Access Microbiology最新文献

{"title":"Molecular epidemiology of antimicrobial resistance in central africa: A systematic review.","authors":"Annicet-Clotaire Dikoumba, Richard Onanga, Laurette G Mangouka, Larson Boundenga, Edgard-Brice Ngoungou, Sylvain Godreuil","doi":"10.1099/acmi.0.000556.v5","DOIUrl":"10.1099/acmi.0.000556.v5","url":null,"abstract":"<p><strong>Background: </strong>In Central Africa, it is difficult to tackle antibiotic resistance, because of a lack of data and information on bacterial resistance, due to the low number of studies carried out in the field. To fill this gap, we carried out a systematic review of the various studies, and devised a molecular epidemiology of antimicrobial resistance from humans, animals and the environmental samples.</p><p><strong>Method: </strong>A systematic search of all publications from 2005 to 2020 on bacterial resistance in Central Africa (Gabon, Cameroon, Democratic Republic of Congo, Central African Republic, Chad, Republic of Congo, Equatorial Guinea, São Tomé and Príncipe, Angola) was performed on Pubmed, Google scholar and African Journals Online (AJOL). All circulating resistance genes, prevalence and genetic carriers of these resistances were collected. The study area was limited to the nine countries of Central Africa.</p><p><strong>Results: </strong>A total of 517 studies were identified through a literature search, and 60 studies carried out in eight countries were included. Among all articles included, 43 articles were from humans. Our study revealed not only the circulation of beta-lactamase and carbapenemase genes, but also several other types of resistance genes. To finish, we noticed that some studies reported mobile genetic elements such as integrons, transposons, and plasmids.</p><p><strong>Conclusion: </strong>The scarcity of data poses difficulties in the implementation of effective strategies against antibiotic resistance, which requires a health policy in a 'One Health' approach.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10219986","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":"A glimpse into the dark – the bacterial and archaeal diversity of tropical anchialine cave sediments","authors":"Kenneth Meland, T. Iliffe, S. Thiele","doi":"10.1099/acmi.0.000622.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000622.v3","url":null,"abstract":"Using ion torrent sequencing of the V4 region of the 16S rRNA gene, we investigated the sediment from four anchialine caves on Eleuthera (Bahamas). Anchialine caves are secluded, landlocked marine ecosystems, with high degrees of endemism. In the cave sediments, the bacterial and archaeal communities differ from marine communities and between caves, while often resembling those from low oxygen or anaerobic marine sediments. The waters of all caves investigated here were mostly saline and oxygenated, with Windermere Abyss differing from the other caves. This was mirrored by the bacterial and archaeal communities, with members of the wb1-A12 clade, \u0000 \u0000 Nitrosopumilaceae\u0000 \u0000 , members of the NB1-j phylum, and \u0000 \u0000 Actinomarinales\u0000 \u0000 being dominant in Preacher’s Blue Hole, Valentine’s Cave, and Bung Hole while \u0000 \u0000 Desulfatiglans\u0000 \u0000 , Bathyarchaeia, and members of the GIF3 and Sva0485 clades were dominant in Windermere Abyss. All communities showed taxa found in oxygenated and anoxic sediments, thus indicating a variety of chemoautotrophic lifestyles, including methane-, nitrogen- and sulphur cycling. The communities were different from other caves and included understudied or otherwise rare taxa, partially from deep sea sediments, implying that the isolation might be an evolutionary factor, and indicating that anchialine caves could be a window into the deep sea.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"104 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75957037","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":"Complete genome sequence of <i>Staphylococcus casei</i> strain DSM 15096.","authors":"Caitlin Wildsmith, Jonathan C Thomas, David Negus","doi":"10.1099/acmi.0.000656.v2","DOIUrl":"10.1099/acmi.0.000656.v2","url":null,"abstract":"<p><p>We present the first complete genome sequence of the species <i>Staphylococcus casei</i> . Strain DSM 15096 was sequenced with a hybrid approach using Oxford Nanopore Technologies long-read sequencing and Illumina short-read sequencing. The assembled sequences produced a 2 808 898 bp chromosomal molecule containing 2705 predicted genes, plus eight plasmids.