1
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Lai HY, Cooper TF. Interaction with a phage gene underlie costs of a β-lactamase. mBio 2024; 15:e0277623. [PMID: 38194254 PMCID: PMC10865808 DOI: 10.1128/mbio.02776-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
The fitness cost of an antibiotic resistance gene (ARG) can differ across host strains, creating refuges that allow the maintenance of an ARG in the absence of direct selection for its resistance phenotype. Despite the importance of such ARG-host interactions for predicting ARG dynamics, the basis of ARG fitness costs and their variability between hosts are not well understood. We determined the genetic basis of a host-dependent cost of a β-lactamase, blaTEM-116*, that conferred a significant cost in one Escherichia coli strain but was close to neutral in 11 other Escherichia spp. strains. Selection of a blaTEM-116*-encoding plasmid in the strain in which it initially had a high cost resulted in rapid and parallel compensation for that cost through mutations in a P1-like phage gene, relAP1. When the wild-type relAP1 gene was added to a strain in which it was not present and in which blaTEM-116* was neutral, it caused the ARG to become costly. Thus, relAP1 is both necessary and sufficient to explain blaTEM-116* costs in at least some host backgrounds. To our knowledge, these findings represent the first demonstrated case of the cost of an ARG being influenced by a genetic interaction with a phage gene. The interaction between a phage gene and a plasmid-borne ARG highlights the complexity of selective forces determining the maintenance and spread of ARGs and, by extension, encoding phage and plasmids in natural bacterial communities.IMPORTANCEAntibiotic resistance genes (ARGs) play a major role in the increasing problem of antibiotic resistance in clinically relevant bacteria. Selection of these genes occurs in the presence of antibiotics, but their eventual success also depends on the sometimes substantial costs they impose on host bacteria in antibiotic-free environments. We evolved an ARG that confers resistance to penicillin-type antibiotics in one host in which it did confer a cost and in one host in which it did not. We found that costs were rapidly and consistently reduced through parallel genetic changes in a gene encoded by a phage that was infecting the costly host. The unmutated version of this gene was sufficient to cause the ARG to confer a cost in a host in which it was originally neutral, demonstrating an antagonism between the two genetic elements and underlining the range and complexity of pressures determining ARG dynamics in natural populations.
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Affiliation(s)
- Huei-Yi Lai
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Tim F. Cooper
- School of Natural Sciences, Massey University, Auckland, New Zealand
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2
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McCallum GE, Rossiter AE, Quraishi MN, Iqbal TH, Kuehne SA, van Schaik W. Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts. Microb Genom 2023; 9:mgen001030. [PMID: 37272920 PMCID: PMC10327510 DOI: 10.1099/mgen.0.001030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/11/2023] [Indexed: 06/06/2023] Open
Abstract
The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C) have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to insertion sequence elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering to remove artefactual links, 87 ARGs were assigned to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes coding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.
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Affiliation(s)
- Gregory E. McCallum
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - Tariq H. Iqbal
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Sarah A. Kuehne
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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3
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Konno N, Iwasaki W. Machine learning enables prediction of metabolic system evolution in bacteria. SCIENCE ADVANCES 2023; 9:eadc9130. [PMID: 36630500 PMCID: PMC9833677 DOI: 10.1126/sciadv.adc9130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Evolution prediction is a long-standing goal in evolutionary biology, with potential impacts on strategic pathogen control, genome engineering, and synthetic biology. While laboratory evolution studies have shown the predictability of short-term and sequence-level evolution, that of long-term and system-level evolution has not been systematically examined. Here, we show that the gene content evolution of metabolic systems is generally predictable by applying ancestral gene content reconstruction and machine learning techniques to ~3000 bacterial genomes. Our framework, Evodictor, successfully predicted gene gain and loss evolution at the branches of the reference phylogenetic tree, suggesting that evolutionary pressures and constraints on metabolic systems are universally shared. Investigation of pathway architectures and meta-analysis of metagenomic datasets confirmed that these evolutionary patterns have physiological and ecological bases as functional dependencies among metabolic reactions and bacterial habitat changes. Last, pan-genomic analysis of intraspecies gene content variations proved that even "ongoing" evolution in extant bacterial species is predictable in our framework.
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Affiliation(s)
- Naoki Konno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding author. (N.K.); (W.I.)
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Corresponding author. (N.K.); (W.I.)
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4
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Apjok G, Számel M, Christodoulou C, Seregi V, Vásárhelyi BM, Stirling T, Eszenyi B, Sári T, Vidovics F, Nagrand E, Kovács D, Szili P, Lantos II, Méhi O, Jangir PK, Herczeg R, Gálik B, Urbán P, Gyenesei A, Draskovits G, Nyerges Á, Fekete G, Bodai L, Zsindely N, Dénes B, Yosef I, Qimron U, Papp B, Pál C, Kintses B. Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains. Nat Microbiol 2023; 8:410-423. [PMID: 36759752 PMCID: PMC9981461 DOI: 10.1038/s41564-023-01320-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.
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Affiliation(s)
- Gábor Apjok
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Mónika Számel
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Chryso Christodoulou
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Viktória Seregi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary
| | - Bálint Márk Vásárhelyi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Tamás Stirling
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary ,grid.481814.00000 0004 0479 9817Institute of Biochemistry, Biological Research Centre, National Laboratory for Health Security, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Bálint Eszenyi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Tóbiás Sári
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Fanni Vidovics
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Erika Nagrand
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Dorina Kovács
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Petra Szili
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Ildikó Ilona Lantos
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Orsolya Méhi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Pramod K. Jangir
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary ,grid.4991.50000 0004 1936 8948Present Address: Department of Zoology, University of Oxford, Oxford, UK
| | - Róbert Herczeg
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Bence Gálik
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary ,grid.48324.390000000122482838Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Péter Urbán
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Attila Gyenesei
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary ,grid.48324.390000000122482838Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Gábor Draskovits
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ákos Nyerges
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Gergely Fekete
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - László Bodai
- grid.9008.10000 0001 1016 9625Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Nóra Zsindely
- grid.9008.10000 0001 1016 9625Department of Genetics, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Béla Dénes
- grid.432859.10000 0004 4647 7293Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - Ido Yosef
- grid.12136.370000 0004 1937 0546Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Udi Qimron
- grid.12136.370000 0004 1937 0546Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Balázs Papp
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.481814.00000 0004 0479 9817Institute of Biochemistry, Biological Research Centre, National Laboratory for Health Security, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Csaba Pál
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
| | - Bálint Kintses
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary. .,HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary. .,Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
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5
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Downing T, Rahm A. Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks. Sci Rep 2022; 12:19203. [PMID: 36357451 PMCID: PMC9649638 DOI: 10.1038/s41598-022-20809-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/19/2022] [Indexed: 11/12/2022] Open
Abstract
Plasmids facilitate horizontal gene transfer, which enables the diversification of pathogens into new anatomical and environmental niches, implying that plasmid-encoded genes can cooperate well with chromosomal genes. We hypothesise that such mobile genes are functionally different to chromosomal ones due to this ability to encode proteins performing non-essential functions like antimicrobial resistance and traverse distinct host cells. The effect of plasmid-driven gene gain on protein-protein interaction network topology is an important question in this area. Moreover, the extent to which these chromosomally- and plasmid-encoded proteins interact with proteins from their own groups compared to the levels with the other group remains unclear. Here, we examined the incidence and protein-protein interactions of all known plasmid-encoded proteins across representative specimens from most bacteria using all available plasmids. We found that plasmid-encoded genes constitute ~ 0.65% of the total number of genes per bacterial sample, and that plasmid genes are preferentially associated with different species but had limited taxonomical power beyond this. Surprisingly, plasmid-encoded proteins had both more protein-protein interactions compared to chromosomal proteins, countering the hypothesis that genes with higher mobility rates should have fewer protein-level interactions. Nonetheless, topological analysis and investigation of the protein-protein interaction networks' connectivity and change in the number of independent components demonstrated that the plasmid-encoded proteins had limited overall impact in > 96% of samples. This paper assembled extensive data on plasmid-encoded proteins, their interactions and associations with diverse bacterial specimens that is available for the community to investigate in more detail.
