Access Microbiology最新文献

{"title":"Infratemporal abscess: a rare complication of a common procedure","authors":"Rajesh Kotagiri, Matthew L Repp, Michael H. Kim, Faissal Stipho","doi":"10.1099/acmi.0.000721.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000721.v3","url":null,"abstract":"The infratemporal fossa (ITF) is an anatomically complex cavity that houses a variety of muscular and neurovascular structures at the base of the skull. Infections involving the ITF, though uncommon, can be fatal due to the difficulties of accessing this anatomical space and its proclivity to evolve into a cavernous venous thrombosis (CVT). As a result, a multi-disciplinary approach involving several surgical and medical subspecialists is often warranted. We present a case of an infratemporal fossa abscess (IFA) after wisdom teeth extraction with a very complicated clinical course and a distinct microbiologic profile.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"40 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139965690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nocardia otitidiscaviarum causing pulmonary nocardiosis: a case report and its review of the literature","authors":"Saumya P. Srivastava, A. Samaddar, Salman Khan, V. Tak, G. Bohra, Deepak Sharma, Arnab Ghosh, V. Nag","doi":"10.1099/acmi.0.000530.v5","DOIUrl":"https://doi.org/10.1099/acmi.0.000530.v5","url":null,"abstract":"\u0000 Background. Infections caused by Nocardia spp. can occur in immunocompromised as well as immunocompetent individuals. Although nocardiosis is rare, it is being increasingly recognized owing to the rise in occurrence rate over the years. The documentation of pleural involvement in nocardiosis is rare in India.\u0000 \u0000 Case. We report a case of pulmonary nocardiosis in an immunocompromised individual caused by Nocardia otitidiscaviarum.\u0000 \u0000 Discussion. Pulmonary nocardiosis caused by Nocardia otitidiscaviarum may go unnoticed without clinical suspicion. Correct and timely identification is the key to proper patient management.\u0000 \u0000 Conclusion. Coordination between clinicians and microbiologists is necessary for early diagnosis and appropriate management of nocardiosis.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"2 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139966795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection and characterization of micro-organisms linked to unsealed drugs sold in Ihiagwa community, Owerri, Imo State, Nigeria","authors":"U. Ekeleme, V. O. Ikwuagwu, U. Chukwuocha, Jane C. Nwakanma, Stephanie A. Adiruo, I. O. Ogini, I. U. Ude","doi":"10.1099/acmi.0.000752.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000752.v3","url":null,"abstract":"The contamination of pharmaceutical products by micro-organisms poses a significant risk to public health. This study was conducted to detect and characterize micro-organisms associated with unsealed drugs sold in Ihiagwa community in Owerri, Imo State, Nigeria. A variety of microbiological techniques were employed to analyse samples from unsealed drug containers. The identification process involved morphological, biochemical and sugar utilization methods, aiding in the accurate determination of microbial species. Microbial contamination was observed in 42 (84 %) out of 50 samples, with contaminants including bacteria and fungi. The range of contamination is between 1.2±0.01×103 and 2.3±0.02×103 c.f.u. ml−1 for viable count, 0.1±0.02×102 and 0.3±0.01×102 c.f.u. g−1 for coliform count and 0.2±0.01×101 and 0.5±0.01×101 c.f.u. g−1 for fungi count. The identified microbes were Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Candida albicans and Aspergillus niger. The most common bacterial isolate was S. aureus (51.8 %), while C. albicans (73.3 %) was the most prevalent fungus. Among the pharmacies and healthcare facilities examined, the Uchems pharmacy had the highest proportion of bacterial isolates (37 %), followed by the Stepwise pharmacy (22.2 %), while the lowest proportion was found at the Roseline Health Clinic (7.4 %). The identification of potentially harmful micro-organisms in these unsealed drug container samples emphasizes the importance of stringent quality control measures and improved handling, storage and packaging practices to ensure product safety and efficacy, especially among pharmacetical dealers.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"12 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139965975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeted genome sequencing for tuberculosis drug susceptibility testing in South Africa: a proposed diagnostic pipeline","authors":"Tayarv J. Bagratee, D. Studholme","doi":"10.1099/acmi.0.000740.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000740.v3","url":null,"abstract":"In July 2023, the World Health Organization (WHO) began recommending targeted next-generation sequencing (tNGS), due to its ability to detect resistance to many drugs with a single test. In March 2023, South Africa further adopted the GeneXpert XDR cartridge, which detects mutations associated with resistance to second-line injectable drugs. Here, we consider the feasibility for implementing tNGS in South Africa, what such a facility might look like and the specific context of this upper-middle-income country. Whilst the WHO now recommends tNGS for TB diagnostics and DST, there are many economic and infrastructural challenges opposing its deployment. In lieu of this, we instead recommend a stratified diagnostic pipeline that utilizes South Africa’s existing GeneXpert technologies, attempting to reduce the costs associated with implementation of tNGS.