Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg

Browsing Posts in Workshops

In two weeks time, on the 15th of June, I will participate in a seminar organised by Landstingens nätverk för läkemedel och miljö (the Swedish county council network for pharmaceuticals and environment; the seminar will be held in Swedish) in Stockholm. I will give a talk on our proposed emission limits for antibiotics published last year (the paper is available here), but there will also be talks on wastewater treatment, sustainable pharmaceutical usage and environmental standards for pharmaceuticals. The full program can be found here, and you may register here until June 9. The seminar is free of charge.

And if you are interested in this, I can also recommend the webinar given by Healthcare Without Harm next week (on June 8), which will deal with sustainable procurement as a means to deal with pharmaceutical pollution in the environment. I will at least tune in to hear how the discussion goes here.

In March, I attended a workshop on the role of NGS technologies in the coordinated action plan against antimicrobial resistance, organised by JRC in Italy. I was, together with 14 other experts, invited to discuss where and how sequencing can be used to investigate and manage antibiotic resistance. The report from the workshop has just recently been published, and is available here. There will be follow-up activities on this workshop, which I also hope that I will be able to participate in, since this is an important and very interesting pet topic of mine.

Reference

  • Angers A, Petrillo P, Patak, A, Querci M, Van den Eede G: The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance. JRC Conference and Workshop Report, EUR 28619 (2017). doi: 10.2760/745099 [Link]
  • I will give a short talk on our findings related to antibiotic resistance associated with pharmaceutical production facilities in India at a one-hour webinar arranged by Healthcare Without Harm, taking place on Thursday, November 3rd, 10.00 CET. The webinar will discuss “hot-spot” environments in which antimicrobial resistance can emerge, such as areas in which there are poor pharmaceutical manufacturing practices, where expired or unused drugs are disposed of in an inappropriate way (i.e. by flushing them down the toilet or sink, or disposing them in household rubbish), and areas in which pharmaceuticals are used for aquaculture or agriculture. This is an important aspect of the resistance problem, but to date most of the actions taken to tackle the spread of AMR don’t take into account this aspect of antimicrobials released into the environment. The webinar is co-organised by HCWH Europe and HCWH Asia, and aims to raise awareness about the issue of AMR and its environmental impact. It features, apart from myself, Lucas Wiarda (Global Marketing Director & Head of Sustainable Antibiotics Program at DSM Sinochem Pharmaceuticals) and Sister Mercilyn Jabel (Pharmacist at Saint Paul Hospital Cavite, Philippines).

    Sign up here to learn about:

    • Antibiotic pollution and waste
    • Recent findings from India regarding antibiotic discharges in rivers from manufacturers and new mechanisms by which resistance spreads in the environment
    • Sustainable antibiotics – how to support the proper and effective use of antibiotics and their responsible production
    • How the pharmaceutical industry is addressing the environmental pollution that leads to AMR
    • The best practices in managing infectious waste at hospital level

    SBW2016

    Comments off

    Today the 15th Swedish Bioinformatics Workshop starts in Linköping. For the first time in many many years, I will not be there, which feels super-strange. (I even took part in organizing the workshop two years ago, in Gothenburg.) I would have thoroughly enjoyed the schedule (the workshops look amazing), and hope that everyone will have a very good time there without me. I do miss you! Please make sure I get another opportunity next year!

    I am part of the organizing committee for the newly invented annual meeting for GOTBIN – the Gothenburg Bioinformatics Network. We will arrange a meeting on December 6 to get the networking activities for 2017 kickstarted, and every bioinformatician in Gothenburg is invited!

    GOTBIN was launched to bridge and bring together all researchers in Gothenburg who fully or partially dealt with bioinformatics in their research. Through the network it should be possible to quickly find other local researchers tackling the same research problems as you are; to find appropriate resources to run your analyses; and to discuss research or infrastructure problems as they arise. To keep the network alive and kicking, it is crucial to keep relations active. Furthermore, it is also crucial to interact with key persons in the GOTBIN network to keep the lists of active researchers, resources and discussion forums up to date.

    To facilitate future communication, we invite everyone who works with bioinformatics in Gothenburg to participate in a get-together workshop. The purpose of this workshop is to find out who is working with what and where, and to better get to know each other. This is a great opportunity to meet your next collaboration partner, post-doc or supervisor! The event will take place in Birgit Thilander at Medicinareberget (just next to the large lecture hall Arvid Carlsson) on December 6th, from 9.00 to 12.00. Fika will be provided and we will arrange ice-breaker activities suitable for the number of participants, so please register at: https://goo.gl/forms/KYdiiZMBDf0F9hvp2 by the 16th of November.