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Affiliation(s)
- Tim Downing
- grid.15596.3e0000000102380260School of Biotechnology, Dublin City University, Dublin, Ireland ,grid.63622.330000 0004 0388 7540Present Address: The Pirbright Institute, Pirbright, UK
| | - Alexander Rahm
- grid.449688.f0000 0004 0647 1487GAATI Lab, University of French Polynesia, Tahiti, French Polynesia
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6
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D'Angelo F, Fernández-Fueyo E, Garcia PS, Shomar H, Pelosse M, Manuel RR, Büke F, Liu S, van den Broek N, Duraffourg N, de Ram C, Pabst M, Bouveret E, Gribaldo S, Py B, Ollagnier de Choudens S, Barras F, Bokinsky G. Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host. eLife 2022; 11:70936. [PMID: 35244541 PMCID: PMC8896826 DOI: 10.7554/elife.70936] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and highly versatile. However, Fe-S proteins and enzymes are often inactive outside their native host species. We sought to systematically investigate the compatibility of Fe-S networks with non-native Fe-S enzymes. By using collections of Fe-S enzyme orthologs representative of the entire range of prokaryotic diversity, we uncovered a striking correlation between phylogenetic distance and probability of functional expression. Moreover, coexpression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be supported by the foreign host. We also find that Fe-S enzymes that require specific electron carrier proteins are rarely functionally expressed unless their taxon-specific reducing partners are identified and co-expressed. We demonstrate how these principles can be applied to improve the activity of a radical S-adenosyl methionine(rSAM) enzyme from a Streptomyces antibiotic biosynthesis pathway in Escherichia coli. Our results clarify how oxygen sensitivity and incompatibilities with foreign Fe-S and electron transfer networks each impede heterologous activity. In particular, identifying compatible electron transfer proteins and heterologous Fe-S biogenesis pathways may prove essential for engineering functional Fe-S enzyme-dependent pathways.
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Affiliation(s)
- Francesca D'Angelo
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Elena Fernández-Fueyo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Pierre Simon Garcia
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France.,Institut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, France
| | - Helena Shomar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Martin Pelosse
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Rita Rebelo Manuel
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Ferhat Büke
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Siyi Liu
- Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, France
| | - Niels van den Broek
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Nicolas Duraffourg
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Carol de Ram
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Emmanuelle Bouveret
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, France
| | - Béatrice Py
- Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, France
| | | | - Frédéric Barras
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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7
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Abstract
By providing the bacterial cell with protection against several antibiotics at once, multiresistance plasmids have an evolutionary advantage in situations where antibiotic treatments are common, such as in hospital environments. However, resistance plasmids can also impose fitness costs on the bacterium in the absence of antibiotics, something that may limit their evolutionary success. The underlying mechanisms and the possible contribution of resistance genes to such costs are still largely not understood. Here, we have specifically investigated the contribution of plasmid-borne resistance genes to the reduced fitness of the bacterial cell. The pUUH239.2 plasmid carries 13 genes linked to antibiotic resistance and reduces bacterial fitness by 2.9% per generation. This cost is fully ameliorated by the removal of the resistance cassette. While most of the plasmid-borne resistance genes individually were cost-free, even when overexpressed, two specific gene clusters were responsible for the entire cost of the plasmid: the extended-spectrum-β-lactamase gene blaCTX-M-15 and the tetracycline resistance determinants tetAR. The blaCTX-M-15 cost was linked to the signal peptide that exports the β-lactamase into the periplasm, and replacement with an alternative signal peptide abolished the cost. Both the tetracycline pump TetA and its repressor TetR conferred a cost on the host cell, and the reciprocal expression of these genes is likely fine-tuned to balance the respective costs. These findings highlight that the cost of clinical multiresistance plasmids can be largely due to particular resistance genes and their interaction with other cellular systems, while other resistance genes and the plasmid backbone can be cost-free. IMPORTANCE Multiresistance plasmids are one of the main drivers of antibiotic resistance development and spread. Their evolutionary success through the accumulation and mobilization of resistance genes is central to resistance evolution. In this study, we find that the cost of the introduction of a multiresistance plasmid was completely attributable to resistance genes, while the rest of the plasmid backbone is cost-free. The majority of resistance genes on the plasmid had no appreciable cost to the host cell even when overexpressed, indicating that plasmid-borne resistance can be cost-free. In contrast, the widespread genes blaCTX-M-15 and tetAR were found to confer the whole cost of the plasmid by affecting specific cellular functions. These findings highlight how the evolution of resistance on plasmids is dependent on the amelioration of associated fitness costs and point at a conundrum regarding the high cost of some of the most widespread β-lactamase genes.
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8
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Hu EZ, Lan XR, Liu ZL, Gao J, Niu DK. A positive correlation between GC content and growth temperature in prokaryotes. BMC Genomics 2022; 23:110. [PMID: 35139824 PMCID: PMC8827189 DOI: 10.1186/s12864-022-08353-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
Background GC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate. Results With a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be strongly shaped by intense UV radiation. Conclusions This study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08353-7.
