Access microbiology最新文献

{"title":"A cautionary tale of false-positive histoplasma urine antigen in an HIV patient: a case report.","authors":"Mohammad Z Khrais, Jake Smith, Tanmay Gandhi, Shahrukh Arif, Juan Carlos Rico","doi":"10.1099/acmi.0.000929.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000929.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Coccidioidomycosis, or Valley fever, is a fungal disease caused by <i>Coccidioides</i> species, prevalent in parts of the southwestern United States. It usually results from inhaling spores from soil and is a common cause of pneumonia in these regions. <b>Case Presentation.</b> We present a unique case of coccidioidomycosis in an immunodeficient male patient secondary to human immunodeficiency virus infection with poor adherence to anti-retroviral treatment. After presenting with non-specific symptoms and pre-syncope, he was initially diagnosed with pneumonia based on chest X-ray findings, but his symptoms failed to improve with antibiotics. He was treated for presumed pulmonary histoplasmosis following a positive histoplasma urine antigen test. However, the patient worsened clinically. Following a computed tomography scan demonstrating a large necrotic lung consolidation, fungal stain and culture of tissue biopsied through endobronchial ultrasound confirmed coccidioidomycosis. The patient received 2 weeks of liposomal amphotericin with clinical improvement before discharge with itraconazole. <b>Conclusion.</b> The histoplasma antigen test can be falsely positive due to cross-reaction with other fungal infections like blastomycosis, paracoccidioidomycosis or talaromycosis, and less frequently, coccidioidomycosis or aspergillosis. Diagnosis of coccidioidomycosis requires a high index of suspicion outside the expected geographic distribution in the appropriate clinical setting. Our case highlights the risk of false-positive antigen test results and the importance of invasive diagnostics, including bronchoscopy to obtain fungal cultures, if the diagnosis remains uncertain.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182686","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":"Are reads required? High-precision variant calling from bacterial genome assemblies.","authors":"Ryan R Wick, Louise M Judd, Timothy P Stinear, Ian R Monk","doi":"10.1099/acmi.0.001025.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.001025.v3","url":null,"abstract":"<p><p>Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related <i>Staphylococcus aureus</i> isolates sequenced on Illumina and Oxford Nanopore Technologies platforms. By benchmarking multiple assembly and variant-calling pipelines against a ground truth dataset, we found that read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality, as errors in the assembly led to false-positive variant calls. These findings underscore the need for improved assembly techniques before the potential benefits of assembly-based variant calling (such as reduced computational requirements and simpler data management) can be realized.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182529","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":"Crystalline lens dislocation as a presenting sign of Streptococcus pyogenes invasive infections.","authors":"Paulina Liberman, Jacob G Light, Shazia Dharssi, Tracy Howard, Jennifer Lu, Patricia J Simner, Karen C Carroll, Cheng-Ying Ho","doi":"10.1099/acmi.0.000903.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000903.v4","url":null,"abstract":"<p><p><b>Introduction.</b> To describe two cases of crystalline lens dislocation as a presenting feature of invasive group A <i>Streptococcus</i> (GAS) infection and its management. <b>Case presentation.</b> We report on a 58-year-old woman and a 36-year-old man who presented in 2024 with acute vision loss and severe ocular and systemic symptoms. Both patients were found to have lens dislocation and were diagnosed with invasive GAS infection. The 58-year-old woman had a complicated clinical course leading to enucleation, while the 36-year-old man responded favourably to early and aggressive treatment with systemic and intravitreal antibiotics. The responsible GAS strains were sequence type (ST) 28 and ST433, respectively. <b>Conclusion.