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10424803","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":"Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations.","authors":"Asmita Gupta,&nbsp;Reelina Basu,&nbsp;Murali Dharan Bashyam","doi":"10.1099/acmi.0.000513.v3","DOIUrl":"10.1099/acmi.0.000513.v3","url":null,"abstract":"<p><p>Despite seminal advances towards understanding the infection mechanism of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), it continues to cause significant morbidity and mortality worldwide. Though mass immunization programmes have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study the role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2-infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April 2020 to October 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this period. We also highlight the presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10356346","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":"Male-killer symbiont screening reveals novel associations in <i>Adalia</i> ladybirds.","authors":"Jack Archer, Gregory D D Hurst, Emily A Hornett","doi":"10.1099/acmi.0.000585.v3","DOIUrl":"10.1099/acmi.0.000585.v3","url":null,"abstract":"<p><p>While male-killing bacteria are known to infect across arthropods, ladybird beetles represent a hotspot for these symbioses. In some host species, there are multiple different symbionts that vary in presence and frequency between populations. To further our understanding of spatial and frequency variation, we tested for the presence of three male-killing bacteria: <i>Wolbachia</i> , <i>Rickettsia</i> and <i>Spiroplasma</i> , in two <i>Adalia</i> ladybird species from a previously unexplored UK population. The two-spot ladybird, <i>A. bipunctata</i>, is known to harbour all three male-killers, and we identified <i>Spiroplasma</i> infection in the Merseyside population for the first time. However, in contrast to previous studies on two-spot ladybirds from continental Europe, evidence from egg-hatch rates indicates the <i>Spiroplasma</i> strain present in the Merseyside population does not cause embryonic male-killing. In the related ten-spot ladybird, <i>A. decempunctata</i>, there is only one previous record of a male-killing symbiont, a <i>Rickettsia</i> , which we did not detect in the Merseyside sample. However, PCR assays indicated the presence of a <i>Spiroplasma</i> in a single <i>A. decempunctata</i> specimen. Marker sequence indicated that this <i>Spiroplasma</i> was divergent from that found in sympatric <i>A. bipunctata</i>. Genome sequencing of the <i>Spiroplasma</i> -infected <i>A. decempunctata</i> additionally revealed the presence of cobionts in the form of a <i>Centistes</i> parasitoid wasp and the parasitic fungi <i>Beauveria</i>. Further study of <i>A. decempunctata</i> from this population is needed to resolve whether it is the ladybird or wasp cobiont that harbours <i>Spiroplasma</i> , and to establish the phenotype of this strain. These data indicate first that microbial symbiont phenotype should not be assumed from past studies conducted in different locations, and second that cobiont presence may confound screening studies aimed to detect the frequency of a symbiont in field collected material from a focal host species.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10436010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10106548","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":"Assessing the evolution of SARS-CoV-2 lineages and the dynamic associations between nucleotide variations","authors":"Asmita Gupta, Reelina Basu, M. Bashyam","doi":"10.1099/acmi.0.000513.v2","DOIUrl":"https://doi.org/10.1099/acmi.0.000513.v2","url":null,"abstract":"Despite seminal advances towards understanding the infection mechanism of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), it continues to cause significant morbidity and mortality worldwide. Though mass immunization programmes have been implemented in several countries, the viral transmission cycle has shown a continuous progression in the form of multiple waves. A constant change in the frequencies of dominant viral lineages, arising from the accumulation of nucleotide variations (NVs) through favourable selection, is understandably expected to be a major determinant of disease severity and possible vaccine escape. Indeed, worldwide efforts have been initiated to identify