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Hughes, Diarmaid
Publications (10 of 119) Show all publications
Brandis, G., Cao, S. & Hughes, D. (2018). Co-evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella. Molecular Microbiology, 108(6), 697-710
Open this publication in new window or tab >>Co-evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella
2018 (English)In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 108, no 6, p. 697-710Article in journal (Refereed) Published
Abstract [en]

Bacteria can have multiple copies of a gene at separate locations on the same chromosome. Some of these gene families, including tuf (translation elongation factor EF-Tu) and rrl (ribosomal RNA), encode functions critically important for bacterial fitness. Genes within these families are known to evolve in concert using homologous recombination to transfer genetic information from one gene to another. This mechanism can counteract the detrimental effects of nucleotide sequence divergence over time. Whether such mechanisms can also protect against the potentially lethal effects of mobile genetic element insertion is not well understood. To address this we constructed two different length insertion cassettes to mimic mobile genetic elements and inserted these into various positions of the tuf and rrl genes. Wemeasured rates of recombinational repair that removed the inserted cassette and studied the underlying mechanism. Our results indicate that homologous recombination can protect the tuf and rrl genes from inactivation by mobile genetic elements, but forinsertions within shorter gene sequences the efficiency of repair is very low. Intriguingly, we found that physical distance separating genes on the chromosome directly affects the rate of recombinational repair suggesting that relative location will influence the ability of homologous recombination to maintain homogeneity.

Place, publisher, year, edition, pages
WILEY, 2018
National Category
Genetics Microbiology Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-358073 (URN)10.1111/mmi.13959 (DOI)000434978300008 ()29603442 (PubMedID)
Funder
Swedish Research Council, 2016-04449Swedish Research Council, 2017-03953Carl Tryggers foundation , CTS16:194Carl Tryggers foundation , CTS17:204
Available from: 2018-08-30 Created: 2018-08-30 Last updated: 2018-08-30Bibliographically approved
Jeannot, F., Taillier, T., Despeyroux, P., Renard, S., Rey, A., Mourez, M., . . . Bacqué, E. (2018). Imidazopyrazinones (IPYs): Non-Quinolone Bacterial Topoisomerase Inhibitors Showing Partial Cross-Resistance with Quinolones. Journal of Medicinal Chemistry, 61(8), 3565-3581
Open this publication in new window or tab >>Imidazopyrazinones (IPYs): Non-Quinolone Bacterial Topoisomerase Inhibitors Showing Partial Cross-Resistance with Quinolones
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2018 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 61, no 8, p. 3565-3581Article in journal (Refereed) Published
Abstract [en]

In our quest for new antibiotics able to address the growing threat of multidrug resistant infections caused by Gram-negative bacteria, we have investigated an unprecedented series of non-quinolone bacterial topoisomerase inhibitors from the Sanofi patrimony, named IPYs for imidazopyrazinones, as part of the Innovative Medicines Initiative (IMI) European Gram Negative Antibacterial Engine (ENABLE) organization. Hybridization of these historical compounds with the quinazolinediones, a known series of topoisomerase inhibitors, led us to a novel series of tricyclic IPYs that demonstrated potential for broad spectrum activity, in vivo efficacy, and a good developability profile, although later profiling revealed a genotoxicity risk. Resistance studies revealed partial cross-resistance with fluoroquinolones (FQs) suggesting that IPYs bind to the same region of bacterial topoisomerases as FQs and interact with at least some of the keys residues involved in FQ binding.

National Category
Medicinal Chemistry
Identifiers
urn:nbn:se:uu:diva-356096 (URN)10.1021/acs.jmedchem.7b01892 (DOI)000431151000021 ()29596745 (PubMedID)
Available from: 2018-07-19 Created: 2018-07-19 Last updated: 2018-07-19Bibliographically approved
Pantel, L., Florin, T., Dobosz-Bartoszek, M., Racine, E., Sarciaux, M., Serri, M., . . . Gualtieri, M. (2018). Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site. Molecular Cell, 70(1), 83-94
Open this publication in new window or tab >>Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site
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2018 (English)In: Molecular Cell, ISSN 1097-2765, E-ISSN 1097-4164, Vol. 70, no 1, p. 83-94Article in journal (Refereed) Published
Abstract [en]

Growing resistance of pathogenic bacteria and shortage of antibiotic discovery platforms challenge the use of antibiotics in the clinic. This threat calls for exploration of unconventional sources of antibiotics and identification of inhibitors able to eradicate resistant bacteria. Here we describe a different class of antibiotics, odilorhabdins (ODLs), produced by the enzymes of the non-ribosomal peptide synthetase gene cluster of the nematode-symbiotic bacterium Xenorhabdus nematophila. ODLs show activity against Gram-positive and Gram-negative pathogens, including carbapenem-resistant Enterobacteriaceae, and can eradicate infections in animal models. We demonstrate that the bactericidal ODLs interfere with protein synthesis. Genetic and structural analyses reveal that ODLs bind to the small ribosomal subunit at a site not exploited by current antibiotics. ODLs induce miscoding and promote hungry codon readthrough, amino acid misincorporation, and premature stop codon bypass. We propose that ODLs' miscoding activity reflects their ability to increase the affinity of non-cognate aminoacyl-tRNAs to the ribosome.

Place, publisher, year, edition, pages
CELL PRESS, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-352693 (URN)10.1016/j.molcel.2018.03.001 (DOI)000429301100010 ()29625040 (PubMedID)
Funder
EU, European Research Council
Available from: 2018-06-08 Created: 2018-06-08 Last updated: 2018-06-08Bibliographically approved
Khan, D., Lagerbäck, P., Malmberg, C., Kristoffersson, A., Gullberg, E., Cao, S., . . . Friberg, L. E. (2018). Predicting mutant selection in competition experiments with ciprofloxacin-exposed Escherichia coli. International Journal of Antimicrobial Agents, 51(3), 399-406, Article ID S0924-8579(17)30392-8.
Open this publication in new window or tab >>Predicting mutant selection in competition experiments with ciprofloxacin-exposed Escherichia coli
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2018 (English)In: International Journal of Antimicrobial Agents, ISSN 0924-8579, E-ISSN 1872-7913, Vol. 51, no 3, p. 399-406, article id S0924-8579(17)30392-8Article in journal (Refereed) Published
Abstract [en]

Predicting competition between antibiotic-susceptible wild-type (WT) and less susceptible mutant (MT) bacteria is valuable for understanding how drug concentrations influence the emergence of resistance. Pharmacokinetic/pharmacodynamic (PK/PD) models predicting the rate and extent of takeover of resistant bacteria during different antibiotic pressures can thus be a valuable tool in improving treatment regimens. The aim of this study was to evaluate a previously developed mechanism-based PK/PD model for its ability to predict in vitro mixed-population experiments with competition between Escherichia coli (E. coli) WT and three well-defined E. coli resistant MTs when exposed to ciprofloxacin. Model predictions for each bacterial strain and ciprofloxacin concentration were made for in vitro static and dynamic time–kill experiments measuring CFU (colony forming units)/mL up to 24 h with concentrations close to or below the minimum inhibitory concentration (MIC), as well as for serial passage experiments with concentrations well below the MIC measuring ratios between the two strains with flow cytometry. The model was found to reasonably well predict the initial bacterial growth and killing of most static and dynamic time–kill competition experiments without need for parameter re-estimation. With parameter re-estimation of growth rates, an adequate fit was also obtained for the 6-day serial passage competition experiments. No bacterial interaction in growth was observed. This study demonstrates the predictive capacity of a PK/PD model and further supports the application of PK/PD modelling for prediction of bacterial kill in different settings, including resistance selection.

Keywords
Ciprofloxacin, Escherichia coli, PK/PD modelling, PK/PD predictions, Pharmacokinetics/Pharmacodynamics, Time–kill experiments
National Category
Pharmaceutical Sciences Pharmaceutical Sciences
Identifiers
urn:nbn:se:uu:diva-343607 (URN)10.1016/j.ijantimicag.2017.10.019 (DOI)000427582000016 ()29127049 (PubMedID)
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research EU, FP7, Seventh Framework Programme, FP7/2007-2013
Available from: 2018-02-28 Created: 2018-02-28 Last updated: 2018-05-18Bibliographically approved
Cao, S., Huseby, D. L., Brandis, G. & Hughes, D. (2017). Alternative Evolutionary Pathways for Drug-Resistant Small Colony Variant Mutants in Staphylococcus aureus. mBio, 8(3), Article ID e00358-17.
Open this publication in new window or tab >>Alternative Evolutionary Pathways for Drug-Resistant Small Colony Variant Mutants in Staphylococcus aureus
2017 (English)In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 8, no 3, article id e00358-17Article in journal (Refereed) Published
Abstract [en]

Staphylococcus aureus is known to generate small colony variants (SCVs) that are resistant to aminoglycoside antibiotics and can cause persistent and recurrent infections. The SCV phenotype is unstable, and compensatory mutations lead to restored growth, usually with loss of resistance. However, the evolution of improved growth, by mechanisms that avoid loss of antibiotic resistance, is very poorly understood. By selection with serial passaging, we isolated and characterized different classes of extragenic suppressor mutations that compensate for the slow growth of small colony variants. Compensation occurs by two distinct bypass mechanisms: (i) translational suppression of the initial SCV mutation by mutant tRNAs, ribosomal protein S5, or release factor 2 and (ii) mutations that cause the constitutive activation of the SrrAB global transcriptional regulation system. Although compensation by translational suppression increases growth rate, it also reduces antibiotic susceptibility, thus restoring a pseudo-wild-type phenotype. In contrast, an evolutionary pathway that compensates for the SCV phenotype by activation of SrrAB increases growth rate without loss of antibiotic resistance. RNA sequence analysis revealed that mutations activating the SrrAB pathway cause upregulation of genes involved in peptide transport and in the fermentation pathways of pyruvate to generate ATP and NAD(+), thus explaining the increased growth. By increasing the growth rate of SCVs without the loss of aminoglycoside resistance, compensatory evolution via the SrrAB activation pathway represents a threat to effective antibiotic therapy of staphylococcal infections. IMPORTANCE Small colony variants (SCVs) of Staphylococcus aureus are a significant clinical problem, causing persistent and antibiotic-resistant infections. However, SCVs are unstable and can rapidly evolve growth-compensated mutants. Previous data suggested that growth compensation only occurred with the loss of antibiotic resistance. We have used selection with serial passaging to uncover four distinct pathways of growth compensation accessible to SCVs. Three of these paths (reversion, intragenic suppression, and translational suppression) increase growth at the expense of losing antibiotic resistance. The fourth path activates an alternative transcriptional program and allows the bacteria to produce the extra ATP required to support faster growth, without losing antibiotic resistance. The importance of this work is that it shows that drug-resistant SCVs can evolve faster growth without losing antibiotic resistance.

Place, publisher, year, edition, pages
AMER SOC MICROBIOLOGY, 2017
Keywords
ATP, experimental evolution, growth compensation, hemin biosynthesis, menaquinone, SrrAB, transcriptional regulation, translational suppression
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-330055 (URN)10.1128/mBio.00358-17 (DOI)000404733300009 ()
Available from: 2017-11-16 Created: 2017-11-16 Last updated: 2017-11-16Bibliographically approved
Banin, E., Hughes, D. & Kuipers, O. P. (2017). Bacterial pathogens, antibiotics and antibiotic resistance: Editorial. FEMS Microbiology Reviews, 41(3), 450-452, Article ID fux016.
Open this publication in new window or tab >>Bacterial pathogens, antibiotics and antibiotic resistance: Editorial
2017 (English)In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 41, no 3, p. 450-452, article id fux016Article in journal, Editorial material (Other academic) Published
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-332902 (URN)10.1093/femsre/fux016 (DOI)000402064900012 ()28486583 (PubMedID)
Available from: 2017-11-06 Created: 2017-11-06 Last updated: 2017-11-06Bibliographically approved
Nielsen, E. I., Khan, D. D., Cao, S., Lustig, U., Hughes, D., Andersson, D. I. & Friberg, L. E. (2017). Can a pharmacokinetic/pharmacodynamic (PKPD) model be predictive across bacterial densities and strains?: External evaluation of a PKPD model describing longitudinal in vitro data. Journal of Antimicrobial Chemotherapy, 72(11), 3108-3116
Open this publication in new window or tab >>Can a pharmacokinetic/pharmacodynamic (PKPD) model be predictive across bacterial densities and strains?: External evaluation of a PKPD model describing longitudinal in vitro data
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2017 (English)In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 72, no 11, p. 3108-3116Article in journal (Refereed) Published
Abstract [en]

