bluuebunny/crossref_metadata_2025 huggingface dataset:
Geographic, clinical, serologic, and molecular evidence of granulocytic ehrlichiosis, a likely zoonotic disease, in Minnesota and Wisconsin dogs
Authors: Greig B , Asanovich K M , Armstrong P J , Dumler J S
Published: January 2020

Seventeen Minnesota and Wisconsin dogs with granulocytic ehrlichosis were studied. The diagnoses were made by finding ehrlichia morulae in peripheral blood neutrophils. Eight dogs were studied retrospectively, and nine dogs were studied prospectively. The medical records of all dogs were reviewed. Eighty-eight percent of the dogs were purebred and 76% were spayed females. The median age was 8 years. Sixty-five percent of the cases were diagnosed in October and November. Fever and lethargy were the most common clinical signs. The most frequent laboratory findings were lymphopenia, thrombocytopenia, elevated activities of serum alkaline phosphatase and amylase, and hypoalbuminemia. No dogs seroreacted to Ehrlichia canis or Ehrlichia chaffeensis antigens, which are cross-reactive. Seventy-five percent of the dogs tested during the acute phase of disease and 100% of the dogs tested during convalescence were seropositive for E. equi antigens. Granulocytic ehrlichial 16S rRNA gene DNAs from six dogs were amplified by PCR. Sequence analysis of a 919-bp sequence of the ehrlichial 16S rRNA gene amplified by PCR from the blood of two dogs revealed the agent to be identical to the agent of human granulocytic ehrlichiosis in Minnesota and Wisconsin and to be very similar to E. equi and Ehrlichia phagocytophila and less similar to E. canis, Ehrlichia ewingii, and E. chaffeensis. The geographic, clinical, serologic, and molecular evidence indicates that granulocytic ehrlichiosis in Minnesota and Wisconsin dogs is not caused by E. ewingii, but suggests that it is a zoonotic disease caused by an agent closely related to E. equi and that dogs likely contribute to the enzootic cycle and human infection.
Simultaneous PCR detection of Haemophilus ducreyi, Treponema pallidum, and herpes simplex virus types 1 and 2 from genital ulcers
Authors: Orle K A , Gates C A , Martin D H , Body B A , Weiss J B
Published: January 2020

A multiplex PCR (M-PCR) assay with colorimetric detection was devised for the simultaneous amplification of DNA targets from Haemophilus ducreyi, Treponema pallidum, and herpes simplex virus (HSV) types 1 and 2. By using target-specific oligonucleotides in a microwell format, 298 genital ulcer swab specimens collected in New Orleans during three intervals from 1992 through 1994 were evaluated. The results of the M-PCR assay were compared with the results of dark-field microscopy and H. ducreyi culture on two different culture media. HSV culture results were available for 99 specimens collected during the third interval. Confirmatory PCR assays targeting different gene sequences for each of the three organisms were used to validate the M-PCR results. Specimens were resolved as positive for the determination of sensitivity if the reference diagnostic test was positive or if the results of both the M-PCR and the confirmatory PCR were positive. The resolved sensitivities of M-PCR for HSV, H. ducreyi, and T. pallidum were 100, 98.4, and 91%, respectively. The resolved sensitivities of HSV culture, H. ducreyi culture, and dark-field microscopy were 71.8, 74.2, and 81%, respectively. These results indicate that the M-PCR assay is more sensitive than standard diagnostic tests for the detection of HSV, H. ducreyi, and T. pallidum from genital ulcers.
Epidemiological typing of Flavimonas oryzihabitans by PCR and pulsed-field gel electrophoresis
Authors: Liu P Y , Shi Z Y , Lau Y J , Hu B S , Shyr J M , Tsai W S , Lin Y H , Tseng C Y
Published: January 2020

Flavimonas oryzihabitans has emerged as a potential nosocomial pathogen in recent years. The typing method for characterization of this species has never been reported before. Pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-based PCR were used to generate DNA fingerprints for 14F. oryzihabitans isolates obtained from eight episodes of nosocomial infections during a 2-year period. Both techniques successfully classified these clinical isolates into eight distinct genotypes, thus indicating that all of these episodes of infections were independent. In contrast, repeated isolates from the same patient were assigned to identical genotypes. The reproducibility of both techniques was good. Therefore, we conclude that both PFGE and ERIC-PCR have comparable reproducible and discriminatory powers for the typing of F. oryzihabitans and may be useful for clarifying the epidemiology of this species; however, ERIC-PCR has the advantages of both speed and simplicity.
Enterohemolytic phenotypes and genotypes of shiga toxin-producing Escherichia coli O111 strains from patients with diarrhea and hemolytic-uremic syndrome
Authors: Schmidt H , Karch H
Published: January 2020

