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A Sustainable Future

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A Sustainable Future
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To highlight the vital role microbiology plays in delivering on the UN Sustainable Development Goals (SDGs), we have created a collection of must-read research on three critical aspects of the SDGs: antimicrobial resistance, soil health, and the circular economy.

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21 - 40 of 107 results

    • Shotgun proteomic analysis of nanoparticle-synthesizing in response to platinum and palladium

      Platinum and palladium are much sought-after metals of critical global importance in terms of abundance and availability. At the nano-scale these metals are of even higher value due to their catalytic abilities for industrial applications. is able to capture ionic forms of both of these metals, reduce them and synthesize elemental nanoparticles. Despite this ability, very little is known about the biological pathways involved in the formation of these nanoparticles. Proteomic analysis of in response to platinum and palladium has highlighted those proteins involved in both the reductive pathways and the wider stress-response system. A core set of 13 proteins was found in both treatments and consisted of proteins involved in metal transport and reduction. There were also seven proteins that were specific to either platinum or palladium. Overexpression of one of these platinum-specific genes, a NiFe hydrogenase small subunit (Dde_2137), resulted in the formation of larger nanoparticles. This study improves our understanding of the pathways involved in the metal resistance mechanism of and is informative regarding how we can tailor the bacterium for nanoparticle production, enhancing its application as a bioremediation tool and as a way to capture contaminant metals from the environment.

    • Restoring the activity of the antibiotic aztreonam using the polyphenol epigallocatechin gallate (EGCG) against multidrug-resistant clinical isolates of

      is an important Gram-negative pathogen that is intrinsically multidrug-resistant (MDR) and frequently associated with healthcare-associated outbreaks. With increasing resistance to antibiotics and with very few novel drugs under development, clinicians often use combinations to treat critically ill patients.

      The aim of this study was to evaluate the ability of epigallocatechin (EGCG) to restore the activity of aztreonam against clinical MDR strains of .

      Checkerboard and time–kill kinetic assays were performed to assess synergy and the model of infection was used to test the efficacy of the combination . Accumulation assays were performed to gain insight into the mechanism of action.

      The results demonstrate that synergy between aztreonam and EGCG exists [fractional inhibitory concentration indices (FICIs) 0.02-0.5], with the combination affording significantly (=<0.05) enhanced bacterial killing, with a >3 log reduction in colony-forming units ml at 24 h. EGCG was able to restore susceptibility to aztreonam to a level equal to or below the breakpoint set by the European Committee for Antimicrobial Susceptibility Testing. In , the combination was superior to monotherapy, with increased larval survival observed (94 % vs ≤63 %). We also demonstrated the relatively low toxicity of EGCG to human keratinocytes and larvae. Accumulation assay data suggest that the mechanism of synergy may be due to EGCG increasing the uptake of aztreonam.

      EGCG was able to restore the activity of aztreonam against MDR . The data presented support further evaluation of the aztreonam–EGCG combination and highlight its potential for use in clinical medicine.

    • Isolation and characterization of novel soil- and plant-associated bacteria with multiple phytohormone-degrading activities using a targeted methodology

      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 . 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.

    • activities of six antifungal agents and their combinations against spp.

      To assess activities of six antifungal agents (amphotericin B, itraconazole, voriconazole, posaconazole, caspofungin and terbinafine) and the combined effects of eight pairs of them (caspofungin or terbinafine with amphotericin B, itraconazole, voriconazole or posaconazole) against 22 isolates of spp.

      The broth microdilution method drafted by the Clinical and Laboratory Standards Institute and the checkerboard method were used in this study to evaluate activities of antifungal drugs both alone and in combination against spp.

      Amphotericin B and triazoles exhibited lower geometric mean, MIC50 and MIC90 than caspofungin and terbinafine. Besides, all the paired drugs displayed varying degrees of synergism, with the interactions between caspofungin and itraconazole ranking first (86.36 %).

      Our study illustrated varying degrees of synergism between caspofungin or terbinafine and itraconazole, voriconazole, posaconazole or amphotericin B towards spp., which could be a reference for the clinical treatment of spp. infections.