Background: Pharmacokinetic/pharmacodynamic (PKPD) models developed based on data from in vitro time-kill experiments have been suggested to contribute to more efficient drug development programmes and better dosing strategies for antibiotics. However, for satisfactory predictions such models would have to show good extrapolation properties. Objectives: To evaluate if a previously described mechanism-based PKPD model was able also to predict drug efficacy for higher bacterial densities and across bacterial strains. Methods: A PKPD model describing the efficacy of ciprofloxacin on Escherichia coli was evaluated. The predictive performance of the model was evaluated across several experimental conditions with respect to: (i) bacterial start inoculum ranging from the standard of similar to 10(6) cfu/mL up to late stationary-phase cultures; and (ii) efficacy for seven additional strains (three laboratory and four clinical strains), not included during the model development process, based only on information regarding their MIC. Model predictions were performed according to the intended experimental protocol and later compared with observed bacterial counts. Results: The mechanism-based PKPD model structure developed based on data from standard start inoculum experiments was able to accurately describe the inoculum effect. The model successfully predicted the time course of drug efficacy for additional laboratory and clinical strains based on only the MIC values. The model structure was further developed to better describe the stationary phase data. Conclusions: This study supports the use of mechanism-based PKPD models based on preclinical data for predictions of untested scenarios.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
National Category
Pharmaceutical Sciences Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-340705 (URN)10.1093/jac/dkx269 (DOI)000413464200019 ()28961946 (PubMedID)
Funder
Swedish Foundation for Strategic Research
Available from: 2018-02-21 Created: 2018-02-21 Last updated: 2018-02-21Bibliographically approved
Pietsch, F., Bergman, J. M., Brandis, G., Marcusson, L. L., Zorzet, A., Huseby, D. L. & Hughes, D. (2017). Ciprofloxacin selects for RNA polymerase mutations with pleiotropic antibiotic resistance effects. Journal of Antimicrobial Chemotherapy, 72(1), 75-84
Open this publication in new window or tab >>Ciprofloxacin selects for RNA polymerase mutations with pleiotropic antibiotic resistance effects
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2017 (English)In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 72, no 1, p. 75-84Article in journal (Refereed) Published
Abstract [en]

Objectives: Resistance to the fluoroquinolone drug ciprofloxacin is commonly linked to mutations that alter the drug target or increase drug efflux via the major AcrAB-TolC transporter. Very little is known about other mutations that might also reduce susceptibility to ciprofloxacin. We discovered that an Escherichia coli strain experimentally evolved for resistance to ciprofloxacin had acquired a mutation in rpoB, the gene coding for the beta-subunit of RNA polymerase. The aim of this work was to determine whether this mutation, and other mutations in rpoB, contribute to ciprofloxacin resistance and, if so, by which mechanism. Methods: Independent lineages of E. coli were evolved in the presence of ciprofloxacin and clones from endpoint cultures were screened for mutations in rpoB. Ciprofloxacin-selected rpoB mutations were identified and characterized in terms of effects on susceptibility and mode of action. Results: Mutations in rpoB were selected at a high frequency in 3 out of 10 evolved lineages, in each case arising after the occurrence of mutations affecting topoisomerases and drug efflux. All ciprofloxacin-selected rpoB mutations had a high fitness cost in the absence of drug, but conferred a competitive advantage in the presence of ciprofloxacin. RNA sequencing and quantitative RT-PCR analysis showed that expression of mdtK, encoding a multidrug efflux transporter, was significantly increased by the ciprofloxacin-selected rpoB mutations. The susceptibility phenotype was shown to depend on the presence of an active mdtK and a mutant rpoB allele. Conclusions: These data identify mutations in RNA polymerase as novel contributors to the evolution of resistance to ciprofloxacin and show that the phenotype is mediated by increased MdtK-dependent drug efflux.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
National Category
Infectious Medicine Microbiology in the medical area Medicinal Chemistry
Identifiers
urn:nbn:se:uu:diva-319816 (URN)10.1093/jac/dkw364 (DOI)000394038700010 ()27621175 (PubMedID)
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research Knut and Alice Wallenberg Foundation
Available from: 2017-04-10 Created: 2017-04-10 Last updated: 2018-01-13Bibliographically approved
De Rosa, M., Lu, L., Zamaratski, E., Szałaj, N., Cao, S., Wadensten, H., . . . Karlen, A. (2017). Design, synthesis and in vitro biological evaluation of oligopeptides targeting E. coli type I signal peptidase (LepB). Bioorganic & Medicinal Chemistry, 25(3), 897-911
Open this publication in new window or tab >>Design, synthesis and in vitro biological evaluation of oligopeptides targeting E. coli type I signal peptidase (LepB)
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2017 (English)In: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 25, no 3, p. 897-911Article in journal (Refereed) Published
Abstract [en]