Thirty-six Shiga toxin-producing Escherichia coli (STEC) O111:H- strains, 18 of which were isolated from patients with hemolytic-uremic syndrome (HUS) and 18 from patients suffering from diarrhea, were investigated for their enterohemolytic phenotypes and genotypes. Twenty-two strains were EHEC hemolysin (EHEC Hly) positive by probe hybridization and by PCR with sequences complementary to the EHEC hlyA gene of E. coli O157:H7, but only 20 of these were hemolytic on blood agar plates. The remaining 14 strains were EHEC Hly negative according to DNA-based methods and did not express the enterohemolytic phenotype. The enterohemolytic phenotype was observed in 16 of 18 (88%) strains from patients with HUS but only in 4 of 18 (22.2%) of the STEC O111:H- strains from patients with diarrhea. All STEC O111:H- strains carried large plasmids, as shown by plasmid analysis, but only plasmids of EHEC Hly probe-positive strains hybridized with the CVD419 probe. A BamHI fragment of approximately 12 kb was cloned from the large plasmid of the E. coli O111:H- strain 78/92 and shown to mediate hemolytic activity when transformed into the E. coli laboratory strain HB101. The EHEC O111 hlyA gene was sequenced completely and shown to have 99.4% sequence identity to the corresponding EHEC O157 hlyA gene of the E. coli O157:H7 strain EDL 933. Our results indicate that detection of EHEC Hly either by DNA-based methods or by investigation of the enterohemolytic phenotype on blood agar alone is insufficient for screening STEC O111 strains. However, the high incidence of EHEC Hly in isolates from patients with HUS and its rare occurrence in isolates from patients with diarrhea may indicate that STEC O111 strains have a distinct pathogenic potential for humans and that the presence of EHEC Hly increases the ability of an STEC O111 strain to cause extraintestinal complications in humans.
Detection of Trypanosoma brucei spp. in human blood by a nonradioactive branched DNA-based technique
Authors: Harris E , Detmer J , Dungan J , Doua F , White T , Kolberg J A , Urdea M S , Agabian N
Published: January 2020

We have developed a nonradioactive branched DNA (bDNA)-based assay for the diagnosis of the African trypanosomiases in simple buffy coat preparations of human blood. Two repetitive DNA sequences specific to the Trypanosoma brucei complex were chosen as targets of the bDNA assay, a technique which amplifies the signal from a target molecule rather than the target itself. Comparable sensitivities were observed with cloned target sequences, purified T. brucei DNA, procyclic trypanosomes, and bloodstream trypomastigotes. The results of bDNA analysis of human blood samples from Côte d'Ivoire (n = 50) showed excellent agreement with those of buffy coat microscopy. The bDNA technology offers certain advantages over alternative molecular biological techniques, including the simplicity of sample preparation and of the procedure itself, the stability of the reagents, the ability to process large numbers of samples simultaneously, and freedom from crosscontamination artifacts. We have successfully applied the bDNA technique to the detection of T. brucei in clinical samples from regions where T. brucei infection is endemic; to our knowledge, this is the first report of the molecular detection of T. brucei in human blood.
Quantitative study of Helicobacter pylori in gastric mucus by competitive PCR using synthetic DNA fragments
Authors: Furuta T , Kaneko E , Suzuki M , Arai H , Futami H
Published: January 2020

Helicobacter pylori is closely related to upper gastrointestinal diseases, and the precise evaluation of H. pylori infection is necessary for the treatment of these diseases. The aim of the present study was to establish a method for the quantitative detection of H. pylori. We applied a competitive PCR method using various amounts of synthetic DNA fragments containing the same primer-binding and a subset of the same template sequences as the target competing for primer binding and amplification in order to quantify H. pylori in gastric mucus. The results obtained by this method were compared with the results of histological examination, the rapid urease test, bacterial culture, the [13C]urea breath test, and urea and ammonia measurements in gastric juice. As the quantity of H. pylori in gastric mucus increased, the rates of positivity of histological examination, the rapid urease test, and bacterial culture increased. The quantity of H. pylori in gastric mucus was also significantly correlated with the results of the [13C]urea breath test and was negatively correlated with the urea/ammonia ratio in gastric juice. The competitive PCR method provides an objective measure of the quantity of H. pylori and makes it possible to distinguish true negatives from false negatives due to incomplete PCR and true positives from false positives due to contamination. This method is very useful for the precise evaluation of gastric H. pylori infection.
Alkaline decontamination of sputum specimens adversely affects stability of mycobacterial mRNA
Authors: Desjardin L E , Perkins M D , Teixeira L , Cave M D , Eisenach K D
Published: January 2020

Reverse transcriptase PCR (RT-PCR) is an important tool for Mycobacterium tuberculosis research and diagnostics. A standard procedure using N-acetyl-L-cysteine (NALC) and NaOH has been widely adopted for digestion and decontamination of sputum specimens for mycobacterial culture. The objective of this study was to determine the compatibility of this method with the recovery of RNA for RT-PCR assays. Nineteen sputum specimens were collected from smear-positive, pretreatment tuberculosis patients. After homogenization with NALC and glass beads, specimens were further processed by the addition of either NaOH, as per the standard decontamination protocol, or phosphate buffer. RNA was prepared by using a modified guanidine-phenol extraction method developed specifically for sputum sediments. DNA was isolated from the same specimens. Reverse transcriptions of alpha antigen (85B protein) mRNA and 16S rRNA were performed together, and aliquots were removed for separate PCRs. In all specimens, the 85B mRNA target was greatly diminished by treatment with NaOH; however, the 16S rRNA target remained unaffected. Storing sputum specimens for 48 h at 4 degrees C before processing did not seem to affect the integrity or yield of RNA; however, some degradation occurred by 72 h. Data suggest that the NaOH-NALC method for processing sputum samples is not suitable for detecting mRNA targets in RT-PCR assays.
Evaluation of an extended blood culture protocol to isolate fastidious organisms from patients with AIDS
Authors: Dougherty M J , Spach D H , Larson A M , Hooton T M , Coyle M B
Published: January 2020