    • activity of mecillinam and nitroxoline against – re-purposing old antibiotics in the multi-drug resistance era

      In 2018, the European Centre for Disease Prevention and Control reported the first cases of extensively drug-resistant infections in Europe. Seeking new options for antimicrobial therapy we investigated the susceptibility of to nitroxoline (NIT) and mecillinam (MCM), both of which are currently only indicated to treat uncomplicated urinary tract infections. Clinical isolates with non-susceptibility to penicillin from two German medical centres were included ( =27). Most isolates were also non-susceptible to a range of other anti-gonococcal antimicrobials (cefotaxime, ciprofloxacin, azithromycin, tetracycline). All isolates were further characterized by multi-locus sequence typing. MICs of penicillin and cefotaxime were determined by agar gradient diffusion. Production of penicillinase was tested by cefinase disk test. Susceptibility of MCM was investigated by agar dilution, NIT by agar dilution and disk diffusion. Penicillin MICs ranged from 0.125 to 64 mg l and MICs of cefotaxime ranged from < 0.016 to 1 mg l . Five isolates were penicillinase-producers. MICs of MCM ranged from 16 to > 128 mg l whereas MICs of NIT ranged from 0.125 to 2 mg l . NIT disk diffusion (median zone diameter 32 mm) correlated well with results from agar dilution. We demonstrated excellent activity of NIT against clinical isolates with non-susceptibility to standard anti-gonococcal antibiotics. MCM activity was unsatisfactory. Correlation of agar dilution and disk diffusion in NIT susceptibility testing is an important aspect with potential clinical implications.

    • efficacy of sodium selenite in reducing toxin production, spore outgrowth and antibiotic resistance in hypervirulent

      This study investigated the efficacy of the essential mineral, selenium (sodium selenite), in reducing the toxin production, spore outgrowth and antibiotic resistance of .

      Two hypervirulent isolates were cultured in brain heart infusion broth with and without a sub-minimum inhibitory concentration (sub-MIC) of sodium selenite, and the supernatant and bacterial pellet were harvested for total toxin quantitation and RT-qPCR analysis of toxin-encoding genes, respectively. Additionally, isolates were cultured in brain heart infusion broth containing 0.5 or 1× the minimum inhibitory concentration (MIC) of either ciprofloxacin or vancomycin with or without sub-MICs of sodium selenite. Further, the effect of sodium selenite on germination and spore outgrowth was also determined by exposing spores to a sub-MIC of sodium selenite in a germination medium and measuring the germination and outgrowth by measuring the optical density at 600  nm.

      Sodium selenite significantly reduced toxin synthesis, cytotoxicity and spore outgrowth. Further, the expression of the toxin production genes, and , was downregulated in the presence of sodium selenite, while sodium selenite significantly increased the sensitivity of to ciprofloxacin , but not vancomycin, as revealed by decreased bacterial growth in samples containing ciprofloxacin+selenium compared to the antibiotic control. Although the sub-MIC of sodium selenite did not inhibit spore germination, it was capable of completely inhibiting spore outgrowth.

      Our results suggest that sodium selenite could potentially be used to control and indicate that future studies are warranted.

    • Rapid antimicrobial susceptibility tests for sepsis; the road ahead

      Current methods for antimicrobial susceptibility testing (AST) are too slow to affect initial treatment decisions in the early stages of sepsis, when the prescriber is most concerned to select effective therapy immediately, rather than finding out what will not work 1 or 2 days later. There is a clear need for much faster differentiation between viral and bacterial infection, and AST, linked to earlier aetiological diagnosis, without sacrificing either the accuracy of quantitative AST or the low cost of qualitative AST. Truly rapid AST methods are eagerly awaited, and there are several candidate technologies that aim to improve the targeting of our limited stock of effective antimicrobial agents. However, none of these technologies are approaching the point of care and nor can they be described as truly culture-independent diagnostic tests. Rapid chemical and genomic methods of resistance detection are not yet reliable predictors of antimicrobial susceptibility and often rely on prior bacterial isolation. In order to resolve the trade-off between diagnostic confidence and therapeutic efficacy in increasingly antimicrobial-resistant sepsis, we propose a series of three linked decision milestones: initial clinical assessment (e.g. qSOFA score) within 10 min, initial laboratory tests and presumptive antimicrobial therapy within 1 h, and definitive AST with corresponding antimicrobial amendment within an 8 h window (i.e. the same working day). Truly rapid AST methods therefore must be integrated into the clinical laboratory workflow to ensure maximum impact on clinical outcomes of sepsis, and diagnostic and antimicrobial stewardship. The requisite series of development stages come with a substantial regulatory burden that hinders the translation of innovation into practice. The regulatory hurdles for the adoption of rapid AST technology emphasize technical accuracy, but progress will also rely on the effect rapid AST has on prescribing behaviour by physicians managing the care of patients with sepsis. Early adopters in well-equipped teaching centres in close proximity to large clinical laboratories are likely to be early beneficiaries of rapid AST, while simplified and lower-cost technology is needed to support poorly resourced hospitals in developing countries, with their higher burden of AMR. If we really want the clinical laboratory to deliver a specific, same-day diagnosis underpinned by definitive AST results, we are going to have to advocate more effectively for the clinical benefits of bacterial detection and susceptibility testing at critical decision points in the sepsis management pathway.

