Access microbiology最新文献

{"title":"A case of pleural Mycobacterium tuberculosis infection with reversion of Quantiferon Gold Plus results from positive to negative.","authors":"N Goire, M S Suchard, A Barling, R Fernando, L Dreyer, A A Mahony","doi":"10.1099/acmi.0.000737.v3","DOIUrl":"10.1099/acmi.0.000737.v3","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Mycobacterium tuberculosis</i> (MTB) infections continue to have a high mortality and morbidity burden globally. Interferon-gamma release assays such as Quantiferon Gold Plus (QFG-Plus) aid in diagnosis of latent TB but diagnosis of pleural TB remains challenging. We present a case of active pleural MTB infection with reversion from positive to negative of IGRA result as well as negative Xpert MTB/RIF Ultra PCR result from tissues obtained from pleural biopsy. <b>Case summary.</b> A 52-year-old otherwise healthy male presented in August 2022 with a 2 week history of pleuritic chest pain associated with modest elevation in inflammatory markers. The patient had had a positive QFG-Plus result in 2018, however QFG-Plus during this admission was negative. Computed-tomography pulmonary angiogram and needle thoracocentesis showed an exudative left pleural effusion with predominant lymphocytes. The patient's symptoms failed to resolve with empiric antimicrobial therapy for community-acquired pneumonia. Broncho-alveolar lavage as well as biopsies of pleural tissues via video-assisted thoracoscopic surgery from the left lower lobe yielded negative results on routine microbiological culture as well as Xpert Ultra PCR. Growth of acid-fast bacilli was noted from mycobacterial cultures of pleural tissues which was identified as MTB. <b>Conclusion.</b> Despite significant technological advances, microbiological diagnosis of MTB infections remains challenging. We document QFG-Plus reversion during development from latent to active pleural TB. Decline in the ability of CD4⁺ and CD8⁺ T cells to produce interferon gamma in response to TB antigens (ESAT-6 and CFP-10) was likely associated with loss of host control of latent MTB. This case serves as a reminder that despite exhaustive testing with state-of-art diagnostic platforms, MTB infections can still elude discovery.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11376222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50.","authors":"Constança Bertrand, Rodrigo Martins, Francisco Nunes, Pedro Brandão, Francisco X Nascimento","doi":"10.1099/acmi.0.000856.v3","DOIUrl":"10.1099/acmi.0.000856.v3","url":null,"abstract":"<p><p>Auxins, mainly in the form of indole-3-acetic acid (IAA), regulate several aspects of plant and algal growth and development. Consequently, plant and algae-associated bacteria developed the ability to modulate IAA levels, including IAA catabolism. In this work, we present and analyse the genome sequence of the IAA-degrading and marine algae-associated bacterium, <i>Marinomonas</i> sp. NFXS50, analyse its IAA catabolism gene cluster and study the prevalence of IAA catabolism genes in other <i>Marinomonas</i> genomes. Our findings revealed the presence of homologs of the <i>Pseudomonas iac</i> gene cluster, implicated in IAA catabolism, in the genome of strain NFXS50; however, differences were observed in the content and organization of the <i>Marinomonas iac</i> gene cluster when compared to that of the model <i>iac</i>-containing <i>Pseudomonas putida</i> 1290. These variations suggest potential adaptations in the IAA catabolism pathway, possibly influenced by substrate availability and evolutionary factors. The prevalence of <i>iac</i> genes across several <i>Marinomonas</i> species underscores the significance of IAA catabolism in marine environments, potentially influencing plant/algae-bacteria interactions. This study provides novel insights into the IAA catabolism in <i>Marinomonas</i>, laying the groundwork for future investigations into the role of <i>iac</i> genes in <i>Marinomonas</i> physiology and the regulation of marine plant/algae-bacteria interactions.