isolated from foals and their environment in Japan, we compared the in vitro antimicrobial susceptibilities to rifampin of 640 isolates from 64 infected foals and 98 soil isolates from their horse-breeding farms. As a control, 39 human isolates from patients with and without AIDS were also tested for susceptibility to rifampin. All of the isolates showed rifampin sensitivity, except isolates from one infected foal and two patients with AIDS that showed rifampin resistance. To investigate the emergence of rifampin-resistant R. equi in the infected foal, which had received rifampin monotherapy for a month before euthanasia, 99 isolates of R. equi from the lesions and 20 isolates from the intestinal contents of the one foal with rifampin-resistant organisms were analyzed for rifampin susceptibilities, pathogenicities, and ribotypes. Of the 99 isolates from the lesions, all of which were virulent R. equi strains containing a virulence plasmid with a size of 85 or 90 kb, 90 (91%) isolates were rifampin resistant (MIC, > or = 12.5 microg/ml). On the other hand, of the 20 isolates from the intestinal contents, 11 (55%) isolates showed rifampin resistance (MIC, > or = 25 microg/ml), and 5 of them were avirulent R. equi strains. Among these 101 rifampin-resistant R. equi isolates with and without virulence plasmids characterized by ribotyping, 58 were type I, 20 were type II, 11 were type III, and 12 were type IV. These results demonstrated that at least eight different rifampin-resistant R. equi strains emerged concurrently and respectively from the different lesions and intestinal contents of the infected foal.
Molecular diagnosis of cat scratch disease: a two-step approach
Authors: Avidor B , Kletter Y , Abulafia S , Golan Y , Ephros M , Giladi M
Published: January 2020

Amplification of Bartonella henselae DNA has been proposed as a diagnostic test for cat scratch disease (CSD). The sensitivities of the following three PCR assays were compared. PCR/rRNA with universal primers amplifies part of the 16S rRNA gene, followed by hybridization with a specific B. henselae probe; PCR/CS and PCR/HSP amplify portions of the gltA and the htrA genes, respectively, each followed by restriction fragment length polymorphism analysis. The threshold of detection of B. henselae DNA in pus was 10(-4), 10(-3), and 10(-2) ng for PCR/rRNA, PCR/CS, and PCR/HSP, respectively. By these three assays, B. henselae DNA was detected in 100, 94, and 69% of 32 pus and lymph node specimens from CSD patients, respectively. The similar sensitivities of the PCR/rRNA and the PCR/CS assays for detecting B. henselae DNA in clinical specimens are in contrast to the 10-fold difference in sensitivities in favor of PCR/rRNA demonstrated with purified B. henselae DNA in sterile pus, suggesting that in the majority of cases, the bacterial load in clinical specimens is large enough to be identified by the PCR/CS assay. A two-step approach is suggested to achieve maximal sensitivity for detecting B. henselae in clinical specimens: initial testing by PCR/CS (which does not require hybridization), followed by PCR/rRNA with PCR/CS-negative specimens when CSD is strongly suspected.
Application of a nested, multiplex PCR to psittacosis outbreaks
Authors: Messmer T O , Skelton S K , Moroney J F , Daugharty H , Fields B S
Published: January 2020

We developed a nested, multiplex PCR for simultaneous detection of three species of chlamydiae in human and avian specimens. The PCR was designed to increase sensitivity and to circumvent inhibitors of PCR present in clinical specimens. The target sequence was the 16S rRNA gene. The first-step PCR was genus specific, and the second-step PCR was multiplexed (i.e., had multiple primer sets in the same tube) and could discriminate among Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia trachomatis on the basis of the molecular weight of the amplicon. The limit of detection of each of the two PCR steps was 5 inclusion-forming units. We used PCR and serologic evidence during outbreaks of psittacosis to infer that C. psittaci had been transmitted from birds purchased in pet stores to humans. We also used this method to test both live and dead birds from pet stores for infection with C. psittaci. Compared with culture, the application of PCR to avian specimens increased the rate of C. psittaci detection.
Detection and identification of mycobacteria by amplification of RNA and DNA in pretreated blood and bone marrow aspirates by a simple lysis method
Authors: Gamboa F , Manterola J M , Lonca J , Matas L , Viñado B , Giménez M , Cardona P J , Padilla E , Ausina V
Published: January 2020