Recent reports of fastidious pathogens suggest the need for special blood cultures for immunocompromised patients. Blood cultures from 45 human immunodeficiency virus (HIV)-infected patients with unexplained fever (> or = 38.0 degrees C) and CD4 counts of < 125 cells per mm3 were collected into a vacuum tube with sodium polyanetholsulfonate, an Isolator tube, and BACTEC aerobic and anaerobic bottles. Blood from the sodium polyanethosulfonate tube was inoculated into BACTEC 13A bottles, which were read weekly for 16 weeks. Isolator sediment was divided among eight agar media, including four sheep blood agar media: chocolate agar, brain heart infusion blood agar, heart infusion blood agar, and brucella blood agar. Other agar plates included Sabouraud's, buffered charcoal-yeast extract, Middlebrook 7H11 (M7H11) with hemoglobin, and M7H11 with mycobactin J. Incubation conditions included air and CO2-enriched aerobic, microaerophilic, and anaerobic atmospheres. Aerobic BACTEC broths received an acridine orange stain on day 8 and were subcultured at 2, 4, and 8 weeks. Anaerobic BACTEC bottles were subcultured at 4 weeks. All solid media, including subcultures, were incubated for 8 weeks, providing a total of 16 weeks of incubation for each specimen. Clinically significant isolates included eight Mycobacterium avium complex isolates and one each of Bartonella henselae, Bartonella quintana, Shigella flexneri, Klebsiella oxytoca, and Cryptococcus neoformans. All isolates were detected with commercially available media and, with the exception of Bartonella spp., were recovered within incubation times routinely used in most clinical laboratories.
Direct identification and typing of Mycobacterium tuberculosis by PCR
Authors: Neimark H , Ali Baig M , Carleton S
Published: January 2020

We have developed a rapid PCR assay that types strains of Mycobacterium tuberculosis by generating distinct DNA fingerprints directly from primary cultures. This assay allows strain identification analogous to that achieved by the standard restriction fragment length polymorphism method, and fingerprints are obtained in less than 8 h. This assay does not require subculturing, DNA purification, restriction digestion, Southern blotting, or nucleic acid hybridization. Rapid and precise identification of M. tuberculosis strains permits immediate molecular epidemiologic studies. The assay can be converted to a computer-automated system by employing fluorescently labeled PCR primers and the Perkin-Elmer DNA sequencer so that unknown-specimen fingerprints are identified by computer comparison to a database of M. tuberculosis strain fingerprints.
Molecular characterization of Salmonella enterica subsp. enterica serovar choleraesuis field isolates and differentiation from homologous live vaccine strains suisaloral and SC-54
Authors: Weide-Botjes M , Liebisch B , Schwarz S , Watts J L
Published: January 2020

Four independent molecular methods were used to characterize the Salmonella enterica subsp. enterica serovar choleraesuis live vaccine strains SC-54 and Suisaloral and to differentiate them from S. choleraesuis field isolates. Plasmid analysis revealed the presence of seven plasmid profiles. A virulence plasmid of 52-kbp was identified by hybridization with an spvB-spvC gene probe in each of the S. choleraesuis field isolates and in the Suisaloral vaccine strain, but not in the SC-54 vaccine strain. Ribotyping, performed with a gene probe that recognized 23S, 16S, and 5S rRNA genes, resulted in three closely related hybridization patterns. IS200 elements were not detected in the field isolates or in the two S. choleraesuis live vaccine strains. Macrorestriction analysis with the enzymes XbaI, SpeI, NotI, and SfiI differentiated the 29 S. choleraesuis strains included in this study into 10, 13, 8, and 13 different fragment patterns, respectively. While the Suisaloral vaccine strain showed a unique XbaI macrorestriction pattern, the fragment patterns of the SC-54 strain obtained with the different enzymes were shared by 2 to 18 S. choleraesuis field strains. A combination of plasmid analysis and macrorestriction analysis proved to be most suitable for the molecular typing of S. choleraesuis and the differentiation of both live vaccine strains from field isolates of this serovar.
PCR detection of DNA specific for Aspergillus species in serum of patients with invasive aspergillosis
Authors: Yamakami Y , Hashimoto A , Tokimatsu I , Nasu M
Published: January 2020

We investigated the possible presence of DNA specific for Aspergillus species in serum samples of patients with invasive aspergillosis (IA) by the nested PCR method. Fourteen strains of fungi including 5 strains of Aspergillus species and 10 strains of common bacteria were used for examination of specificity and sensitivity of the nested PCR. Two sets of oligonucleotide primers were derived from the sequence of the variable regions V7 to V9 of the 18S rRNA genes of Aspergillus fumigatus. The specific fragment was amplified from five strains of Aspergillus species in the single and nested PCR but not from other microorganisms. Target DNA was detected by the nested PCR with as little as 50 fg of the extracted DNA of A. fumigatus. We investigated the detection of DNA specific for Aspergillus species in serum samples of a murine model of aspergillosis and 20 patients with IA. The specific fragment was detected by the nested PCR in 71% of serum samples of infected mice and 70% of serum samples of patients with IA, while galactomannan antigen was detected in 43 and 60% of samples, respectively. The high sensitivity and specificity of the nested PCR indicate that the assay can provide early diagnosis with sufficient accuracy to be clinically useful for immunocompromised patients with IA.
Rapid identification of Toscana virus by nested PCR during an outbreak in the Siena area of Italy
Authors: Valassina M , Cusi M G , Valensin P E
Published: January 2020