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"49 13","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139965627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Draft genomes announcement of Vietnamese Xanthomonas euvesicatoria strains causing bacterial spot on pepper","authors":"Aastha Subedi, Nguyen Thi Thu Nga, Doan Thi Kieu Tien, G. Minsavage, Pamela D. Roberts, Erica M. Goss, Jeffrey B. Jones","doi":"10.1099/acmi.0.000741.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000741.v3","url":null,"abstract":"\u0000 \u0000 \u0000 Xanthomonas euvesicatoria\u0000 \u0000 the primary causal agent of bacterial spot of pepper (BSP), poses a significant global challenge, resulting in severe defoliation and yield losses for pepper growers. We present the whole genome sequences of eight \u0000 \u0000 X. euvesicatoria\u0000 \u0000 strains associated with BSP in Vietnam. These genomes contribute to representation of pepper production regions in the global sample of \u0000 \u0000 X. euvesicatoria\u0000 \u0000 genomes, enabling the development of precise global disease management strategies.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"6 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139632725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Listeria innocua infection in an old case of total knee replacement – an unusual case report","authors":"Minakshi Gupta, Uma Shankar Saha, Ritesh Kumar, J. Laik, Minakshi Mishra","doi":"10.1099/acmi.0.000524.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000524.v3","url":null,"abstract":"<jats:p>Prosthetic implant-associated arthritis due to <jats:italic>\u0000 <jats:named-content content-type=\"genus\">\u0000 <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://doi.org/10.1601/nm.5095\" xlink:type=\"simple\">Listeria</jats:ext-link>\u0000 </jats:named-content>\u0000 </jats:italic> is mostly reported for <jats:italic>\u0000 <jats:named-content content-type=\"species\">\u0000 <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://doi.org/10.1601/nm.5096\" xlink:type=\"simple\">Listeria monocytogenes</jats:ext-link>\u0000 </jats:named-content>\u0000 </jats:italic>. Here, we describe a patient who underwent total knee replacement 12 years ago and presented with pain, tenderness, redness and local rise in temperature in the right knee. Purulent fluid was aspirated. Upon microbiological analysis, culture yielded <jats:italic>\u0000 <jats:named-content content-type=\"species\">\u0000 <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://doi.org/10.1601/nm.5099\" xlink:type=\"simple\">Listeria innocua</jats:ext-link>\u0000 </jats:named-content>\u0000 </jats:italic>. <jats:italic>\u0000 <jats:named-content content-type=\"species\">\u0000 <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://doi.org/10.1601/nm.5099\" xlink:type=\"simple\">L. innocua</jats:ext-link>\u0000 </jats:named-content>\u0000 </jats:italic> is rare. <jats:italic>\u0000 <jats:named-content content-type=\"genus\">\u0000 <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"http://doi.org/10.1601/nm.5095\" xlink:type=\"simple\">Listeria</jats:ext-link>\u0000 </jats:named-content>\u0000 </jats:italic> is not reported as a contaminant and routine cultures may be negative. Because of the long interval between surgery and the onset of symptoms, clinical suspicion, radiological investigations and analysing multiple samples are of immense help.</jats:p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"54 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139637543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome sequencing and genotyping Klebsiella pneumoniae multi-drug resistant hospital isolates from Western Kenya","authors":"Victor Dinda, A. Kimang’a, D. Kariuki, A. Sifuna, Thomas James O’Brien, Martin Welch, O.N. Reva","doi":"10.1099/acmi.0.000667.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000667.v4","url":null,"abstract":"\u0000 Objectives.\u0000 \u0000 \u0000 Klebsiella pneumoniae\u0000 \u0000 are a frequent cause of nosocomial infections worldwide. Sequence type 147 (ST147) has been reported as a major circulating high-risk lineage in many countries, and appears to be a formidable platform for the dissemination of antimicrobial resistance (AMR) determinants. However, the distribution of this pathogen in Western African hospitals has been scarcely studied. The main objective of this work was to perform whole genome sequencing of \u0000 \u0000 K. pneumoniae\u0000 \u0000 isolates from a referral hospital in Kakamega (Kenya) for genotyping and identification of AMR and virulence determinants.\u0000 \u0000 Methods. In total, 15 \u0000 \u0000 K\u0000 \u0000 . \u0000 \u0000 pneumoniae\u0000 \u0000 isolates showing a broad spectrum antimicrobial resistance were selected for whole genome sequencing by Illumina HiSeq 2500 platform.