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Analysis of Whole-Genome Sequences of Pathogenic Gram-Positive and Gram-Negative Isolates from the Same Hospital Environment to Investigate Common Evolutionary Trends Associated with Horizontal Gene Exchange, Mutations and DNA Methylation Patterning. Microorganisms 2023; 11:microorganisms11020323. [PMID: 36838287 PMCID: PMC9961978 DOI: 10.3390/microorganisms11020323] [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: 12/22/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
Hospital-acquired infections are a generally recognized problem for healthcare professionals. Clinical variants of Gram-negative and Gram-positive pathogens are characterized with enhanced antibiotic resistance and virulence due to mutations and the horizontal acquisition of respective genetic determinants. In this study, two Escherichia coli, two Klebsiella pneumoniae, three Pseudomonas aeruginosa, two Staphylococcus aureus, one Staphylococcus epidermidis and one Streptococcus pneumoniae showing broad spectra of antibiotic resistance were isolated from patients suffering from nosocomial infections in a local hospital in Almaty, Kazakhstan. The aim of the study was to compare general and species-specific pathways of the development of virulence and antibiotic resistance through opportunistic pathogens causing hospital-acquired infections. The whole-genome PacBio sequencing of the isolates allowed for the genotyping and identification of antibiotic resistance and virulence genetic determinants located in the chromosomes, plasmids and genomic islands. It was concluded that long-read sequencing is a useful tool for monitoring the epidemiological situation in hospitals. Marker antibiotic resistance mutations common for different microorganisms were identified, which were acquired due to antibiotic-selective pressure in the same clinical environment. The genotyping and identification of strain-specific DNA methylation motifs were found to be promising in estimating the risks associated with hospital infection outbreaks and monitoring the distribution and evolution of nosocomial pathogens.
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Monteiro Pires S, Morabito S, Niskanen T, Scheutz F, da Silva Felício MT, Messens W, Bolton D. Pathogenicity assessment of Shiga toxin‐producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC. EFSA J 2020. [DOI: 10.2903/j.efsa.2020.5967] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Hazard Identification and Characterization: Criteria for Categorizing Shiga Toxin-Producing Escherichia coli on a Risk Basis †. J Food Prot 2019; 82:7-21. [PMID: 30586326 DOI: 10.4315/0362-028x.jfp-18-291] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) comprise a large, highly diverse group of strains. Since the emergence of STEC serotype O157:H7 as an important foodborne pathogen, serotype data have been used for identifying STEC strains, and this use continued as other serotypes were implicated in human infections. An estimated 470 STEC serotypes have been identified, which can produce one or more of the 12 known Shiga toxin (Stx) subtypes. The number of STEC serotypes that cause human illness varies but is probably higher than 100. However, many STEC virulence genes are mobile and can be lost or transferred to other bacteria; therefore, STEC strains that have the same serotype may not carry the same virulence genes or pose the same risk. Although serotype information is useful in outbreak investigations and surveillance studies, it is not a reliable means of assessing the human health risk posed by a particular STEC serotype. To contribute to the development of a set of criteria that would more reliably support hazard identification, this review considered each of the factors contributing to a negative human health outcome: mild diarrhea, bloody diarrhea, and hemolytic uremic syndrome (HUS). STEC pathogenesis involves entry into the human gut (often via ingestion), attachment to the intestinal epithelial cells, and elaboration of Stx. Production of Stx, which disrupts normal cellular functions and causes cell damage, alone without adherence of bacterial cells to gut epithelial cells is insufficient to cause severe illness. The principal adherence factor in STEC is the intimin protein coded by the eae gene. The aggregative adherence fimbriae adhesins regulated by the aggR gene of enteroaggregative E. coli strains are also effective adherence factors. The stx2a gene is most often present in locus of enterocyte effacement ( eae)-positive STEC strains and has consistently been associated with HUS. The stx2a gene has also been found in eae-negative, aggR-positive STEC that have caused HUS. HUS cases where other stx gene subtypes were identified indicate that other factors such as host susceptibility and the genetic cocktail of virulence genes in individual isolates may affect their association with severe diseases.