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Delving deep into the draft genome of Mangrovibacter sp. SLW1, isolated from Sundarbans mangrove.","authors":"Arindam Roy, Anwesha Ghosh, Punyasloke Bhadury","doi":"10.1099/acmi.0.000847.v3","DOIUrl":"10.1099/acmi.0.000847.v3","url":null,"abstract":"<p><p><i>Mangrovibacter</i> sp. SLW1, a Gram-negative, aerobic, motile bacterium, was isolated from mangrove litterfall in Sundarbans mangrove. The draft genome is 5.5 Mbp in size with 49.45 mol% guanine-cytosine (GC) content. The linear chromosome of the bacterium consists of 27 contigs with 7339 coding sequences. The detailed <i>in silico</i> analyses of the genome of <i>Mangrovibacter</i> sp. SLW1 provide information on ecological adaptation. The genome is a reservoir for multiple heavy metals and metalloid resistance gene clusters as well as exhibit metabolic capabilities for utilization of a wide range of carbohydrates. It also encodes for tris-catecholate siderophore and can regulate uptake of iron thereby may influence plant growth such as mangrove vegetation.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11652732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142857477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial infection among SARS-COV-2-infected patients in a COVID-19-dedicated tertiary care hospital of Bangladesh: a cross-sectional study.","authors":"A N M Shamsul Islam, Nasreen Farhana, Rafaat Choudhury, Naznin Akter Jahan, Mohammad Jamal Uddin, Md Nazmul Hassan Refat, Fatima Nasreen, Fahmida Khanam","doi":"10.1099/acmi.0.000727.v3","DOIUrl":"10.1099/acmi.0.000727.v3","url":null,"abstract":"<p><p><b>Objectives.</b> This study aimed to determine patterns of respiratory, blood-borne and uropathogenic microbial pathogens among SARS-CoV-2-infected patients in a COVID-19-(coronavirus disease 2019) dedicated tertiary care hospital in Dhaka, Bangladesh. <b>Design.</b>This was a cross-sectional study. <b>Setting.</b> In a COVID-19-dedicated tertiary care hospital in Dhaka, Bangladesh, conducted from March to June 2021. <b>Participants.</b> Hospitalized individuals with COVID-19 infection regardless of age or sex. <b>Primary and secondary outcome measures.</b> The percentage of co-infected COVID-19 patients and the characterization of the micro-organisms responsible for co-infection served as the primary outcome measures. Finding any associations between co-infection and age, co-infection and sex and co-infection and comorbidity was the secondary outcome variable. <b>Interventions.</b> Not applicable. <b>Results.</b>Out of 79 patients, 61 % were male, and the mean age was 49.53 years. Co-infection was seen in 7.7 % of patients, out of which 5.1 % of isolates were from urine samples, followed by 2.6 % from blood. Bacteria isolated from urine were <i>Enterococcus</i> (2.6 %), coagulase-negative <i>Staphylococcus</i> (CONS) (1.3 %) and <i>Enterobacter</i> spp. (1.3 %). <i>Pseudomonas</i> spp. was the only organism isolated from blood sample. Mixed growth was found in nasopharyngeal and throat swabs, with the predominant species being Staphylococcus aureus and Streptococcus spp. At the time of data collection, 55.7 % of patients had been given antimicrobials, and 30.4 % of patients had been given a single antimicrobial. HBsAg was positive in 1.3 % of patients and none were anti-hepatitis C or dengue NS1Ag positive. <b>Conclusion.</b> Microbial infection has been seen to be associated with SARS-CoV-2 infections and is of great value in prescribing antimicrobials and reducing fatal outcomes of hospitalized patients.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142010208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel Gammapapillomavirus type in the nasal cavity of a wild red colobus (Piliocolobus tephrosceles).","authors":"Taylor E Weary, Kavi P M Mehta, Tony L Goldberg","doi":"10.1099/acmi.0.000866.v3","DOIUrl":"10.1099/acmi.0.000866.v3","url":null,"abstract":"<p><p>Papillomaviruses (PVs) are double-stranded, circular, epitheliotropic DNA viruses causing benign warts (papillomas) or inducing dysplasia that can progress to cancer. Although they have been identified in all vertebrate taxa, most classified types are human PVs (HPVs); relatively little is known about PVs in other species. Here we characterize a novel <i>Gammapapillomavirus</i> type, PtepPV1, from