The sand fly-transmitted Toscana virus is recognized as an etiologic agent of an aseptic meningitis with a long convalescence. This infection has been reported overall in many tourists or in a seronegative population circulating in endemic Mediterranean areas (Italy, Portugal, Egypt, and Cyprus). We report a cluster of acute Toscana virus infections in the local population during the summer of 1995. Twenty-one clinical cases of meningitis were investigated for the presence of Toscana virus by nested PCR performed on the S segment of the virus RNA extracted from cerebrospinal fluid samples.
Direct activity of recombinant human lactoferrin against Helicobacter pylori
Authors: Miehlke S , Reddy R , Osato M S , Ward P P , Conneely O M , Graham D Y
Published: January 2020

We report the activity of recombinant human lactoferrin against Helicobacter pylori. Lactoferrin exerted a time- and dose-dependent action against 8 of the 13 clinical isolates of H. pylori tested in vitro. These results highlight a potential therapeutic use for lactoferrin against H.pylori infection.
Comparison of reverse transcription-PCR with tissue culture and other rapid diagnostic assays for detection of type A influenza virus
Authors: Atmar R L , Baxter B D , Dominguez E A , Taber L H
Published: January 2020

We applied a reverse transcription (RT)-PCR assay for influenza A virus to combined nasal wash-throat swab specimens previously obtained from an outpatient pediatric population with acute respiratory illness during concurrent epidemics of influenza A virus and respiratory syncytial virus. The results of the RT-PCR assay were compared with those previously reported with virus cultivation and commercially available rapid diagnostic kits (E.A. Dominguez, L.H. Taber, and R.B. Couch, J. Clin. Microbiol. 31:2286-2290, 1993). With virus cultivation as the "gold standard", the RT-PCR assay had a sensitivity, specificity, and efficiency of 95, 98, and 97%, respectively, compared with 75, 100, and 93%, respectively, for the best diagnostic kit (Becton Dickinson Directigen). RT-PCR is an effective alternative to virus isolation for the detection of influenza A virus in clinical specimens.
Clonality of multidrug-resistant nontypeable strains of Haemophilus influenzae
Authors: Fusté M C , Pineda M A , Palomar J , Viñas M , Lorén J G
Published: January 2020

The genetic structure of a population of multidrug-resistant nontypeable (unencapsulated) Haemophilus influenzae strains isolated at a hospital in Barcelona, Spain, was investigated by using multilocus enzyme electrophoresis to determine the allelic variation in 15 structural loci. In our study we have also included some antimicrobial agent-susceptible strains isolated at the same hospital. All enzymes were polymorphic for two to eight electromorphs, and the analysis revealed 43 distinct electrophoretic types among the 44 isolates. The mean genetic diversity of the entire population was 0.55. Multilocus linkage disequilibrium analysis of the isolates revealed a strong association between alleles, suggesting little possibility of recombination. Furthermore, the dendrogram and the allele mismatch distribution are typical of a population with no extensive genetic mixing.
Comparison of PCR with blood smear and inoculation of small animals for diagnosis of Babesia microti parasitemia
Authors: Krause P J , Telford S , Spielman A , Ryan R , Magera J , Rajan T V , Christianson D , Alberghini T V , Bow L , Persing D
Published: January 2020

The specific diagnosis of babesiosis, which is caused by the piroplasm Babesia microti, is made by microscopic identification of the organism in Giemsa-stained thin blood smears, detection of babesial antibody in acute-and convalescent-phase sera, or identification of the organism following the injection of patient blood into laboratory animals. Although rapid diagnosis can be made with thin blood smears, parasites are often not visualized early in the course of infection. PCR is a new, rapid diagnostic technique for the detection of Babesia spp. that has not yet been systematically evaluated. We conducted a blinded study of the sensitivity, specificity, and reproducibility of the PCR-based test with patients with babesiosis and a group of asymptomatic subjects residing in a region in southern New England where babesiosis is enzootic. Among 19 patients with recent babesial illness, we found that PCR was as sensitive and specific as the use of Giemsa-stained blood smears and inoculation of hamsters. Among asymptomatic subjects, the PCR result was positive for 3 persons with recent babesial infection and was negative for 41 persons without previous babesial infection. We conclude that the B. microti PCR procedure is sufficiently sensitive, specific, and reproducible for use in the diagnosis of acute babesiosis.
Influence of relative humidity and suspending menstrua on survival of Acinetobacter spp. on dry surfaces
Authors: Jawad A , Heritage J , Snelling A M , Gascoyne-Binzi D M , Hawkey P M
Published: January 2020

Acinetobacter spp. are being reported with increasing frequency as a cause of nosocomial infection and have been isolated from the skin of healthy individuals, patients, hospital staff, dry nonbiotic objects, and different pieces of medical equipment. Factors affecting the survival of Acinetobacter spp. under conditions closely similar to those found in the hospital environment were investigated in the present study to help us understand the epidemiology of nosocomial Acinetobacter infection. Bacterial cells were suspended in distilled water or bovine serum albumin and were dried onto glass coverslips and kept at different relative humidities. Cells washed from coverslips were used to determined viable counts. Freshly isolated strains of Acinetobacter spp. belonging to the clinically important Acinetobacter calcoaceticus-Acinetobacter baumannii complex were found to be more resistant to drying conditions (e.g., 30 days for A. baumannii 16/49) than American Type Culture Collection strains (e.g., 2 days for A. baumannii ATCC 9955). The majority of strains belonging to the Acb complex had survival times similar to those observed for the gram-positive organism Staphylococcus aureus tested in the experiment. Survival times were prolonged for almost all the strains tested when they were suspended in bovine serum albumin (e.g., 60 days for A. baumannii R 447) compared with those for strains suspended in distilled water (11 days for R 447). The survival times for strains at higher relative humidity (31 or 93%) were longer than those for strains of Acinetobacter kept at a relative humidity of 10% (11 days at 31% relative humidity and 4 days at 10% relative humidity for R447). These findings are consistent with the observed tendency of Acinetobacter spp. to survive on dry surfaces, and they can be transferred not only by moist vectors but also under dry conditions in a hospital environment during nosocomial infection outbreaks. The results obtained in the experiment support the previously suggested airborne spread of Acinetobacter spp. in hospital wards and repeated outbreaks after incomplete disinfection of contaminated dry surfaces.
Heterogeneity in phenotypic and genotypic characteristics among strains of Hafnia alvei
Authors: Ismaili A , Bourke B , de Azavedo J C , Ratnam S , Karmali M A , Sherman P M
Published: January 2020