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Affiliation(s)
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- The Joint FAO/WHO Expert Meetings on Microbiological Risk Assessment (JEMRA) Secretariat, * Food Safety and Quality Unit, Agriculture and Consumer Protection Department, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153 Rome, Italy
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Li YP, Carraro N, Yang N, Liu B, Xia X, Feng R, Saquib Q, Al-Wathnani HA, van der Meer JR, Rensing C. Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine. Genes (Basel) 2018; 9:genes9120573. [PMID: 30477188 PMCID: PMC6316836 DOI: 10.3390/genes9120573] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/16/2018] [Accepted: 11/19/2018] [Indexed: 01/29/2023] Open
Abstract
Heavy metals (HMs) are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu(II), 21 mM Zn(II), 1.2 mM Cd(II), and 10.0 mM As(III). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative PIB-1-ATPase, 5 putative PIB-3-ATPase, 4 putative Zn(II)/Cd(II) PIB-4 type ATPase, and 16 putative resistance-nodulation-division (RND)-type metal transporter systems. Moreover, the four genomes contained a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci included genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system), respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.
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Affiliation(s)
- Yuan Ping Li
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne 1015, Switzerland.
| | - Nan Yang
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Bixiu Liu
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xian Xia
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Renwei Feng
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Hend A Al-Wathnani
- Department of Botany & Microbiology, College of Sciences, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | | | - Christopher Rensing
- Institute of Environmental Microbiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academic of Sciences, 361021 Xiamen, China.
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5
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Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, LaCono V, Smedile F, Slesarev A, Rojo D, Barbas C, Ferrer M, Yakimov MM, Golyshin PN. Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y T. Sci Rep 2017; 7:3682. [PMID: 28623373 PMCID: PMC5473848 DOI: 10.1038/s41598-017-03904-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/02/2017] [Indexed: 12/19/2022] Open
Abstract
Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by 'ancient' CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the mutation rate of ≥1.3 × 10-8 single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum YT variants from geographically distant populations.
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Affiliation(s)
- Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK.
| | - Hai Tran
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK
| | - Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, 0002, South Africa
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S3E5, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S3E5, Toronto, Ontario, Canada
| | - Alexander Goesmann
- CeBiTec Bielefeld University, Universitätsstraße 25, D-33615, Bielefeld, Germany
- Department of Bioinformatics and Systems Biology, Justus Liebig Universität Gießen, Heinrich-Buff-Ring 58, D-35392, Gießen, Germany
| | - Taras Y Nechitaylo
- Insect Symbiosis Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Violetta LaCono
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Alexei Slesarev
- Fidelity Systems, Zylacta Corporation, 7965 Cessna Avenue, Gaithersburg, MD, 20879, USA
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Manuel Ferrer
- Institute of Catalysis CSIC, Campus Cantoblanco, 28049, Madrid, Spain
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
- Immanuel Kant Baltic Federal University, Universitetskaya 1, 36040, Kaliningrad, Russia
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK
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Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TBK, Klenk HP, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Front Microbiol 2017; 8:195. [PMID: 28265262 PMCID: PMC5317091 DOI: 10.3389/fmicb.2017.00195] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 01/26/2017] [Indexed: 11/13/2022] Open
Abstract
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.
