Application of vacA Sequencing in Helicobacter pylori for Classification of Specimens from Healthy Persons, and from Hepatobiliary and Gastroduodenal Patients

Helicobacter pylori is an important causative agent of gastrointestinal and hepatobiliary diseases. The aim of this study was to investigate phylogenetic relationships among H. pylori strains from the oral cavities of healthy individuals, gastric biopsies from gastroduodenal (GI) patients and bile samples from hepatobiliary (HB) patients in the northeast of Thailand. The DNA sequences of a portion of the vacuolating cytotoxin A gene (vacA) were investigated. Phylogenetic trees were constructed using the neighbor-joining and maximum-likelihood methods. The vacA sequences of H. pylori fell into four main groups on the trees. Strains from healthy persons fell into two widely separated but well-supported groups, while most H. pylori vacA sequences from HB patients were distributed in another two groups. In contrast, the H. pylori strains from GI patients were scattered across the tree, without a clear geographical pattern. In conclusion, the sequence of vacA may be useful to classify the genetic relationship of H. pylori derived from different sources

A Lung Granuloma Case Possibly Associated with a Working Environment: A Case Report

Lung granulomas are uncommon in Thailand. The disease typically develops from an occupational environment and is mostly caused by infection. Herein is a case report of a female patient, aged 48, working as a nurse in an Accident and Emergency Department at a hospital. Eighteen years prior to admission the patient was diagnosed with myasthenia gravis and pulmonary tuberculosis. The chest X-ray and CT scans showed a solitary pulmonary nodule in the lower left lung. The patient received an open thoracotomy with a left lobectomy. Granulomatous and nonseptate hyphae were found in the pathology diagnosis. The patient was thus diagnosed as having a lung granuloma. The galactomannan antigen test was positive. The solitary pulmonary nodule—found from the use of a Polymerase Chain Reaction (PCR) test—was an Aspergillus spp. The fungus culture was collected from air samples. The air samples were collected by the impaction technique using a microbial air sampler. Three types of Aspergillus spp. were found as well as Penicillium spp. and Monilia sitophila. The Aspergillus spp. was a match for the patient's disease. The patient was diagnosed as having a lung granuloma possibly Aspergillus nodule which was caused by airborne Aspergillus spp. from the occupational environment

Occurrence of Ochroconis and Verruconis species in clinical specimens from the United States

Ochroconis is a dematiaceous fungus able to infect immunocompetent people. Recently, the taxonomy of the genus has been reevaluated, and the most relevant species, Ochroconis gallopava, was transferred to the new genus Verruconis. Due to the important clinical implications of these fungi and based on the recent classification, it was of interest to know the spectra of Ochroconis and Verruconis species in clinical samples received in a reference laboratory in the United States. A set of 51 isolates was identified morphologically and molecularly based on sequence analyses of the nuclear ribosomal RNA (nrRNA), actin, and β-tubulin genes. Verruconis gallopava was the most common species (68.6%), followed by Ochroconis mirabilis (21.5%). One isolate of Ochroconis cordanae was found, being reported for the first time in a clinical setting. The most common anatomical site of isolation was the lower respiratory tract (58.8%), followed by superficial and deep tissues at similar frequencies (21.6 and 19.6%, respectively). Interestingly, three new species were found, which are Ochroconis olivacea and Ochroconis ramosa from clinical specimens and Ochroconis icarus of an environmental origin. The in vitro antifungal susceptibilities of eight antifungal drugs against the Ochroconis isolates revealed that terbinafine and micafungin were the most active drugs

Subcutaneous infection by Ochroconis mirabilis in an immunocompetent patient

Recently, the taxonomy of Ochroconis (Ascomycota, Pezizomycotina, Venturiales, Sympoventuriaceae) has been revised with the recognition of an additional genus, Verruconis. Ochroconis comprises mesophilic saprobes that occasionally infect vertebrates which mostly are cold-blooded, while Verruconis contains thermophilic species which is a neurotrope in humans and birds. On the basis of molecular data it is noted that only a single Ochroconis species regularly infects immunocompetent human hosts. Here we report a subcutaneous infection due to Ochroconis mirabilis in a 50-year-old immunocompetent female patient. In vitro antifungal susceptibility tests revealed that terbinafine was the most effective drug. The patient was successfully cured with oral administration of terbinafine 250 mg daily in combination with 3 times of topical ALA-photodynamic therapy for 9 months

Ochroconis globalis infecting Atlantic salmon (Salmo salar), with a review of Ochroconis species in cold-blooded animals

Necropsy examination of an adult Atlantic salmon (Salmo salar) from the Dalälven River in Sweden revealed numerous large, white nodules, with spherical cysts and granulomata in kidney and liver. Histopathology showed dark, septate, thin-walled hyphae. The aetiologic agent was found to be an Ochroconis species (Venturiales) that differed from known fish-associated species of the genus. Molecular phylogenetic studies of the culture (strain UIII09 = CBS 135766) demonstrated that Ochroconis globalis was concerned. The isolate proved to be susceptible to all investigated antifungals, as it is known for another Ochroconis species. The role of Ochroconis in opportunism of cold-blooded animals was discussed, and the diagnostic methods using DNA sequences for routine identification of the fungus were proposed

One fungus, which genes? : development and assessment of universal primers for potential secondary fungal DNA barcodes

The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1–D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β-tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5–6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail