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Górniak M, Zalewska A, Jurczak-Kurek A. Recombination Events in Putative Tail Fibre Gene in Litunavirus Phages Infecting Pseudomonas aeruginosa and Their Phylogenetic Consequences. Viruses 2022; 14:v14122669. [PMID: 36560673 PMCID: PMC9786124 DOI: 10.3390/v14122669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Recombination is the main driver of bacteriophage evolution. It may serve as a tool for extending the phage host spectrum, which is significant not only for phages' ecology but also for their utilisation as therapeutic agents of bacterial infections. The aim of this study was to detect the recombination events in the genomes of Litunavirus phages infecting Pseudomonas aeruginosa, and present their impact on phylogenetic relations within this phage group. The phylogenetic analyses involved: the whole-genome, core-genome (Schitoviridae conserved genes), variable genome region, and the whole-genome minus variable region. Interestingly, the recombination events taking place in the putative host recognition region (tail fibre protein gene and the adjacent downstream gene) significantly influenced tree topology, suggesting a strong phylogenetic signal. Our results indicate the recombination between phages from two genera Litunavirus and Luzeptimavirus and demonstrate its influence on phage phylogeny.
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Paetzold C, Barke BH, Hörandl E. Evolution of Transcriptomes in Early-Generation Hybrids of the Apomictic Ranunculus auricomus Complex ( Ranunculaceae). Int J Mol Sci 2022; 23:ijms232213881. [PMID: 36430360 PMCID: PMC9697309 DOI: 10.3390/ijms232213881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
Hybridisation in plants may cause a shift from sexual to asexual seed formation (apomixis). Indeed, natural apomictic plants are usually hybrids, but it is still unclear how hybridisation could trigger the shift to apomixis. The genome evolution of older apomictic lineages is influenced by diverse processes such as polyploidy, mutation accumulation, and allelic sequence divergence. To disentangle the effects of hybridisation from these other factors, we analysed the transcriptomes of flowering buds from artificially produced, diploid F2 hybrids of the Ranunculus auricomus complex. The hybrids exhibited unreduced embryo sac formation (apospory) as one important component of apomixis, whereas their parental species were sexual. We revealed 2915 annotated single-copy genes that were mostly under purifying selection according to dN/dS ratios. However, pairwise comparisons revealed, after rigorous filtering, 79 genes under diversifying selection between hybrids and parents, whereby gene annotation assigned ten of them to reproductive processes. Four genes belong to the meiosis-sporogenesis phase (ASY1, APC1, MSP1, and XRI1) and represent, according to literature records, candidate genes for apospory. We conclude that hybridisation could combine novel (or existing) mutations in key developmental genes in certain hybrid lineages, and establish (together with altered gene expression profiles, as observed in other studies) a heritable regulatory mechanism for aposporous development.
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Affiliation(s)
- Claudia Paetzold
- Department of Botany and Molecular Evolution, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany
| | - Birthe H. Barke
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Goettingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Goettingen, Germany
- Correspondence:
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3
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Ge D, Feijó A, Wen Z, Abramov AV, Lu L, Cheng J, Pan S, Ye S, Xia L, Jiang X, Vogler AP, Yang Q. Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats. Mol Biol Evol 2021; 38:1905-1923. [PMID: 33386846 PMCID: PMC8097305 DOI: 10.1093/molbev/msaa334] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Shengkai Pan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Sicheng Ye
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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4
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Gu Z, Sun Y, Wu F. Mechanism of Growth Regulation of Yeast Involving Hydrogen Sulfide From S-Propargyl-Cysteine Catalyzed by Cystathionine-γ-Lyase. Front Microbiol 2021; 12:679563. [PMID: 34276612 PMCID: PMC8285084 DOI: 10.3389/fmicb.2021.679563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022] Open
Abstract