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Affiliation(s)
- Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Olga M Sigalova
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia QLD, Australia
| | - Olga Kovaleva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Nikolai A Chernyh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | | | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Oleg N Reva
- Center for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria Pretoria, South Africa
| | - Margarita L Miroshnichenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, USA; Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, BerkeleyCA, USA
| | - Mikhail S Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia; Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State UniversityMoscow, Russia; Skolkovo Institute of Science and TechnologyMoscow, Russia; Faculty of Computer Science, National Research University - Higher School of EconomicsMoscow, Russia
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7
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Zwonitzer MR, Soupir ML, Jarboe LR, Smith DR. Quantifying Attachment and Antibiotic Resistance of from Conventional and Organic Swine Manure. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:609-617. [PMID: 27065408 DOI: 10.2134/jeq2015.05.0245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Broad-spectrum antibiotics are often administered to swine, contributing to the occurrence of antibiotic-resistant bacteria in their manure. During land application, the bacteria in swine manure preferentially attach to particles in the soil, affecting their transport in overland flow. However, a quantitative understanding of these attachment mechanisms is lacking, and their relationship to antibiotic resistance is unknown. The objective of this study is to examine the relationships between antibiotic resistance and attachment to very fine silica sand in collected from swine manure. A total of 556 isolates were collected from six farms, two organic and four conventional (antibiotics fed prophylactically). Antibiotic resistance was quantified using 13 antibiotics at three minimum inhibitory concentrations: resistant, intermediate, and susceptible. Of the 556 isolates used in the antibiotic resistance assays, 491 were subjected to an attachment assay. Results show that isolates from conventional systems were significantly more resistant to amoxicillin, ampicillin, chlortetracycline, erythromycin, kanamycin, neomycin, streptomycin, tetracycline, and tylosin ( < 0.001). Results also indicate that isolated from conventional systems attached to very fine silica sand at significantly higher levels than those from organic systems ( < 0.001). Statistical analysis showed that a significant relationship did not exist between antibiotic resistance levels and attachment in from conventional systems but did for organic systems ( < 0.001). Better quantification of these relationships is critical to understanding the behavior of in the environment and preventing exposure of human populations to antibiotic-resistant bacteria.
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Staehlin BM, Gibbons JG, Rokas A, O'Halloran TV, Slot JC. Evolution of a Heavy Metal Homeostasis/Resistance Island Reflects Increasing Copper Stress in Enterobacteria. Genome Biol Evol 2016; 8:811-26. [PMID: 26893455 PMCID: PMC4824010 DOI: 10.1093/gbe/evw031] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2016] [Indexed: 12/24/2022] Open
Abstract
Copper homeostasis in bacteria is challenged by periodic elevation of copper levels in the environment, arising from both natural sources and human inputs. Several mechanisms have evolved to efflux copper from bacterial cells, including thecus(copper sensing copper efflux system), andpco(plasmid-borne copper resistance system) systems. The genes belonging to these two systems can be physically clustered in a Copper Homeostasis and Silver Resistance Island (CHASRI) on both plasmids and chromosomes in Enterobacteria. Increasing use of copper in agricultural and industrial applications raises questions about the role of human activity in the evolution of novel copper resistance mechanisms. Here we present evidence that CHASRI emerged and diversified in response to copper deposition across aerobic and anaerobic environments. An analysis of diversification rates and a molecular clock model suggest that CHASRI experienced repeated episodes of elevated diversification that could correspond to peaks in human copper production. Phylogenetic analyses suggest that CHASRI originated in a relative ofEnterobacter cloacaeas the ultimate product of sequential assembly of several pre-existing two-gene modules. Once assembled, CHASRI dispersed via horizontal gene transfer within Enterobacteriaceae and also to certain members of Shewanellaceae, where the originalpcomodule was replaced by a divergentpcohomolog. Analyses of copper stress mitigation suggest that CHASRI confers increased resistance aerobically, anaerobically, and during shifts between aerobic and anaerobic environments, which could explain its persistence in facultative anaerobes and emergent enteric pathogens.
