Access Microbiology最新文献

{"title":"Draft genome sequences of 11 <i>Xanthomonas</i> strains associated with bacterial spot disease in Turkey.","authors":"Aastha Subedi,&nbsp;Serhat Kara,&nbsp;Yesim Aysan,&nbsp;Gerald V Minsavage,&nbsp;Sujan Timilsina,&nbsp;Pamela D Roberts,&nbsp;Erica M Goss,&nbsp;Jeffrey B Jones","doi":"10.1099/acmi.0.000586.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000586.v3","url":null,"abstract":"<p><p>Bacterial spot is an economically significant disease in tomato and pepper-producing countries globally. We report the whole-genome sequence of 11 <i>Xanthomonas</i> strains associated with bacterial spot disease on pepper, tomato and eggplant in the Southeastern Anatolia Region, Turkey. This genomic information can be used as a reference to study the genetic diversity of these species and contribute to illuminating pathogen evolution with respect to host specificity.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9799119","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":"<i>Streptococcus parasanguinis</i>: An emerging pathogen causing neonatal endocarditis: A case report.","authors":"Twishi Shrimali,&nbsp;Shikhir Malhotra,&nbsp;Nidhi Relhan,&nbsp;Vibhor Tak,&nbsp;Sushil Kumar Choudhary,&nbsp;Neeraj Gupta,&nbsp;Arun Kumarendu Singh","doi":"10.1099/acmi.0.000576.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000576.v4","url":null,"abstract":"<p><p><b>Background.</b> The microbial infection of the endocardium, popularly known as Infective Endocarditis (IE), is typically classified on the basis of anatomy, valve nativity and its associated microbiology. As per the associated microbiology, <i>Staphylococcus aureus</i> is the most common microorganism responsible for the cause of IE. Even though, the Streptococcus group accounts for a smaller percentage of IE, however this doesn't give us the liberty of ignoring the high mortality and morbidity associated with this pathogen. <b>Case presentation.</b> We report an unusual case of neonatal sepsis, complicated with endocarditis, caused by penicillin resistant <i>Streptococcus parasanguinis</i> . The neonate however died of the same despite all efforts. The said baby was given birth by a mother with gestational diabetes mellitus.</p><p><strong>Conclusion: </strong>High index of clinical suspicion and prompt diagnosis are the most important factors of patient management, especially in cases of life threatening neonatal infections. In such conditions a coordinated interdepartmental approach is very much needed.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9810398","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":"Fluoroquinolone resistance does not facilitate phage Φ13 integration or excision in <i>Staphylococcus aureus</i>.","authors":"Helena Leinweber,&nbsp;Raphael N Sieber,&nbsp;Martin S Bojer,&nbsp;Jesper Larsen,&nbsp;Hanne Ingmer","doi":"10.1099/acmi.0.000583.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000583.v4","url":null,"abstract":"<p><p>Prophages of the ΦSa3int family are commonly found in human-associated strains of <i>Staphylococcus aureus</i> where they encode factors for evading the human innate immune system. In contrast, they are usually absent in livestock-associated methicillin-resistant <i>S. aureus</i> (LA-MRSA) strains where the phage attachment site is mutated compared to the human strains. However, ΦSa3int phages have been found in a subset of LA-MRSA strains belonging to clonal complex 398 (CC398), including a lineage that is widespread in pig farms in Northern Jutland, Denmark. This lineage contains amino acid changes in the DNA topoisomerase IV and the DNA gyrase encoded by <i>grlA</i> and <i>gyrA</i>, respectively, which have been associated with fluoroquinolone (FQ) resistance. As both of these enzymes are involved in DNA supercoiling, we speculated that the mutations might impact recombination between the ΦSa3int phage and the bacterial chromosome. To examine this, we introduced the FQ resistance mutations into <i>S. aureus</i> 8325-4<i>attB_LA</i> that carry the mutated CC398-like bacterial attachment site for ΦSa3int phages. When monitoring phage integration and release of Φ13, a well-described representative of the ΦSa3int phage family, we did not observe any significant differences between the FQ-resistant mutant and the wild-type strain. Thus our results suggest that mutations in <i>grlA</i> and <i>gyrA</i> do not contribute to the presence of the ΦSa3int phages in LA-MRSA CC398.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323784/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9812466","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":"<i>Rhizopus homothallicus,</i> an emerging pathogen causing cavitary lung lesions.","authors":"Juhi Taneja,&nbsp;Kuhu Chatterjee,&nbsp;Ruchi Arora Sachdeva,&nbsp;S Zafar Abbas,&nbsp;M K Sen","doi":"10.1099/acmi.0.000526.