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Affiliation(s)
- En-Ze Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xin-Ran Lan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Zhi-Ling Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jie Gao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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9
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López C, Delmonti J, Bonomo RA, Vila AJ. Deciphering the evolution of metallo-β-lactamases: a journey from the test tube to the bacterial periplasm. J Biol Chem 2022; 298:101665. [PMID: 35120928 DOI: 10.1016/j.jbc.2022.101665] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the evolution of metallo-β-lactamases (MBLs) is fundamental to deciphering the mechanistic basis of resistance to carbapenems in pathogenic and opportunistic bacteria. Presently, these MBL producing pathogens are linked to high rates of morbidity and mortality worldwide. However, the study of the biochemical and biophysical features of MBLs in vitro provides an incomplete picture of their evolutionary potential, since this limited and artificial environment disregards the physiological context where evolution and selection take place. Herein, we describe recent efforts aimed to address the evolutionary traits acquired by different clinical variants of MBLs in conditions mimicking their native environment (the bacterial periplasm) and considering whether they are soluble or membrane-bound proteins. This includes addressing the metal content of MBLs within the cell under zinc starvation conditions, and the context provided by different bacterial hosts that result in particular resistance phenotypes. Our analysis highlights recent progress bridging the gap between in vitro and in-cell studies.
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Affiliation(s)
- Carolina López
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Juliana Delmonti
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Robert A Bonomo
- Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA; Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina.
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10
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Hall JPJ, Harrison E, Baltrus DA. Introduction: the secret lives of microbial mobile genetic elements. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200460. [PMID: 34839706 PMCID: PMC8628069 DOI: 10.1098/rstb.2020.0460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Ellie Harrison
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 1EA, UK
| | - David A. Baltrus
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721‐0036, USA
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11
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Evolutionary Processes Driving the Rise and Fall of Staphylococcus aureus ST239, a Dominant Hybrid Pathogen. mBio 2021; 12:e0216821. [PMID: 34903061 PMCID: PMC8669471 DOI: 10.1128/mbio.02168-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Selection plays a key role in the spread of antibiotic resistance, but the evolutionary drivers of clinically important resistant strains remain poorly understood. Here, we use genomic analyses and competition experiments to study Staphylococcus aureus ST239, a prominent MRSA strain that is thought to have been formed by large-scale recombination between ST8 and ST30. Genomic analyses allowed us to refine the hybrid model for the origin of ST239 and to date the origin of ST239 to 1920 to 1945, which predates the clinical introduction of methicillin in 1959. Although purifying selection has dominated the evolution of ST239, parallel evolution has occurred in genes involved in antibiotic resistance and virulence, suggesting that ST239 has evolved toward an increasingly pathogenic lifestyle. Crucially, ST239 isolates have low competitive fitness relative to both ST8 and ST30 isolates, supporting the idea that fitness costs have driven the demise of this once-dominant pathogen strain.
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12
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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13
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den Haan R, Rose SH, Cripwell RA, Trollope KM, Myburgh MW, Viljoen-Bloom M, van Zyl WH. Heterologous production of cellulose- and starch-degrading hydrolases to expand Saccharomyces cerevisiae substrate utilization: Lessons learnt. Biotechnol Adv 2021; 53:107859. [PMID: 34678441 DOI: 10.1016/j.biotechadv.2021.107859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Selected strains of Saccharomyces cerevisiae are used for commercial bioethanol production from cellulose and starch, but the high cost of exogenous enzymes for substrate hydrolysis remains a challenge. This can be addressed through consolidated bioprocessing (CBP) where S. cerevisiae strains are engineered to express recombinant glycoside hydrolases during fermentation. Looking back at numerous strategies undertaken over the past four decades to improve recombinant protein production in S. cerevisiae, it is evident that various steps in the protein production "pipeline" can be manipulated depending on the protein of interest and its anticipated application. In this review, we briefly introduce some of the strategies and highlight lessons learned with regards to improved transcription, translation, post-translational modification and protein secretion of heterologous hydrolases. We examine how host strain selection and modification, as well as enzyme compatibility, are crucial determinants for overall success. Finally, we discuss how lessons from heterologous hydrolase expression can inform modern synthetic biology and genome editing tools to provide process-ready yeast strains in future. However, it is clear that the successful expression of any particular enzyme is still unpredictable and requires a trial-and-error approach.
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Affiliation(s)
- Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Kim M Trollope
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marthinus W Myburgh
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa.
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14
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Petitjean M, Condamine B, Burdet C, Denamur E, Ruppé E. Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes. Microb Genom 2021; 7. [PMID: 34435947 PMCID: PMC8549366 DOI: 10.1099/mgen.0.000489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Escherichia coli is a ubiquitous bacterium that has been widely exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic-resistance genes (ARGs), the census of which we aim to characterize here. To do so, we analysed 70 301 E. coli genomes obtained from the EnteroBase database and detected 1 027 651 ARGs using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup and clonal lineage specific distribution of some ARGs, supporting the argument for epistasis between ARGs and the strain genetic background. However, each phylogroup had ARGs conferring a similar antibiotic class resistance pattern, indicating phenotypic adaptive convergence. The G+C content or the type of ARG was not associated with the frequency of the ARG in the database. In addition, we identified ARGs from anaerobic, non-Proteobacteria bacteria in four genomes of E. coli, supporting the hypothesis that the transfer between anaerobic bacteria and E. coli can spontaneously occur but remains exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of a resistome in E. coli.
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Affiliation(s)
| | | | - Charles Burdet
- IAME, INSERM, Université de Paris, F-75018 Paris, France.,Département d'Epidémiologie, Biostatistique et Recherche Clinique, Hôpital Bichat, APHP, F-75018 Paris, France
| | - Erick Denamur
- IAME, INSERM, Université de Paris, F-75018 Paris, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat, APHP, F-75018 Paris, France
| | - Etienne Ruppé
- IAME, INSERM, Université de Paris, F-75018 Paris, France.,Laboratoire de Bactériologie, Hôpital Bichat, APHP, F-75018 Paris, France
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15
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Ellabaan MMH, Munck C, Porse A, Imamovic L, Sommer MOA. Forecasting the dissemination of antibiotic resistance genes across bacterial genomes. Nat Commun 2021; 12:2435. [PMID: 33893312 PMCID: PMC8065159 DOI: 10.1038/s41467-021-22757-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 03/19/2021] [Indexed: 01/22/2023] Open
Abstract
Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. We identify 152 gene exchange networks containing 22,963 bacterial genomes. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. Certain ARGs appear to be frequently mobilised by different mobile genetic elements. We characterise the phylogenetic reach of these mobilisation elements to predict the potential future dissemination of known ARGs. Using a separate database with 472,798 genomes from Streptococcaceae, Staphylococcaceae and Enterobacteriaceae, we confirm 34 of 94 predicted mobilisations. We explore transfer barriers beyond mobilisation and show experimentally that physiological constraints of the host can explain why specific genes are largely confined to Gram-negative bacteria although their mobile elements support dissemination to Gram-positive bacteria. Our approach may potentially enable better risk assessment of future resistance gene dissemination.