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Affiliation(s)
- Benjamin M Staehlin
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University
| | - John G Gibbons
- Department of Biological Sciences, Vanderbilt University Present address: Biology Department, Clark University, Worcester, MA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
| | - Thomas V O'Halloran
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus
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Pierneef R, Cronje L, Bezuidt O, Reva ON. Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015. [PMID: 26200753 PMCID: PMC5630688 DOI: 10.1093/database/bav058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Predicted Genomic Islands database (Pre_GI) is a comprehensive repository of prokaryotic genomic islands (islands, GIs) freely accessible at http://pregi.bi.up.ac.za/index.php. Pre_GI, Version 2015, catalogues 26 744 islands identified in 2407 bacterial/archaeal chromosomes and plasmids. It provides an easy-to-use interface which allows users the ability to query against the database with a variety of fields, parameters and associations. Pre_GI is constructed to be a web-resource for the analysis of ontological roads between islands and cartographic analysis of the global fluxes of mobile genetic elements through bacterial and archaeal taxonomic borders. Comparison of newly identified islands against Pre_GI presents an alternative avenue to identify their ontology, origin and relative time of acquisition. Pre_GI aims to aid research on horizontal transfer events and materials through providing data and tools for holistic investigation of migration of genes through ecological niches and taxonomic boundaries.
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Affiliation(s)
- Rian Pierneef
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Gauteng 0002, South Africa
| | - Louis Cronje
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Gauteng 0002, South Africa
| | - Oliver Bezuidt
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Gauteng 0002, South Africa
| | - Oleg N Reva
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Gauteng 0002, South Africa
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Jalasvuori M, Koonin EV. Classification of prokaryotic genetic replicators: between selfishness and altruism. Ann N Y Acad Sci 2015; 1341:96-105. [PMID: 25703428 PMCID: PMC4390439 DOI: 10.1111/nyas.12696] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Prokaryotes harbor a variety of genetic replicators, including plasmids, viruses, and chromosomes, each having different effects on the phenotype of the hosting cell. Here, we propose a classification for replicators of bacteria and archaea on the basis of their horizontal-transfer potential and the type of relationships (mutualistic, symbiotic, commensal, or parasitic) that they have with the host cell vehicle. Horizontal movement of replicators can be either active or passive, reflecting whether or not the replicator encodes the means to mediate its own transfer from one cell to another. Some replicators also have an infectious extracellular state, thus separating viruses from other mobile elements. From the perspective of the cell vehicle, the different types of replicators form a continuum from genuinely mutualistic to completely parasitic replicators. This classification provides a general framework for dissecting prokaryotic systems into evolutionarily meaningful components.
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Affiliation(s)
- Matti Jalasvuori
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
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Microbiological Quality of Ready-to-Eat Vegetables Collected in Mexico City: Occurrence of Aerobic-Mesophilic Bacteria, Fecal Coliforms, and Potentially Pathogenic Nontuberculous Mycobacteria. BIOMED RESEARCH INTERNATIONAL 2015; 2015:789508. [PMID: 25918721 PMCID: PMC4396000 DOI: 10.1155/2015/789508] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 09/24/2014] [Indexed: 01/08/2023]
Abstract
The aims of this study were to evaluate the microbiological quality and the occurrence of nontuberculous mycobacteria (NTM) in a variety of salads and sprouts from supermarkets and street vendors in Mexico City. Aerobic-mesophilic bacteria (AMB) were present in 100% of RTE-salads samples; 59% of samples were outside guidelines range (>5.17 log10 CFU per g). Although fecal coliforms (FC) were present in 32% of samples, only 8% of them exceeded the permissible limit (100 MPN/g). Regarding the 100 RTE-sprouts, all samples were also positive for AMB and total coliforms (TC) and 69% for FC. Seven NTM species were recovered from 7 salad samples; they included three M. fortuitum, two M. chelonae, one M. mucogenicum, and one M. sp. Twelve RTE-sprouts samples harbored NTM, which were identified as M. porcinum (five), M. abscessus (two), M. gordonae (two), M. mucogenicum (two), and M. avium complex (one). Most RTE-salads and RTE-sprouts had unsatisfactory microbiological quality and some harbored NTM associated with illness. No correlation between the presence of coliforms and NTM was found. Overall, these results suggest that RTE-salads and RTE-sprouts might function as vehicles for NTM transmission in humans; hence, proper handling and treatment before consumption of such products might be recommendable.