Hafnia alvei is an emerging human pathogen associated with sporadic cases and outbreaks of diarrhea. Bangladeshi isolates of H. alvei possess the Escherichia coli attaching and effacing (eaeA) gene and demonstrate an attaching and effacing phenotype. In the present study we examined 11 Canadian H. alvei isolates and strain 19,982 from Bangladesh to determine if the formation of attaching and effacing lesions is a property shared among multiple isolates. Attaching and effacing lesions were detected by induction of tyrosine kinase protein phosphorylation and cytoskeletal rearrangements in infected tissue culture epithelial cells with immunofluorescence microscopy and by the examination of infected cells with transmission electron microscopy. The presence of the eaeA gene was examined by PCR and colony blot hybridization. Profiles of outer membrane protein extracts, chromosomal macrorestriction fragments, and plasmids were also examined. Accumulation of host phosphotyrosine proteins and rearrangement of the cytoskeletal protein alpha-actinin were both observed in HEp-2 cells infected with H. alvei 19,982. In contrast, none of the other 11 clinical H. alvei isolates demonstrated either of these responses, nor did they form attaching and effacing lesions under electron microscopy. Consistent with the absence of the attaching and effacing phenotype, these clinical isolates did not possess the eaeA gene. The outer membrane protein profiles of all the Canadian isolates were identical but differed from that of H. alvei 19,982. Pulsed-field gel electrophoresis and plasmid profile analyses of the clinical H. alvei isolates differed substantially from those of the Bangladeshi strain. These results indicate that there is heterogeneity among H. alvei strains with respect to signal transduction, attaching and effacing adhesion, outer membrane constituents, and genotype. Epidemiological studies on enteropathogenic H. alvei thus need to go beyond simple species designations and require specific identification of the virulent clones.
Shiga toxin-producing Escherichia coli strains from bovines: association of adhesion with carriage of eae and other genes
Authors: Wieler L H , Vieler E , Erpenstein C , Schlapp T , Steinrück H , Bauerfeind R , Byomi A , Baljer G
Published: January 2020

Out of 174 bovine Shiga toxin-producing Escherichia coli (STEC) strains isolated from diarrheic calves in Germany and Belgium, 122 strains (70.1%) were selected because of their reactivity with the eae (E. coli attaching and effacing gene) probe ECW1-ECW2. One hundred seven of these eae-positive strains (87.7%) harbored stx1 genes, 13 strains (10.7%) had stx2 genes, and 2 strains (1.6%) had both stx genes. The strains displayed 17 different O types, the majority (97 strains) [79.5%]) belonging to O5 (5 strains), O26 (21 strains), O111 (13 strains) O118 (36 strains), O145 (9 strains), and O157 (13 strains). In the HEp-2 cell adhesion assay, 99 strains (81.1%) showed a localized adhesion, and 80 strains (65.6%) stimulated actin accumulation, as determined in the fluorescence actin staining test. None of the strains harbored genes coding for bundle-forming pili (bfpA), clearly differentiating them from enteropathogenic. E. cole. espB gene sequences were only detectable in 23 (18.9%) of the eae-positive bovine STEC strains. Three different PCRs were established, differentiating between eae sequences of enteropathogenic E. coli strain E2348/69 (O127:H6) and STEC strain EDL933 (O157: H7). Primers matching in the more heterologous downstream eae sequences gave amplicons in only 8 of the 17 O types (O84:H-, O103:H2, O111:H-, O111:H2, O119:H25, O128:H-, O145:H28, and O157:H-). Only 15 STEC strains, belonging to serotypes O111H:-, O111H:2, O145:H28, and O157:H-, gave amplicons in all three eae-specific PCRs. These data demonstrate that bovine STEC strains are a heterogeneous group of pathogenic bacteria, a lot of which share virulence markers with STEC strains causing infections in humans. However, in contrast to human STEC strains, bovine eae-positive STEC strains are mainly restricted to the stx1 genotype. The observation that espB sequences are not highly conserved might have consequences for the serological recognition of the ESPB protein in patients. Like in human STEC strains, eae-related sequences are closely associated with certain E. coli O groups; however, they are not serotype specific.
Group-specific identification of polioviruses by PCR using primers containing mixed-base or deoxyinosine residue at positions of codon degeneracy
Authors: Kilpatrick D R , Nottay B , Yang C F , Yang S J , Mulders M N , Holloway B P , Pallansch M A , Kew O M
Published: January 2020