a nasal swab of a wild red colobus (<i>Piliocolobus tephrosceles</i>) in Kibale National Park, Uganda. The virus has a genome of 6576 bases, encoding the seven canonical early (E) ORFs (E6, E7, E1, E2, E4, E1^E4 and E8^E2) and two late (L) ORFs (L1 and L2) of the gammapapillomaviruses, and is 81.0% similar to HPV-mSK_118, detected in a cutaneous wart from an immunocompromised human patient, in the L1 gene at the amino acid level. Alphapapillomaviruses (genus <i>Alphapapillomavirus</i>) cause anogenital carcinomas such as cervical cancer and have been described previously in several nonhuman primates. However, the first gammapapillomavirus (genus <i>Gammapapillomavirus</i>), which cause transient cutaneous infections, was not described until 2019 in a healthy rhesus macaque (<i>Macaca mulatta</i>) genital swab. The new virus from red colobus, PtepPV1, has many genomic features encoded by high-risk oncogenic PVs, such as the E7 gene LXSXE and CXXC motifs, suggesting potential for pRb and zinc-finger binding, respectively. To our knowledge, PtepPV1 is also the first reported nonhuman primate PV found in the nasal cavity. PtepPV1 expands the known host range, geographical distribution, tissue tropism and biological characteristics of nonhuman primate PVs.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142010210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mycotic aneurysms: uncommon pathogens and treatment conundrums.","authors":"Akshatha Ravindra, Santhanam Naguthevar, Deepak Kumar, Rengarajan Rajagopal, Pushpinder Singh Khera, Vibhor Tak, Neetha Thayil Ramankutty, Durga Shankar Meena, Naresh Midha, Gopal Krishana Bohra, Mahendra Kumar Garg","doi":"10.1099/acmi.0.000777.v5","DOIUrl":"10.1099/acmi.0.000777.v5","url":null,"abstract":"<p><p><b>Introduction.</b> Mycotic aneurysms, characterized by vessel wall dilation resulting from infections including bacteria, fungi, and viruses, are a rare but severe consequence of systemic infections. The term 'mycotic' was coined by William Osler to describe the first instance of a fungal-induced infected aneurysm. These aneurysms, accounting for 0.6% of aneurysms in Western countries, carry a higher risk of rupture compared to uninfected aneurysms. While the femoral artery, aorta, and intracranial arteries are commonly affected, pathogens causing mycotic aneurysms vary across regions. Diagnostic challenges arise from nonspecific symptoms such as fever, and discomfort. To prevent the substantial morbidity and mortality associated with mycotic aneurysms, timely identification and treatment are paramount. We present a case series highlighting mycotic aneurysms caused by some rare pathogens - <i>Salmonella Paratyphi A, Streptococcus pneumoniae</i>, and <i>Pseudomonas aeruginosa</i>. <b>Methods.</b> This case series involves three patients diagnosed with mycotic aneurysms due to unusual pathogens. We describe each patient's clinical presentation, medical history, physical examination findings, laboratory results, imaging studies, and the diagnostic process leading to the identification of the causative pathogens. <b>Results.</b> The first patient is a 70-year-old gentleman who presented with a ruptured infra-renal abdominal aortic pseudoaneurysm caused by <i>Salmonella Paratyphi A</i>. The second patient is a 66-year-old gentleman with a <i>Streptococcus pneumoniae</i>-associated descending thoracic aortic pseudoaneurysm. The third patient is a 70-year-old gentleman with a ruptured descending thoracic aortic aneurysm with an occult aorto-oesophageal fistula due to <i>Pseudomonas aeruginosa</i> infection. The description highlights unique clinical features, laboratory findings, imaging results, and the management approaches undertaken in each patient. <b>Conclusion.</b> Mycotic aneurysms, pose diagnostic challenges due to their nonspecific symptoms. Early identification and intervention are essential to mitigate the severe complications associated with these aneurysms. The presented cases underscore the need for a comprehensive approach to diagnosis and management, ensuring optimal outcomes for patients affected by mycotic aneurysms.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142010209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characteristics of soil origin Pseudomonas batumici Koz11 isolated from a remote island in Japan.","authors":"Hui Zuo, Yuh Morimoto, Kenzo Muroi, Tadashi Baba","doi":"10.1099/acmi.0.000799.v3","DOIUrl":"10.1099/acmi.0.000799.v3","url":null,"abstract":"<p><p>Soil samples from a remote Japanese island (Kozushima) were processed and investigated for organisms exhibiting antimicrobial activity against pathogenic strains. A <i>Pseudomonas</i> strain demonstrating antimicrobial activity against <i>Staphylococcus aureus</i> (<i>S. aureus</i>) was identified, prompting further investigation. Whole-genome sequencing was employed to identify the species and conduct phylogenetic analysis, followed by <i>in silico</i> molecular analysis. Chemotaxonomic and biochemical analyses were conducted to further characterize the strain. Genomic analysis identified the strain of interest as <i>Pseudomonas batumici</i> (<i>P. batumici</i>), originally isolated from soil of the Black Sea coast of the Caucasus in 1980. <i>P. batumici</i> Koz11 is the second <i>P. batumici</i> strain to be isolated and identified outside its initial area of discovery. Similar to the type strain, <i>P. batumici</i> Koz11 showed antimicrobial activity against various <i>S. aureus</i> strains, including methicillin-resistant <i>S. aureus</i> (MRSA) and vancomycin-resistant <i>S. aureus</i> (VRSA). However, the previously reported 'batumin gene cluster', which synthesizes antimicrobial compounds, was absent from <i>P. batumici</i> Koz11. This study provides new insights into <i>P. batumici</i>. Since the type strain of <i>P. batumici</i> is exclusively deposited in the Ukrainian Collection of Microorganisms, the Koz11 strain may serve as a surrogate to facilitate continued study of <i>P. batumici</i>.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11328868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142001677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic investigations of diverse corbiculate bee gut-associated Gilliamella reveal conserved pathways for energy metabolism, with diverse and variable energy sources.","authors":"Viet Hung Nguyen","doi":"10.1099/acmi.0.000793.v3","DOIUrl":"10.1099/acmi.0.000793.v3","url":null,"abstract":"<p><p><i>Gilliamella</i> is a genus of bacteria commonly found as symbionts of corbiculate bees. Research into energy metabolism by this genus has predominantly been done through <i>in vivo</i> and <i>in vitro</i> experiments focused on the type species <i>Gilliamella apicola</i>. This study examined 95 publicly available genomes representing at least 18 <i>Gilliamella</i> species isolated predominantly from the hindgut of corbiculate bees. Energy metabolism pathways were found to be highly conserved across not only the <i>Gilliamella</i> but also other members of the family <i>Orbaceae</i>. Evidence suggests <i>Gilliamella</i> are capable of fermentation of both fumarate and pyruvate. Fermentation of the former produces succinate. Fermentation of the latter can produce acetate, ethanol, formate, and both isoforms of lactate for all <i>Gilliamella</i> and acetoin for some <i>G. apicola</i> strains. According to genomic evidence examined, all <i>Gilliamella</i> are only capable of respiration under microoxic conditions, while higher oxygen conditions likely inhibits respiration. Evidence suggests that the glycolysis and pentose phosphate pathways are essential mechanisms for the metabolism of energy sources, with the TCA cycle playing little to no role in energy metabolism for all <i>Gilliamella</i> species. Uptake of energy sources, i.e. sugars and derivatives, likely relies predominantly on the phospho<i>enol</i>-pyruvate-dependent phosphotransferase system. Differences in the utilized energy sources may confer fitness advantages associated with specific host species.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11325843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir.","authors":"Adriele Jéssica do Carmo Santos, Roberto Sousa Dias, Carlos Henrique Martins da Silva, Pedro Marcus Pereira Vidigal, Maíra Paula de Sousa, Cynthia Canedo da Silva, Sérgio Oliveira de Paula","doi":"10.1099/acmi.0.000801.v3","DOIUrl":"10.1099/acmi.0.000801.v3","url":null,"abstract":"<p><p>Bacteria of the species <i>Oceanotoga teriensis</i> belong to the family <i>Petrotogaceae</i>, are Gram-negative bacilli, are moderately thermophilic and are included in the group of thiosulfate-reducing bacteria, being capable of significantly accelerating corrosion in metallic structures. However, no in-depth study on the genome, antibiotic resistance and mobile elements has been carried out so far. In this work, the isolation, phenotypic and genotypic characterization of the multi-resistant <i>O. teriensis</i> UFV_LIMV02 strain was carried out, from water samples from an offshore oil extraction platform in Rio de Janeiro (Brazil). We determined that the isolate has a genome of 2 812 778 bp in size, with 26 % GC content, organized into 34 contigs. Genomic annotation using Rapid Annotation using Subsystem Technology revealed the presence of genes related to resistance to antibiotics and heavy metals. By evaluating the antimicrobial resistance of the isolate using the disc diffusion technique, resistance was verified for the classes of antibiotics, beta-lactams, fluoroquinolones, aminoglycosides, sulfonamides, lincosamides and rifamycins, a total of 14 antibiotics. The search for genomic islands, prophages and defence systems against phage infection revealed the presence of five genomic islands in its genome, containing genes related to resistance to heavy metals and antibiotics, most of which are efflux pumps and several transposases. No prophage was found in its genome; however, nine different defence systems against phage infection were detected. When analysing the clustered regularly interspaced short palindromic repeat (CRISPR) systems, four CRISPR arrays, classified as types I-B and III-B, with 272 spacers, can provide the strain with immunity to different mobile genetic elements and bacteriophage infection. The results found in this study show that the isolate UFV_LIVM02 is an environmental bacterium, resistant to different classes of antibiotics, and that the proteins encoded by the predicted genomic islands may be associated with the development of greater resistance to antibiotics and heavy metals. They provide evidence that environmental bacteria found in offshore oil exploration residues may pose a risk for the spread of antibiotic resistance genes. More comprehensive studies on the microbial community present in oil waste are needed to assess the risks of horizontal gene transfer.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11326445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of causative fungus from sterile abscess using metagenomics followed by in situ hybridization.","authors":"Hiroya Oki, Ryotaro Niwa, Somboonthum Pranee, Daisuke Motooka, Yoshiyuki Onda, Jun Nakata, Hiroko Nakajima, Yoshihiro Oka, Haruo Sugiyama, Yuka Yoshii, Naoyuki Anzai, Shota Nakamura, Tetsuya Iida","doi":"10.1099/acmi.0.000779.v3","DOIUrl":"10.1099/acmi.0.000779.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Invasive fungal infections require early diagnosis for treatment. Microscopic observation of biopsy and blood culture is the gold standard for the identification of the causative fungus, but it is difficult to identify the causative pathogen by a sterile abscess biopsy. <b>Case Presentation.</b> We present a case report of breakthrough invasive trichosporonosis in a 65-year-old Japanese male with acute myeloid leukaemia receiving antifungal prophylaxis. Blood cultures showed no fungal growth, and a liver biopsy and a removed spleen with abscess showed fragmented fungi, but no fungal identification was possible. This report demonstrates that retrospective analyses were able to identify the causative fungus. <b>Conclusion.</b> We narrowed down the candidate fungi by deep sequencing of the ITS1 region of fungal genome and confirmed that the fungus observed in the specimen was <i>Trichosporon asahii</i> by <i>in situ</i> hybridization using a DNA probe targeting 26S rRNA.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"6 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11325578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}