Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg

Browsing Posts in Thoughts

This morning as I was leaving my daughter at daycare, I got asked by one of the other kids at kindergarten what I do for work. Trying to communicate what you do as a researcher to a five-year-old is a quite interesting task. Five-year-olds are smart – but not very knowledgeable, which leads to very interesting turns to the conversation. Here’s the entire dialogue, transcribed from memory and translated to English:

– What do you do for work?
– I work at the hospital, but I’m not a doctor.
– So you are a physiologist?
– No, I am something called a researcher. I try to understand why bacteria turn evil and make us sick.
– Does someone need to do that?
– Not really. But if we can understand why bugs go bad, we may be able to be sick for much shorter in the future. Or perhaps not get sick at all.
– Okay. Isn’t that hard?
– Yes it is.
– Okay. Bye!

A few things I learned from this conversation: 1) explaining your research to young kids really makes you think about how to present what you do. 2) Kids really question the usefulness of your work (“Does someone need to do that?”). This is actually quite cool, because you need to think about how useful your work really is, in terms that a five-year-old can understand. 3) Society is awesome! To some extent, my work is a “luxury job”, i.e. maybe someone does not need to do my work, but it something we can afford because we share responsibilities and work together as a society, improving (hopefully) the world for all of us. In some sense, nobody strictly needs to be building houses; everyone could just build their own cottage. But building houses improve the standards for everyone, setting time aside for curing diseases, making music, researching microbial interactions, gardening, coffee roasting… Society is awesome.

First of all, I am happy to announce that the webinar I participated in on the (un)recognised pathways of AMR: Air pollution and food, organised by Healthcare Without Harm is now put online so that you can view it, in case you missed out on this event. To be honest it is probably not one of my best public appearances, but the topic is highly interesting.

Second, next week I am taking part in Vetenskapsfestivalen – the Science Festival in Gothenburg. Specifically, I will be on of the researchers participating in the Science Roulette, taking place in the big ferris wheel at Liseberg. This will take place between 17.00 and 18.00 on May 11th. The idea is that people will be paired with researchers in diverse subjects, of which I am one, and then have a 20 minute chat while the wheel is spinning. Sounds like potential for lot of fun, and I hope to see you there! I will discuss antibiotic resistance, and for how much longer we can trust that our antibiotics will work.

Sorry for the late notice, but if you have half an hour to spare later today I will discuss our findings on resistance genes in Beijing air on a webinar organised by Healthcare Without Harm on “The (un)recognised pathways of AMR: Air pollution and food“. Tune in a few minutes before 16.00 CEST!

I am happy to announce that the opinion/review piece I wrote for Current Opinion in Food Science has been published. The paper (1) extends on some of my thoughts on how high-throughput sequencing and metagenomics can aid in risk assessment of antibiotic resistant bacteria that I outlined in my PhD thesis (2), but specifically focuses on the food supply chain and its role in resistance dissemination and selection.

In the paper, I argue for that the food supply chain is a special type of setting in the resistance puzzle, as it not only serves as a connection between environmental habitats for bacteria and humans, but also sometimes presents a substantial selection for resistance, due to use of antibiotics in agri- and aquaculture. International food standards are clear that both selection and dissemination of foodborne resistance should be considered in the risk analysis of food production (3). However, the current main use of DNA sequencing in food safety is whole genome sequencing to delineate which specific strains that are involved in foodborne disease outbreaks, including the resistance factors they may carry (4,5). Further, I argue that while shotgun metagenomics could be used to screen samples for a large number of genes involved in resistance and virulence in the food supply chain, it would at present be very costly and therefore of doubtful benefit to employ in routine screening programs. Still, metagenomics can contribute knowledge that can be used in quantitative risk assessment of antibiotic resistance in the food supply chain.

The entire paper can be read here.

References

  1. Bengtsson-Palme J: Antibiotic resistance in the food supply chain: Where can sequencing and metagenomics aid risk assessment? Current Opinion in Food Science, in press (2017). doi: 10.1016/j.cofs.2017.01.010 [Paper link]
  2. Bengtsson-Palme J: Antibiotic resistance in the environment: a contribution from metagenomic studies. Doctoral thesis (medicine), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 2016. [Link]
  3. Codex Alimentarius Commission: Guidelines for risk analysis of foodborne antimicrobial resistance. Food and Agriculture Organization of the United Nations & World Health Organization2011. [Link]
  4. Franz E, Gras LM, Dallman T: Significance of whole genome sequencing for surveillance, source attribution and microbial risk assessment of foodborne pathogens. Current Opinion in Food Science, 8, 74-79 (2016). doi: 10.1016/j.cofs.2016.04.004
  5. Stasiewicz MJ, Bakker den HC, Wiedmann M: Genomics tools in microbial food safety. Current Opinion in Food Science, 4, 105-110 (2015). doi: 10.1016/j.cofs.2015.06.002

So 2017 has begun, and this year will bring new challenges and exciting opportunities. First of all, my application for a 3.5 year grant from the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS) to go to Prof. Jo Handelsman’s lab in the US was granted. Since Prof. Handelsman in is moving her lab to University of Wisconsin in Madison, where she will be heading the Wisconsin Institute of Discovery (after returning from the White House), it means that this summer I will be moving to Wisconsin. I will retain a link to the University of Gothenburg and the Joakim Larsson lab though, and part of the grant is actually for covering my salary after returning from the US, so Gothenburg won’t get rid of me so easily.