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12
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Reva O, Korotetskiy I, Ilin A. Role of the horizontal gene exchange in evolution of pathogenic Mycobacteria. BMC Evol Biol 2015; 15 Suppl 1:S2. [PMID: 25708825 PMCID: PMC4331801 DOI: 10.1186/1471-2148-15-s1-s2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis is one of the most dangerous human pathogens, the causative agent of tuberculosis. While this pathogen is considered as extremely clonal and resistant to horizontal gene exchange, there are many facts supporting the hypothesis that on the early stages of evolution the development of pathogenicity of ancestral Mtb has started with a horizontal acquisition of virulence factors. Episodes of infections caused by non-tuberculosis Mycobacteria reported worldwide may suggest a potential for new pathogens to appear. If so, what is the role of horizontal gene transfer in this process? RESULTS Availing of accessibility of complete genomes sequences of multiple pathogenic, conditionally pathogenic and saprophytic Mycobacteria, a genome comparative study was performed to investigate the distribution of genomic islands among bacteria and identify ontological links between these mobile elements. It was shown that the ancient genomic islands from M. tuberculosis still may be rooted to the pool of mobile genetic vectors distributed among Mycobacteria. A frequent exchange of genes was observed between M. marinum and several saprophytic and conditionally pathogenic species. Among them M. avium was the most promiscuous species acquiring genetic materials from diverse origins. CONCLUSIONS Recent activation of genetic vectors circulating among Mycobacteria potentially may lead to emergence of new pathogens from environmental and conditionally pathogenic Mycobacteria. The species which require monitoring are M. marinum and M. avium as they eagerly acquire genes from different sources and may become donors of virulence gene cassettes to other micro-organisms.
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Reva O, Bezuidt O. Distribution of horizontally transferred heavy metal resistance operons in recent outbreak bacteria. Mob Genet Elements 2014; 2:96-100. [PMID: 22934243 PMCID: PMC3429527 DOI: 10.4161/mge.19963] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mankind is confronted by the outbreaks of highly virulent and multi-drug resistant pathogens. The outbreak strains often belong to well-known diseases associated species such as Salmonella, Klebsiella and Mycobacterium, but even normally commensal and environmental microorganisms may suddenly acquire properties of virulent bacteria and cause nosocomial infections. The acquired virulence is often associated with lateral exchange of pathogenicity genomic islands containing drug and heavy metal resistance determinants. Metal ions are used by the immune system of macro-organisms against bactericidal agents. The ability to control heavy metal homeostasis is a factor that allows the survival of pathogenic microorganisms in macrophages. In this paper, we investigate the origin of heavy metal resistance operons in the recent outbreak strains and the possible routes which may lead to acquisitions of these genes by potentially new pathogens. We hypothesize that new outbreak microorganisms appear intermittently on an intersection of the non-specialized, genetically naïve strains of potential pathogens and virulence factor comprising vectors (plasmid and/or phages) newly generated in the environmental microflora. Global contamination of the environment and climate change may also have an effect toward the acceleration and appearance of new pathogens.
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Affiliation(s)
- Oleg Reva
- Bioinformatics and Computational Biology Unit; Department of Biochemistry; University of Pretoria; Pretoria, South Africa
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Kumwenda B, Litthauer D, Reva O. Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species. BMC Genomics 2014; 15:813. [PMID: 25257245 PMCID: PMC4180962 DOI: 10.1186/1471-2164-15-813] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 09/17/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Bacteria of genus Thermus inhabit both man-made and natural thermal environments. Several Thermus species have shown biotechnological potential such as reduction of heavy metals which is essential for eradication of heavy metal pollution; removing of organic contaminants in water; opening clogged pipes, controlling global warming among many others. Enzymes from thermophilic bacteria have exhibited higher activity and stability than synthetic or enzymes from mesophilic organisms. RESULTS Using Meiothermus silvanus DSM 9946 as a reference genome, high level of coordinated rearrangements has been observed in extremely thermophilic Thermus that may imply existence of yet unknown evolutionary forces controlling adaptive re-organization of whole genomes of thermo-extremophiles. However, no remarkable differences were observed across species on distribution of functionally related genes on the chromosome suggesting constraints imposed by metabolic networks. The metabolic network exhibit evolutionary pressures similar to levels of rearrangements as measured by the cross-clustering index. Using stratigraphic analysis of donor-recipient, intensive gene exchanges were observed from Meiothermus species and some unknown sources to Thermus species confirming a well established DNA uptake mechanism as previously proposed. CONCLUSION Global genome rearrangements were found to play an important role in the evolution of Thermus bacteria at both genomic and metabolic network levels. Relatively higher level of rearrangements was observed in extremely thermophilic Thermus strains in comparison to the thermo-tolerant Thermus scotoductus. Rearrangements did not significantly disrupt operons and functionally related genes. Thermus species appeared to have a developed capability for acquiring DNA through horizontal gene transfer as shown by the donor-recipient stratigraphic analysis.
