FEMS microbes最新文献

{"title":"Long-term survival of <i>Dehalococcoides mccartyi</i> strains in mixed cultures under electron acceptor and ammonium limitation.","authors":"Nadia Morson,&nbsp;Olivia Molenda,&nbsp;Katherine J Picott,&nbsp;Ruth E Richardson,&nbsp;Elizabeth A Edwards","doi":"10.1093/femsmc/xtac021","DOIUrl":"https://doi.org/10.1093/femsmc/xtac021","url":null,"abstract":"<p><p>Few strains of <i>Dehalococcoides mccartyi</i> harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The <i>vcrA</i> operon is found on a Genomic Island (GI) and, therefore, believed to participate in horizontal gene transfer (HGT). To try to induce HGT of the <i>vcrA</i>-GI, we blended two enrichment cultures in medium without ammonium while providing VC. We hypothesized that these conditions would select for a mutant strain of <i>D. mccartyi</i> that could both fix nitrogen and respire VC. However, after more than 4 years of incubation, we found no evidence for HGT of the <i>vcrA</i>-GI. Rather, we observed VC-dechlorinating activity attributed to the trichloroethene reductase TceA. Sequencing and protein modelling revealed a mutation in the predicted active site of TceA, which may have influenced substrate specificity. We also identified two nitrogen-fixing <i>D. mccartyi</i> strains in the KB-1 culture. The presence of multiple strains of <i>D. mccartyi</i> with distinct phenotypes is a feature of natural environments and certain enrichment cultures (such as KB-1), and may enhance bioaugmentation success. The fact that multiple distinct strains persist in the culture for decades and that we could not induce HGT of the <i>vcrA</i>-GI suggests that it is not as mobile as predicted, or that mobility is restricted in ways yet to be discovered to specific subclades of <i>Dehalococcoides</i>.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac021"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10035913","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":"Improving correlation of wastewater SARS-CoV-2 gene copy numbers with COVID-19 public health cases using readily available biomarkers.","authors":"Justin M Hutchison,&nbsp;Zhengxi Li,&nbsp;Chi-Ning Chang,&nbsp;Yasawantha Hiripitiyage,&nbsp;Megan Wittman,&nbsp;Belinda S M Sturm","doi":"10.1093/femsmc/xtac010","DOIUrl":"10.1093/femsmc/xtac010","url":null,"abstract":"<p><p>The COVID-19 pandemic has highlighted the potential role that wastewater-based epidemiology can play in assessing aggregate community health. However, efforts to translate SARS-CoV-2 gene copy numbers obtained from wastewater samples into meaningful community health indicators are nascent. In this study, SARS-CoV-2 nucleocapsid (N) genes (N1 and N2) were quantified weekly using reverse transcriptase droplet digital PCR from two municipal wastewater treatment plants for seven months. Four biomarkers (ammonium, biological oxygen demand (BOD), creatinine, and human mitochondrial gene NADH dehydrogenase subunit 5) were quantified and used to normalize SARS-CoV-2 gene copy numbers. These were correlated to daily new case data and one-, two-, and three-week cumulative case data. Over the course of the study, the strongest correlations were observed with a one-day case data lag. However, early measurements were strongly correlated with a five-day case data lag. This indicates that in the early stages of the pandemic, the wastewater samples may have indicated active COVID-19 cases before clinical indications. Mitochondrial and creatinine normalization methods showed the strongest correlations throughout the study, indicating that human-specific biomarkers were better at normalizing wastewater data than ammonium or BOD. Granger causality tests supported this observation and showed that gene copies in wastewater could be predictive of new cases in a sewershed.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/20/e2/xtac010.PMC9480869.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9633403","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":"Concentrations of mesophilic bacteria in a poultry farm over two fattening periods focusing on the presence of staphylococci and enterococci.","authors":"Doris Haas,&nbsp;Tea Miskovic,&nbsp;Theresa Fritz,&nbsp;Herbert Galler,&nbsp;Juliana Habib,&nbsp;Sabine Köck,&nbsp;Michael Kropsch,&nbsp;Peter Pless,&nbsp;Martin Stonitsch,&nbsp;Eduard Zentner,&nbsp;Franz F Reinthaler","doi":"10.1093/femsmc/xtac023","DOIUrl":"https://doi.org/10.1093/femsmc/xtac023","url":null,"abstract":"<p><p>The increasing animal numbers have a potential impact on the air quality of stables. The aim of this study was to assess the microbial load in the barn air from the day of entry of the chickens to the day of removal for slaughter. A total of 10 measurements in two fattening periods were conducted in a poultry farm with