Johan Bengtsson-Palme

Johan Bengtsson-Palme
University of Gothenburg | GU · Department of Infectious Diseases

BSc Biology, MSc Bioinformatics, PhD Medicine

About

150
Publications
67,391
Reads
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10,742
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Introduction
I am doing research in microbiology and microbial ecology, primarily focusing on investigating antibiotic resistance of bacterial communities through the use of metagenomics and bioinformatics. I also have an interest in molecular taxonomy, building bioinformatics tools and improving the quality of reference databases.
Additional affiliations
January 2019 - present
University of Gothenburg
Position
  • Professor (Assistant)
Description
  • I lead a research group working with interactions in microbial communities and antibiotic resistance
August 2017 - January 2021
University of Gothenburg
Position
  • Professor
Description
  • Antibiotic resistance and microbial invasion processes
August 2017 - December 2018
University of Wisconsin–Madison
Position
  • PostDoc Position
Education
August 2009 - April 2011
University of Gothenburg
Field of study
  • Bioinformatics and Systems biology
August 2006 - June 2009
University of Gothenburg
Field of study
  • Biology

Publications

Publications (150)
Article
Full-text available
The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of...
Article
The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The Metaxa software tool is a popular uti...
Article
In a recent Opinion article, Martínez et al. outline the obstacles associated with determining the risks presented by antibiotic resistance genes in environmental microbial communities in terms of their potential to transfer to human pathogens. The authors then propose a system for ranking the risks associated with the detection of such genes. With...
Article
Full-text available
Antibiotic resistance and its wider implications present us with a growing healthcare crisis. Recent research points to the environment as an important component for the transmission of resistant bacteria and in the emergence of resistant pathogens. However, a deeper understanding of the evolutionary and ecological processes that lead to clinical a...
Article
Full-text available
Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and s...
Preprint
The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, current AMR monitoring initiatives lack comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is nece...
Article
Full-text available
It is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in transmission of resistant bacteria, its role in the emergence of novel antibiotic resistance genes (ARGs) is less clear. I...
Article
Full-text available
Abstract The specific concentrations of florfenicol and thiamphenicol in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in ter...
Article
Full-text available
Abstract The specific concentrations of tilmicosin, tylosin and tylvalosin in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect i...
Article
Full-text available
Abstract The specific concentrations of tetracycline, chlortetracycline, oxytetracycline and doxycycline in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations...
Article
Full-text available
Abstract The specific concentrations of apramycin, paromomycin, neomycin and spectinomycin in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which...
Article
Full-text available
Abstract The specific concentrations of amprolium in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promoti...
Article
Full-text available
Abstract The specific concentrations of colistin in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotio...
Article
Full-text available
Abstract The specific concentrations of trimethoprim in non‐target feed for food‐producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promo...
Article
Full-text available
Abstract The specific concentrations of tiamulin and valnemulin in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of...
Article
Full-text available
Abstract The specific concentrations of lincomycin in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promot...
Article
Full-text available
Abstract The specific concentrations of amoxicillin and penicillin V in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in term...
Article
Full-text available
Abstract The European Commission requested EFSA to assess, in collaboration with EMA, the specific concentrations of antimicrobials resulting from cross‐contamination in non‐target feed for food‐producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in microbial agents relevant for human and...
Article
Full-text available
Abstract The specific concentrations of flumequine and oxolinic acid in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in term...
Article
Full-text available
Abstract The specific concentrations of sulfonamides in non‐target feed for food‐producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth prom...
Article
Full-text available
Current knowledge about the microbial communities that occur in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strain...
Article
Full-text available
Microbial communities are essential for human and environmental health, often forming complex interaction networks responsible for driving ecosystem processesaffecting their local environment and their hosts. Disturbances of these communitiescan lead to loss of interactions and thereby important ecosystem functionality. Theresearch on what drives i...