specific virus lineage(s) and/or NVs that may cause a severe clinical presentation or facilitate vaccination breakthrough. Since host genetics is expected to play a major role in shaping virus evolution, it is imperative to study the role of genome-wide SARS-CoV-2 NVs across various populations. In the current study, we analysed the whole genome sequence of 3543 SARS-CoV-2-infected samples obtained from the state of Telangana, India (including 210 from our previous study), collected over an extended period from April 2020 to October 2021. We present a unique perspective on the evolution of prevalent virus lineages and NVs during this period. We also highlight the presence of specific NVs likely to be associated favourably with samples classified as vaccination breakthroughs. Finally, we report genome-wide intra-host variations at novel genomic positions. The results presented here provide critical insights into virus evolution over an extended period and pave the way to rigorously investigate the role of specific NVs in vaccination breakthroughs.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"61 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89489297","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":"Metabolic perturbations and key pathways associated with the bacteriostatic activity of <i>Clitoria ternatea</i> flower anthocyanin fraction against <i>Escherichia coli</i>.","authors":"Ethel Jeyaseela Jeyaraj, Mei-Ling Han, Jian Li, Wee Sim Choo","doi":"10.1099/acmi.0.000535.v5","DOIUrl":"10.1099/acmi.0.000535.v5","url":null,"abstract":"<p><p><i>Clitoria ternatea</i> flowers are rich in anthocyanins and possess various biological activities. Specifically, the antibacterial mechanism of action of <i>C. ternatea</i> anthocyanins remains unknown and was investigated in <i>Escherichia coli</i> . A time-kill assay was used to assess the antibacterial activity and the metabolic perturbations in <i>E. coli</i> were investigated utilizing liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. Pathway analyses were carried out for metabolites showing ≥2-fold changes. The anthocyanin fraction remarkably reduced the growth of <i>E. coli</i> at 4 h by 95.8 and 99.9 % at minimum inhibitory concentration (MIC) and 2× MIC, respectively. The anthocyanin fraction (MIC) had a bacteriostatic effect and was shown to have perturbed glycerophospholipids (1-acyl-sn-glycero-3-phosphoethanolamine, phosphatidylglycerol, diacylglycerol and cardiolipin), amino acids (valine, tyrosine and isoleucine) and energy (ubiquinone and NAD) metabolites at 1 and 4 h. This study demonstrated significant metabolic perturbations of the glycerophospholipid, amino acid and energy metabolism, with these being the key pathways involved in the bacteriostatic activity of anthocyanins from <i>C. ternatea</i>, which may have promise as bacteriostatic agents for <i>E. coli</i> -related infections.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9812463","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 <i>Enterococcus</i> secretome inhibits the growth of <i>Mycobacterium tuberculosis</i> complex mycobacteria.","authors":"Wafaa Achache, Jean Louis Mege, Mustapha Fellag, Michel Drancourt","doi":"10.1099/acmi.0.000471.v3","DOIUrl":"10.1099/acmi.0.000471.v3","url":null,"abstract":"<p><p><i>Enterococcus mundtii</i> , a commensal intestinal bacterium, was demonstrated to inhibit the growth of some <i>Mycobacterium tuberculosis</i> complex (MTC) species that cause tuberculosis in humans and mammals. To further explore this preliminary observation, we cross-investigated five <i>E. mundtii</i> strains and seven MTC strains representative of four MTC species using a standardized quantitative agar well diffusion assay. All five <i>E. mundtii</i> strains, calibrated at 10 MacFarland, inhibited the growth of all <i>M. tuberculosis</i> strains with various susceptibility profiles, but no inhibition was observed with lower inoculums. Further, eight <i>E. mundtii</i> freeze-dried cell-free culture supernatants (CFCS) inhibited the growth of <i>M. tuberculosis</i> , <i>Mycobacterium africanum, Mycobacterium bovis</i> and <i>Mycobacterium canettii</i>, the most susceptible MTC species (inhibition diameter 25±1 mm), proportionally to CFCS protein concentrations. The data reported here indicate that the <i>E. mundtii</i> secretome inhibited growth of all MTC species of medical interest, which broadens previously reported data. In the gut, the <i>E. mundtii</i> secretome may modulate the expression of tuberculosis, exhibiting an anti-tuberculosis effect, with some protective roles in human and animal health.