a capacity of 400 chickens in Styria, Austria. The samples were collected with an Air-Sampling Impinger for the investigation of mesophilic bacteria, staphylococci and enterococci. Chicken skin swab samples were collected to detect <i>Staphylococcus aureus</i>. The total colony forming units per cubic meter of mesophilic bacteria of the first measurement series of period I was 7.8 × 10⁴ and increased to 1.4 × 10⁸ at the end and at the fattening period II it increased from 2.5 × 10⁵ to 4.2 × 10⁷. In the measurement series of the fattening period I, the concentration of <i>Staphylococcus</i> spp. increased from 0 to 4.9 × 10⁷ CFUs/m³ and from 0 to 2.1 × 10⁷ CFUs/m³ in the fattening period II. <i>Staphylococcus aureus</i> could not be found on the chicken skin. An interesting finding was the increase of staphylococci while the intestinal enterococci were not detectable in the air of the barn toward the end of both fattening periods.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac023"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117851/pdf/xtac023.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9653274","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":"Bacteriophages in sewage: abundance, roles, and applications.","authors":"Elisenda Ballesté,&nbsp;Anicet R Blanch,&nbsp;Maite Muniesa,&nbsp;Cristina García-Aljaro,&nbsp;Lorena Rodríguez-Rubio,&nbsp;Julia Martín-Díaz,&nbsp;Miriam Pascual-Benito,&nbsp;J Jofre","doi":"10.1093/femsmc/xtac009","DOIUrl":"https://doi.org/10.1093/femsmc/xtac009","url":null,"abstract":"<p><p>The raw sewage that flows through sewage systems contains a complex microbial community whose main source is the human gut microbiome, with bacteriophages being as abundant as bacteria or even more so. Phages that infect common strains of the human gut bacteriome and transient bacterial pathogens have been isolated in raw sewage, as have other phages corresponding to non-sewage inputs. Although human gut phages do not seem to replicate during their transit through the sewers, they predominate at the entrance of wastewater treatment plants, inside which the dominant populations of bacteria and phages undergo a swift change. The sheer abundance of phages in the sewage virome prompts several questions, some of which are addressed in this review. There is growing concern about their potential role in the horizontal transfer of genes, including those related with bacterial pathogenicity and antibiotic resistance. On the other hand, some phages that infect human gut bacteria are being used as indicators of fecal/viral water pollution and as source tracking markers and have been introduced in water quality legislation. Other potential applications of enteric phages to control bacterial pathogens in sewage or undesirable bacteria that impede the efficacy of wastewater treatments, including biofilm formation on membranes, are still being researched.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac009"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/df/e6/xtac009.PMC10117732.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10035912","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":"Anti-malarial plants in Ethiopia and their activities on drug-resistant malaria.","authors":"Yimeslal Atnafu Sema,&nbsp;Teshale Areda Waktola","doi":"10.1093/femsmc/xtac001","DOIUrl":"https://doi.org/10.1093/femsmc/xtac001","url":null,"abstract":"<p><p>In Ethiopia, the impacts of malaria continue to cause a many number of morbidity and mortality that accounts to most-outpatient observations. Ethiopia recently designed to attain nationwide malaria control by 2030 by beginning sub-national elimination in districts with low malaria transmission. However, the rise of drug-resistant parasites, especially <i>Plasmodium falciparum</i> hinder the malaria-containment strategies. <i>Plasmodium falciparum</i> and <i>Plasmodium vivax</i> are dispersed all over Ethiopia, and account for 60% and 40% of malaria cases, respectively. The aim of this report was to overview the phytochemical constituents, diversity, and effect of some compound extracts on drug-resistant plasmodium species. Many plant species, a total 200 identified by 82 studies, are used in traditional malaria treatments throughout the country. <i>Allium sativum, Croton macrostachyus</i>, and <i>Carica papaya</i> were the more frequently used medicinal plant species. There are so many phytochemical constituents found in medicinal plants used to treat malaria. Alkaloids, flavonoids, phenolics, terpenoids, and glycosides are the most-reported for their effective activity on drug-resistant malaria.