Preprint
Full-text available
It is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in the transmission of resistant bacteria, it is less clear what role it plays in the emergence of novel types of resistance....
Preprint
Full-text available
The microbiomes of tropical reef-building corals are actively studied using 16S rRNA gene amplicons to understand microbial roles in coral health, metabolism, and disease resistance. However, primers targeting bacterial and archaeal 16S rRNA genes may additionally amplify organelle rRNA genes from the coral, associated microbial eukaryotes, and enc...
Preprint
Full-text available
Current knowledge about the microbial communities inhabiting the stormwater quality improvement devices (SQIDs) for road runoff is scarce. However, as a bioactive compound of these systems, microbes can facilitate water quality improvement through the biodegradation or precipitation of dissolved contaminants. On the other hand, these contaminants m...
Article
Full-text available
Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE—Coefficient-based Analysis of Fitness by read Enrichment—a software package that ca...
Article
Full-text available
Natural microbial communities are complex ecosystems with myriads of interactions. To deal with this complexity, we can apply lessons learned from the study of model organisms and try to find simpler systems that can shed light on the same questions. Here, microbial model communities are essential, as they can allow us to learn about the metabolic...
Article
Full-text available
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translate...
Article
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translate...
Chapter
The ability for bacteria to exchange resistance genes with each other through horizontal gene transfer introduces a fundamental conundrum for management: resistance genes may be transferred from environmental bacteria to human pathogens over and over again, essentially erasing progress made toward eradicating resistant pathogens. This limits our mi...
Article
Full-text available
Metagenomics has emerged as a central technique for studying the structure and function of microbial communities. Often the functional analysis is restricted to classification into broad functional categories. However, important phenotypic differences, such as resistance to antibiotics, are often the result of just one or a few point mutations in o...
Article
Antibiotic resistance is an emerging global health crisis, driven largely by overuse and misuse of antibiotics. However, there are examples in which the production of these antimicrobial agents has polluted the environment with active antibiotic residues, selecting for antibiotic resistant bacteria and the genes they carry. In this work, we have us...
Article
Full-text available
Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we deter...
Data
Quantification results for diarrheal bacterial pathogens in water samples from the La Paz River basin. a) EHEC-stx1, b) S.enterica-invA and c) K. pneumoniae-ntrA. The bars show the number of copies per pathogen gene per 100 ml of river water (N° gc/100mL H2O) per month (April to March 2013–14, January results are absent) and per site obtained by qP...
Data
Sequencing data from the four multi-resistant bacterial isolates from the Choqueyapu River positive for blaCTX-M in PCR. (DOCX)
Article
Full-text available
UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustered into ∼459 000 species hypothe...
Article
Full-text available
Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms. In the implementation of any novel technology fo...
Preprint
Full-text available
Metagenomics has emerged as a central technique for studying the structure and function of microbial communities. Often the functional analysis is restricted to classification into broad functional categories. However, important phenotypic differences, such as resistance to antibiotics, are often the result of just one or a few point mutations in o...
Article
Full-text available
The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here, we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element...
Article
Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new fungal environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom both in terms of taxonomy and marker coverage in the refere...
Article
Full-text available
Background: Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abundance and diversity of known resistance genes are representative also for the non-characterized fraction of the resistome in a gi...
Article
Full-text available
Metabarcoding is a popular application which warrants continued methods optimization. To maximize barcoding inferences, hierarchy-based sequence classification methods are increasingly common. We present methods for the construction and curation of a database designed for hierarchical classification of a 157 bp barcoding region of the arthropod cyt...
Article
Full-text available
Motivation: Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adopti...
Article
Full-text available
There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in...
Article
Full-text available
Many pathogenic bacteria utilise sialic acids as an energy source or use them as an external coating to evade immune detection. As such, bacteria that colonise sialylated environments deploy specific transporters to mediate import of scavenged sialic acids. Here, we report a substrate-bound 1.95 Å resolution structure and subsequent characterisatio...