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000526.v3","url":null,"abstract":"<p><strong>Introduction: </strong><i>Rhizopus homothallicus</i> is an emerging pathogen that causes pulmonary mucormycosis.</p><p><strong>Case presentation: </strong>We report a case of pneumonia caused by <i>R. homothallicus</i> in a 54-year-old type 2 diabetic patient. The organism was isolated from bronchoalveolar lavage fluid and preliminarily identified by fungal morphology and finally by sequencing of the internal transcribed spacer region.</p><p><strong>Conclusion: </strong>Mucormycosis may be associated with cavitary lung lesions against a backdrop of poorly controlled diabetes or other immunosuppressed states. Pulmonary mucormycosis may have variable clinical and radiological presentations. Therefore, strong clinical suspicion and prompt management can address the high fatality associated with the disease.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521516","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":"The relationship between microbial community vitality and ATP bioburden in bottom waters under fuel microcosms.","authors":"Frederick Jay Passman,&nbsp;Jordan Schmidt,&nbsp;Russell P Lewis","doi":"10.1099/acmi.0.000411","DOIUrl":"https://doi.org/10.1099/acmi.0.000411","url":null,"abstract":"<p><p>Adenylate energy charge (AEC) - computed from the ATP, ADP and AMP concentrations in a specimen - reflect the net physiological state of the microbial population in that specimen. Previous research has demonstrated that healthy microbial populations maintain AEC≥0.8. As populations are subjected to stresses, or - in closed systems - deplete the available nutrients, respond to the accumulation of toxic metabolites, or both, AEC decreases (often to <0.5). Aqueous-phase samples from a set of fuel-water microcosms were tested for cellular ATP (cATP) and AEC. This paper reports on the precision of the AEC test method and the relationship between cellular AEC and cATP bioburdens in the aqueous phase of fuel over aqueous-phase microcosms.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 4","pages":"acmi000411"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9521518","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":"<i>Gordonia sputi</i>-associated bloodstream infection in a renal transplant patient with chronic indwelling central venous catheter: a case report and literature review.","authors":"Calvin Ka-Fung Lo,&nbsp;Conor Broderick,&nbsp;Aleksandra Stefanovic,&nbsp;William Connors,&nbsp;Melanie Murray","doi":"10.1099/acmi.0.000560.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000560.v3","url":null,"abstract":"<p><strong>Introduction: </strong>Although rare, human infections caused by <i>Gordonia</i> spp. have been reported, especially within the immunocompromised population and those with long-term indwelling devices. We report a case of <i>Gordonia</i> spp. bacteraemia in a renal transplant patient and present a literature review on microbiological identification methods of this organism.</p><p><strong>Case presentation: </strong>A 62-year-old female renal transplant recipient admitted to hospital with a 2-month history of dry cough and fevers occurring weekly when receiving electrolyte replacement infusions via a Groshong line. Over 2 weeks, blood cultures repeatedly isolated a Gram-positive bacillus solely in aerobic bottles, and this was initially reported as <i>Rhodococcus</i> spp. by the local microbiology laboratory. Chest computed tomography (CT) showed multiple ground-glass lung opacities suggestive of septic pulmonary emboli. As central line-associated bloodstream infection was suspected, empirical antibiotics were initiated and the Groshong line was removed. The Gram-positive bacillus was later confirmed by the reference laboratory as <i>Gordonia sputi</i> via 16S rRNA sequencing. Vancomycin and ciprofloxacin for a duration of 6 weeks were completed as targeted antimicrobial therapy. After treatment, the patient remained symptom-free with marked improvement on repeat CT chest imaging.</p><p><strong>Conclusion: </strong>This case illustrates the challenges surrounding identification of <i>Gordonia</i> spp. and other aerobic actinomycetes. 16S rRNA gene sequencing may be a preferred identification method, especially when initial workup of a weakly acid-fast organism fails to make an identification or shows discrepant results using traditional diagnostic modalities.