    We hope to find everyone with a research interest in bioinformatics there and that this will be the launch of the next era of GOTBIN in 2017! See you there!

    I just want to highlight that the paper on strategies to improve database accuracy and usability we recently published in Proteomics (1) has been included in their most recent issue, which is a special issue focusing on Data Quality Issues in Proteomics. I highly recommend reading our paper (of course) and many of the other in the special issue. Happy reading!

    On another note, I will be giving a talk next Wednesday (October 5th) on a seminar day on next generation sequencing in clinical microbiology, titled “Antibiotic resistance in the clinic and the environment – There and back again“. You are very welcome to the lecture hall at floor 3 in our building at Guldhedsgatan 10A here in Gothenburg if you are interested! (Bear in mind though that it all starts at 8.15 in the morning.)

    Finally, it seems that I am going to the Next Generation Sequencing Congress in London this year, which will be very fun! Hope to see some of you dealing with sequencing there!

    References

    1. Bengtsson-Palme J, Boulund F, Edström R, Feizi A, Johnning A, Jonsson VA, Karlsson FH, Pal C, Pereira MB, Rehammar A, Sánchez J, Sanli K, Thorell K: Strategies to improve usability and preserve accuracy in biological sequence databases. Proteomics, 16, 18, 2454–2460 (2016). doi: 10.1002/pmic.201600034 [Paper link]

    I have been asked to give a short talk on the metals and biocides and antibiotic resistance co-selection conference I mentioned in February. My presentation will take place late Tuesday afternoon, and is entitled “Elucidating biocide and metal co-selection for antibiotic resistance in sewage treatment plants using metagenomics“. I hope to see you there!

    I have had the pleasure to be chosen as a speaker for next week’s (ten days from now) Swedish Bioinformatics Workshop. My talk is entitled “Turn up the signal – wipe out the noise: Gaining insights into bacterial community functions using metagenomic data“, and will largely deal with the same questions as my talk on EDAR3 in May this year. As then, the talk will highlight the some particular pitfalls related to interpretation of data, and exemplify how flawed analysis practices can result in misleading conclusions regarding community function, and use examples from our studies of environments subjected to pharmaceutical pollution in India, the effect of travel on the human resistome, and modern municipal wastewater treatment processes.

    The talk will take place on Thursday, September 24, 2015 at 16:30. The full program for the conference can be found here. And also, if you want a sneak peak of the talk, you can drop by on Friday 13.00 at Chemistry and Molecular Biology, where I will give a seminar on the same topic in the Monthly Bioinformatic Practical Meetings series.

    One of the highlights of the Swedish Bioinformatics Workshop 2014 was of course the dinner entertainment, a song specially crafted for the event. It has now, fortunately, been put online. For anyone who might not catch all the words, here’s the complete lyrics for the song (which is based on the song “Java Jive” in the Manhattan Transfer arrangement):

    The Bioinformatics ABC

    Grab your coffee
    Grab your tea
    Put down your spoon now and listen to me
    For the bioinformatics ABC
    Wake up, wake up, wake up, wake up, wake up
    (Boy)

    A for ABYSS
    B for BLAST
    And C for Clustal, though it’s not that fast
    Alternatives are Muscle and MAFFT
    ABYSS and BLAST and Clustal, Muscle, MAFFT
    (Yeah)

    D count reads with DESeq or E for EdgeR
    And F for FastQC and G for GLIMMER
    H for HMMER using Markov Chains
    (Explain)
    Hidden hidden Markov model

    I for Inchworm;
    Jellyfish
    Add Chrysalis and Butterfly and wish
    Assemble fast with a sound that goes swish
    Contig, contig, contig, contig, transcript
    (Girl)

    KBASE
    Lasergene
    And the ton of tools for metagenomics
    MEGAN, Megraft,
    MetaPhlan, MG-RAST, Meta-GeneMark
    And that’s just mentioning a few of them
    (Talk it boy)

    N for Newbler, old-school it is
    If you’re still using 454 it’s a bliss
    O for Oases, P for PyroNoise
    45-45-45-454-454

    Q is for Quake for that great quality
    And R is for all those neat statistics
    S for the Spades assembler, oh yeah

    T for TopHat
    U for Uclust
    V for Velvet

    There is Wham to align
    XMatchView to review
    And YASS to pursue
    (But do you)
    Know any tools beginning with Z?
    What?
    Yeah, Zorro, Zorro, Zorro
    Oh yeah

    I would like to bring your attention to that the abstract deadline for the Swedish Bioinformatics Workshop held in Gothenburg in October has been extended to September 15. So hurry on and contribute with your latest research, we look forward to get to know what you’re doing!