Microbiology - Journal Articles

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    Bioactivity screening and genomic analysis reveals deep-sea fish microbiome isolates as sources of novel antimicrobials
    (MDPI, 2023) Uniacke-Lowe, Shona; Collins, Fergus W. J.; Hill, Colin; Ross, R. Paul; Science Foundation Ireland
    With the increase in antimicrobial resistance and the subsequent demand for novel therapeutics, the deep-sea fish microbiome can be a relatively untapped source of antimicrobials, including bacteriocins. Previously, bacterial isolates were recovered from the gut of deep-sea fish sampled from the Atlantic Ocean.In this study, we used in vitro methods to screen a subset of these isolates for antimicrobial activity, and subsequently mined genomic DNA from isolates of interest for bacteriocin and other antimicrobial metabolite genes. We observed antimicrobial activity against foodborne pathogens, including Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis and Micrococcus luteus. In total, 147 candidate biosynthetic gene clusters were identified in the genomic sequences, including 35 bacteriocin/RiPP-like clusters. Other bioactive metabolite genes detected included non-ribosomal peptide synthases (NRPS), polyketide synthases (PKS; Types 1 and 3), beta-lactones and terpenes. Moreover, four unique bacteriocin gene clusters were annotated and shown to encode novel peptides: a class IIc bacteriocin, two class IId bacteriocins and a class I lanthipeptide (LanM subgroup). Our dual in vitro and in silico approach allowed for a more comprehensive understanding of the bacteriocinogenic potential of these deep-sea isolates and an insight into the antimicrobial molecules that they may produce.
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    Bovine mastitis is a polymicrobial disease requiring a polydiagnostic approach
    (Elsevier Ltd, 2019) Angelopoulou, Angeliki; Holohan, Ross; Rea, Mary C.; Warda, Alicja K.; Hill, Colin; Science Foundation Ireland
    Bovine mastitis, an inflammation of the udder, is associated with increases in milk somatic cell count usually resulting from bacterial infection. We analysed 50 mastitic milk samples via cultivation, 16S rRNA sequencing and a combination of the two (culturomics) to define the complete microbial content of the milk. Most samples contained over 10,000 cfu mL−1 total bacterial counts including isolates that were haemolysin positive (n = 36). Among colonies isolated from blood agar plates, Streptococcus uberis was dominant (11/50) followed by Streptococcus dysgalactiae (6/50), Pseudomonas (6/50), Enterococcus faecalis (6/50), Escherichia coli (6/50), Staphylococcus argenteus (4/50), Bacillus (4/50) and Staphylococcus aureus (2/50). 16S rRNA profiling revealed that amplicons were dominated by Rhodococcus, Staphylococcus, Streptococcus and Pseudomonas. A higher inter-sample diversity was noted in the 16S rRNA readouts, which was not always reflected in the plating results. The combination of the two methods highlights the polymicrobial complexity of bovine mastitis. © 2019 Elsevier Ltd
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    Analysis of selection methods to develop novel phage therapy cocktails against antimicrobial resistant clinical isolates of bacteria
    (Frontiers Media S.A., 2021) Haines, Melissa E. K.; Hodges, Francesca E.; Nale, Janet Y.; Mahony, Jennifer; van Sinderen, Douwe; Kaczorowska, Joanna; Alrashid, Bandar; Akter, Mahmuda; Brown, Nathan; Sauvageau, Dominic; Sicheritz-Pontén, Thomas; Thanki, Anisha M.; Millard, Andrew D.; Galyov, Edouard E.; Clokie, Martha R. J.; National Institute for Health and Care Research; Ministry of Education in Saudi Arabia
    Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) associated sepsis are E. coli and Klebsiella along with Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which are featured on the WHO priority pathogens list as “critical” for research. Bacteriophages (phages), as viruses that can infect and kill bacteria, could provide an effective tool to tackle these AMR strains. There is currently no “gold standard” for developing a phage cocktail. Here we describe a novel approach to develop an effective phage cocktail against a set of ESBL-producing E. coli and Klebsiella largely isolated from patients in United Kingdom hospitals. By comparing different measures of phage efficacy, we show which are the most robust, and suggest an efficient screening cascade that could be used to develop phage cocktails to target other AMR bacterial species. A target panel of 38 ESBL-producing clinical strains isolated from urine samples was collated and used to test phage efficacy. After an initial screening of 68 phages, six were identified and tested against these 38 strains to determine their clinical coverage and killing efficiency. To achieve this, we assessed four different methods to assess phage virulence across these bacterial isolates. These were the Direct Spot Test (DST), the Efficiency of Plating (EOP) assay, the planktonic killing assay (PKA) and the biofilm assay. The final ESBL cocktail of six phages could effectively kill 23/38 strains (61%), for Klebsiella 13/19 (68%) and for E. coli 10/19 (53%) based on the PKA data. The ESBL E. coli collection had six isolates from the prevalent UTI-associated ST131 sequence type, five of which were targeted effectively by the final cocktail. Of the four methods used to assess phage virulence, the data suggests that PKAs are as effective as the much more time-consuming EOPs and data for the two assays correlates well. This suggests that planktonic killing is a good proxy to determine which phages should be used in a cocktail. This assay when combined with the virulence index also allows “phage synergy” to inform cocktail design.