We have developed a method for differentiating polioviruses from nonpolio enteroviruses using PCR. A pair of panpoliovirus PCR primers were designed to match intervals encoding amino acid sequences within VP1 that are strongly conserved among polioviruses. The initiating primer hybridizes with codons of a 7-amino-acid sequence that has been found only in polioviruses; the second primer matches codons of a domain thought to interact with the cell receptor. The panpoliovirus PCR primers contain mixed-base and deoxyinosine residues to compensate for the high degeneracy of the targeted codons. All RNAs from 48 vaccine-related and 110 wild poliovirus isolates of all three serotypes served as efficient templates for amplification of 79-bp product. None of the genomic sequences of 49 nonpolio enterovirus reference strains were amplified under equivalent reaction conditions. Sensitivities of poliovirus detection were as low as 100 fg (equivalent to approximately 25,000 genomic copies or 25 to 250 PFU) when the amplified products were visualized by ethidium bromide fluorescence. These degenerate PCR primers should aid in the detection of all polioviruses, including those wild poliovirus isolates for which genotype-specific reagents are unavailable.
Phylogenetic analysis of hepatitis D viruses indicating a new genotype I subgroup among African isolates
Authors: Zhang Y Y , Tsega E , Hansson B G
Published: January 2020

Genetic analysis was performed on 13 hepatitis D virus (HDV) isolates from Ethiopia, Somalia, Jordan, Kuwait, Bulgaria, Moldavia, and Sweden. The complete nucleotide sequence and genomic organization are described for the first time for two African HDV isolates. Phylogenetic analysis showed all the African isolates to be intrarelated and to form a novel group within HDV genotype I; the suggested designation for this group is IC. The genetic distance to previously described type I isolates was about 0.15. The HDV genotype I isolates (total of 22 examined) phylogenetically formed three clusters, each of them corresponding to certain geographic regions; the "western" group consisted of six HDV isolates from western Europe and the United States plus one from Kuwait; the "eastern" group consisted of two isolates from Moldavia and one each from Bulgaria, Nauru, mainland China, and Taiwan; and the "African-Middle East" group consisted of six HDV isolates from Ethiopia and one from Somalia, Jordan, and Lebanon.
In vitro susceptibility testing and DNA typing of Saccharomyces cerevisiae clinical isolates
Authors: Zerva L , Hollis R J , Pfaller M A
Published: January 2020

Saccharomyces spp. are widely distributed in nature and may colonize the normal human gastrointestinal tract. Although Saccharomyces cerevisiae isolates have been previously considered nonpathogenic, they appear to be increasingly associated with infections in immunocompromised or otherwise debilitated patients. The antifungal susceptibility and epidemiology of S. cerevisiae are poorly defined at present. A series of 76 isolates (mostly stool surveillance and throat swab isolates) from 70 bone marrow transplant patients hospitalized at two different medical centers were characterized by antifungal susceptibility testing and restriction endonuclease analysis of chromosomal DNA. For DNA typing, digestion with NotI followed by pulsed-field gel electrophoresis was applied. Typing results revealed 62 distinct DNA types among the 76 clinical isolates. Despite this genomic diversity, clusters of identical isolates were identified among different patients hospitalized concurrently in the same unit, indicating possible nosocomial transmission. The MICs of amphotericin B, 5-fluorocytosine, fluconazole, and itraconazole were determined by a broth microdilution method, as recommended by the National Committee for Clinical Laboratory Standards. The MICs at which 90% of the strains were inhibited were as follows: amphotericin B, 1.0 micrograms/ml; 5-fluorocytosine, 0.25 micrograms/ml; fluconazole, 8.0 micrograms/ml; and itraconazole, 1.0 micrograms/ml. The relative resistance of S. cerevisiae to fluconazole and itraconazole may promote the emergence of this species as a pathogen among immunosuppressed patients.
Two related strains of feline infectious peritonitis virus isolated from immunocompromised cats infected with a feline enteric coronavirus
Authors: Poland A M , Vennema H , Foley J E , Pedersen N C
Published: January 2020

Two groups of cats were experimentally infected orally with the cat-passaged RM strain of feline enteric coronavirus (FECV-RM). One group of cats (n = 19) had been chronically infected with feline immunodeficiency virus (FIV) for over 6 years, while a second control group (n = 20) consisted of FIV-naive siblings. Fecal virus shedding of FECV occurred in both groups starting on day 3 postinfection, nearly ceased by 4 weeks in FIV-uninfected cats, but remained at high levels in FIV-infected animals. FIV-infected cats shed virus for a longer period of time and at levels 10 to 100 times greater than those for FIV-uninfected cats. The coronavirus antibody response of the FIV-infected cats was delayed and of reduced titer compared with that of the FIV-uninfected animals. Cats in both groups remained asymptomatic for the first two months following FECV-RM infection; however, 8 to 10 weeks postinfection two cats in the FIV-infected group developed feline infectious peritonitis (FIP). The FIP viruses (designated FIPV-UCD9 and -UCD10) isolated from these two cats had almost complete genetic homology to each other and to the infecting FECV-RM. However, unlike FECV-RM, they readily induced FIP when inoculated intraperitoneally into specific-pathogen-free cats. This study confirms that FIPVs are frequently and rapidly arising mutants of FECV. Immunosuppression caused by chronic FIV infection may have enhanced the creation and selection of FIPV mutants by increasing the rate of FECV replication in the bowel and inhibiting the host's ability to combat the mutant viruses once they occurred.
Molecular analysis of outer capsid glycoprotein (VP7) genes from two isolates of human group C rotavirus with different genome electropherotypes
Authors: Kuzuya M , Fujii R , Hamano M , Nakamura J , Yamada M , Nii S , Mori T
Published: January 2020