A sodium dodecyl (lauryl) sulfate method was evaluated for the preparation of blood specimens and bone marrow aspirates for use in two amplification procedures (Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test [AMTDT] and Roche Amplicor M. avium/M. intracellulare [MAI] Test) for the detection and identification of Mycobacterium tuberculosis and M. avium and M. intracellulare, respectively. The AMTDT is based on amplification of rRNA, whereas the Amplicor MAI Test amplifies a specific DNA region of the 16S rRNA gene. The results of amplification techniques were compared with those of standard culture and culture in BACTEC 13A and BACTEC 12B liquid media. A total of 121 blood specimens and 15 bone marrow aspirates were collected from 136 AIDS patients. Mycobacterial growth was recovered for 103 specimens; 35 yielded M. tuberculosis, 62 yielded M. avium, 5 yielded M. genavense, and 1 yielded M. kansasii. The values of sensitivity and specificity in pretreated specimens for detection of M. tuberculosis by the AMTDT were 94.3 and 100%, respectively, and those for detection of M. avium by the Amplicor MAI Test were 91.9 and 100%, respectively. The simple lysis method described in the present work allows the recovery of mycobacteria from blood specimens and bone marrow aspirates and may be used in combination with the AMTDT and the Amplicor MAI Test to detect and identify different members of the genus Mycobacterium. This method might also be applicable for the identification of mycobacteria from blood culture fluids with acridinium-ester-labeled DNA probes.
Detection of equine arteritis virus in the semen of carrier stallions by using a sensitive nested PCR assay
Authors: Gilbert S A , Timoney P J , McCollum W H , Deregt D
Published: January 2020

A nested PCR, developed for the detection of equine arteritis virus (EAV) in semen, detected less than 2.5 PFU of EAV per ml of naturally infected seminal plasma. Based on results from testing 88 semen samples from 70 stallions, the sensitivity and specificity of the test were 100 and 97%, respectively.
Serological responses to Ehrlichia equi, Ehrlichia chaffeensis, and Borrelia burgdorferi in patients from New York State
Authors: Wong S J , Brady G S , Dumler J S
Published: January 2020

Serological testing at the New York State Department of Health for human granulocytic ehrlichiosis in the residents of Westchester County, N.Y., was performed with specimens from 176 patients by the indirect fluorescent-antibody (IFA) technique with Ehrlichia equi MRK-infected neutrophils. To understand whether human monocytotropic ehrlichiosis also occurs in this northeastern geographic region, specimens were also tested for antibodies to Ehrlichia chaffeensis Arkansas. Screening tests and immunoblots for Lyme disease (Borrelia burgdorferi infection) were also performed. Thirty-two patients had antibodies only to E. equi and 21 patients had antibodies to both E. equi and E. chaffeensis, whereas 12 patients had only E. chaffeensis antibodies by the IFA technique. The remaining patients did not have antibodies to either ehrlichia. Eighteen serum samples from 13 of these patients were coded and sent to the Ehrlichia Research Laboratory (Baltimore, Md.) for repeat analysis by the IFA test and for E. equi and E. chaffeensis immunoblots. Immunoblot analysis for E. equi in samples with positive IFA test results confirmed the results for eight of the nine specimens. Immunoblot analyses for E. chaffeensis were negative for all 18 serum samples. Borrelia-reactive antibodies were found in sera both from patients with granulocytic ehrlichiosis and from patients with monocytotropic ehrlichiosis from New York State. Our results suggest that E. equi antigen is an appropriate substrate for identifying human granulocytic ehrlichiosis. E. chaffeensis antigen lacks appropriate sensitivity to serve as a surrogate substrate for the detection of human granulocytic ehrlichiosis and should be used solely for the diagnosis of human monocytotropic ehrlichiosis. Heat shock proteins may, in some cases, cause cross-reactivity between B. burgdorferi and ehrlichiae.
Isolation of verotoxin-producing Escherichia coli O-rough:K1:H7 from two patients with traveler's diarrhea
Authors: Vila J , Vargas M , Ruiz J , Gallardo F , Jimenez de Anta M T , Gascón J
Published: January 2020

Two Escherichia coli O-rough:K1:H7 strains producing verotoxin 1 that were isolated from stool samples of two travelers with diarrhea who consulted our clinic after trips to the Indian Subcontinent and Central America were characterized. Both strains were sorbitol negative, the same phenotype presented by E. coli O157:H7, but in contrast they were beta-glucuronidase positive. Low-frequency restriction analysis of chromosomal DNA and pulsed-field gel electrophoresis and repetitive extragenic palindrome-PCR showed that both strains were epidemiologically related. The illness was self-limited in both cases but involved long-duration, watery diarrhea (10 to 50 days) accompanied by abdominal cramps and flatulence. This serotype should be taken into account as a possible cause of traveler's diarrhea.
Identification and DNA fingerprinting of Legionella strains by randomly amplified polymorphic DNA analysis
Authors: Bansal N S , McDonell F
Published: January 2020

