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Articles by Patrick Munk
Starstruck og med tobakshunger i Melbourne: Hun ændrede min forståelse af liv
Som de fleste andre dage i 2018 hoppede jeg af bussen i Kongens Lyngby ved et af stoppestederne på Danmarks Tekniske Universitet. Derfra tog autopiloten over og førte mig til mit kontor. Her arbejdede jeg som nyuddannet forsker (ph.d.), primært med at undersøge bakterier i svinelort. Hvad, jeg troede, skulle blive en ordinær dag med møder, data-analyse og rygepauser, blev pludselig meget mere spændende. En mail tikkede ind i fra selveste professor Jillian Fiona Banfield.
Unveiling the global urban virome through wastewater metagenomics
Five years on, Google DeepMind’s AlphaFold shows why science may be AI’s killer app While many businesses continue to seek AI’s killer app, biochemists have already found it. That application is protein folding. This week marks the …
Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes
Antimicrobial resistance genes (ARGs) have rapidly emerged and spread globally, but the pathways driving their spread remain poorly understood. We analyzed 1240 sewage samples from 351 cities across 111 countries, comparing ARGs known to be mobilized with those identified through functional meta- genomics (FG).
Fra svinestalden til tv-skærmen: Sådan ser dagligdagen ud for forsker i mikrobiologi
Jeg har oplevet, at folk omkring mig har vidt forskellige indtryk af, hvad mit arbejde som forsker går ud på. Studerende, venner, kollegaer og familie ser hver især en lille bid af mig, og tænker nok, at netop dén må være repræsentativ for, ‘hvad en forsker går og laver’. Der er dog ikke nogen enkel opgave, som kan give et retvisende billede, for en forsker løser en bred vifte af opgaver.
Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa
Loading metrics Open Access Peer-reviewed Research Article Citation: Smith AM, Ramudzulu M, Munk P, Avot BJP, Esterhuyse KCM, van Blerk N, et al. (2024) Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa. PLoS ONE 19(8): e0309409.
Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome
Abstract The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is essential to identify which pairs of ARGs co-occur. Given the wealth of NGS data available in public repositories, we have investigated the correlation between ARG abundances in a collection of 214,095 metagenomic datasets.
Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering - Communications Biology
Global sewage dataset Samples were collected and handled as part of the Global Sewage project2,35 . In brief, untreated sewage samples were collected before the inlet to the wastewater treatment plant at sample sites. DNA was extracted and fragmented from the untreated sewage and libraries were sequenced using Illumina paired-end sequencing to an average sequencing depth of approximately 42 mio reads.
Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome
PLOS ONE, Mar 2023 This is a preview of a remote PDF: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0283676&type=printable Line Jensen Ostenfeld, Patrick Munk, Frank M. Aarestrup, Saria Otani. , PLOS ONE, 2023, Volume 18, Issue 3, DOI: 10.1371/journal.pone.0283676
Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance - Nature Communications
Correction to: Nature Communications https://doi.org/10.1038/s41467-022-34312-7, published online 01 December 2022 In this article, the author name Antoinette Ngandjio was incorrectly written as Antoinette Ngandijo.
Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome
New Results doi: https://doi.org/10.1101/2022.12.19.519133 Abstract The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is essential to identify which pairs of ARGs co-occur.
Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance - Nature Communications
Sampling, DNA-purification, and sequencing Collection of sewage from global sites, DNA-purification, and sequencing were organized and conducted similarly to the previous study7. Briefly, on request, empty bottles were shipped to worldwide project partners, who were briefed on sample inclusion criteria. Only samples of raw, untreated, urban sewage prior to any processing were requested.
A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome
Loading metrics Abstract The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods, as well as a deeper understanding of how antimicrobial resistance genes (ARGs) have been transmitted around the world. The large pool of sequencing data available in public repositories provides an excellent resource for monitoring the temporal and spatial dissemination of AMR in different ecological settings.
Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study
Summary Background Semi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy and speed by sequencing the microbiota and resistome directly from urine. We aimed to compare metagenomics to culture for semi-quantitative pathogen and resistome detection from urine.
A curated data resource of 214K metagenomes for characterization of the global resistome
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A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds
Objectives Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring. Methods We evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E.
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