</b> These cases highlight the importance of recognizing crystalline lens dislocation as a potential sign of ocular GAS infection. Two specific strain types of GAS associated with these findings, ST28 and ST433, are reported. In patients with GAS sepsis presenting with corneal oedema and zonular loss, clinicians should immediately initiate treatment, including intravitreal antibiotic injections and systemic therapy. Prompt and aggressive management can be crucial in preserving ocular structures.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144176344","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":"Multi-metal-resistant Staphylococcus warneri strain TWSL_1: revealing heavy metal-resistant genomic features by whole-genome sequencing and analysis.","authors":"Dilani Chathurika Dissanayake, Naduviladath Vishvanath Chandrasekharan, Champika Dilrukshi Wijayarathna","doi":"10.1099/acmi.0.000954.v5","DOIUrl":"https://doi.org/10.1099/acmi.0.000954.v5","url":null,"abstract":"<p><p>This study explores the genomic basis of heavy metal resistance in <i>Staphylococcus warneri</i> strain TWSL_1, isolated from industrial textile effluent. The strain exhibited strong resistance to Cd²⁺, Pb²⁺ and Cu²⁺, with MICs of 50, 1,200 and 75 mg l^-1, respectively. Whole-genome sequencing revealed a 2.66 Mb genome with 2,567 CDSs and a 99.81% average nucleotide identity to <i>S. warneri</i> WS479. Comparative genomic analysis at the genus level revealed that <i>S. warneri</i> strain TWSL_1 possesses a unique and expanded repertoire of heavy metal resistance genes, including the cadmium efflux system accessory protein and cadmium resistance protein, which are absent in pathogenic <i>Staphylococcus</i> sp. used for the comparison. Phylogenetic analysis confirmed its classification within <i>S. warneri</i>, with strong bootstrap support (100). Functional annotation highlighted metabolic versatility and stress response capabilities, supporting its adaptation to metal-rich environments. <i>S. warneri</i> TWSL_1 demonstrated high Pb²⁺ removal efficiency, reducing concentrations by over 70%. These findings highlight <i>S. warneri</i> TWSL_1 as a promising candidate for heavy metal bioremediation with potential applications in environmental detoxification and monitoring strategies.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144176478","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":"Derivatization of pBACpAK entrapment vectors for enhanced mobile genetic element transposition detection in multidrug-resistant Escherichia coli.","authors":"Supathep Tansirichaiya, Wasawat Leartsiwawinyu, Nattharee Thanawan, Richard N Goodman, Chanwit Tribuddharat, Adam P Roberts","doi":"10.1099/acmi.0.001013.v3","DOIUrl":"10.1099/acmi.0.001013.v3","url":null,"abstract":"<p><p><b>Aim.</b> Antimicrobial resistance poses a critical global health threat, driven by the dissemination of resistance genes via mobile genetic elements (MGEs). This study aims to enhance the detection of MGE insertions in multidrug-resistant <i>Escherichia coli</i> by derivatizing the pBACpAK entrapment vector. <b>Methods and results.</b> Three derivatives were constructed with additional nucleotides upstream of the <i>cI</i> repressor gene, based on conserved regions identified from GenBank sequences containing known IS<i>26</i> and IS<i>1</i> insertions. Using colony PCR, intracellular transposition screening was performed on 194 tetracycline-resistant colonies from four <i>E. coli</i> ESI123 strains carrying different pBACpAK constructs. The derivatives showed increased MGE capture rates (10.7-73.1 %) compared to the WT vector (3.75%), identifying multiple MGEs, including the novel composite transposon Tn<i>7824</i>. Tn<i>7824</i> harbours the <i>bla</i> _OXA-181 carbapenem resistance gene and the <i>qnrS1</i> quinolone resistance gene, highlighting the clinical relevance of these findings. Long-read sequencing of transposants confirmed the accuracy of MGE identification and structural characterization, which also revealed chromosomal integration events of the pBACpAK derivatives mediated by flanking insertion sequences. <b>Conclusions.</b> The modifications introduced in the pBACpAK derivatives could increase the detection of transposition events by alleviating spatial constraints, allowing for more robust MGE detection.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144145347","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":"Detection and antibiotic resistance of Salmonella isolates from selected poultry farms in Dar es Salaam, Tanzania.","authors":"Saxon J Mwambene, Adelard B Mtenga, Augustino A Chengula, Abubakar S Hoza","doi":"10.1099/acmi.0.000879.v5","DOIUrl":"10.1099/acmi.0.000879.v5","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;Introduction.&lt;/b&gt; &lt;i&gt;Salmonella&lt;/i&gt; is one of the most prevalent foodborne bacteria, posing a significant global health concern and responsible for ~155,000 deaths and 93.8 million human foodborne illnesses annually. The rampant use of antibiotic agents to combat salmonellosis in poultry has contributed to the emergence of resistance against commonly used antibiotics. &lt;b&gt;Methodology.&lt;/b&gt; The cross-sectional study was conducted between January and June 2023 across three districts in the Dar es Salaam region, Tanzania. &lt;i&gt;Salmonella&lt;/i&gt; isolates were detected and confirmed by using standard microbiological conventional methods and molecular methods such as PCR and genomic sequencing. PCR was used for detecting the presence of the &lt;i&gt;invA&lt;/i&gt; gene, and partial DNA sequencing was performed to identify species and their close relatedness. A Kirby-Bauer disc diffusion method was employed to evaluate &lt;i&gt;Salmonella&lt;/i&gt; sensitivity to seven different commonly used antibiotics, namely ampicillin, azithromycin, chloramphenicol, ciprofloxacin, gentamycin, trimethoprim/sulfamethoxazole and tetracycline. &lt;i&gt;Salmonella&lt;/i&gt; strain with reference number ATCC 8739 was used as a control. &lt;b&gt;Results.&lt;/b&gt; The overall &lt;i&gt;Salmonella&lt;/i&gt; isolates from faecal droppings were 6.04% (&lt;i&gt;n&lt;/i&gt;=796). Of the PCR-confirmed isolates, 64.3% (&lt;i&gt;n&lt;/i&gt;=28) were resistant to more than two classes of antibiotics and hence considered multidrug resistant. The highest resistance was observed with ampicillin (92.9%, &lt;i&gt;n&lt;/i&gt;=26), followed by tetracycline (71.43%, &lt;i&gt;n&lt;/i&gt;=20), ciprofloxacin (42.9%, &lt;i&gt;n&lt;/i&gt;=12), sulphonamide (42.85%, &lt;i&gt;n&lt;/i&gt;=12), gentamicin (35.7%, &lt;i&gt;n&lt;/i&gt;=10) and azithromycin (28.9%, &lt;i&gt;n&lt;/i&gt;=8). All the isolates were susceptible to chloramphenicol (100%, &lt;i&gt;n&lt;/i&gt;=28). Twenty-eight isolates were sent for sequencing, out of which 16 sequences (OR021717-OR021739) met the criteria for phylogenetic analysis. All 16 sequences had a per cent identity to EU348369 strains Senftenberg isolated from China, OL581594 &lt;i&gt;Salmonella&lt;/i&gt; Newport isolated from China and EU348368 &lt;i&gt;Salmonella&lt;/i&gt; Pullorum isolates from China. Other sequences diverged more distantly; these are &lt;i&gt;Salmonella&lt;/i&gt; Abony with accession number CP007541 and &lt;i&gt;Salmonella&lt;/i&gt; Kentucky with accession number OL581592. The tree also included an outgroup species, &lt;i&gt;Salmonella bongori&lt;/i&gt;, which was downloaded from GenBank with accession numbers NC015761 and NC021870 &lt;i&gt;S. bongori&lt;/i&gt;. &lt;b&gt;Conclusion.&lt;/b&gt; The high level of antibiotic resistance found in this study could be due to the misuse of antibiotics in poultry management, and/or, probably, there were circulating resistant &lt;i&gt;Salmonella&lt;/i&gt; strains in the environment. To reverse the trend observed, immediate interventions such as advocating for the prudent use of antibiotics in poultry production systems by strengthening extension services to poultry farmers and the use of a farmer field school model to improve poultry management through improved fa","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129947","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":"Fortuitous discovery of a microfilaria of the genus Loa loa during a routine blood smear at the Hematology Laboratory of the Mohamed V Military Instruction Hospital in Rabat: a case report.","authors":"Mohammed Labrigui, Hamza Layat, Manal Bouikhif, Fatima Ziad, Zimi Khalil, Zineb Jerroundi, Hafid Zahid, Zohra Ouzzif","doi":"10.1099/acmi.0.000895.v3","DOIUrl":"10.1099/acmi.0.000895.v3","url":null,"abstract":"<p><p>Loiasis is a parasitic infection transmitted by a vector, specifically through the bites of Chrysops genus tabanid flies. It is often associated with marked and persistent eosinophilia in affected individuals. We report the case of a 28-year-old Cameroonian male patient. His medical history includes an episode of malaria treated on an outpatient basis. As part of a diving internship in Morocco, the young serviceman underwent a medical fitness examination at the Medical Expertise Center for Aircrew Personnel of the Mohamed V Military Hospital, which included a biological assessment. This revealed a mildly elevated bilirubin level, lactate dehydrogenase activity at the upper limit of normal and eosinophilia at 1500 µl^-1, without anaemia or thrombocytopaenia. A blood smear was prepared and stained with May-Grünwald Giemsa, revealing the presence of several small worms, with an appearance consistent with <i>Loa loa</i> microfilariae. This case of <i>L. loa</i>, identified in the haematology laboratory, is one of the rare diagnoses in Morocco. Therefore, biologists need to remain vigilant and carry out a thorough analysis of the blood count and blood smear.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129951","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":"Haematological abnormalities as diagnostic indicators of malaria in returning travellers: a retrospective study at Mohamed V Military Instruction Hospital.","authors":"Nabil Mohamed Zniber, Hamid Laatiris, Hamza Siyar, Abdelouahab Erraji, Ismail Labrouzi, Mohamed Jnah, Mehdi Talbi, Maryem Iken, Badreddine Lmimouni, Hafida Naoui","doi":"10.1099/acmi.0.000919.v3","DOIUrl":"10.1099/acmi.0.000919.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Malaria remains a significant global health concern, particularly in travellers returning from endemic regions. Haematological abnormalities are often associated with malaria and can serve as diagnostic indicators, especially when clinical symptoms are nonspecific. <b>Objective.</b> This study aims to identify the most relevant haematological parameters for diagnosing malaria in travellers returning from endemic areas, who sought care at the Mohamed V Military Instruction Hospital in Rabat. <b>Methods.</b> We conducted a retrospective comparative study involving 829 patients who returned from malaria-endemic regions between January 2017 and December 2023. Data collected included demographic information, parasitological test results and comprehensive haematological profiles. Statistical analysis was performed to determine the sensitivity and specificity of various haematological parameters in diagnosing malaria. <b>Results.</b> Thrombocytopenia, lymphocytopenia and anaemia were the most significant haematological abnormalities associated with malaria. Thrombocytopenia, defined as a platelet count below 150×10³ µl^-1, demonstrated a sensitivity of 75.91% and a specificity of 84.11%. Lymphocytopenia, with a threshold of less than 1.5×10³ µl^-1, showed a sensitivity of 69.47% and a specificity of 78.39%. Anaemia, defined by haemoglobin levels below 13 g dl^-1 in men and 12 g dl^-1 in women, also significantly correlated with malaria diagnosis. <b>Discussion.</b> This study highlights the significance of haematological abnormalities as key diagnostic markers for imported malaria cases. By analysing retrospective data, we observed that these abnormalities, especially thrombocytopenia and anaemia, are common amongst returning travellers with confirmed malaria. These findings suggest that clinicians can use such markers as a valuable tool for early malaria diagnosis, potentially improving patient outcomes. Additionally, the study reinforces the need for heightened awareness amongst healthcare providers in non-endemic regions regarding the presentation of malaria in travellers. <b>Conclusion.