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9805954","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":"Shiga toxin-producing <i>Escherichia coli</i> (STEC) and atypical enteropathogenic <i>E. coli</i> (aEPEC) in Swedish retail wheat flour.","authors":"Robert Söderlund,&nbsp;Catarina Flink,&nbsp;Anna Aspán,&nbsp;Erik Eriksson","doi":"10.1099/acmi.0.000577.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000577.v3","url":null,"abstract":"Wheat flour has been identified as the source of multiple outbreaks of gastrointestinal disease caused by shiga toxin-producing Escherichia coli (STEC). We have investigated the presence and genomic characteristics of STEC and related atypical enteropathogenic E. coli (aEPEC) in 200 bags of Swedish-produced retail wheat flour, representing 87 products and 25 brands. Samples were enriched in modified tryptone soya broth (mTSB) and screened with real-time PCR targeting stx1 , stx2 and eae, and the serogroups O157, O121 and O26. Isolation was performed by immunomagnetic separation (IMS) for suspected STEC/aEPEC O157, O121 and O26, and by screening pools of colonies for other STEC. Real-time PCR after enrichment revealed 12 % of samples to be positive for shiga toxin genes (stx1 and/or stx2 ) and 11 % to be positive for intimin (eae). Organic production, small-scale production or whole grain did not significantly influence shiga toxin gene presence or absence in a generalized linear mixed model analysis. Eight isolates of STEC were recovered, all of which were intimin-negative. Multiple serotype/sequence type/shiga toxin subtype combinations that have also been found in flour samples in other European countries were recovered. Most STEC types recovered were associated with sporadic cases of STEC among humans in Sweden, but no types known to have caused outbreaks or severe cases of disease (i.e. haemolytic uraemic syndrome) were found. The most common finding was O187:H28 ST200 with stx2g , with possible links to cervid hosts. Wildlife associated with crop damage is a plausible explanation for at least some of the surprisingly high frequency of STEC in wheat flour.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10267659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9647126","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":"Evaluation of five commercial DNA extraction kits using <i>Salmonella</i> as a model for implementation of rapid Nanopore sequencing in routine diagnostic laboratories.","authors":"Shannon H C Eagle,&nbsp;James Robertson,&nbsp;D Patrick Bastedo,&nbsp;Kira Liu,&nbsp;John H E Nash","doi":"10.1099/acmi.0.000468.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000468.v3","url":null,"abstract":"<p><p>Oxford Nanopore long-read sequencing offers advantages over Illumina short reads for the identification and characterization of bacterial pathogens for outbreak detection and surveillance activities within a diagnostic public health laboratory context. Compared to Illumina, Nanopore is more cost-effective for small batches, has a lower capital cost and has a faster turnaround time, in addition to the ability to assemble complete bacterial genomes. The quantity and quality of DNA required for Nanopore sequencing are greater than for Illumina, and the DNA extraction methods recommended for obtaining high-molecular-weight DNA are different from those typically used in diagnostic laboratories. Using a <i>Salmonella</i> isolate with a previously closed PacBio genome as a model Enterobacteriaceae organism, we evaluated the quantity, quality and fragmentation of five commercial DNA extraction kits. Nanopore sequencing performance was evaluated for the top three methods: Qiagen EZ1 DNA Tissue, Qiagen DNeasy Blood and Tissue, and a modified, in-house version of the MasterPure Complete DNA and RNA purification. To evaluate the effect of post-extraction DNA purification methods, we subjected extracted DNA from the three selected extraction methods to purification by AMPure beads or ethanol precipitation and compared these outputs with untreated DNA as a control. All methods are suitable for routine whole-genome sequencing (WGS), since all 60 replicates had very high genome recovery rates, with ≥98 % of the reference genome covered by mapped Nanopore reads. For 85 % of the replicates, assembly was able to produce a complete, circular chromosome using either Flye or Canu. In most cases, it is recommended to move directly from extraction to sequencing, as untreated DNA had the highest rates of genome closure regardless of extraction method. Using our evaluation criteria, the Qiagen DNeasy Blood and Tissue kit was found to be the best overall method due to its low cost, ability to scale from single tubes to 96-well plates, and high consistency in yield and sequencing performance.