    • Semisynthetic eugenol derivatives as antifungal agents against dermatophytes of the genus

      Eugenol, the main component of clove bud essential oil () has been linked to antimicrobial, anti-inflammatory, insecticidal and immunomodulatory properties. The purpose of this study was to evaluate the antifungal and cytotoxic activity of eugenol, the essential oil of , and some semisynthetic derivatives of eugenol against dermatophytes of the genus .

      We evaluated the antifungal effect of the compounds, determining the minimum inhibitory concentrations (MICs) by the microdilution method and the minimum fungicidal concentrations by cultures from the inhibitions. Additionally, the inhibition of the radial growth of the mycelium of the dermatophyte fungi was tested by poisoned substrate. Cytotoxicity was measured by the colorimetric method on Vero cells.

      All of the eugenol compounds tested exhibited antifungal properties, showing MICs of 62.5–500 µg ml , determined within three dermatophyte species: and . Among these derivatives, methyl isoeugenol, at concentrations of 300 and 100 µg ml, was found to completely inhibit (100 %) radial growth of the mycelium of all three species after 20 days of treatment. Additionally, phenotypic variations related to the decrease in pigment production of were observed after treatment with O-ethyl and O-butyl isoeugenol derivatives. Meanwhile, all of the tested (iso)eugenol molecules exhibited moderate toxicity in Vero cells [50 % cytotoxic concentration (the concentration required for a 50 % reduction in cell viability; CC): 54.06–265.18 µg ml ).

      The results suggest that the semisynthetic eugenol derivatives (SEDs) show promising antifungal activity and selectivity against dermatophyte fungi.

    • Casing microbiome dynamics during button mushroom cultivation: implications for dry and wet bubble diseases

      The casing material required in mushroom cultivation presents a very rich ecological niche, which is inhabited by a diverse population of bacteria and fungi. In this work three different casing materials, blonde peat, black peat and a 50 : 50 mixture of both, were compared for their capacity to show a natural suppressive response against dry bubble, Lecanicillium fungicola (Preuss) Zare and Gams, and wet bubble, Mycogone perniciosa (Magnus) Delacroix. The highest mushroom production was collected from crops cultivated using the mixed casing and black peat, which were not significantly different in yield. However, artificial infection with mycoparasites resulted in similar yield losses irrespective of the material used, indicating that the casing materials do not confer advantages in disease suppression. The composition of the microbiome of the 50 : 50 casing mixture along the crop cycle and the compost and basidiomes was evaluated through next-generation sequencing (NGS) of the V3–V4 region of the bacterial 16S rRNA gene and the fungal ITS2 region. Once colonized by Agaricus bisporus, the bacterial diversity of the casing microbiome increased and the fungal diversity drastically decreased. From then on, the composition of the casing microbiome remained relatively stable. Analysis of the composition of the bacterial microbiome in basidiomes indicated that it is highly influenced by the casing microbiota. Notably, L. fungicola was consistently detected in uninoculated control samples of compost and casing using NGS, even in asymptomatic crops. This suggests that the naturally established casing microbiota was able to help to suppress disease development when inoculum levels were low, but was not effective in suppressing high pressure from artificially introduced fungal inoculum. Determination of the composition of the casing microbiome paves the way for the development of synthetic casing communities that can be used to investigate the role of specific components of the casing microbiota in mushroom production and disease control.

