Access Microbiology: Most Cited Articles http://www.microbiologyresearch.org/content/journal/acmi?TRACK=RSS Please follow the links to view the content. Cutaneous geotrichosis due to Geotrichum candidum in a burn patient http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000001?TRACK=RSS Geotrichum candidum is a saprophytic yeast known to colonize the human skin, respiratory tract and gastrointestinal tract. It can cause local or disseminated disease (geotrichosis), mainly in the immunocompromised host. Trauma, indwelling catheter use, prolonged broad-spectrum antibiotic treatment and critical illness have also been implicated as risk factors. Here we report the first case, to our knowledge, of cutaneous G. candidum infection in a burn patient. The isolate had a high amphotericin B minimum inhibitory concentration (MIC) and the patient experienced concomitant Candida orthopsilosis fungaemia, and so was treated with a combination of voriconazole and micafungin. This case highlights the importance of source control, rapid identification of G. candidum infection and MIC determination to guide antifungal therapy, which typically consists of amphotericin B with or without flucytosine or voriconazole alone. Clinicians should be aware of geotrichosis as a clinical entity in burn patients as well as in the immunocompromised. Antifungal resistance and breakthrough disease are an ongoing concern due to the increasing number of immunocompromised at-risk patients and the use of routine mould prophylaxis. Sarah Keene, Manbeer S. Sarao, Philip J. McDonald and Jennifer Veltman Wed Mar 20 09:57:11 UTC 2019Z Isolation and characterization of novel soil- and plant-associated bacteria with multiple phytohormone-degrading activities using a targeted methodology http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000053?TRACK=RSS Ethylene (ET), salicylic acid (SA) and indole-3-acetic acid (IAA) are important phytohormones regulating plant growth and development, as well as plant-microbe interactions. Plant growth-promoting bacteria (PGPB) naturally associate with plants and facilitate plant growth through a variety of mechanisms, including the ability to modulate the concentrations of these phytohormones in planta. Importantly, the wide presence of phytohormone degradation mechanisms amongst symbiotic and other soil- and plant-associated bacteria indicates that the ability to modulate phytohormone concentrations plays an important role in bacterial colonization and plant-growth promotion abilities. Obtaining phytohormone-degrading bacteria is therefore key for the development of novel solutions aiming to increase plant growth and protection. In this paper, we report an optimized targeted methodology and the consequent isolation of novel soil- and plant-associated bacteria, including rhizospheric, endophytic and phyllospheric strains, with the ability to degrade the phytohormones, SA and IAA, as well as the ET precursor, 1-aminocyclopropane-1-carboxylic acid (ACC). By using an optimized targeted methodology, we rapidly isolated diverse soil- and plant-associated bacteria presenting phytohormone-degrading abilities from several plants, plant tissues and environments, without the need for prior extensive and laborious isolation and maintenance of large numbers of isolates. The developed methodology facilitates PGPB research, especially in developing countries. Here, we also report, for the first time, the isolation of bacterial strains able to concomitantly catabolize three phytohormones (SA, IAA and ACC). Ultimately, the described targeted methodology and the novel phytohormone-degrading bacteria obtained in this work may be useful tools for future plant-microbe interaction studies, and in the development of new inoculant formulations for agriculture and biotechnology. Francisco X. Nascimento, Bernard R. Glick and Márcio J. Rossi Wed Aug 28 14:21:03 UTC 2019Z Sensitivity of shotgun metagenomics to host DNA: abundance estimates depend on bioinformatic tools and contamination is the main issue http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000104?TRACK=RSS A recent study reported that increasing host DNA abundance and reducing read depth impairs the sensitivity of detection of low-abundance micro-organisms by shotgun metagenomics. The authors used DNA from a synthetic bacterial community with abundances varying across several orders of magnitude and added varying proportions of host DNA. However, the use of a marker-gene-based abundance estimation tool (MetaPhlAn2) requires considerable depth to detect marker genes from low-abundance organisms. Here, we reanalyse the deposited data, and place the study in the broader context of low microbial biomass metagenomics. We opted for a fast and sensitive read binning tool (Kraken 2) with abundance estimates from Bracken. With this approach all organisms are detected even