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Affiliation(s)
- Mostafa M H Ellabaan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Christian Munck
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Andreas Porse
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lejla Imamovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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16
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Nawaz M, Li L, Azeem F, Shabbir S, Zohaib A, Ashraf U, Yang H, Wang Z. Insight of transcriptional regulators reveals the tolerance mechanism of carpet-grass (Axonopus compressus) against drought. BMC PLANT BIOLOGY 2021; 21:71. [PMID: 33530948 PMCID: PMC7851936 DOI: 10.1186/s12870-021-02844-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/19/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Carpet grass [Axonopus compressus (L.)] is an important warm-season perennial grass around the world and is known for its adaptability to varied environmental conditions. However, Carpet grass lacks enough data in public data banks, which confined our comprehension of the mechanisms of environmental adaptations, gene discovery, and development of molecular markers. In current study, the DEGs (differentially expressed genes) in Axonopus compressus under drought stress (DS) were identified and compared with CK (control) by RNA-Seq. RESULTS A total of 263,835 unigenes were identified in Axonopus compressus, and 201,303 (also added to the numbers of the remaining 2 databases) a sequence of unigenes significantly matched in at least one of the seven databases. A total of 153,697 (58.25%) unigenes classified to 144 KEGG pathways, and 7444 unigenes were expressed differentially between DS and CK, of which 4249 were up-regulated and 3195 were down-regulated unigenes. Of the 50 significantly enriched GO terms, 18, 6, and 14 items were related to BP, CC, and MF respectively. Analysis of KEGG enrichment revealed 2569 DEGs involved in 143 different pathways, under drought stress. 2747 DEGs were up-regulated and 2502 DEGs were down-regulated. Moreover, we identified 352 transcription factors (TFs) in Axonopus compressus, of which 270 were differentially expressed between CK and DS. The qRT-PCR validation experiment also supports the transcriptional response of Axonopus compressus against drought. Accuracy of transcriptome unigenes of Axonopus compressus was assessed with BLAST, which showed 3300 sequences of Axonopus compressus in the NCBI. CONCLUSION The 7444 unigenes were found to be between DS and CK treatments, which indicate the existence of a strong mechanism of drought tolerance in Axonopus compressus. The current findings provide the first framework for further investigations for the particular roles of these unigenes in Axonopus compressus in response to drought.
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Affiliation(s)
- Mohsin Nawaz
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry and College of Tropical Crops, Hainan University, Haikou, 570228, People's Republic of China
| | - Liao Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry and College of Tropical Crops, Hainan University, Haikou, 570228, People's Republic of China.
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad, Pakistan
| | - Samina Shabbir
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu, 610041, China
| | - Ali Zohaib
- Adaptive Research Farm, Gujranwala, 52250, Pakistan
| | - Umair Ashraf
- Department of Botany, University of Education, Lahore, Faisalabad-Campus, Faisalabad, 38000, Pakistan
| | - Hubiao Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737, Hainan, China
| | - Zhiyong Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry and College of Tropical Crops, Hainan University, Haikou, 570228, People's Republic of China.
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17
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Beyond horizontal gene transfer: the role of plasmids in bacterial evolution. Nat Rev Microbiol 2021; 19:347-359. [PMID: 33469168 DOI: 10.1038/s41579-020-00497-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 12/27/2022]
Abstract
Plasmids have a key role in bacterial ecology and evolution because they mobilize accessory genes by horizontal gene transfer. However, recent studies have revealed that the evolutionary impact of plasmids goes above and beyond their being mere gene delivery platforms. Plasmids are usually kept at multiple copies per cell, producing islands of polyploidy in the bacterial genome. As a consequence, the evolution of plasmid-encoded genes is governed by a set of rules different from those affecting chromosomal genes, and these rules are shaped by unusual concepts in bacterial genetics, such as genetic dominance, heteroplasmy or segregational drift. In this Review, we discuss recent advances that underscore the importance of plasmids in bacterial ecology and evolution beyond horizontal gene transfer. We focus on new evidence that suggests that plasmids might accelerate bacterial evolution, mainly by promoting the evolution of plasmid-encoded genes, but also by enhancing the adaptation of their host chromosome. Finally, we integrate the most relevant theoretical and empirical studies providing a global understanding of the forces that govern plasmid-mediated evolution in bacteria.
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18
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Kang Y, Yuan L, Shi X, Chu Y, He Z, Jia X, Lin Q, Ma Q, Wang J, Xiao J, Hu S, Gao Z, Chen F, Yu J. A fine-scale map of genome-wide recombination in divergent Escherichia coli population. Brief Bioinform 2020; 22:6034796. [PMID: 33319232 DOI: 10.1093/bib/bbaa335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 01/09/2023] Open
Abstract
Recombination is one of the most important molecular mechanisms of prokaryotic genome evolution, but its exact roles are still in debate. Here we try to infer genome-wide recombination within a species, utilizing a dataset of 149 complete genomes of Escherichia coli from diverse animal hosts and geographic origins, including 45 in-house sequenced with the single-molecular real-time platform. Two major clades identified based on physiological, clinical and ecological characteristics form distinct genetic lineages based on scarcity of interclade gene exchanges. By defining gene-based syntenies for genomic segments within and between the two clades, we build a fine-scale recombination map for this representative global E. coli population. The map suggests extensive within-clade recombination that often breaks physical linkages among individual genes but seldom interrupts the structure of genome organizational frameworks as well as primary metabolic portfolios supported by the framework integrity, possibly due to strong natural selection for both physiological compatibility and ecological fitness. In contrast, the between-clade recombination declines drastically when phylogenetic distance increases to the extent where a 10-fold reduction can be observed, establishing a firm genetic barrier between clades. Our empirical data suggest a critical role for such recombination events in the early stage of speciation where recombination rate is associated with phylogenetic distance in addition to sequence and gene variations. The extensive intraclade recombination binds sister strains into a quasisexual group and optimizes genes or alleles to streamline physiological activities, whereas the sharply declined interclade recombination split the population into clades adaptive to divergent ecological niches.
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Affiliation(s)
- Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Shi
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, PR China
| | - Yanan Chu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zilong He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, 100191, PR China
| | - Xinmiao Jia
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Qiang Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qin Ma
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songnian Hu
- University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Zhancheng Gao
- Department of Respiratory & Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, PR China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, PR China.,China National Center for Bioinformation, Beijing 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, China
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19
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Abstract
The genomes of bacteria contain fewer genes and substantially less noncoding DNA than those of eukaryotes, and as a result, they have much less raw material to invent new traits. Yet, bacteria are vastly more taxonomically diverse, numerically abundant, and globally successful in colonizing new habitats compared to eukaryotes. Although bacterial genomes are generally considered to be optimized for efficient growth and rapid adaptation, nonadaptive processes have played a major role in shaping the size, contents, and compact organization of bacterial genomes and have allowed the establishment of deleterious traits that serve as the raw materials for genetic innovation.