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Affiliation(s)
- Benjamin Kumwenda
- />Department of Biochemistry, Bioinformatics and Computational Biology Unit, University of Pretoria, Pretoria, South Africa
| | - Derek Litthauer
- />Department of Microbial Biochemical and Food Biotechnology, University of Free State, Bloemfontein, South Africa
| | - Oleg Reva
- />Department of Biochemistry, Bioinformatics and Computational Biology Unit, University of Pretoria, Pretoria, South Africa
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15
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Cao X, Zhang Z, Shen H, Ning M, Chen J, Wei H, Zhang K. Genotypic characteristics of multidrug-resistant Escherichia coli isolates associated with urinary tract infections. APMIS 2014; 122:1088-95. [PMID: 24698634 DOI: 10.1111/apm.12260] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/07/2014] [Indexed: 01/18/2023]
Abstract
Escherichia coli is an important pathogen involved in community-acquired urinary tract infections (CA-UTIs). In this study, we analyzed the prevalence of frequently occurring genes and the distribution of integrons in 51 multidrug-resistant (MDR) E. coli isolates associated with CA-UTIs. The clonality of these strains was investigated by phylogrouping, multi-locus sequence typing, and pulsed-field gel electrophoresis (PFGE). All these strains were found to produce two or more resistance determinants, ceftazidime-hydrolyzing CTX-M-type extended-spectrum β-lactamases (ESBLs) and plasmid-mediated quinolone resistance determinants were the most prevalent (92.2% and 51.0%, respectively). A sulfhydryl variable-61-producing E. coli strain was identified for the first time in China. The prevalence of class 1 integrons was 54.9%, class 2 integrons were detected in three isolates but no isolate contained a class 3 integron. Phylogenetic group D was the dominant, observed in 70.6% of the isolates. PFGE analysis revealed a high level of diversity. Twenty-four distinctive sequence types (STs) including four major STs (ST648, ST224, ST38, and ST405) were identified. To our knowledge, this is the first report on the characterization of MDR E. coli isolates associated with CA-UTIs in China; our results suggest that an MDR D-ST648 clone producing CTX-M-ESBLs has emerged as a major clone in the community setting.
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Affiliation(s)
- Xiaoli Cao
- Department of Laboratory Medicine, The affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Jiangsu, China
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16
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Enterohemorrhagic Escherichia coli (EHEC). Emerg Infect Dis 2014. [DOI: 10.1016/b978-0-12-416975-3.00017-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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17
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Bapteste E, Dupré J. Towards a processual microbial ontology. BIOLOGY & PHILOSOPHY 2013; 28:379-404. [PMID: 23487350 PMCID: PMC3591535 DOI: 10.1007/s10539-012-9350-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 10/17/2012] [Indexed: 05/26/2023]
Abstract
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely "processually equivalent" entities, "processually versatile" entities, and "stabilized" entities.