Nucleotide sequences for the VP7 gene of human group C rotavirus were determined for two strains isolated in Okayama, Japan, during a 1988-1990 epidemic. These isolates, OK118 and OK450, were selected as prototypes of two different electropherotypes, patterns I and II, respectively. The genes were identical in size (1,063 bp), and both contained singled open reading frames encoding 332 amino acids. The alignment of two sequences revealed 46 nucleotide substitutions, 11 of which were predicted to give amino acid changes. The deduced amino acid sequence of VP7 from OK118 was similar to published sequences of a Japanese isolate and three foreign isolates (more than 98.4% identity), whereas the VP7 sequence of OK450 revealed around 96% identity with these isolates and had nine unique amino acid substitutions. The VP7 genes of nine Okayama isolated were than analyzed by dot blot hybridization with the VP7 probes of OK118 and OK450. Under highly stringent conditions, the OK118 probe produced strong hybridization signals with the genes of five pattern I strains and one pattern II strain, while the OK450 probe strongly reacted only with those of three pattern II strains. Our results concluded that relative sequence diversity in the VP7 gene was observed between two different electropherotypes prevalent in a limited area.
An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma
Authors: Kern D , Collins M , Fultz T , Detmer J , Hamren S , Peterkin J J , Sheridan P , Urdea M , White R , Yeghiazarian T , Todd J
Published: January 2020

The quantification of human immunodeficiency virus type 1 (HIV-1) RNA has facilitated clinical research and expedited the development of antiretroviral drugs. The branched-DNA (bDNA) assay provides a reliable method for the quantification of HIV-1 RNA in human plasma and is considered one of the most reproducible assays ready for use in clinical trials. A series of oligonucleotide probe design and solution changes have been developed to enhance the sensitivity of the bDNA assay while maintaining its performance characteristics. Among the changes incorporated into the enhanced-sensitivity bDNA (ES bDNA) assay to reduce the background level and enhance the signal are the use of shorter overhang sequences of target probes for capture, the cruciform design of target probes for amplification, and the addition of preamplifier molecules. The ES bDNA assay is at least 20-fold more sensitive than the first-generation bDNA assay, yet it maintains a high level of accuracy, linearity, and reproducibility. Further, quantification values obtained with the ES bDNA assay and the first-generation bDNA assay are highly correlated, thus allowing for meaningful comparisons of HIV-1 RNA levels in specimens tested with either assay. The ES bDNA assay may be useful in determining the prognostic value of HIV-1 RNA levels of below 10,000 copies per ml and in assessing the clinical benefit of antiretroviral therapy-induced decreases in plasma HIV-1 RNA sustained at levels of below 10,000 copies per ml.
Case of bacterial endophthalmitis caused by an Agrobacterium radiobacter-like organism
Authors: Miller J M , Novy C , Hiott M
Published: January 2020

A case of postsurgical endophthalmitis caused by Agrobacterium radiobacter in a 70-year-old male is reported. A. radiobacter organisms are normally environmental bacteria but may occasionally be opportunistic pathogens. Infection in this case occurred after the patient was discharged following routine cataract surgery. The infection cleared after empiric therapy intraocular administration of vancomycin and gentamicin.
Comparative evaluation of macrodilution and chromogenic agar screening for determining fluconazole susceptibility of Candida albicans
Authors: Patterson T F , Kirkpatrick W R , Revankar S G , McAtee R K , Fothergill A W , McCarthy D I , Rinaldi M G
Published: January 2020

A simple screening method for fluconazole susceptibility using CHROMagar Candida with fluconazole was compared with the National Committee for Clinical Laboratory Standards (NCCLS) macrobroth method. In this agar dilution method, susceptible Candida albicans colonies are smaller on medium with fluconazole than on fluconazole-free medium. Yeasts with decreased susceptibility have normal-sized colonies on medium containing fluconazole. On agar with 16 micrograms of fluconazole per ml, 32 of 34 strains with NCCLS MICs of > or = 16 micrograms/ml were correctly predicted, as were 66 of 68 with MICs of < 16, an agreement of 96%. On agar with 8 micrograms of fluconazole per ml, 38 of 41 isolates with MICs of > or = 8 were correctly predicted, as were 59 of 61 isolates with MICs of < 8, an agreement of 95%. This agar dilution methods appears to highly correlate with NCCLS macrobroth methods for detection of C. albicans and may be an effective screen for fluconazole susceptibility.
Use of recombinant antigens of Borrelia burgdorferi in serologic tests for diagnosis of lyme borreliosis
Authors: Magnarelli L A , Fikrig E , Padula S J , Anderson J F , Flavell R A
Published: January 2020

Recombinant antigens of outer surface proteins (Osps) OspA, OspB, OspC, OspE, and OspF of Borrelia burgdorferi sensu stricto and of p41-G, an antigenic region of flagellin of this spirochete, were tested with human sera in class-specific and polyvalent enzyme-linked immunosorbent assays (ELISAs). In analyses for immunoglobulin M (IgM) antibodies, 18 (85.7%) of 21 serum samples from persons who had been diagnosed as having Lyme borreliosis on the basis of the presence of erythema migrans reacted positively in ELISAs with one or more Osp antigens or the p41-G antigen. Eleven serum samples contained antibodies to OspC antigen, and of these, six also reacted to the p41-G antigen and to one or more of the other recombinant antigens. The remaining five serum samples reacted solely to OspC (n = 4) or to OspC plus OspA and OspE without reactivity to p41-G (n = 1). In analyses for IgG antibodies, seropositivity was comparable to that of IgM analyses and was marked by predominant reactivity to p41-G, OspC, and OspF. Similarly, all 21 serum samples were positive in polyvalent and class-specific ELISAs with whole-cell B. burgdorferi. Minor cross-reactivity was noted when sera from persons who had syphilis, periodontitis or other oral infections, or rheumatoid arthritis were tested with OspC, OspE, OspF, and p41-G. With relatively high degrees of specificity, ELISAs with recombinant antigens, particularly OspC and p41-G, can help to confirm B. burgdorferi infections.
Isolation of Mycoplasma genitalium strains from the male urethra
Authors: Jensen J S , Hansen H T , Lind K
Published: January 2020