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Affiliation(s)
- Paul C Kirchberger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Marian L Schmidt
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA; ; ;
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20
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Bohr LL, Mortimer TD, Pepperell CS. Lateral Gene Transfer Shapes Diversity of Gardnerella spp. Front Cell Infect Microbiol 2020; 10:293. [PMID: 32656099 PMCID: PMC7324480 DOI: 10.3389/fcimb.2020.00293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
Gardnerella spp. are pathognomonic for bacterial vaginosis, which increases the risk of preterm birth and the transmission of sexually transmitted infections. Gardnerella spp. are genetically diverse, comprising what have recently been defined as distinct species with differing functional capacities. Disease associations with Gardnerella spp. are not straightforward: patients with BV are usually infected with multiple species, and Gardnerella spp. are also found in the vaginal microbiome of healthy women. Genome comparisons of Gardnerella spp. show evidence of lateral gene transfer (LGT), but patterns of LGT have not been characterized in detail. Here we sought to define the role of LGT in shaping the genetic structure of Gardnerella spp. We analyzed whole genome sequencing data for 106 Gardnerella strains and used these data for pan genome analysis and to characterize LGT in the core and accessory genomes, over recent and remote timescales. In our diverse sample of Gardnerella strains, we found that both the core and accessory genomes are clearly differentiated in accordance with newly defined species designations. We identified putative competence and pilus assembly genes across most species; we also found them to be differentiated between species. Competence machinery has diverged in parallel with the core genome, with selection against deleterious mutations as a predominant influence on their evolution. By contrast, the virulence factor vaginolysin, which encodes a toxin, appears to be readily exchanged among species. We identified five distinct prophage clusters in Gardnerella genomes, two of which appear to be exchanged between Gardnerella species. Differences among species are apparent in their patterns of LGT, including their exchange with diverse gene pools. Despite frequent LGT and co-localization in the same niche, our results show that Gardnerella spp. are clearly genetically differentiated and yet capable of exchanging specific genetic material. This likely reflects complex interactions within bacterial communities associated with the vaginal microbiome. Our results provide insight into how such interactions evolve and are maintained, allowing these multi-species communities to colonize and invade human tissues and adapt to antibiotics and other stressors.
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Affiliation(s)
- Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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21
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Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria. Proc Natl Acad Sci U S A 2020; 117:15755-15762. [PMID: 32571917 PMCID: PMC7355013 DOI: 10.1073/pnas.2001240117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.
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22
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Emamalipour M, Seidi K, Zununi Vahed S, Jahanban-Esfahlan A, Jaymand M, Majdi H, Amoozgar Z, Chitkushev LT, Javaheri T, Jahanban-Esfahlan R, Zare P. Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression. Front Cell Dev Biol 2020; 8:229. [PMID: 32509768 PMCID: PMC7248198 DOI: 10.3389/fcell.2020.00229] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
Flexibility in the exchange of genetic material takes place between different organisms of the same or different species. This phenomenon is known to play a key role in the genetic, physiological, and ecological performance of the host. Exchange of genetic materials can cause both beneficial and/or adverse biological consequences. Horizontal gene transfer (HGT) or lateral gene transfer (LGT) as a general mechanism leads to biodiversity and biological innovations in nature. HGT mediators are one of the genetic engineering tools used for selective introduction of desired changes in the genome for gene/cell therapy purposes. HGT, however, is crucial in development, emergence, and recurrence of various human-related diseases, such as cancer, genetic-, metabolic-, and neurodegenerative disorders and can negatively affect the therapeutic outcome by promoting resistant forms or disrupting the performance of genome editing toolkits. Because of the importance of HGT and its vital physio- and pathological roles, here the variety of HGT mechanisms are reviewed, ranging from extracellular vesicles (EVs) and nanotubes in prokaryotes to cell-free DNA and apoptotic bodies in eukaryotes. Next, we argue that HGT plays a role both in the development of useful features and in pathological states associated with emerging and recurrent forms of the disease. A better understanding of the different HGT mediators and their genome-altering effects/potentials may pave the way for the development of more effective therapeutic and diagnostic regimes.
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Affiliation(s)
- Melissa Emamalipour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khaled Seidi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hasan Majdi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zohreh Amoozgar
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - L T Chitkushev
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States.,Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Tahereh Javaheri
- Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, United States
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland.,Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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23
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de Sousa Silveira Z, Macêdo NS, Sampaio dos Santos JF, Sampaio de Freitas T, Rodrigues dos Santos Barbosa C, Júnior DLDS, Muniz DF, Castro de Oliveira LC, Júnior JPS, da Cunha FAB, Melo Coutinho HD, Balbino VQ, Martins N. Evaluation of the Antibacterial Activity and Efflux Pump Reversal of Thymol and Carvacrol against Staphylococcus aureus and Their Toxicity in Drosophila melanogaster. Molecules 2020; 25:E2103. [PMID: 32365898 PMCID: PMC7249103 DOI: 10.3390/molecules25092103] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022] Open
Abstract
The antibacterial activity and efflux pump reversal of thymol and carvacrol were investigated against the Staphylococcus aureus IS-58 strain in this study, as well as their toxicity against Drosophila melanogaster. The minimum inhibitory concentration (MIC) was determined using the broth microdilution method, while efflux pump inhibition was assessed by reduction of the antibiotic and ethidium bromide (EtBr) MICs. D. melanogaster toxicity was tested using the fumigation method. Both thymol and carvacrol presented antibacterial activities with MICs of 72 and 256 µg/mL, respectively. The association between thymol and tetracycline demonstrated synergism, while the association between carvacrol and tetracycline presented antagonism. The compound and EtBr combinations did not differ from controls. Thymol and carvacrol toxicity against D. melanogaster were evidenced with EC50 values of 17.96 and 16.97 µg/mL, respectively, with 48 h of exposure. In conclusion, the compounds presented promising antibacterial activity against the tested strain, although no efficacy was observed in terms of efflux pump inhibition.
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Affiliation(s)
- Zildene de Sousa Silveira
- Laboratory of Semi-Arid Bioprospecting (LABSEMA), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (Z.d.S.S.); (N.S.M.); (J.F.S.d.S.); (D.L.d.S.J.); (L.C.C.d.O.); (F.A.B.d.C.)
- Graduate Program in Biological Sciences-PPGCB, Federal University of Pernambuco-UFPE, Recife 50670-901, PE, Brazil;
| | - Nair Silva Macêdo
- Laboratory of Semi-Arid Bioprospecting (LABSEMA), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (Z.d.S.S.); (N.S.M.); (J.F.S.d.S.); (D.L.d.S.J.); (L.C.C.d.O.); (F.A.B.d.C.)