Pathogenic fungi are recognized as a progressive threat to humans, particularly those with the immunocompromised condition. The growth of fungi is controlled by several factors, one of which is signaling molecules, such as hydrogen sulfide (H2S), which was traditionally regarded as a toxic gas without physiological function. However, recent studies have revealed that H2S is produced enzymatically and endogenously in several species, where it serves as a gaseous signaling molecule performing a variety of critical biological functions. However, the influence of this endogenous H2S on the biological activities occurring within the pathogenic fungi, such as transcriptomic and phenotypic alternations, has not been elucidated so far. Therefore, the present study was aimed to decipher this concern by utilizing S-propargyl-cysteine (SPRC) as a novel and stable donor of H2S and Saccharomyces cerevisiae as a fungal model. The results revealed that the yeast could produce H2S by catabolizing SPRC, which facilitated the growth of the yeast cells. This implies that the additional intracellularly generated H2S is generated primarily from the enhanced sulfur-amino-acid-biosynthesis pathways and serves to increase the growth rate of the yeast, and presumably the growth of the other fungi as well. In addition, by deciphering the implicated pathways and analyzing the in vitro enzymatic activities, cystathionine-γ-lyase (CYS3) was identified as the enzyme responsible for catabolizing SPRC into H2S in the yeast, which suggested that cystathionine-γ-lyase might play a significant role in the regulation of H2S-related transcriptomic and phenotypic alterations occurring in yeast. These findings provide important information regarding the mechanism underlying the influence of the gaseous signaling molecules such as H2S on fungal growth. In addition, the findings provide a better insight to the in vivo metabolism of H2S-related drugs, which would be useful for the future development of anti-fungal drugs.
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Affiliation(s)
- Zhongkai Gu
- The Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yufan Sun
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Department of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Feizhen Wu
- The Institute of Biomedical Sciences, Fudan University, Shanghai, China
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5
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Huber KT, Linz S, Moulton V. The rigid hybrid number for two phylogenetic trees. J Math Biol 2021; 82:40. [PMID: 33770290 PMCID: PMC7997861 DOI: 10.1007/s00285-021-01594-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/25/2021] [Accepted: 03/13/2021] [Indexed: 11/29/2022]
Abstract
Recently there has been considerable interest in the problem of finding a phylogenetic network with a minimum number of reticulation vertices which displays a given set of phylogenetic trees, that is, a network with minimum hybrid number. Such networks are useful for representing the evolution of species whose genomes have undergone processes such as lateral gene transfer and recombination that cannot be represented appropriately by a phylogenetic tree. Even so, as was recently pointed out in the literature, insisting that a network displays the set of trees can be an overly restrictive assumption when modeling certain evolutionary phenomena such as incomplete lineage sorting. In this paper, we thus consider the less restrictive notion of rigidly displaying which we introduce and study here. More specifically, we characterize when two trees can be rigidly displayed by a certain type of phylogenetic network called a temporal tree-child network in terms of fork-picking sequences. These are sequences of special subconfigurations of the two trees related to the well-studied cherry-picking sequences. We also show that, in case it exists, the rigid hybrid number for two phylogenetic trees is given by a minimum weight fork-picking sequence for the trees. Finally, we consider the relationship between the rigid hybrid number and three closely related numbers; the weak, beaded, and temporal hybrid numbers. In particular, we show that these numbers can all be different even for a fixed pair of trees, and also present an infinite family of pairs of trees which demonstrates that the difference between the rigid hybrid number and the temporal-hybrid number for two phylogenetic trees on the same set of n leaves can grow at least linearly with n.
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Affiliation(s)
| | - Simone Linz
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich, UK
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Brian JI, Davy SK, Wilkinson SP. Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts. PeerJ 2019; 7:e7178. [PMID: 31289699 PMCID: PMC6598746 DOI: 10.7717/peerj.7178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.