when the sample comprises 99 % host DNA and similarly accurate abundance estimates are provided (mean squared error 0.45 vs. 0.3 in the original study). We show that off-target genera, whether contaminants or misidentified reads, come to represent over 10 % of reads when the sample is 99 % host DNA and exceed counts of many target genera. Therefore, we applied Decontam, a contaminant detection tool, which was able to remove 61 % of off-target species and 79 % of off-target reads. We conclude that read binning tools can remain sensitive to low-abundance organisms even with high host DNA content, but even low levels of contamination pose a significant problem due to low microbial biomass. Analytical mitigations are available, such as Decontam, although steps to reduce contamination are critical. Andrew J. McArdle and Myrsini Kaforou Mon Feb 17 14:25:46 UTC 2020Z Antibiofilm properties of Clitoria ternatea flower anthocyanin-rich fraction towards Pseudomonas aeruginosa http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000343?TRACK=RSS In Asia, Clitoria ternatea flowers are commonly used as a traditional medicinal herb and as a food colourant. Their bioactive compounds have anti-inflammatory, anti-microbial and anti-biofilm activities. Pseudomonas aeruginosa is one of the major pathogens that cause biofilm-associated infections resulting in an increase in antimicrobial resistance. Hence, the aim of this study was to investigate if the anti-biofilm properties of the anthocyanin-rich fraction of C. ternatea flowers were effective against P. aeruginosa . The effect of the anthocyanin-rich fraction of C. ternatea flowers on P. aeruginosa biofilms formed on a polystyrene surface was determined using the crystal violet assay and scanning electron microscopy (SEM). The anthocyanin-rich fraction reduced biofilm formation by four P. aeruginosa strains with a minimum biofilm inhibitory concentration value ranging between 0.625 and 5.0 mg ml−1. We further show that the biofilm-inhibiting activity of C. ternatea flowers is not due to the flavonols but is instead attributed to the anthocyanins, which had significant biofilm inhibitory activity (64.0±1.1 %) at 24 h in a time–response study. The anthocyanin-rich fraction also significantly reduced bacterial attachment on the polystyrene by 1.1 log c.f.u. cm−2 surface based on SEM analysis. Hence, anthocyanins from C. ternatea flowers have potential as an agent to decrease the risk of biofilm-associated infections. Ethel Jeyaseela Jeyaraj, Sheila Nathan, Yau Yan Lim and Wee Sim Choo Tue Apr 26 12:59:53 UTC 2022Z Biosynthesis of silver nanoparticles using baker’s yeast, Saccharomyces cerevisiae and its antibacterial activities http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.ac2019.po0316?TRACK=RSS The biosynthesis of silver nanoparticles extracellularly using baker’s yeast, Saccharomyces cerevisiae and its antibacterial activity was investigated in this study. Biosynthesised silver nanoparticles were chaterized by using UV-Visible spectroscopy, which showed a distinct observed absorption peak at 429.00 nm that is attributed to the plasmon resonance of silver nanoparticles; X-ray diffraction, which determined the average size of the silver nanoparticles to be approximately 16.07 nm; presence of oval shaped silver nanoparticles determined by scanning electron microscopy; and Fourier-transform infrared, which revealed notable peaks at 3332.2, 2903.6 and 1636.3 cm−1 corresponding to the binding of the silver nanoparticles to active biomolecules, alcohols and phenols, carboxylic acids and aromatic amines respectively. The silver nanoparticles were also found to be stable for ninety days. Antibacterial activity of the silver nanoparticles was also studied. The silver nanoparticles was significantly active (P>0.05) against the test organisms at an extract concentration of 75 µg ml−1. Concentrations less than or equal to 50 µg ml−1 were not as effective as the colony forming units at this concentration, 1.61×106 for methicillin-resistant Staphylococcus aureus and 1.45×106 for Pseudomonas aeruginosa respectively were about the same range a small the colony forming units of the controls. The silver nanoparticles inhibited methicillin-resistant S. aureusmore than they inhibited P. aeruginosa. The LD50 of the synthesized silver nanoparticles after oral administration was seen to be greater than 5000 mg kg−1 body weight and is therefore thought to be safe. This study supports the use of silver nanoparticles as therapeutic agents. Ifeyomi Olobayotan and Bukola Akin-Osanaiye Mon Apr 08 14:56:43 UTC 2019Z In praise of preprints http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000013?TRACK=RSS This article has been co-published in all Society journals Norman K. Fry, Helina Marshall and Tasha Mellins-Cohen Tue Apr 02 14:44:00 UTC 2019Z Antibacterial activity of high-dose nitric