- Graduate Program in Biological Sciences-PPGCB, Federal University of Pernambuco-UFPE, Recife 50670-901, PE, Brazil;
| | - Joycy Francely Sampaio dos Santos
- Laboratory of Semi-Arid Bioprospecting (LABSEMA), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (Z.d.S.S.); (N.S.M.); (J.F.S.d.S.); (D.L.d.S.J.); (L.C.C.d.O.); (F.A.B.d.C.)
| | - Thiago Sampaio de Freitas
- Laboratory of Microbiology and Molecular Biology (LMBM), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (T.S.d.F.); (C.R.d.S.B.); (D.F.M.)
| | - Cristina Rodrigues dos Santos Barbosa
- Laboratory of Microbiology and Molecular Biology (LMBM), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (T.S.d.F.); (C.R.d.S.B.); (D.F.M.)
| | - Dárcio Luiz de Sousa Júnior
- Laboratory of Semi-Arid Bioprospecting (LABSEMA), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (Z.d.S.S.); (N.S.M.); (J.F.S.d.S.); (D.L.d.S.J.); (L.C.C.d.O.); (F.A.B.d.C.)
| | - Débora Feitosa Muniz
- Laboratory of Microbiology and Molecular Biology (LMBM), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (T.S.d.F.); (C.R.d.S.B.); (D.F.M.)
| | - Lígia Claudia Castro de Oliveira
- Laboratory of Semi-Arid Bioprospecting (LABSEMA), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (Z.d.S.S.); (N.S.M.); (J.F.S.d.S.); (D.L.d.S.J.); (L.C.C.d.O.); (F.A.B.d.C.)
| | - José Pinto Siqueira Júnior
- Laboratory of Microorganism Genetics (LGM), Federal University of Paraiba-UFPB, João Pessoa 58051-900, PB, Brazil;
| | - Francisco Assis Bezerra da Cunha
- Laboratory of Semi-Arid Bioprospecting (LABSEMA), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (Z.d.S.S.); (N.S.M.); (J.F.S.d.S.); (D.L.d.S.J.); (L.C.C.d.O.); (F.A.B.d.C.)
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Regional University of Cariri-URCA, Crato 63105-000, CE, Brazil; (T.S.d.F.); (C.R.d.S.B.); (D.F.M.)
| | - Valdir Queiroz Balbino
- Graduate Program in Biological Sciences-PPGCB, Federal University of Pernambuco-UFPE, Recife 50670-901, PE, Brazil;
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
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24
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McInnes RS, McCallum GE, Lamberte LE, van Schaik W. Horizontal transfer of antibiotic resistance genes in the human gut microbiome. Curr Opin Microbiol 2020; 53:35-43. [PMID: 32143027 DOI: 10.1016/j.mib.2020.02.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/28/2020] [Accepted: 02/02/2020] [Indexed: 01/05/2023]
Abstract
Infections caused by antibiotic-resistant bacteria are a major threat to public health. The pathogens causing these infections can acquire antibiotic resistance genes in a process termed horizontal gene transfer (HGT). HGT is a common event in the human gut microbiome, that is, the microbial ecosystem of the human intestinal tract. HGT in the gut microbiome can occur via different mechanisms of which transduction and conjugation have been best characterised. Novel bioinformatic tools and experimental approaches have been developed to determine the association of antibiotic resistance genes with their microbial hosts and to quantify the extent of HGT in the gut microbiome. Insights from studies into HGT in the gut microbiome may lead to the development of novel interventions to minimise the spread of antibiotic resistance genes among commensals and opportunistic pathogens.
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Affiliation(s)
- Ross S McInnes
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Gregory E McCallum
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Lisa E Lamberte
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
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25
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Phylogenomics of Rhodocyclales and its distribution in wastewater treatment systems. Sci Rep 2020; 10:3883. [PMID: 32127605 PMCID: PMC7054561 DOI: 10.1038/s41598-020-60723-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/11/2020] [Indexed: 11/09/2022] Open
Abstract
Rhodocyclales is an abundant bacterial order in wastewater treatment systems and putatively plays key roles in multiple functions. Its phylogenomics, prevalence of denitrifying genes in sub-lineages and distribution in wastewater treatment plants (WWTPs) worldwide have not been well characterized. In the present study, we collected 78 Rhodocyclales genomes, including 17 from type strains, non-type strains and genome bins contributed by this study. Phylogenomics indicated that the order could be divided into five family-level lineages. With only a few exceptions (mostly in Rhodocyclaceae), nirS-containing genomes in this order usually contained the downstream genes of norB and nosZ. Multicopy of denitrifying genes occurred frequently and events of within-order horizontal transfer of denitrifying genes were phylogenetically deduced. The distribution of Rhodocyclaceae, Zoogloeaceae and Azonexaceae in global WWTPs were significantly governed by temperature, mixed liquor suspended solids, etc. Metagenomic survey showed that the order generally ranked at the top or second for different denitrifying genes in wastewater treatment systems. Our results provided comprehensive genomic insights into the phylogeny and features of denitrifying genes of Rhodocyclales. Its contribution to the denitrifying gene pool in WWTPs was proved.
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26
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The Peril and Promise of Integrons: Beyond Antibiotic Resistance. Trends Microbiol 2020; 28:455-464. [PMID: 31948729 DOI: 10.1016/j.tim.2019.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/13/2019] [Accepted: 12/09/2019] [Indexed: 12/11/2022]
Abstract
Integrons are bacterial genetic elements that can capture, rearrange, and express mobile gene cassettes. They are best known for their role in disseminating antibiotic-resistance genes among pathogens. Their ability to rapidly spread resistance phenotypes makes it important to consider what other integron-mediated traits might impact human health in the future, such as increased virulence, pathogenicity, or resistance to novel antimicrobial strategies. Exploring the functional diversity of cassettes and understanding their de novo creation will allow better pre-emptive management of bacterial growth, while also facilitating development of technologies that could harness integron activity. If we can control integrons and cassette formation, we could use integrons as a platform for enzyme discovery and to construct novel biochemical pathways, with applications in bioremediation or biosynthesis of industrial and therapeutic molecules. Integron activity thus holds both peril and promise for humans.
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27
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Close DM, Cooper CJ, Wang X, Chirania P, Gupta M, Ossyra JR, Giannone RJ, Engle N, Tschaplinski TJ, Smith JC, Hedstrom L, Parks JM, Michener JK. Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Mol Microbiol 2019; 112:1784-1797. [PMID: 31532038 DOI: 10.1111/mmi.14393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2019] [Indexed: 11/28/2022]
Abstract
A microbe's ecological niche and biotechnological utility are determined by its specific set of co-evolved metabolic pathways. The acquisition of new pathways, through horizontal gene transfer or genetic engineering, can have unpredictable consequences. Here we show that two different pathways for coumarate catabolism failed to function when initially transferred into Escherichia coli. Using laboratory evolution, we elucidated the factors limiting activity of the newly acquired pathways and the modifications required to overcome these limitations. Both pathways required host mutations to enable effective growth with coumarate, but the necessary mutations differed. In one case, a pathway intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid replacements in IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii, is resistant to inhibition by the relevant intermediate, suggesting that natural pathway transfers have faced and overcome similar challenges. Molecular dynamics simulation of the wild type and a representative single-residue mutant provide insight into the structural and dynamic changes that relieve inhibition. These results demonstrate how deleterious interactions can limit pathway transfer, that these interactions can be traced to specific molecular interactions between host and pathway, and how evolution or engineering can alleviate these limitations.