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    METAnnotatorX2: a comprehensive tool for deep and shallow metagenomic data set analyses
    (American Society for Microbiology, 2021) Milani, Christian; Lugli, Gabriele A.; Fontana, Federico; Mancabelli, Leonardo; Alessandri, Giulia; Longhi, Giulia; Anzalone, Rosaria; Viappiani, Alice; Turroni, Francesca; van Sinderen, Douwe; Ventura, Marco; Mani Arumugam; Science Foundation Ireland; Fondazione Cariparma; GenProbio srl; Università degli Studi di Parma
    The use of bioinformatic tools for read-based taxonomic and functional analyses of metagenomic data sets, including their assembly and management, is rather fragmentary due to the absence of an accepted gold standard. Moreover, most currently available software tools need input of millions of reads and rely on approximations in data analysis in order to reduce computing times. These issues result in suboptimal results in terms of accuracy, sensitivity, and specificity when used either for the reconstruction of taxonomic or functional profiles through read analysis or analysis of genomes reconstructed by metagenomic assembly. Moreover, the recent introduction of novel DNA sequencing technologies that generate long reads, such as Nanopore and PacBio, represent a valuable data resource that still suffers from a lack of dedicated tools to perform integrated hybrid analysis alongside short read data. In order to overcome these limitations, here we describe a comprehensive bioinformatic platform, METAnnotatorX2, aimed at providing an optimized user-friendly resource which maximizes output quality, while also allowing user-specific adaptation of the pipeline and straightforward integrated analysis of both short and long read data. To further improve performance quality and accuracy of taxonomic assignment of reads and contigs, custom preprocessed and taxonomically revised genomic databases for viruses, prokaryotes, and various eukaryotes were developed.The performance of METAnnotatorX2 was tested by analysis of artificial data sets encompassing viral, archaeal, bacterial, and eukaryotic (fungal) sequence reads that simulate different biological matrices. Moreover, real biological samples were employed to validate in silico results.
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    COVID‐19 pandemic and allergen immunotherapy - an EAACI survey
    (John Wiley & Sons, Inc., 2021-03-02) Pfaar, Oliver; Agache, Ioana; Bonini, Matteo; Brough, Helen Annaruth; Chivato, Tomás; Del Giacco, Stefano R.; Gawlik, Radoslaw; Gelincik, Aslı; Hoffmann‐Sommergruber, Karin; Jutel, Marek; Klimek, Ludger; Knol, Edward F.; Lauerma, Antti; Ollert, Markus; O’Mahony, Liam; Mortz, Charlotte G.; Palomares, Oscar; Riggioni, Carmen; Schwarze, Jürgen; Skypala, Isabel; José Torres, María; Untersmayr, Eva; Walusiak‐Skorupa, Jolanta; Chaker, Adam; Giovannini, Mattia; Heffler, Enrico; Jensen‐Jarolim, Erika; Quecchia, Cristina; Sandoval‐Ruballos, Mónica; Sahiner, Umit; Tomić Spirić, Vesna; Alvaro‐Lozano, Montserrat
    Background: As in many fields of medical care, the coronavirus disease 2019 (COVID-19) resulted in an increased uncertainty regarding the safety of allergen immunotherapy (AIT). Therefore, the European Academy of Allergy and Clinical Immunology (EAACI) aimed to analyze the situation in different countries and to systematically collect all information available regarding tolerability and possible amendments in daily practice of sublingual AIT (SLIT), subcutaneous AIT (SCIT) for inhalant allergies and venom AIT. Methods: Under the framework of the EAACI, a panel of experts in the field of AIT coordinated by the Immunotherapy Interest Group set-up a web-based retrospective survey (SurveyMonkey®) including 27 standardized questions on practical and safety aspects on AIT in worldwide clinical routine. Results: 417 respondents providing AIT to their patients in daily routine answered the survey. For patients (without any current symptoms to suspect COVID-19), 60% of the respondents informed of not having initiated SCIT (40% venom AIT, 35% SLIT) whereas for the maintenance phase of AIT, SCIT was performed by 75% of the respondents (74% venom AIT, 89% SLIT). No tolerability concern arises from this preliminary analysis. 16 physicians reported having performed AIT despite (early) symptoms of COVID-19 and/or a positive test result for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Conclusions: This first international retrospective survey in atopic diseases investigated practical aspects and tolerability of AIT during the COVID-19 pandemic and gave no concerns regarding reduced tolerability under real-life circumstances. However, the data indicate an undertreatment of AIT, which may be temporary, but could have a long-lasting negative impact on the clinical care of allergic patients.