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Affiliation(s)
- Joshua I Brian
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Shaun P Wilkinson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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7
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Sillo F, Gonthier P, Lockman B, Kasuga T, Garbelotto M. Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids. Ecol Evol 2019; 9:6588-6605. [PMID: 31236246 PMCID: PMC6580273 DOI: 10.1002/ece3.5238] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/14/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Hybridization may be a major driver in the evolution of plant pathogens. In a high elevation Alpine larch stand in Montana, a novel hybrid fungal pathogen of trees originating from the mating of Heterobasidion irregulare with H. occidentale has been recently discovered. In this study, sequence analyses of one mitochondrial and four nuclear loci from 11 Heterobasidion genotypes collected in the same Alpine larch stand indicated that hybridization has increased allelic diversity by generating novel polymorphisms unreported in either parental species. Sequence data and ploidy analysis through flow cytometry confirmed that heterokaryotic (n + n) genotypes were not first-generation hybrids, but were the result of multiple backcrosses, indicating hybrids are fertile. Additionally, all admixed genotypes possessed the H. occidentale mitochondrion, indicating that the hybrid progeny may have been backcrossing mostly with H. occidentale. Based on reticulate phylogenetic network analysis by PhyloNet, Bayesian assignment, and ordination tests, alleles can be defined as H. irregulare-like or H. occidentale-like. H. irregulare-like alleles are clearly distinct from all known H. irregulare alleles and are derived from the admixing of both Heterobasidion species. Instead, all but one H. occidentale alleles found in hybrids, although novel, were not clearly distinct from alleles found in the parental H. occidentale population. This discovery demonstrates that Alpine larch can be a universal host favouring the interspecific hybridization between H. irregulare and H. occidentale and the hybridization-mediated evolution of a nucleus, derived from H. irregulare parental species but clearly distinct from it.
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Affiliation(s)
- Fabiano Sillo
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoGrugliasco (TO)Italy
| | - Paolo Gonthier
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoGrugliasco (TO)Italy
| | - Blakey Lockman
- Pacific Northwest Region, State and Private ForestryUSDA Forest ServicePortlandOregon
| | - Takao Kasuga
- Crops Pathology and Genetics Research UnitUSDA Agricultural Research ServiceDavisCalifornia
| | - Matteo Garbelotto
- Department of Agricultural, Forest and Food Sciences (DISAFA)University of TorinoGrugliasco (TO)Italy
- Department of Environmental Science, Policy and Management, Forest Pathology and Mycology LaboratoryUniversity of California, BerkeleyBerkeleyCalifornia
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8
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Baltrušis P, Halvarsson P, Höglund J. Exploring benzimidazole resistance in Haemonchus contortus by next generation sequencing and droplet digital PCR. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:411-419. [PMID: 30266023 PMCID: PMC6159336 DOI: 10.1016/j.ijpddr.2018.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 12/25/2022]
Abstract
Anthelmintic resistance in gastrointestinal nematode (GIN) parasites of grazing ruminants is on the rise in countries across the world. Haemonchus contortus is one of most frequently encountered drug-resistant GINs in small ruminants. This blood-sucking abomasal nematode contributes to massive treatment costs and poses a serious threat to farm animal health. To prevent the establishment of resistant strains of this parasite, up-to-date molecular techniques need to be proposed which would allow for quick, cheap and accurate identification of individuals infected with resistant worms. The effort has been made in the previous decade, with the development of the pyrosequencing method to detect resistance-predicting alleles. Here we propose a novel droplet digital PCR (ddPCR) assay for rapid and precise identification of H. contortus strains as being resistant or susceptible to benzimidazole drugs based on the presence or absence of the most common resistance-conferring mutation F200Y (TAC) in the β tubulin isotype 1 gene. The newly developed ddPCR assay was first optimized and validated utilizing DNA templates from single-worm samples, which were previously sequenced using the next generation PacBio RSII Sequencing (NGS) platform. Subsequent NGS results for faecal larval cultures were then used as a reference to compare the obtained values for fractional abundances of the resistance-determining mutant allele between ddPCR and NGS techniques in each sample. Both methods managed to produce highly similar results and ddPCR proved to be a reliable tool which, when utilized at full capacity, can be used to create a powerful mutation detection and quantification assay.
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Affiliation(s)
- Paulius Baltrušis
- Swedish University of Agricultural Sciences, Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036, Uppsala, Sweden
| | - Peter Halvarsson
- Swedish University of Agricultural Sciences, Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036, Uppsala, Sweden
| | - Johan Höglund
- Swedish University of Agricultural Sciences, Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, P.O. Box 7036, Uppsala, Sweden.
