The McArthur lab and the Comprehensive Antibiotic Resistance Database are proud to have contributed to the Genome Canada – Canadian Food Inspection Agency Forum on Genomics and Antimicrobial Resistance. The two-day event brought together over sixty leading experts from academic, government, industry and commodities groups to address the challenge of AMR and discuss a path forward. A summary of the Forum and the Workshop Report are now online.
Ni X, Davis JH, Jain N, Razi A, Benlekbir S, McArthur AG, Rubinstein JL, Britton RA, Williamson JR, Ortega J.
Nucleic Acids Res. 2016 Sep 30;44(17):8442-55.
YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were under the control of an inducible promoter. Under depletion conditions, they accumulated incomplete ribosomal subunits that we named 45SYphC and 44.5SYsxC particles. Quantitative mass spectrometry analysis and the 5-6 Å resolution cryo-EM maps of the 45SYphC and 44.5SYsxC particles revealed that the two GTPases participate in the maturation of the central protuberance, GTPase associated region and key RNA helices in the A, P and E functional sites of the 50S subunit. We observed that YphC and YsxC bind specifically to the two immature particles, suggesting that they represent either on-pathway intermediates or that their structure has not significantly diverged from that of the actual substrate. These results describe the nature of these immature particles, a widely used tool to study the assembly process of the ribosome. They also provide the first insights into the function of YphC and YsxC in 50S subunit assembly and are consistent with this process occurring through multiple parallel pathways, as it has been described for the 30S subunit.
Williams LM, Lago BA, McArthur AG, Raphenya AR, Pray N, Saleem N, Salas S, Paulson K, Mangar RS, Liu Y, Vo AH, Shavit JA.
Aquat Toxicol. 2016 Oct 1;180:141-154.
Development is a complex and well-defined process characterized by rapid cell proliferation and apoptosis. At this stage in life, a developmentally young organism is more sensitive to toxicants as compared to an adult. In response to pro-oxidant exposure, members of the Cap’n’Collar (CNC) basic leucine zipper (b-ZIP) transcription factor family (including Nfe2 and Nfe2-related factors, Nrfs) activate the expression of genes whose protein products contribute to reduced toxicity. Here, we studied the role of the CNC protein, Nfe2, in the developmental response to pro-oxidant exposure in the zebrafish (Danio rerio). Following acute waterborne exposures to diquat or tert-buytlhydroperoxide (tBOOH) at one of three developmental stages, wildtype (WT) and nfe2 knockout (KO) embryos and larvae were morphologically scored and their transcriptomes sequenced. Early in development, KO animals suffered from hypochromia that was made more severe through exposure to pro-oxidants; this phenotype in the KO may be linked to decreased expression of alas2, a gene involved in heme synthesis. WT and KO eleutheroembryos and larvae were phenotypically equally affected by exposure to pro-oxidants, where tBOOH caused more pronounced phenotypes as compared to diquat. Comparing diquat and tBOOH exposed embryos relative to the WT untreated control, a greater number of genes were up-regulated in the tBOOH condition as compared to diquat (tBOOH: 304 vs diquat: 148), including those commonly found to be differentially regulated in the vertebrate oxidative stress response (OSR) (e.g. hsp70.2, txn1, and gsr). When comparing WT and KO across all treatments and times, there were 1170 genes that were differentially expressed, of which 33 are known targets of the Nrf proteins Nrf1 and Nrf2. More specifically, in animals exposed to pro-oxidants a total of 968 genes were differentially expressed between WT and KO across developmental time, representing pathways involved in coagulation, embryonic organ development, body fluid level regulation, erythrocyte differentiation, and oxidation-reduction, amongst others. The greatest number of genes that changed in expression between WT and KO occurred in animals exposed to diquat at 2h post fertilization (hpf). Across time and treatment, there were six genes (dhx40, cfap70, dnajb9b, slc35f4, spi-c, and gpr19) that were significantly up-regulated in KO compared to WT and four genes (fhad1, cyp4v7, nlrp12, and slc16a6a) that were significantly down-regulated. None of these genes have been previously identified as targets of Nfe2 or the Nrf family. These results demonstrate that the zebrafish Nfe2 may be a regulator of both primitive erythropoiesis and the OSR during development.
Authors: Dearborn DC, Gager AB, McArthur AG, Gilmour ME, Mandzhukova E, Mauck RA.
Mol Ecol. 2016 Sep;25(17):4355-67.