\u0000 \u0000 Results. ST147 was the dominant lineage among the highly-resistant \u0000 \u0000 K. pneumoniae\u0000 \u0000 isolates that we sequenced. ST147 was associated with both community- and the hospital-acquired infections, and with different infection sites, whereas other STs were predominantly uropathogens. Multiple antibiotic resistance and virulence determinants were detected in the genomes including extended-spectrum β-lactamases (ESBL) and carbapenemases. Many of these genes were plasmid-borne.\u0000 \u0000 Conclusions. Our data suggest that the evolutionary success of ST147 may be linked with the acquisition of broad host-range plasmids, and their propensity to accrue AMR and virulence determinants. Although ST147 is a dominant lineage in many countries worldwide, it has not been previously reported as prevalent in Africa. Our data suggest an influx of new nosocomial pathogens with new virulence genes into African hospitals from other continents.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"345 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139635777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The longitudinal effect of disseminating handwashing public health education to children in India via co-created, culturally relevant resources","authors":"Sapphire Crosby, S. Younie, Harnesh Vijay Ujenia, Katie Laird","doi":"10.1099/acmi.0.000677.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000677.v3","url":null,"abstract":"Infectious diseases are a leading cause of death for children from low- and middle-income countries (LMICs), often due to inadequate hand-hygiene. This study evaluates culturally relevant educational resources as a vehicle to disseminate the importance of handwashing amongst children in India. Employing a participatory action research (PAR) model and mixed methods, this follow-up longitudinal study evaluates a set of innovate educational handwashing resources and workshops specifically co-created for use in the State of Gujarat, and how they aid teachers in the teaching of hand-hygiene over a 3 year period. Working alongside local NGOs on-the-ground, teacher questionnaires (n=58) and focus groups including a brief questionnaire with teachers (n=35) were conducted to assess the impact of trainer workshops. In addition, pre- and post-workshop worksheets were conducted with children (n=98). Percentage change was calculated between children’s pre-and post-worksheet scores and a cumulative frequency of responses to each questionnaire criterion was measured. Data from the focus group found that the resources had been used in over 200 schools by more than 5000 children. In addition, 92.28 % of teachers said they would use the resources within their classrooms in India, with 58.16 % of pupils having an increased understanding of germs/handwashing directly after the workshop. Teachers reported that they are able to teach microbiology and handwashing more effectively. Furthermore, following a focus group, 100 % of teachers noted a reduction in childhood vomiting and diarrhoeal illnesses linked with insufficient hand-hygiene across 46 schools in the State of Gujarat since using the Germ’s Journey resources.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"80 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139638302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenome-assembled genomes from mineral tundra soils in Rásttigáisá, northern Norway","authors":"I. Pessi, Aino Rutanen, J. Hultman","doi":"10.1099/acmi.0.000655.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000655.v3","url":null,"abstract":"Microbial communities in tundra soils remain largely unknown despite their important roles in the cycling of greenhouse gases. Here, we report 59 non-redundant metagenome-assembled genomes (MAGs) recovered from mineral tundra soils in Rásttigáisá, northern Norway. The MAGs were obtained by clustering contigs according to tetranucleotide frequency and differential coverage and were manually curated to remove contigs with outlying GC content and/or mean coverage. Most MAGs were assigned to the bacterial phyla Candidatus Dormibacterota (n=12), Verrucomicrobiota (n=10), and Acidobacteriota (n=9). All archaeal MAGs (n=4) belong to the genus Candidatus Nitrosopolaris (phylum Thermoproteota). The 59 Rásttigáisá MAGs expand our knowledge of the diversity and ecological roles of tundra microbiomes.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139637837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BactEXTRACT: an R Shiny app to quickly extract, plot and analyse bacterial growth and gene expression data","authors":"Julien Dénéréaz, J. Veening","doi":"10.1099/acmi.0.000742.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000742.v3","url":null,"abstract":"To streamline the analysis and visualization of bacterial growth and gene expression data obtained by microtitre plate readers, we developed BactEXTRACT, an intuitive, easy-to-use R Shiny application. BactEXTRACT simplifies the transition from raw optical density, fluorescence and luminescence measurements to publication-ready plots. This package offers a user-friendly interface that reduces the complexity involved in growth curve and gene expression analysis and is generally applicable. BactEXTRACT is available at https://veeninglab.com/bactextract.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"208 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139636489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}