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Affiliation(s)
- Eric Bapteste
- />UMR CNRS 7138, Université Pierre et Marie Curie, 75005 Paris, France
| | - John Dupré
- />ESRC Centre for Genomics in Society (Egenis), University of Exeter, Exeter, UK
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18
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Kube M, Chernikova TN, Al-Ramahi Y, Beloqui A, Lopez-Cortez N, Guazzaroni ME, Heipieper HJ, Klages S, Kotsyurbenko OR, Langer I, Nechitaylo TY, Lünsdorf H, Fernández M, Juárez S, Ciordia S, Singer A, Kagan O, Egorova O, Alain Petit P, Stogios P, Kim Y, Tchigvintsev A, Flick R, Denaro R, Genovese M, Albar JP, Reva ON, Martínez-Gomariz M, Tran H, Ferrer M, Savchenko A, Yakunin AF, Yakimov MM, Golyshina OV, Reinhardt R, Golyshin PN. Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. Nat Commun 2013; 4:2156. [PMID: 23877221 PMCID: PMC3759055 DOI: 10.1038/ncomms3156] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 06/18/2013] [Indexed: 01/21/2023] Open
Abstract
Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis--the paradigm of mesophilic hydrocarbonoclastic bacteria--O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.
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Affiliation(s)
- Michael Kube
- Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany
- Section Phytomedicine, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin-Dahlem D-14195, Germany
| | - Tatyana N. Chernikova
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
- School of Biological Sciences, Bangor University, Gwynedd, Wales LL57 2UW, UK
| | | | - Ana Beloqui
- Institute of Catalysis, CSIC, Madrid 28049, Spain
| | | | - María-Eugenia Guazzaroni
- Institute of Catalysis, CSIC, Madrid 28049, Spain
- Departamento de Química, Universidade de São Paulo, Ribeirao Preto 14049 901, Brazil
| | - Hermann J. Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig D-04318, Germany
| | - Sven Klages
- Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany
| | - Oleg R. Kotsyurbenko
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Ines Langer
- Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany
| | - Taras Y. Nechitaylo
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Heinrich Lünsdorf
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Marisol Fernández
- Proteomic Facility, National Centre for Biotechnology, CSIC, Madrid 28049, Spain
| | - Silvia Juárez
- Proteomic Facility, National Centre for Biotechnology, CSIC, Madrid 28049, Spain
| | - Sergio Ciordia
- Proteomic Facility, National Centre for Biotechnology, CSIC, Madrid 28049, Spain
| | - Alexander Singer
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Olga Kagan
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Olga Egorova
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Pierre Alain Petit
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Youngchang Kim
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Anatoli Tchigvintsev
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
| | - Robert Flick
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
| | - Renata Denaro
- Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
| | - Maria Genovese
- Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
| | - Juan P. Albar
- Proteomic Facility, National Centre for Biotechnology, CSIC, Madrid 28049, Spain
| | - Oleg N. Reva
- Department of Biochemistry, University of Pretoria, Pretoria 0002, South Africa
| | | | - Hai Tran
- School of Biological Sciences, Bangor University, Gwynedd, Wales LL57 2UW, UK
| | | | - Alexei Savchenko
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Michail M. Yakimov
- Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
| | - Olga V. Golyshina
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
- School of Biological Sciences, Bangor University, Gwynedd, Wales LL57 2UW, UK
| | - Richard Reinhardt
- Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany
- Present address: Max-Planck Genome Centre Cologne, Max-Planck Institute for Plant Breeding Research, Cologne D-50829, Germany
| | - Peter N. Golyshin
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
- School of Biological Sciences, Bangor University, Gwynedd, Wales LL57 2UW, UK
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19
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Merabishvili M, De Vos D, Verbeken G, Kropinski AM, Vandenheuvel D, Lavigne R, Wattiau P, Mast J, Ragimbeau C, Mossong J, Scheres J, Chanishvili N, Vaneechoutte M, Pirnay JP. Selection and characterization of a candidate therapeutic bacteriophage that lyses the Escherichia coli O104:H4 strain from the 2011 outbreak in Germany. PLoS One 2012; 7:e52709. [PMID: 23285164 PMCID: PMC3528706 DOI: 10.1371/journal.pone.0052709] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 11/20/2012] [Indexed: 11/18/2022] Open
Abstract
In 2011, a novel strain of O104:H4 Escherichia coli caused a serious outbreak of foodborne hemolytic uremic syndrome and bloody diarrhea in Germany. Antibiotics were of questionable use and 54 deaths occurred. Candidate therapeutic bacteriophages that efficiently lyse the E. coli O104:H4 outbreak strain could be selected rather easily from a phage bank or isolated from the environment. It is argued that phage therapy should be more considered as a potential armament against the growing threat of (resistant) bacterial infections.