Genes of the major histocompatibility complex (MHC) exhibit heterozygote advantage in immune defence, which in turn can select for MHC-disassortative mate choice. However, many species lack this expected pattern of MHC-disassortative mating. A possible explanation lies in evolutionary processes following gene duplication: if two duplicated MHC genes become functionally diverged from each other, offspring will inherit diverse multilocus genotypes even under random mating. We used locus-specific primers for high-throughput sequencing of two expressed MHC Class II B genes in Leach’s storm-petrels, Oceanodroma leucorhoa, and found that exon 2 alleles fall into two gene-specific monophyletic clades. We tested for disassortative vs. random mating at these two functionally diverged Class II B genes, using multiple metrics and different subsets of exon 2 sequence data. With good statistical power, we consistently found random assortment of mates at MHC. Despite random mating, birds had MHC genotypes with functionally diverged alleles, averaging 13 amino acid differences in pairwise comparisons of exon 2 alleles within individuals. To test whether this high MHC diversity in individuals is driven by evolutionary divergence of the two duplicated genes, we built a phylogenetic permutation model. The model showed that genotypic diversity was strongly impacted by sequence divergence between the most common allele of each gene, with a smaller additional impact of monophyly of the two genes. Divergence of allele sequences between genes may have reduced the benefits of actively seeking MHC-dissimilar mates, in which case the evolutionary history of duplicated genes is shaping the adaptive landscape of sexual selection.
McMaster Interdisciplinary Research Exposition (MIREx); Ontario Biology Day; Biomedical Discovery and Commercialization Engage Symposium; Rapid Microbial NGS and Bioinformatics: Translation Into Practice (Germany); Canadian Food Inspection Agency Forum on Genomics and Antimicrobial Resistance; New Antibacterial Discovery & Development Gordon Research Conference (Italy); McMaster Women in Science and Engineering (WISE) Current Research in Engineering, Science & Technology (CREST) Meeting; 6th Biennial National IDeA Symposium of Biomedical Research Excellence (USA).
Presenter underlined, trainees in bold.
- Dave, B.M., J.A. Klein, L.A. Knodler, A.R. Raphenya, & A.G. McArthur. 2016. A phylogenetic analysis of Inv/Mxi-Spa proteins and implications for functional complementation. Poster presentation at McMaster Interdisciplinary Research Exposition (MIREx), Hamilton, Ontario, Canada.
- Dave, B.M., J.A. Klein, L.A. Knodler, A.R. Raphenya, & A.G. McArthur. 2016. A phylogenetic analysis of Inv/Mxi-Spa proteins and implications for functional complementation. Poster presentation at Ontario Biology Day 2016, Toronto, Ontario, Canada.
- Lin, Z. & A.G. McArthur. 2016. Adapting Galaxy bioinformatics to outbreak-associated Clostridium difficile. Poster presentation at McMaster’s Biomedical Discovery and Commercialization Engage Symposium, Hamilton, Ontario, Canada.
- McArthur, A.G., B. Jia, A.R. Raphenya, P. Guo, K. Tsang, B. Dave, B. Alcock, B. Lago, N. Waglechner, & G.D. Wright. 2016. The Comprehensive Antibiotic Resistance Database – A Platform for Antimicrobial Resistance Surveillance. Invited presentation at the 2nd Conference Rapid Microbial NGS and Bioinformatics: Translation Into Practice, Hamburg, Germany.
- McArthur, A.G. 2016. Bioinformatic resources for antimicrobial resistance. Invited presentation at Canadian Food Inspection Agency (CFIA) Forum on Genomics and Antimicrobial Resistance, Ottawa, Ontario, Canada.
- McArthur, A.G. 2016. Combatting Antibiotic Resistance Using Surveillance. Invited presentation at McMaster Interdisciplinary Research Exposition (MIREx), Hamilton, Ontario, Canada.
- Pawlowski, A.C., W. Wang, K. Koteva, H.A. Barton, B. Jia, A.R. Raphenya, P. Guo, A.G. McArthur, G.D. Wright. 2016. A multi-antibiotic resistant genotype is maintained for millions of years. Presentation at the New Antibacterial Discovery & Development Gordon Research Conference, Lucca, Italy.
- Tsang, K. & A.G. McArthur. 2016. Translation of biocuration to metagenomic analysis. Poster presentation at McMaster Interdisciplinary Research Exposition (MIREx), Hamilton, Ontario, Canada.
- Tsang, K. & A.G. McArthur. 2016. Translation of biocuration to metagenomic analysis. Poster presentation at Ontario Biology Day 2016, Toronto, Ontario, Canada.
- Tsang, K. & A.G. McArthur. 2016. Translation of biocuration to metagenomic analysis. Poster presentation at McMaster Women in Science and Engineering (WISE) Current Research in Engineering, Science & Technology (CREST) Meeting, Hamilton, Ontario, Canada.