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Affiliation(s)
- Dan M Close
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Connor J Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Xingyou Wang
- Graduate Program in Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Payal Chirania
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Madhulika Gupta
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John R Ossyra
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Nancy Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Jeremy C Smith
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee, 37996, USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA, 02454, USA.,Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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28
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29
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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30
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Metagenomics Approaches in Discovery and Development of New Bioactive Compounds from Marine Actinomycetes. Curr Microbiol 2019; 77:645-656. [PMID: 31069462 DOI: 10.1007/s00284-019-01698-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/26/2019] [Indexed: 02/06/2023]
Abstract
Marine actinomycetes are prolific sources of marine drug discovery system contributing for several bioactive compounds of biomedical prominence. Metagenomics, a culture-independent technique through its sequence- and function-based screening has led to the discovery and synthesis of numerous biologically significant compounds like polyketide synthase, Non-ribosomal peptide synthetase, antibiotics, and biocatalyst. While metagenomics offers different advantages over conventional sequencing techniques, they also have certain limitations including bias classification, non-availability of quality DNA samples, heterologous expression, and host selection. The assimilation of advanced amplification and screening methods such as φ29 DNA polymerase, Next-Generation Sequencing, Cosmids, and recent bioinformatics tools like automated genome mining, anti-SMASH have shown promising results to overcome these constrains. Consequently, functional genomics and bioinformatics along with synthetic biology will be crucial for the success of the metagenomic approach and indeed for exploring new possibilities among the microbial consortia for the future drug discovery process.
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31
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Microbial evolutionary medicine: from theory to clinical practice. THE LANCET. INFECTIOUS DISEASES 2019; 19:e273-e283. [PMID: 31053492 DOI: 10.1016/s1473-3099(19)30045-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 11/21/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022]
Abstract
Medicine and clinical microbiology have traditionally attempted to identify and eliminate the agents that cause disease. However, this traditional approach is becoming inadequate for dealing with a changing disease landscape. Major challenges to human health are non-communicable chronic diseases, often driven by altered immunity and inflammation, and communicable infections from agents which harbour antibiotic resistance. This Review focuses on the so-called evolutionary medicine framework, to study how microbial communities influence human health. The evolutionary medicine framework aims to predict and manipulate microbial effects on human health by integrating ecology, evolutionary biology, microbiology, bioinformatics, and clinical expertise. We focus on the potential of evolutionary medicine to address three key challenges: detecting microbial transmission, predicting antimicrobial resistance, and understanding microbe-microbe and human-microbe interactions in health and disease, in the context of the microbiome.
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32
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Abstract
Production of fuels and chemicals from renewable lignocellulosic feedstocks is a promising alternative to petroleum-derived compounds. Due to the complexity of lignocellulosic feedstocks, microbial conversion of all potential substrates will require substantial metabolic engineering. Non-model microbes offer desirable physiological traits, but also increase the difficulty of heterologous pathway engineering and optimization. The development of modular design principles that allow metabolic pathways to be used in a variety of novel microbes with minimal strain-specific optimization will enable the rapid construction of microbes for commercial production of biofuels and bioproducts. In this review, we discuss variability of lignocellulosic feedstocks, pathways for catabolism of lignocellulose-derived compounds, challenges to heterologous engineering of catabolic pathways, and opportunities to apply modular pathway design. Implementation of these approaches will simplify the process of modifying non-model microbes to convert diverse lignocellulosic feedstocks.
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33
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Kintses B, Méhi O, Ari E, Számel M, Györkei Á, Jangir PK, Nagy I, Pál F, Fekete G, Tengölics R, Nyerges Á, Likó I, Bálint A, Molnár T, Bálint B, Vásárhelyi BM, Bustamante M, Papp B, Pál C. Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota. Nat Microbiol 2019; 4:447-458. [PMID: 30559406 PMCID: PMC6387620 DOI: 10.1038/s41564-018-0313-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/30/2018] [Indexed: 01/10/2023]
Abstract
The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.
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Affiliation(s)
- Bálint Kintses
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
| | - Orsolya Méhi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Eszter Ari
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Mónika Számel
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Ádám Györkei
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Pramod K Jangir
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd, Mórahalom, Hungary
- Sequencing Platform, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ferenc Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Gergely Fekete
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Roland Tengölics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - István Likó
- Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Anita Bálint
- 1st Department of Internal Medicine, Albert Szent-Györgyi Health Centre, University of Szeged, Szeged, Hungary
| | - Tamás Molnár
- 1st Department of Internal Medicine, Albert Szent-Györgyi Health Centre, University of Szeged, Szeged, Hungary
| | | | | | | | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
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Socha RD, Chen J, Tokuriki N. The Molecular Mechanisms Underlying Hidden Phenotypic Variation among Metallo-β-Lactamases. J Mol Biol 2019; 431:1172-1185. [PMID: 30769117 DOI: 10.1016/j.jmb.2019.01.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
Abstract
Genetic variation among orthologous genes has been largely formed through neutral genetic drift while maintaining the functional role of these genes. However, because the evolution of gene occurs in the context of each host organism, their sequence changes are also associated with adaptation to a specific environment. Thus, genetic variation can create critical phenotypic variation, particularly when genes are transferred to a new host by horizontal gene transfer. Unveiling "hidden phenotypic variation" is particularly important for genes that confer resistance to antibiotics. However, our understanding of the molecular mechanisms that underlie phenotypic variation remains limited. Here we sought to determine the extent of phenotypic variation in the B1 metallo-β-lactamase (MBL) family and its molecular basis by systematically characterizing eight MBL orthologs, including NDM-1 and VIM-2 and IMP-1. We found that these MBLs confer diverse levels of resistance. The phenotypic variation cannot be explained by variation in catalytic efficiency alone; rather, it is the combination of the catalytic efficiency and abundance of functional periplasmic enzyme that best predicts the observed variation in resistance. The level of functional periplasmic expression varied dramatically between MBL orthologs. This was the result of changes at multiple levels of each ortholog's: (1) quantity of mRNA, (2) amount of MBL expressed, and (3) efficacy of functional enzyme translocation to the periplasm. Overall, it is the interaction between each gene and the host's underlying cellular processes (transcription, translation, and translocation) that determines MBL genetic incompatibility through horizontal gene transfer. These host-specific processes may constrain the effective spread and deployment of MBLs to certain host species and could explain the current observed distribution bias.