</b> Haematological parameters such as thrombocytopenia, lymphocytopenia and anaemia are valuable diagnostic tools for malaria in returning travellers. These findings suggest that these parameters should be integrated into diagnostic protocols to improve the accuracy and timeliness of malaria diagnosis, particularly in clinical settings with limited access to advanced diagnostic tools.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129952","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":"First case of infective endocarditis due to NDM-type carbapenemase-producing Serratia marcescens in a preterm infant: a case report.","authors":"Zakaria Malihy, Ikram El Abdallaoui, Tilila Abassor, Salah Sghir, Yassine Ben Lahlou, Rachid Abilkassem, Elmostafa Benaissa, Mariama Chadli","doi":"10.1099/acmi.0.000933.v3","DOIUrl":"10.1099/acmi.0.000933.v3","url":null,"abstract":"<p><p><i>Serratia marcescens (S. marcescens)</i> is a Gram-negative rod-shaped bacterium belonging to the <i>Enterobacteriaceae</i> family, commonly found in various environments. This opportunistic pathogen can cause urinary tract infections, respiratory infections and septicaemia, but endocarditis is particularly rare and concerning due to its rapid and devastating progression. We report the first documented case worldwide of infective endocarditis (IE) caused by <i>S. marcescens</i> producing NDM-type carbapenemase, and the second reported case of <i>S. marcescens</i> endocarditis in a preterm infant. The patient was a preterm male infant born at 34 weeks of gestation, from a triplet pregnancy, admitted to the neonatal intensive care unit on day 2 of life for respiratory distress. The mother, aged 39, had undiagnosed gestational diabetes. Premature rupture of membranes had occurred 10 days before delivery, necessitating prophylactic treatment with amoxicillin. On day 4 of life, the newborn developed a fever with elevated C-reactive protein (CRP) levels and leucocytosis, leading to antibiotic therapy with colistin, imipenem and amikacin. Blood cultures revealed the presence of carbapenemase-producing <i>S. marcescens</i> sensitive to fluoroquinolones. A cardiac ultrasound showed a vegetation on the mitral valve, confirming the diagnosis of IE. Despite intensive treatment, the newborn died on day 16 of life due to septic shock. This rare case of endocarditis caused by <i>S. marcescens</i> highlights the severity of this infection in preterm infants. Treatment relies on appropriate antibiotic therapy. Prevention requires strict hygiene measures. Further research is needed to establish optimal therapeutic recommendations.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144096141","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":"Draft genome sequences of four potential new species of the genus Bradyrhizobium isolated from root nodules of native legumes in Costa Rican forests.","authors":"Rachelle Fernández-Vargas, Sara Jiménez-Alpízar, Valeria Leandro-Arce, Bradd Mendoza-Guido, Keilor Rojas-Jimenez","doi":"10.1099/acmi.0.000990.v3","DOIUrl":"10.1099/acmi.0.000990.v3","url":null,"abstract":"<p><p>Here, we report the draft genome sequences of four <i>Bradyrhizobium</i> spp. isolates obtained from root nodules of the native legumes <i>Pentaclethra macroloba</i>, <i>Chamaecrista nictitans</i>, <i>Erythrina fusca</i> and <i>Zygia engelsingii</i> in tropical forests of Costa Rica. Genomes ranged from 8.6 to 9.8 Mb with GC contents between 62.8% and 63.8%. Phylogenomic analysis, along with average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons, confirmed that these isolates represent potential new species. ANI values ranged from 88.3% to 90.3%, and dDDH values from 28.8% to 41.8%, compared with their closest <i>Bradyrhizobium</i> species. Functional annotation revealed some genes related to nitrogen fixation (<i>nifA</i>, <i>nifB</i>, <i>nifH</i>) and nodulation capacity (<i>nodB</i>, <i>nodC</i>, <i>nodJ</i>). These results provide insights into the diversity and symbiotic capabilities of <i>Bradyrhizobium</i> in tropical ecosystems.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144096137","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}