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac001"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9665819","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":"Macromolecular composition and substrate range of three marine fungi across major cell types.","authors":"Seth Thomas,&nbsp;Sabine K Lengger,&nbsp;Kimberley E Bird,&nbsp;Ro Allen,&nbsp;Michael Cunliffe","doi":"10.1093/femsmc/xtab019","DOIUrl":"https://doi.org/10.1093/femsmc/xtab019","url":null,"abstract":"<p><p>Marine fungi exist as three major cell types: unicellular yeasts, filamentous hyphae and zoosporic early-diverging forms, such as the Chytridiomycota (chytrids). To begin to understand the ecological and biogeochemical influence of these cell types within the wider context of other plankton groups, cell size and macromolecular composition must be assessed across all three cell types. Using a mass-balance approach to culture, we describe quantitative differences in substrate uptake and subsequent macromolecular distribution in three model marine fungi: the yeast <i>Metschnikowia zobellii</i>, the filamentous <i>Epicoccum nigrum</i> and chytrid <i>Rhizophydium littoreum</i>. We compared these model cell types with select oleaginous phytoplankton of specific biotechnological interest through metanalysis. We hypothesise that fungal cell types will maintain a significantly different macromolecular composition to one another and further represent an alternative grazing material to bacterioplankton and phytoplankton for higher trophic levels. Assessment of carbon substrate range and utilisation using phenotype arrays suggests that marine fungi have a wide substrate range. Fungi also process organic matter to an elevated-lipid macromolecular composition with reduced-protein content. Because of their size and increased lipid composition compared to other plankton groups, we propose that fungi represent a compositionally distinct, energy-rich grazing resource in marine ecosystems. We propose that marine fungi could act as vectors of organic matter transfer across trophic boundaries, and supplement our existing understanding of the microbial loop and carbon transfer in marine ecosystems.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtab019"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/48/1d/xtab019.PMC10117802.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9660446","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":"Repurposing the PDMA-approved drugs in Japan using an insect model of staphylococcal infection.","authors":"Atsushi Miyashita,&nbsp;Shuhei Mitsutomi,&nbsp;Tohru Mizushima,&nbsp;Kazuhisa Sekimizu","doi":"10.1093/femsmc/xtac014","DOIUrl":"https://doi.org/10.1093/femsmc/xtac014","url":null,"abstract":"<p><p>A total of 1253 compounds approved as therapeutic drugs in Japan (Pharmaceuticals and Medical Devices Agency (PMDA)-approved compounds) were screened for their therapeutic effects against <i>Staphylococcus aureus</i> infection using the silkworm infection model. In the first stage of screening with an index of prolonged survival, 80 compounds were identified as hits. Of these, 64 compounds were clinically used as antimicrobial agents, and the remaining 16 compounds were not. The 16 compounds were examined for their dose-dependent therapeutic effects on the silkworm model as a second screening step, and we obtained five compounds as a result. One of the compounds (capecitabine) had no documented <i>in vitro</i> minimum inhibitory concentration (MIC) value against <i>S. aureus</i>. The MIC value of capecitabine against <i>S. aureus</i> strains ranged from 125 to 250 µg/ml, and capecitabine was therapeutically effective at a dose of 200 mg/kg in a murine model of <i>S. aureus</i> infection. These results suggest that silkworm-based drug repositioning studies are of potential value. Furthermore, the therapeutic effects of capecitabine demonstrated in this study provide an important scientific rationale for clinical observational studies examining the association between staphylococcal infection events and capecitabine administration in cancer chemotherapy patients.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"3 ","pages":"xtac014"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9661875","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":"Erratum to \"Enterococcus faecalis Colonizes and Forms Persistent Biofilm Microcolonies on Undamaged Endothelial Surfaces in a Rabbit Endovascular Infection Model\".","authors":"Aaron M T Barnes","doi":"10.1093/femsmc/xtab018","DOIUrl":"https://doi.org/10.1093/femsmc/xtab018","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/femsmc/xtab014.].</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":" ","pages":"xtab018"},"PeriodicalIF":0.0,"publicationDate":"2021-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8b/76/xtab018.PMC8684440.