oxide against pulmonary Mycobacterium abscessus disease http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000154?TRACK=RSS Introduction. Mycobacterium abscessus is an emerging pulmonary pathogen with limited treatment options. Nitric oxide (NO) demonstrates antibacterial activity against various bacterial species, including mycobacteria. In this study, we evaluated the effect of adjunctive inhaled NO therapy, using a novel NO generator, in a CF patient with pulmonary M. abscessus disease, and examined heterogeneity of response to NO in vitro. Methods. In the compassionate-use treatment, a 24-year-old CF patient with pulmonary M. abscessus was treated with two courses of adjunctive intermittent NO, first at 160 p.p.m. for 21 days and subsequently by escalating the dose up to 240 p.p.m. for 8 days. Methemoglobin, pulmonary function, 6 min walk distance (6MWD), qualify of life and sputum microbiology were assessed. In vitro susceptibility tests were performed against patient’s isolate and comparison clinical isolates and quantified by Hill’s slopes calculated from time–kill curves. Results. M. abscessus lung infection eradication was not achieved, but improvements in selected qualify of life domains, lung function and 6MWD were observed during the study. Inhaled NO was well tolerated at 160 p.p.m. Dosing at 240 p.p.m. was stopped due to adverse symptoms, although methemoglobin levels remained within safety thresholds. In vitro susceptibility tests showed a dose-dependent NO effect on M. abscessus susceptibility and significant heterogeneity in response between M. abscessus clinical isolates. The patient’s isolate was found to be the least susceptible strain in vitro. Conclusion. These results demonstrate heterogeneity in M. abscessus susceptibility to NO and suggest that longer treatment regimens could be required to see the reduction or eradication of more resistant pulmonary strains. Kristijan Bogdanovski, Trisha Chau, Chevalia J. Robinson, Sandra D. MacDonald, Ann M. Peterson, Christine M. Mashek, Windy A. Wallin, Mark Rimkus, Frederick Montgomery, Joas Lucas da Silva, Shashank Gupta, Abdi Ghaffari, Adrian M. Zelazny and Kenneth N. Olivier Mon Aug 10 14:13:42 UTC 2020Z Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000143?TRACK=RSS The Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont – a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/. Nicholas R. Waters, Florence Abram, Fiona Brennan, Ashleigh Holmes and Leighton Pritchard Fri Jun 19 14:39:05 UTC 2020Z A comparison of methodologies for the staining and quantification of intracellular components of arbuscular mycorrhizal fungi in the root cortex of two varieties of winter wheat http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000083?TRACK=RSS Arbuscular mycorrhizal (AM) fungi are one of the most common fungal organisms to exist in symbiosis with terrestrial plants, facilitating the growth and maintenance of arable crops. Wheat has been studied extensively for AM fungal symbiosis using the carcinogen trypan blue as the identifying stain for fungal components, namely arbuscles, vesicles and hyphal structures. The present study uses Sheaffer blue ink with a lower risk as an alternative to this carcinogenic stain. Justification for this is determined by stained wheat root sections (n=120), with statistically significant increases in the observed abundance of intracellular root cortical fungal structures stained with Sheaffer blue ink compared to trypan blue for both Zulu (P=0.003) and Siskin (P=0.0003) varieties of winter wheat. This new alternative combines an improved quantification of intracellular fungal components with a lower hazard risk at a lower cost. Thomas I. Wilkes, Douglas J. Warner, Veronica Edmonds-Brown, Keith G. Davies and Ian Denholm Thu Nov 21 15:54:54 UTC 2019Z Characterization of the φCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota http://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000002?TRACK=RSS Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37 152 bp genome that closely resembles the temperate P. aeruginosa phage φCTX, a member of the P2 phage group. Dobby does not, however, encode for the cytotoxin CTX. Dobby’s genome was queried against publicly available bacterial sequences identifying 44 other φCTX-like prophages. These prophages are integrated within the genomes of P. aeruginosa strains from a variety of environments, including strains isolated from urine samples and other niches of the human body. Phylogenetic analysis suggests that the temperate φCTX phage species is widespread. With the isolation of Dobby, we now have evidence that phages are members of the kidney stone microbiota. Further investigation, however, is needed to determine their abundance and diversity within these communities. Genevieve Johnson, Alan J. Wolfe and Catherine Putonti Wed Mar 20 09:56:54 UTC 2019Z