    • Alginate genes are required for optimal soil colonization and persistence by Pseudomonas fluorescens Pf0-1

      Pseudomonas fluorescens strains are important candidates for use as biological control agents to reduce fungal diseases on crop plants. To understand the ecological success of these bacteria and for successful and stable biological control, determination of how these bacteria colonize and persist in soil environments is critical. Here we show that P. fluorescens Pf0-1 is negatively impacted by reduced water availability in soil, but adapts and persists. A pilot transcriptomic study of Pf0-1 colonizing moist and dehydrated soil was used to identify candidate genetic loci, which could play a role in the adaptation to dehydration. Genes predicted to specify alginate production were identified and chosen for functional evaluation. Using deletion mutants, predicted alginate biosynthesis genes were shown to be important for optimal colonization of moist soil, and necessary for adaptation to reduced water availability in dried soil. Our findings extend in vitro studies of water stress into a more natural system and suggest alginate may be an essential extracellular product for the lifestyle of P. fluorescens when growing in soil.

    • Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes

      We examined whether genomic surveillance of Escherichia coli in wastewater could capture the dominant E. coli lineages associated with bloodstream infection and livestock in the East of England, together with the antibiotic-resistance genes circulating in the wider E. coli population. Treated and untreated wastewater was taken from 20 municipal treatment plants in the East of England, half in direct receipt of acute hospital waste. All samples were culture positive for E. coli , and all but one were positive for extended-spectrum β-lactamase (ESBL)-producing E. coli . The most stringent wastewater treatment (tertiary including UV light) did not eradicate ESBL- E. coli in 2/3 cases. We sequenced 388 E. coli (192 ESBL, 196 non-ESBL). Multilocus sequence type (ST) diversity was similar between plants in direct receipt of hospital waste versus the remainder (93 vs 95 STs, respectively). We compared the genomes of wastewater E. coli with isolates from bloodstream infection (n=437), and livestock farms and retail meat (n=431) in the East of England. A total of 19/20 wastewater plants contained one or more of the three most common STs associated with bloodstream infection (ST131, ST73, ST95), and 14/20 contained the most common livestock ST (ST10). In an analysis of 1254 genomes (2 cryptic E. coli were excluded), wastewater isolates were distributed across the phylogeny and intermixed with isolates from humans and livestock. Ten bla CTX-M elements were identified in E. coli isolated from wastewater, together with a further 47 genes encoding resistance to the major antibiotic drug groups. Genes encoding resistance to colistin and the carbapenems were not detected. Genomic surveillance of E. coli in wastewater could be used to monitor new and circulating lineages and resistance determinants of public-health importance.

    • Molecular characterization and antifungal susceptibility testing of from blood samples – an Iranian multicentre study and a review of the literature

      . Identification of the emerging yeast species among presumptively identified Iranian isolates.

      . Clinical species complex isolates from blood (=100; 46.9%), vaginal swabs (=20; 9.4%), bronchoalveolar lavage (=10; 4.7%) and sputum (=12; 5.6%) from 68 patients from Iran were investigated. Isolates were characterized by CHROMagar, multiplex PCRs, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), amplified fragment length polymorphism (AFLP) fingerprinting, internal transcribed spacer (ITS)/large subunit (LSU) rDNA and / sequencing, and the European Committee on Antimicrobial Susceptibility Testing broth microdilution method. A comprehensive literature review was conducted and all the relevant clinical and microbiological data were collected.

      . Four isolates were recovered from blood samples of three subjects and were all consistently identified by nine-plex PCR, Bruker MALDI-TOF MS, and LSU and ITS rDNA sequencing. AFLP genotyping clustered the isolates into two groups. Sequencing of the and hotspots showed no accountable amino acid substitutions. All isolates were susceptible to amphotericin B, fluconazole, itraconazole, posaconazole, voriconazole, anidulafungin and micafungin.

      . In total, 4 out of 213 clinical species complex candidemia isolates were . Improvement of the BioMerieux Vitek MS database is required to accurately identify and it is advised to alternatively use CHROMagar and/or PCR-based techniques. As other species within the clade may cause infection and showed high MIC values for antifungals, inclusion of their spectra into the MALDI-TOF MS database seems relevant. Due to developing resistance to fluconazole and insufficient efficacy of caspofungin, the combination of catheter removal plus treatment with caspofungin, or voriconazole, or micafungin might be effective for patients.