The granted project will use high-throughput sequencing techniques to identify genes improving colonization and invasion ability or resistance to invasion in microbial communities, using a model system developed by the Handelsman lab. The project will focus on genes important for colonization, invasion and resistance to invasion under exposure to sub-lethal antibiotics concentrations. The project will contribute important knowledge towards the understanding of microbial colonization and invasion and highlight disturbances to the interactions in microbial communities caused by anthropogenic activities. In addition, the results of the project will hopefully allow for prediction of secondary effects of antibiotic exposure in the environment, and the preparation for future challenges related to infections with pathogenic bacteria. The project has already been highlighted by CARe (although this was before Jo announced her move from Yale) and a FORMAS press release (in Swedish).

The project will go under the acronym InSiDER, and I intend to write about it in a special section of the website, called the Wisconsin Blog. My intention is to include personal reflections on life in Wisconsin and work in the Handelsman lab there, but we’ll see how those plans turn out. Anyway, I am very thankful for FORMAS funding this project and giving me the opportunity to work with one of the leading scientists within microbial ecology in the world!

Merry Christmas

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From today, I will shut down my activities on the website and over mail to spend the Christmas holidays with my family. I will likely not read e-mails until the first week of January, and as I might then have a large pile of mail to go through, please re-send any messages to me after January 3.

I apologise to everyone who might have outstanding support issues for Metaxa2 or ITSx. If you feel that I have neglected your e-mail, please re-send it after January 3 as well, to make sure that I have not missed it.

I wish you all a very Merry Christmas and a Happy new year!

As the 8th Next Generation Sequencing Congress in London is drawing to a close as I write this, I have a few reflections that might warrant sharing. The first thing that has been apparent this year compared to the two previous times I have visited the event (in 2012 and 2013) is that there was very little talk about where Illumina sequencing is heading next. Instead the discussion was about the applications of Illumina sequencing in the clinical setting; so apparently this is now so mainstream that we only expect slow progress towards longer reads. Apart from that, Illumina is a completed, mature technology. Instead, the flashlight is now pointing entirely towards long-read sequencing (PacBio, NanoPore) as the next big thing. However, the excitement around these technologies has also sort of faded compared to in 2013 when they were soon-to-arrive. Indeed, it seems like there’s not much to be excited about in the sequencing field at the moment, or at least Oxford Global (who are hosting the conference) has failed to get these technologies here.

What also strikes me is the vast amounts of talk about RNAseq of cancer cells. The scope of this event has narrowed dramatically in the past three years. Which makes me substantially less interested in returning next year. If there is not much to be excited about, and the focus is only on cancer sequencing – despite the human microbiota being a very hot topic at the moment – what is the reason for non-cancer researchers to come to the event? There will need to be a stark shift towards another direction of this event if the arrangers want it to remain a broad NGS event. Otherwise, they may just as well go all in and rename the event the Next Generation Sequencing of Cancer Congress. But I hope they choose to widen the scope again; conferences discussing technology as a foundation for a variety of applications are important meeting points and spawning grounds for novel ideas.

Yesterday, Molecular Ecology Resources put online an unedited version of a recent paper which I co-authored. This time, Rodney Richardson at Ohio State University has made a tremendous work of evaluating three taxonomic classification software – the RDP Naïve Bayesian Classifier, RTAX and UTAX – on a set of DNA barcoding regions commonly used for plants, namely the ITS2, and the matK, rbcL, trnL and trnH genes.

In the paper (1), we discuss the results, merits and limitations of the classifiers. In brief, we found that:

  • There is a considerable trade-off between accuracy and sensitivity for the classifiers tested, which indicates a need for improved sequence classification tools (2)
  • UTAX was superior with respect to error rate, but was exceedingly stringent and thus suffered from a low assignment rate
  • The RDP Naïve Bayesian Classifier displayed high sensitivity and low error at the family and order levels, but had a genus-level error rate of 9.6 percent
  • RTAX showed high sensitivity at all taxonomic ranks, but at the same time consistently produced the high error rates
  • The choice of locus has significant effects on the classification sensitivity of all tested tools
  • All classifiers showed strong relationships between database completeness, classification sensitivity and classification accuracy

We believe that the methods of comparison we have used are simple and robust, and thereby provides a methodological and conceptual foundation for future software evaluations. On a personal note, I will thoroughly enjoy working with Rodney and Reed again; I had a great time discussing the ins and outs of taxonomic classification with them! The paper can be found here.

References and notes

  1. Richardson RT, Bengtsson-Palme J, Johnson RM: Evaluating and Optimizing the Performance of Software Commonly Used for the Taxonomic Classification of DNA Sequence Data. Molecular Ecology Resources, Early view (2016). doi: 10.1111/1755-0998.12628 [Paper link]
  2. This is something that several classifiers also showed in the evaluation we did for the Metaxa2 paper (3). Interestingly enough, Metaxa2 is better at maintaining high accuracy also as sensitivity is increased.
  3. Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 6, 1403–1414 (2015). doi: 10.1111/1755-0998.12399 [Paper 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

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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!