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Affiliation(s)
- Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
- Laboratory of Bacteriology Research, Ghent University, Ghent, Belgium
| | - Daniel De Vos
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Andrew M. Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Ontario, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | | | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Heverlee, Belgium
| | - Pierre Wattiau
- Unit of Highly Pathogenic & Foodborne Zoonoses, Veterinary and Agrochemical Research Centre, Brussels, Belgium
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical 8 Research Centre, Brussels, Belgium
| | - Catherine Ragimbeau
- Surveillance and Epidemiology of Infectious Diseases, Laboratoire National de Santé, Luxembourg, Luxembourg
| | - Joel Mossong
- Surveillance and Epidemiology of Infectious Diseases, Laboratoire National de Santé, Luxembourg, Luxembourg
| | - Jacques Scheres
- Maastricht University Medical Centre, Maastricht, The Netherlands
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Nina Chanishvili
- Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
| | | | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
- * E-mail:
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20
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Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proc Natl Acad Sci U S A 2012; 109:18266-72. [PMID: 23090996 DOI: 10.1073/pnas.1206541109] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.
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21
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Antimicrobial-resistant Bacteria: An Unrecognized Work-related Risk in Food Animal Production. Saf Health Work 2012; 3:85-91. [PMID: 22993711 PMCID: PMC3440465 DOI: 10.5491/shaw.2012.3.2.85] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 03/06/2012] [Accepted: 03/28/2012] [Indexed: 11/16/2022] Open
Abstract
The occupations involved in food animal production have long been recognized to carry significant health risks for workers, with special attention to injuries. However, risk of pathogen exposure in these occupations has been less extensively considered. Pathogens are a food safety issue and are known to be present throughout the food animal production chain. Workers employed at farms and slaughterhouses are at risk of pathogen exposure and bacterial infections. The industrialization of animal farming and the use of antimicrobials in animal feed to promote growth have increased the development of antimicrobial resistance. The changed nature of these pathogens exposes workers in this industry to new strains, thus modifying the risks and health consequences for these workers. These risks are not yet recognized by any work-related health and safety agency in the world.
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Vehicles, replicators, and intercellular movement of genetic information: evolutionary dissection of a bacterial cell. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:874153. [PMID: 22567533 PMCID: PMC3332184 DOI: 10.1155/2012/874153] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/06/2012] [Accepted: 02/08/2012] [Indexed: 11/18/2022]
Abstract
Prokaryotic biosphere is vastly diverse in many respects. Any given bacterial cell may harbor in different combinations viruses, plasmids, transposons, and other genetic elements along with their chromosome(s). These agents interact in complex environments in various ways causing multitude of phenotypic effects on their hosting cells. In this discussion I perform a dissection for a bacterial cell in order to simplify the diversity into components that may help approach the ocean of details in evolving microbial worlds. The cell itself is separated from all the genetic replicators that use the cell vehicle for preservation and propagation. I introduce a classification that groups different replicators according to their horizontal movement potential between cells and according to their effects on the fitness of their present host cells. The classification is used to discuss and improve the means by which we approach general evolutionary tendencies in microbial communities. Moreover, the classification is utilized as a tool to help formulating evolutionary hypotheses and to discuss emerging bacterial pathogens as well as to promote understanding on the average phenotypes of different replicators in general. It is also discussed that any given biosphere comprising prokaryotic cell vehicles and genetic replicators may naturally evolve to have horizontally moving replicators of various types.
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