Type I signal peptidases are potential targets for the development of new antibacterial agents. Here we report finding potent inhibitors of E. coli type I signal peptidase (LepB), by optimizing a previously reported hit compound, decanoyl-PTANA-CHO, through modifications at the N- and C-termini. Good improvements of inhibitory potency were obtained, with IC50s in the low nanomolar range. The best inhibitors also showed good antimicrobial activity, with MICs in the low μg/mL range for several bacterial species. The selection of resistant mutants provided strong support for LepB as the target of these compounds. The cytotoxicity and hemolytic profiles of these compounds are not optimal but the finding that minor structural changes cause the large effects on these properties suggests that there is potential for optimization in future studies.

Keywords
Antibacterials, Escherichia coli, Oligopeptides, Solid-phase peptide synthesis, Type I signal peptidase
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-314110 (URN)10.1016/j.bmc.2016.12.003 (DOI)000394201900009 ()28038943 (PubMedID)
Funder
Swedish Research Council, 521-2014-6711 521-2013-2904 521-2013-3105 621-2014-6215Swedish Foundation for Strategic Research , RIF14-0078Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

Maria De Rosa and Lu Lu contributed equally to this work.

Available from: 2017-01-27 Created: 2017-01-27 Last updated: 2018-01-13Bibliographically approved
Petursdottir, D. H., Nordlander, S., Qazi, K. R., Carvalho-Queiroz, C., Osman, O. A., Hell, E., . . . Sverremark-Ekstrom, E. (2017). Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice. Frontiers in Immunology, 8, Article ID 1699.
Open this publication in new window or tab >>Early-Life Human Microbiota Associated With Childhood Allergy Promotes the T Helper 17 Axis in Mice
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2017 (English)In: Frontiers in Immunology, ISSN 1664-3224, E-ISSN 1664-3224, Vol. 8, article id 1699Article in journal (Refereed) Published
Abstract [en]

The intestinal microbiota influences immune maturation during childhood, and is implicated in early-life allergy development. However, to directly study intestinal microbes and gut immune responses in infants is difficult. To investigate how different types of early-life gut microbiota affect immune development, we collected fecal samples from children with different allergic heredity (AH) and inoculated germ-free mice. Immune responses and microbiota composition were evaluated in the offspring of these mice. Microbial composition in the small intestine, the cecum and the colon were determined by 16S rRNA sequencing. The intestinal microbiota differed markedly between the groups of mice, but only exposure to microbiota associated with AH and known future allergy in children resulted in a T helper 17 (Th17)-signature, both systemically and in the gut mucosa in the mouse offspring. These Th17 responses could be signs of a particular microbiota and a shift in immune development, ultimately resulting in an increased risk of allergy.

Place, publisher, year, edition, pages
FRONTIERS MEDIA SA, 2017
Keywords
infant microbiota, allergic heredity, immune development, germ-free, T helper 17-responsesIN
National Category
Immunology in the medical area
Identifiers
urn:nbn:se:uu:diva-343555 (URN)10.3389/fimmu.2017.01699 (DOI)000416803000001 ()
Funder
Swedish Research Council, 2013-02904Swedish Heart Lung FoundationTorsten Söderbergs stiftelseStiftelsen Olle Engkvist ByggmästareCarl Tryggers foundation Swedish Research Council, 2016-04449
Available from: 2018-03-02 Created: 2018-03-02 Last updated: 2018-03-02Bibliographically approved
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