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9
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Ottenburghs J, Megens HJ, Kraus RHS, van Hooft P, van Wieren SE, Crooijmans RPMA, Ydenberg RC, Groenen MAM, Prins HHT. A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evol Biol 2017; 17:201. [PMID: 28830337 PMCID: PMC5568201 DOI: 10.1186/s12862-017-1048-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022] Open
Abstract
Background The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. Results We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. Conclusions Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1048-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jente Ottenburghs
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Robert H S Kraus
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg, 1D-78315, Radolfzell, Germany.,Department of Biology, University of Konstanz, D-78457, Constance, Germany
| | - Pim van Hooft
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| | - Sipke E van Wieren
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Ronald C Ydenberg
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.,Centre for Wildlife Ecology, Simon Fraser University, V5A 1S6, Burnaby, BC, Canada
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Herbert H T Prins
- Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands
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10
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Escobar-Perez J, Reyes N, Marquez-Ortiz RA, Rebollo J, Pinzón H, Tovar C, Moreno-Castañeda J, Corredor ZL, Castro BE, Moncada MV, Vanegas N. Emergence and spread of a new community-genotype methicillin-resistant Staphylococcus aureus clone in Colombia. BMC Infect Dis 2017; 17:108. [PMID: 28143440 PMCID: PMC5282769 DOI: 10.1186/s12879-017-2193-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 01/06/2017] [Indexed: 11/15/2022] Open
Abstract
Background Community-genotype methicillin-resistant Staphylococcus aureus (CG-MRSA) clones are a global concern due to their resistance and increased virulence and their ability to cause infections both hospitalized patients and healthy people in the community. Here, we characterize 32 isolates of a new CG-MRSA clone. These isolates were identified in four cities in Colombia, South America. Methods The isolates were recovered from four different epidemiological and prospective studies that were conducted in several regions of Colombia. Molecular characterizations included multilocus sequence typing; pulsed-field gel electrophoresis; SCCmec, agr and spa typing; and whole-genome sequencing. Results All isolates belonged to ST923 (clonal complex 8), harbouring SCCmec IVa and a spa type t1635 and lacking an arginine catabolism mobile element. The isolates were classified as COL923, were resistant to at least one non-beta-lactam antibiotic, and exhibited high frequencies (>60%) of resistance to macrolides and tetracycline. Using whole-genome sequencing, we found that this new clone harbours novel prophage 3 and beta-island structures and a slightly different pathogenicity island 5. Moreover, isolates belonging to the COL923 clone are grouped in a different clade than USA300 and USA300-LV. Conclusion Our results show the emergence and spread of the COL923 clone in different cities in Colombia. This clone is resistant to several antibiotics and possesses new structures in its mobile genetic elements. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2193-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Javier Escobar-Perez
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Carrera 9 #131A-02, 110121274, Bogotá, DC, Colombia.
| | - Niradiz Reyes
- Grupo de Genética y Biología Molecular, Universidad de Cartagena, Cartagena, Colombia
| | | | - Juan Rebollo
- Grupo de Genética y Biología Molecular, Universidad de Cartagena, Cartagena, Colombia
| | - Hernando Pinzón
- Grupo de Genética y Biología Molecular, Universidad de Cartagena, Cartagena, Colombia
| | - Catalina Tovar
- Grupo de Investigación en Enfermedades Tropicales y Resistencia Bacteriana, Montería, Colombia
| | | | - Zayda Lorena Corredor
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Carrera 9 #131A-02, 110121274, Bogotá, DC, Colombia
| | - Betsy Esperanza Castro
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Carrera 9 #131A-02, 110121274, Bogotá, DC, Colombia
| | - Maria Victoria Moncada
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Carrera 9 #131A-02, 110121274, Bogotá, DC, Colombia
| | - Natasha Vanegas
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Carrera 9 #131A-02, 110121274, Bogotá, DC, Colombia.,I3 Institute, Faculty of Science, University of Technology, Sydney, Australia
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