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9996181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9102083","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":"Characterization and <i>in vitro</i> antibacterial activity of sulfated polysaccharides from freshwater alga <i>Cladophora crispata</i>.","authors":"Mohanad Khaled Jasem,&nbsp;Abd-Alwahab Merai,&nbsp;Adnan Ali Nizam","doi":"10.1099/acmi.0.000537.v5","DOIUrl":"https://doi.org/10.1099/acmi.0.000537.v5","url":null,"abstract":"<p><p>Barada River is characterized by an abundant growth of freshwater algae. <i>Cladophora</i> sp. algae have emerged as a new source of bioactive compounds. In this research <i>Cladophora crispata</i> was cultivated with the outdoor method, and algal sulfated polysaccharides (SPs) were extracted by an ultrasonic-assisted extraction method. After extraction, gel filtration was used to purify the crude SPs, SP compounds were determined and selected, and the effect of purified SPs as antibacterial agents was investigated. The purified extract gave two fractions (F1 and F2). The chemical components of both crude and purified SPs were then determined. The highest carbohydrate content (74.12%) and protein content (4.02%) was found in the crude extract, while the highest sulfate content (12.17%) was found in purified fraction F2, and the highest uronic acid content (18.46%) was found in purified fraction F1. Fourier transform infrared spectroscopy (FT-IR) was used to confirm that the crude extract and fractions consist of sugar, uronic acids, protein and sulfate groups. Both F1 and F2 consisted of rhamnose, galactose, xylose and ribose based on high performance liquid chromatography (HPLC) separation. Each fraction showed an inhibitory effect on Gram-positive and Gram-negative bacteria. F2 has the lowest minimum inhibitory concentration (MIC) value against <i>Staphylococcus aureus</i> , <i>Bacillus anthracis</i> , <i>Enterobacter aerogenes</i> and <i>Pseudomonas aeruginosa</i> , where its MIC values were 6, 13, 25 and 30 mg ml^-1, respectively. Algae polysaccharides are of key interest due to their antibacterial properties, which has led to them being included in pharmaceutics and food applications.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10406154","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":"<i>Bordetella trematum</i> bacteraemia secondary to an empyema in an immunocompromised host: A case report and review of the literature.","authors":"Crystal Wong,&nbsp;Lynna Grace Calungsud,&nbsp;My-Van La","doi":"10.1099/acmi.0.000602.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000602.v3","url":null,"abstract":"<p><strong>Introduction: </strong><i>Bordetella trematum</i> infection remains uncommon. More cases of bacteraemia are reported in recent years with the primary infection largely originating from skin and soft tissue sites. Yet, our understanding of its virulence, antibiotic susceptibility profile and treatment is still limited.</p><p><strong>Case presentation: </strong><b>Case presentation.</b> We report the first case of <i>B. trematum</i> bacteraemia from a left-sided empyema. An 87-year-old female patient with a past medical history of ischaemic heart disease, diabetes mellitus complicated by nephropathy and locally advanced left breast adenocarcinoma presented with fever, productive cough and shortness of breath. The <i>B. trematum</i> isolates from blood and pleural fluid were identified by MALDI-TOF and 16S rRNA sequencing. Ceftriaxone and azithromycin commenced empirically on admission were switched to piperacillin-tazobactam after 2 days due to lack of clinical improvement. Despite a pleurocentesis and 1 week of piperacillin-tazobactam with microbiological clearance in blood, the patient continued to deteriorate. Decision to withdraw treatment was made in view of the patient's prognosis, and the patient succumbed on the fourteenth day of admission. The isolate was susceptible to piperacillin-tazobactam, imipenem and meropenem but had reduced susceptibility or was non-susceptible to cefuroxime, cefotaxime, ceftazidime, cefepime, the aminoglycosides and fluoroquinolones.</p><p><strong>Conclusion: </strong>Invasive <i>B. trematum</i> infection is associated with significant mortality. Consensus for antibiotic treatment remains unclear, with limited susceptibility data to support specific antibiotic use. We expect more clinical cases will surface with improved microbial identification systems, as well as enhanced clinical awareness. Standardized and more robust susceptibility work are needed to provide clear recommendations and establish consensus in treating invasive infections.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10424801","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}