- Tsang, K. & A.G. McArthur. 2016. Translation of biocuration to metagenomic analysis. Poster presentation at McMaster’s Biomedical Discovery and Commercialization Engage Symposium, Hamilton, Ontario, Canada.
- Williams, L., A.G. McArthur, B. Lago, A.R. Raphenya, N. Pray, N. Saleem, S. Salas, K. Paulson, R. Mangar, Y. Liu, A. Vo, & J. Shavit. 2016. Nuclear factor, erythoid 2 (Nfe2) is a transcriptional regulator of oxidative stress during zebrafish development. Presentation at the 6th Biennial National IDeA Symposium of Biomedical Research Excellence, Washington, DC.
Authors: Freschi et al. Front Microbiol. 2015 Sep 29;6:1036.
The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.
Authors: Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM. Mol Ecol Resour. 2015 Nov;15(6):1304-15.
Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situ DNA degradation on data generation for a modified double-digest RADSeq approach (3RAD). We generated libraries using genomic DNA serially extracted from the muscle tissue of 8 individual lake whitefish (Coregonus clupeaformis) following 0-, 12-, 48- and 96-h incubation at room temperature posteuthanasia. This treatment of the tissue resulted in input DNA that ranged in quality from nearly intact to highly sheared. All samples were sequenced as a multiplexed pool on an Illumina MiSeq. Libraries created from low to moderately degraded DNA (12-48 h) performed well. In contrast, the number of RADtags per individual, number of variable sites, and percentage of identical RADtags retained were all dramatically reduced when libraries were made using highly degraded DNA (96-h group). This reduction in performance was largely due to a significant and unexpected loss of raw reads as a result of poor quality scores. Our findings remained consistent after changes in restriction enzymes, modified fold coverage values (2- to 16-fold), and additional read-length trimming. We conclude that starting DNA quality is an important consideration for RADSeq; however, the approach remains robust until genomic DNA is extensively degraded.
Authors: McArthur AG, Wright GD.
Curr Opin Microbiol. 2015 Jul 31;27:45-50.
Antimicrobial resistance is a global health challenge and has an evolutionary trajectory ranging from proto-resistance in the environment to untreatable clinical pathogens. Resistance is not static, as pathogenic strains can move among patient populations and individual resistance genes can move among pathogens. Effective treatment of resistant infections, antimicrobial stewardship, and new drug discovery increasingly rely upon genotype information, powered by decreasing costs of DNA sequencing. These new approaches will require advances in microbial informatics, particularly in development of reference databases of molecular determinants such as our Comprehensive Antibiotic Resistance Database and clinical metadata, new algorithms for prediction of resistome and resistance phenotype from genotype, and new protocols for global collection and sharing of high-throughput molecular epidemiology data.
Authors: Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG, Brinkman FS.
Nucleic Acids Res. 2015 Jul 1;43(W1):W104-8.
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization.
Authors: Dearborn DC, Gager AB, Gilmour ME, McArthur AG, Hinerfeld DA, Mauck RA.
Immunogenetics. 2015 Feb;67(2):111-23.
The major histocompatibility complex (Mhc) is subject to pathogen-mediated balancing selection and can link natural selection with mate choice. We characterized two Mhc class II B loci in Leach’s storm-petrel, Oceanodroma leucorhoa, focusing on exon 2 which encodes the portion of the protein that binds pathogen peptides. We amplified and sequenced exon 2 with locus-specific nested PCR and Illumina MiSeq using individually barcoded primers. Repeat genotyping of 78 single-locus genotypes produced identical results in 77 cases (98.7 %). Sequencing of messenger RNA (mRNA) from three birds confirmed expression of both loci, consistent with the observed absence of stop codons or frameshifts in all alleles. In 48 birds, we found 9 and 12 alleles at the two loci, respectively, and all 21 alleles translated to unique amino acid sequences. Unlike many studies of duplicated Mhc genes, alleles of the two loci clustered into monophyletic groups. Consistent with this phylogenetic result, interlocus gene conversion appears to have affected only two short fragments of the exon. As predicted under a paradigm of pathogen-mediated selection, comparison of synonymous and non-synonymous substitution rates found evidence of a history of positive selection at putative peptide binding sites. Overall, the results suggest that the gene duplication event leading to these two loci is not recent and that point mutations and positive selection on the peptide binding sites may be the predominant forces acting on these genes. Characterization of these loci sets the stage for population-level work on the evolutionary ecology of Mhc in this species.