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39749337","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":"Microbiological characteristics of bacteremias among COVID-19 hospitalized patients in a tertiary referral hospital in Northern Greece during the second epidemic wave.","authors":"Efthymia Protonotariou,&nbsp;Paraskevi Mantzana,&nbsp;Georgios Meletis,&nbsp;Areti Tychala,&nbsp;Angeliki Kassomenaki,&nbsp;Olga Vasilaki,&nbsp;Georgia Kagkalou,&nbsp;Ioanna Gkeka,&nbsp;Maria Archonti,&nbsp;Styliani Kati,&nbsp;Simeon Metallidis,&nbsp;Lemonia Skoura","doi":"10.1093/femsmc/xtab021","DOIUrl":"https://doi.org/10.1093/femsmc/xtab021","url":null,"abstract":"<p><p>Northern Greece was struck by an intense second COVID-19 (coronavirus disease 2019) epidemic wave during the fall of 2020. Because of the coinciding silent epidemic of multidrug-resistant organisms, the handling of COVID-19 patients became even more challenging. In the present study, the microbiological characteristics of bacteremias in confirmed cases of hospitalized COVID-19 patients were determined. Data from 1165 patients hospitalized between September and December 2020 were reviewed regarding the frequency of bloodstream infections, the epidemiology and the antibiotic susceptibility profiles of the causative bacteria. The hospital's antibiotic susceptibility data for all major nosocomial pathogens isolated from bacteremias of COVID-19 patients between September and December 2020 versus those between September and December 2019 were also compared. Overall, 122 patients developed bacteremia (10.47%). The average of time interval between hospitalization date and development of bacteremia was 13.98 days. Admission to ICU occurred in 98 out of 122 patients with an average stay time of 15.85 days and 90.81% in-hospital mortality. In total, 166 pathogens were recovered including 114 Gram-negative bacteria and 52 Gram-positive cocci. <i>Acinetobacter baumannii</i> was the most frequent (<i>n</i> = 51) followed by <i>Klebsiella pneumoniae</i> (<i>n</i> = 45) and <i>Enterococcus faecium</i> (<i>n</i> = 31). Bacteremias in hospitalized COVID-19 patients were related with prolonged time of hospitalization and higher in-hospital mortality, and the isolated microorganisms represented the bacterial species that were present in our hospital before the COVID-19 pandemic. Worryingly, the antibiotic resistance rates were increased compared with the pre-pandemic era for all major opportunistic bacterial pathogens. The pandemic highlighted the need for continuous surveillance of patients with prolonged hospitalization.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":" ","pages":"xtab021"},"PeriodicalIF":0.0,"publicationDate":"2021-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8847882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40308977","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":"Wastewater surveillance of SARS-CoV-2 corroborates heightened community infection during the initial peak of COVID-19 in Bexar County, Texas.","authors":"Haya Al-Duroobi, Sina V Moghadam, Duc C Phan, Arash Jafarzadeh, Akanksha Matta, Vikram Kapoor","doi":"10.1093/femsmc/xtab015","DOIUrl":"10.1093/femsmc/xtab015","url":null,"abstract":"<p><p>The purpose of this study was to conduct a preliminary assessment of the levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater at the Salitrillo Wastewater Treatment Plant in Texas during the initial peak of coronavirus disease 2019 (COVID-19) outbreak. Raw wastewater influent (24 h composite, time-based 1 L samples, <i>n</i> = 13) was collected weekly during June-August 2020. We measured SARS-CoV-2 RNA in wastewater by reverse transcription droplet digital PCR using the same N1 and N2 primer sets as employed in COVID-19 clinical testing. Virus RNA copies for positive samples (77%) ranged from 1.4 × 10² to 4.1 × 10⁴ copies per liter of wastewater, and exhibited both increasing and decreasing trends, which corresponded well with the COVID-19 weekly infection rate (N1: ρ = 0.558, <i>P</i> = 0.048; N2: ρ = 0.487, <i>P</i> = 0.092). A sharp increase in virus RNA concentrations was observed during July sampling dates, consistent with the highest number of COVID-19 cases reported. This could be attributed to an increase in the spread of COVID-19 infection due to the Fourth of July holiday week gatherings (outdoor gatherings were limited to 100 people during that time). Our data show that wastewater surveillance is an effective tool to determine trends in infectious disease prevalence, and provide complementary information to clinical testing.</p>","PeriodicalId":73024,"journal":{"name":"FEMS microbes","volume":"2 ","pages":"xtab015"},"PeriodicalIF":0.0,"publicationDate":"2021-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ca/de/xtab015.PMC10117867.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9667296","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}