The randomly amplified polymorphic DNA (RAPD) technique was used in the development of a fingerprinting (typing) and identification protocol for Legionella strains. Twenty decamer random oligonucleotide primers were screened for their discriminatory abilities. Two candidate primers were selected. By using a combination of these primers, RAPD analysis allowed for the differentiation between all different species, between the serogroups, and further differentiation between subtypes of the same serogroup. The usefulness of RAPD analysis was also evaluated with outbreak-related clinical and environmental isolates previously typed by the restriction fragment length polymorphism technique. RAPD analysis proved to be as accurate as other genotypic methods, reproducible, and highly discriminatory and is a valuable new alternative to traditional fingerprinting and identification of Legionella species and strains.
Development of a rapid assay for detecting gyrA mutations in Escherichia coli and determination of incidence of gyrA mutations in clinical strains isolated from patients with complicated urinary tract infections
Authors: Ozeki S , Deguchi T , Yasuda M , Nakano M , Kawamura T , Nishino Y , Kawada Y
Published: January 2020

The MICs of ofloxacin for 743 strains of Escherichia coli isolated from 1988 to 1994 were determined by testing. The strains were from patients with urinary tract infections complicated by functional or anatomical disorders of the urinary tract. Those determined to be ofloxacin resistant (MIC, > or =12.5 microg/ml) comprised 3 of 395 strains (1.3%) from the 1988 to 1990 group, 2 of 166 strains (1.2%) from the 1991 to 1992 group, and 7 of 182 strains (3.8%) from the 1993 to 1994 group. The incidence of resistant strains increased significantly during this period. The percentage of isolates with moderately decreased susceptibilities to ofloxacin (MIC, 0.39 to 3.13 microg/ml) also rose during the same period. To determine the incidence of gyrA mutations in urinary-tract-derived strains of E. coli, we developed a simple and rapid assay based on PCR amplification of the region of the gyrA gene containing the mutation sites followed by digestion of the PCR product with a restriction enzyme. Using this assay, we examined all 182 strains isolated in 1993 and 1994 for the presence of mutations at Ser-83 and Asp-87 in the gyrA gene. Of these strains, 33 (18.1%) had mutations in the gyrA gene. The incidences of mutations at Ser-83, at Asp-87, and at both codons were 10.4 (19 strains), 4.4 (8 strains), and 3.3% (6 strains), respectively. To determine the correlation of the mutations in the gyrA gene with susceptibilities to quinolones (nalidixic acid, ofloxacin, norfloxacin, and ciprofloxacin), we further examined 116 strains for which the MICs of ofloxacin were > or =0.2 microg/ml that were chosen from the isolates in the 1988 to 1992 group. The MICs of nalidixic acid for the strains without mutations at either Ser-83 or Asp-87 were < or =25 microg/ml, whereas those for the strains with single mutations or double mutations were from 50 to >800 microg/ml. For the fluoroquinolones, significant differences in the distributions of the MICs were observed among the strains without mutations, with single mutations, and with double mutations. The accumulation of mutations in the gyrA gene was associated with an increase in fluoroquinolone resistance. Ofloxacin MICs for the majority of the strains with single and double mutations were 0.39 to 3.13 and 6.25 to 100 microg/ml, respectively. This study demonstrates a chronological increase in the percentage of not only highly fluoroquinolone-resistant strains, corresponding to those with double mutations in the gyrA gene, but also strains with moderately decreased susceptibilities to fluoroquinolones, corresponding to those with single mutations. This increase in the incidence of strains with a single mutation in the gyrA gene portends a further increase in the incidence of strains with clinically significant resistance to fluoroquinolones.
DNA fingerprinting of Mycobacterium tuberculosis strains from patients with pulmonary tuberculosis in Honduras
Authors: Pineda-Garcia L , Ferrera A , Hoffner S E
Published: January 2020

Mycobacterium tuberculosis isolates from 84 patients with pulmonary tuberculosis in Honduras were characterized by restriction fragment length polymorphism analysis. Seventy-three different IS6110 patterns were found; 63 of these were unique and 10 were shared by two to three strains each. Thus, no ongoing spread of any specific clone of bacteria could be demonstrated.
A molecular scheme based on 23S rRNA gene polymorphisms for rapid identification of Campylobacter and Arcobacter species
Authors: Hurtado A , Owen R J
Published: January 2020

23S rRNA gene PCR amplicons from 118 strains representing 15 species of Campylobacter and four species of Arcobacter were consecutively digested with HpaII, CfoI, and HinfI. A reproducible and discriminatory identification scheme based on combined restriction patterns was developed by using reference strains and was applied to the identification of a variety of isolates.
Use of a single swab in multi-microbe or flex trans transport medium for detection of Chlamydia trachomatis by Roche Amplicor PCR and culture in specimens from two different patient populations
Authors: Fong C K , Falcone J , Landry M L
Published: January 2020

The Roche Amplicor PCR increased the detection of Chlamydia trachomatis compared with culture in promptly processed clinical specimens from a local clinic (100 and 86.5%, respectively) and in samples with delayed processing transported from distant facilities (100 and 72.7%, respectively). A single swab collected in culture transport medium was used. Two media, Multi-Microbe and Flex Trans, were tested and found to be equally acceptable.