Mycoplasma genitalium is a human mycoplasma species which, on the basis of detection by PCR, has been incriminated as a cause of nongonococcal urethritis. Previously, only two strains from the urogenital tract and five strains from extragenital sites have been isolated. We have developed a method for the isolation of this fastidious microbe. M. genitalium from PCR-positive urethral specimens was initially propagated in Vero cell cultures grown in serum-free medium supplemented with Ultroser HY serum substitute. Growth was monitored by PCR. The M. genitalium strains grown in cell cultures could subsequently be subcultured in modified Friis's FF broth medium. Several passages in broth medium were required before growth on agar medium was attained. A total of 11 urethral specimens positive for M. genitalium by PCR from male patients with urethritis were investigated. Six strains were adapted to growth in broth medium, and four of these strains were cloned. Three specimens were overgrown by other mycoplasmas during propagation in the cell cultures. In only two PCR-positive specimens was propagation of M. genitalium unsuccessful. The use of cell culture combined with PCR monitoring of mycoplasmal growth may prove to be more widely applicable for the isolation of other fastidious mollicutes.
Typing of Mycobacterium avium isolates by PCR
Authors: Picardeau M , Vincent V
Published: January 2020

A Mycobacterium avium typing method based on PCR amplification of genomic sequences located between the recently described repetitive elements IS1245 and IS1311 was developed. This method was applied to a set of epidemiologically related and unrelated strains and compared with restriction fragment length polymorphism analysis with IS1245 as the probe. This PCR typing consists of a rapid and simple technique, providing a reproducible M. avium characterization as discriminant as restriction fragment length polymorphism analysis.
Evaluation of in vitro spectra of activity of azithromycin, clarithromycin, and erythromycin tested against strains of Neisseria gonorrhoeae by reference agar dilution, disk diffusion, and Etest methods
Authors: Mehaffey P C , Putnam S D , Barrett M S , Jones R N
Published: January 2020

The macrolide-azilide susceptibility testing (agar dilution, disk diffusion, Etest) criteria for 105 Neisseria gonorrhoeae strains were evaluated. In addition, the potencies of azithromycin, clarithromycin, and erythromycin were studied. The most active macrolide-azilide agent was azithromycin (MIC at which 90% of the isolates are inhibited [MIC90], 0.5 microgram/ml) compared with clarithromycin (MIC90, 1.5 to 2 micrograms/ml) and erythromycin (MIC90, 2 to 4 micrograms/ml). The Etest (AB Biodisk, Solna, Sweden) was observed to produce MIC results very similar to those of the reference agar dilution test (GC agar base), with 100% of the results within 1 log2 dilution step of the reference MICs. The disk diffusion test zone diameters for all three drugs correlated at an acceptable level (r = -0.81 to -0.92) with the reference agar dilution MICs. Interpretive criteria for susceptibility were proposed for azithromycin at a MIC of < or = 2 micrograms/ml and a disk diffusion test zone of > or = 25 mm. No category for resistance was proposed because of the paucity of strains for which MICs were > 2 micrograms/ml. These tentative criteria should be further validated by correlations with clinical trial data for gonococcal strains (as they emerge) that have azithromycin MICs above the proposed susceptible category range.
New PCR assay for rapid and quantitative detection of human cytomegalovirus in cerebrospinal fluid
Authors: Vogel J U , Cinatl J , Lux A , Weber B , Driesel A J , Doerr H W
Published: January 2020

Rapid Chelex extraction combined with an automated hybridization assay for the detection of PCR-amplified human cytomegalovirus DNA from cerebrospinal fluid was established. Quantitation of DNA was performed with a plasmid being used as an external standard. The detection limit was 10 copies per microliter. Quantitative detection of human cytomegalovirus DNA could be achieved over a range from 10 to 10(4) copies per microliter.
Is urine leukocyte esterase test a useful screening method to predict Chlamydia trachomatis infection in women?
Authors: Chow J M , Moncada J , Brooks D , Bolan G , Shaw H , Schachter J
Published: January 2020

We evaluated the use of the leukocyte esterase test (LET) on first-catch urine specimens from women as a screening test to predict infection with Chlamydia trachomatis. For diagnosis, we used Abbott's ligase chain reaction (LCR) on urine specimens and isolation by tissue culture (TC) on cervical brushes. Of 4,053 women attending sexually transmitted disease and family planning clinics, 4.3% (n = 174) were positive by TC and 5.9% (n = 239) were positive by LCR. When LET was compared to TC, the sensitivity, specificity, positive predictive value, and negative predictive value were 54.0, 67.0, 6.8, and 97.0%, respectively. The corresponding performance of LET versus LCR was 53.1, 67.3, 10.1, and 95.8%. Almost half of the laboratory-confirmed chlamydial infections were negative by LET. The low specificity probably reflects multiple causes of pyuria in women and results in a low positive predictive value. LET is neither sensitive nor specific as a predictor of chlamydial infection and cannot be recommended for use as a screening test for C. trachomatis with first-catch urine samples from females from low- or moderate-prevalence populations.