    • Streptomyces fodineus sp. nov., an actinobacterium with antifungal activity isolated from mine area soil

      A novel actinobacterial strain producing an antifungal substance was isolated from a sample of acidic mine area soil, and its taxonomic position was evaluated. The novel strain, designated TW1S1, formed white-grey aerial mycelium and yellow substrate mycelium on oatmeal agar. Growth occurred at 10–45 °C (optimum, 30 °C), pH 4–9 (pH 6–7) and in the presence of up to 8 % (w/v) NaCl. Melanin was produced on peptone–yeast extract–iron agar. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that the novel strain should be assigned to the genus Streptomyces , and the closest species was Streptomyces puniciscabiei S77 with 99.1 % sequence similarity, which was followed by Streptomyces durhamensis NRRL B-3309 (99.0 %), Streptomyces filipinensis NBRC 12860 (98.9 %) and Streptomyces yaanensis Z4 (98.7 %). The chemotaxonomic properties were consistent with those of Streptomyces . ll-Diaminopimelic acid was the diagnostic diamino acid, and alanine, glutamic acid and glycine were present in the peptidoglycan. The cell-wall hydrolysate also contained galactose, glucose, mannose and ribose. The predominant isoprenoid quinones were MK-9(H4) and MK-9(H6), the major polar lipids were phosphatidylglycerol and an unidentified phospholipid, and the main fatty acids were iso-C16 : 0 and anteiso-C15 : 0. However, strain TW1S1 could be distinguished from its neighbouring species by its phenotypic properties. In addition, the genome-based comparison with the closest species indicated that strain TW1S1 should be recognized as a separate species. The phylogenetic, phenotypic and chemotaxonomic as well as genomic evidence supported that TW1S1 represents a novel species of Streptomyces , for which the name Streptomyces fodineus sp. nov. is proposed (type strain, TW1S1 = KCTC 49013 = JCM 32404).

    • Use of whole genome sequencing in surveillance for antimicrobial-resistant Shigella sonnei infections acquired from domestic and international sources

      Shigella species are a major cause of gastroenteritis worldwide, and Shigella sonnei is the most common species isolated within the United States. Previous surveillance work in Pennsylvania documented increased antimicrobial resistance (AMR) in S. sonnei associated with reported illnesses. The present study examined a subset of these isolates by whole genome sequencing (WGS) to determine the relationship between domestic and international isolates, to identify genes that may be useful for identifying specific Global Lineages of S. sonnei and to test the accuracy of WGS for predicting AMR phenotype. A collection of 22 antimicrobial-resistant isolates from patients infected within the United States or while travelling internationally between 2009 and 2014 was chosen for WGS. Phylogenetic analysis revealed both international and domestic isolates were one of two previously defined Global Lineages of S. sonnei , designated Lineage II and Lineage III. Twelve of 17 alleles tested distinguish these two lineages. Lastly, genome analysis was used to identify AMR determinants. Genotypic analysis was concordant with phenotypic resistance for six of eight antibiotic classes. For aminoglycosides and trimethoprim, resistance genes were identified in two and three phenotypically sensitive isolates, respectively. This article contains data hosted by Microreact.

    • Antifungal susceptibilities, biofilms, phospholipase and proteinase activities in the Candida rugosa complex and Candida pararugosa isolated from tertiary teaching hospitals

      Purpose. Non-albicans Candida species have emerged as fungal pathogens that cause invasive infections, with many of these species displaying resistance to commonly used antifungal agents. This study was confined to studying the characteristics of clinical isolates of the C. rugosa complex and C. pararugosa species.

      Methodology. Seven isolates of the C. rugosa complex and one isolate of C. pararugosa were obtained from two tertiary referral hospitals in Malaysia. Their antifungal susceptibilities, biofilm, proteinase, phospholipase, esterase and haemolysin activities were characterized. Biofilms were quantified using crystal violet (CV) and tetrazolium (XTT) reduction assays at 1.5, 6, 18, 24, 48 and 72 h.

      Results/Key findings. The E-test antifungal tests showed that both species have elevated MICs compared to C. albicans and C. tropicalis. The highest biomass was observed in one of the C. rugosa isolates (0.237), followed by C. pararugosa (0.206) at 18 h of incubation. However, the highest bioactivity was observed in the C. rugosa ATCC 10571 strain at 24 h (0.075), followed by C. pararugosa at 48 h (0.048) and the same C. rugosa strain at 24 h (0.046), with P<0.05. All isolates exhibited high proteinase activity (+++) whereas six isolates showed very strong esterase activity (++++). All the isolates were alpha haemolytic producers. None of the isolates exhibited phospholipase activity.

      Conclusion. Elevated MICs were shown for the C. rugosa complex and C. pararugosa for commonly used antifungal drugs. Further studies to identify virulence genes involved in the pathogenesis and genes that confer reduced drug susceptibility in these species are proposed.

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