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Affiliation(s)
- Raymond D Socha
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - John Chen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Collateral sensitivity constrains resistance evolution of the CTX-M-15 β-lactamase. Nat Commun 2019; 10:618. [PMID: 30728359 PMCID: PMC6365502 DOI: 10.1038/s41467-019-08529-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/15/2019] [Indexed: 11/25/2022] Open
Abstract
Antibiotic resistance is a major challenge to global public health. Discovery of new antibiotics is slow and to ensure proper treatment of bacterial infections new strategies are needed. One way to curb the development of antibiotic resistance is to design drug combinations where the development of resistance against one drug leads to collateral sensitivity to the other drug. Here we study collateral sensitivity patterns of the globally distributed extended-spectrum β-lactamase CTX-M-15, and find three non-synonymous mutations with increased resistance against mecillinam or piperacillin–tazobactam that simultaneously confer full susceptibility to several cephalosporin drugs. We show in vitro and in mice that a combination of mecillinam and cefotaxime eliminates both wild-type and resistant CTX-M-15. Our results indicate that mecillinam and cefotaxime in combination constrain resistance evolution of CTX-M-15, and illustrate how drug combinations can be rationally designed to limit the resistance evolution of horizontally transferred genes by exploiting collateral sensitivity patterns. Development of bacterial resistance to an antibiotic can lead to collateral sensitivity to another drug. Here, the authors study collateral sensitivity conferred by mutations in the horizontally acquired β-lactamase CTX-M-15, and identify antibiotic combinations that constrain the evolution of resistance.
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Yano H, Shintani M, Tomita M, Suzuki H, Oshima T. Reconsidering plasmid maintenance factors for computational plasmid design. Comput Struct Biotechnol J 2018; 17:70-81. [PMID: 30619542 PMCID: PMC6312765 DOI: 10.1016/j.csbj.2018.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/08/2018] [Accepted: 12/09/2018] [Indexed: 12/18/2022] Open
Abstract
Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University, 5180, Kurokawa, Imizu, Toyama 939-0398, Japan
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Krogh TJ, Møller-Jensen J, Kaleta C. Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes. Front Microbiol 2018; 9:2019. [PMID: 30210483 PMCID: PMC6119826 DOI: 10.3389/fmicb.2018.02019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Much attention has been devoted to investigating the dynamic topology and organization of the nucleoid. In contrast, the specific nucleoid organization, and the relationship between nucleoid structure and function is often neglected with regard to importance for adaption to changing environments and horizontal gene acquisition. In this review, we focus on the structure-function relationship in the bacterial nucleoid. We provide an overview of the fundamental properties that shape the chromosome as a structured yet dynamic macromolecule. These fundamental properties are then considered in the context of the living cell, with focus on how the informational flow affects the nucleoid structure, which in turn impacts on the genetic output. Subsequently, the dynamic living nucleoid will be discussed in the context of evolution. We will address how the acquisition of foreign DNA impacts nucleoid structure, and conversely, how nucleoid structure constrains the successful and sustainable chromosomal integration of novel DNA. Finally, we will discuss current challenges and directions of research in understanding the role of chromosomal architecture in bacterial survival and adaptation.
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Affiliation(s)
- Thøger J Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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Integrative analysis of fitness and metabolic effects of plasmids in Pseudomonas aeruginosa PAO1. ISME JOURNAL 2018; 12:3014-3024. [PMID: 30097663 PMCID: PMC6246594 DOI: 10.1038/s41396-018-0224-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/09/2018] [Accepted: 05/25/2018] [Indexed: 01/25/2023]
Abstract
Horizontal gene transfer (HGT) mediated by the spread of plasmids fuels evolution in prokaryotes. Although plasmids provide bacteria with new adaptive genes, they also produce physiological alterations that often translate into a reduction in bacterial fitness. The fitness costs associated with plasmids represent an important limit to plasmid maintenance in bacterial communities, but their molecular origins remain largely unknown. In this work, we combine phenomics, transcriptomics and metabolomics to study the fitness effects produced by a collection of diverse plasmids in the opportunistic pathogen Pseudomonas aeruginosa PAO1. Using this approach, we scan the physiological changes imposed by plasmids and test the generality of some main mechanisms that have been proposed to explain the cost of HGT, including increased biosynthetic burden, reduced translational efficiency, and impaired chromosomal replication. Our results suggest that the fitness effects of plasmids have a complex origin, since none of these mechanisms could individually provide a general explanation for the cost of plasmid carriage. Interestingly, our results also showed that plasmids alter the expression of a common set of metabolic genes in PAO1, and produce convergent changes in host cell metabolism. These surprising results suggest that there is a common metabolic response to plasmids in P. aeruginosa PAO1.
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Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach CF, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Plant L, Ploy MC, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel AJ, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson AS. Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. ENVIRONMENT INTERNATIONAL 2018; 117:132-138. [PMID: 29747082 DOI: 10.1016/j.envint.2018.04.041] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/30/2018] [Accepted: 04/21/2018] [Indexed: 05/24/2023]
Abstract
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 establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1.
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Affiliation(s)
- D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.
| | - Antoine Andremont
- INSERM, IAME, UMR 1137, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, 75018 Paris, France
| | - Johan Bengtsson-Palme
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.
| | - Kristian Koefoed Brandt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.
| | - Ana Maria de Roda Husman
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80175, 3508 TD Utrecht, The Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands.
| | | | - Jerker Fick
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, Cornwall TR1 3HD, UK.
| | - Makoto Kuroda
- National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
| | - Kristian Kvint
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy at University of Gothenburg, Guldhedsdsgatan 10A, SE-413 46, Sweden.
| | | | - Celia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal.
| | - Kaare Magne Nielsen
- Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, 0130 Oslo, Norway.
| | - Laura Plant
- Swedish Research Council, Box 1035, SE-101 38 Stockholm, Sweden.
| | | | - Carlos Segovia
- Unidad funcional de Acreditación de Institutos de Investigación Sanitaria, Instituto de Salud Carlos III, Spain.
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratory Ampère, UMR CNRS 5005, École Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 Écully Cedex, France.
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.
| | - Jason Snape
- Global Environment, AstraZeneca, Cheshire SK10 4TF, UK; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Edward Topp
- London Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Department of Biology, University of Western Ontario, London, ON N5V 4T3, Canada.
| | - Arjon J van Hengel
- Directorate Health, Directorate-General for Research and Innovation, European Commission, Brussels, Belgium.
| | - David W Verner-Jeffreys
- Cefas Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset DT4 8UB, UK.
| | - Marko P J Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | | | - Ann-Sofie Wernersson
- Swedish Agency for Marine and Water Management, Box 11 930, SE-404 39 Gothenburg, Sweden.
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