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9805958","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":"Evidence for some antimicrobial properties of English churchyard lichens.","authors":"J A Taylor, Toscane Fourie, Mark Powell, Iva Chianella","doi":"10.1099/acmi.0.000536.v4","DOIUrl":"10.1099/acmi.0.000536.v4","url":null,"abstract":"<p><p>The emergence of multidrug-resistant bacteria has driven the need for novel antibiotics. Our investigations have focussed on lichens as they naturally produce a wide range of unique and very effective defence chemicals. The aim of this study was to evaluate some of the antimicrobial properties of ten common British churchyard lichens. The lichen material was sampled from ten species, namely <i>Caloplaca flavescens</i>, <i>Diploicia canescens</i>, <i>Cladonia fimbriata</i>, <i>Psilolechia lucida</i>, <i>Lecanora campestris</i> subsp. <i>Campestris</i>, <i>Lecanora sulphurea, Pertusaria amara f.amara</i>, <i>Lepraria incana</i>, <i>Porpidia tuberculosa</i> and <i>Xanthoria calcicola</i>. Crude acetone extracts of these lichens were tested against six bacteria (<i>Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonela typhimurium, Listeria monocytogenes</i> and <i>Lactobacillus acidophilus</i> ) and two fungi (<i>Trichophyton interdigitale</i> and <i>Aspergillus flavus</i>) by the disc-diffusion susceptibility test method. Extracts of <i>Diploicia canescens, Psilolechia lucida, Lecanora sulphurea, Pertusaria amara</i> and <i>Lepraria incana</i> showed clear inhibition of the Gram-positive bacteria tested (<i>S. aureus, L. monocytogenes, L. plantarum</i>). <i>Diploicia canescens, Pertusaria amara</i> and <i>Lepraria incana</i> extracts also inhibited the dermatophyte fungi tested. The <i>Lepraria incana</i> sample tested here was the only extract that showed activity against any of the Gram-negative bacteria tested; it showed inhibition of <i>Pseudomnas aeruginosa</i>. Overall, our results showed that crude extracts of <i>Diploicia canescens</i> and <i>Pertusaria amara</i> had the most potent antimicrobial activity of all the extracts tested. Our results are in general agreement with published findings elsewhere. The activity of the <i>Porpidia tuberculosa</i> margin sample being different from that of the main colony material was an interesting and new finding reported here for the first time.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9799117","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":"Going through phages: a computational approach to revealing the role of prophage in <i>Staphylococcus aureus</i>.","authors":"Tyrome Sweet, Suzanne Sindi, Mark Sistrom","doi":"10.1099/acmi.0.000424","DOIUrl":"10.1099/acmi.0.000424","url":null,"abstract":"<p><p>Prophages have important roles in virulence, antibiotic resistance, and genome evolution in <i>Staphylococcus aureus</i> . Rapid growth in the number of sequenced <i>S. aureus</i> genomes allows for an investigation of prophage sequences at an unprecedented scale. We developed a novel computational pipeline for phage discovery and annotation. We combined PhiSpy, a phage discovery tool, with VGAS and PROKKA, genome annotation tools to detect and analyse prophage sequences in nearly 10 011  <i>S</i> . <i>aureus</i> genomes, discovering thousands of putative prophage sequences with genes encoding virulence factors and antibiotic resistance. To our knowledge, this is the first large-scale application of PhiSpy on a large-scale set of genomes (10 011  <i>S</i> . <i>aureus</i> ). Determining the presence of virulence and resistance encoding genes in prophage has implications for the potential transfer of these genes/functions to other bacteria via transduction and thus can provide insight into the evolution and spread of these genes/functions between bacterial strains. While the phage we have identified may be known, these phages were not necessarily known or characterized in <i>S. aureus</i> and the clustering and comparison we did for phage based on their gene content is novel. Moreover, the reporting of these genes with the <i>S. aureus</i> genomes is novel.</p>","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"5 6","pages":"acmi000424"},"PeriodicalIF":0.0,"publicationDate":"2023-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9805959","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}