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Catchpole RJ, Barbe V, Magdelenat G, Marguet E, Terns M, Oberto J, Forterre P, Da Cunha V. A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea. Nat Microbiol 2023; 8:1339-1347. [PMID: 37277532 PMCID: PMC10788138 DOI: 10.1038/s41564-023-01387-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/19/2023] [Indexed: 06/07/2023]
Abstract
Conjugative plasmids are self-transmissible mobile genetic elements that transfer DNA between host cells via type IV secretion systems (T4SS). While T4SS-mediated conjugation has been well-studied in bacteria, information is sparse in Archaea and known representatives exist only in the Sulfolobales order of Crenarchaeota. Here we present the first self-transmissible plasmid identified in a Euryarchaeon, Thermococcus sp. 33-3. The 103 kbp plasmid, pT33-3, is seen in CRISPR spacers throughout the Thermococcales order. We demonstrate that pT33-3 is a bona fide conjugative plasmid that requires cell-to-cell contact and is dependent on canonical, plasmid-encoded T4SS-like genes. Under laboratory conditions, pT33-3 transfers to various Thermococcales and transconjugants propagate at 100 °C. Using pT33-3, we developed a genetic toolkit that allows modification of phylogenetically diverse Archaeal genomes. We demonstrate pT33-3-mediated plasmid mobilization and subsequent targeted genome modification in previously untransformable Thermococcales species, and extend this process to interphylum transfer to a Crenarchaeon.
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Affiliation(s)
- Ryan J Catchpole
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Institut Pasteur, Paris, France.
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Ghislaine Magdelenat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Evelyne Marguet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France
| | - Michael Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Jacques Oberto
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France
| | - Patrick Forterre
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Institut Pasteur, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France
| | - Violette Da Cunha
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Département de Microbiologie, Institut Pasteur, Paris, France.
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Gif-sur-Yvette, Cedex, France.
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.
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Dionisio F, Zilhão R, Gama JA. Interactions between plasmids and other mobile genetic elements affect their transmission and persistence. Plasmid 2019; 102:29-36. [DOI: 10.1016/j.plasmid.2019.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 10/27/2022]
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3
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Tasmin R, Hasan NA, Grim CJ, Grant A, Choi SY, Alam MS, Bell R, Cavanaugh C, Balan KV, Babu US, Parveen S. Genotypic and phenotypic characterization of multidrug resistant Salmonella Typhimurium and Salmonella Kentucky strains recovered from chicken carcasses. PLoS One 2017; 12:e0176938. [PMID: 28481935 PMCID: PMC5421757 DOI: 10.1371/journal.pone.0176938] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/19/2017] [Indexed: 01/18/2023] Open
Abstract
Salmonella Typhimurium is the leading cause of human non-typhoidal gastroenteritis in the US. S. Kentucky is one the most commonly recovered serovars from commercially processed poultry carcasses. This study compared the genotypic and phenotypic properties of two Salmonella enterica strains Typhimurium (ST221_31B) and Kentucky (SK222_32B) recovered from commercially processed chicken carcasses using whole genome sequencing, phenotype characterizations and an intracellular killing assay. Illumina MiSeq platform was used for sequencing of two Salmonella genomes. Phylogenetic analysis employing homologous alignment of a 1,185 non-duplicated protein-coding gene in the Salmonella core genome demonstrated fully resolved bifurcating patterns with varying levels of diversity that separated ST221_31B and SK222_32B genomes into distinct monophyletic serovar clades. Single nucleotide polymorphism (SNP) analysis identified 2,432 (ST19) SNPs within 13 Typhimurium genomes including ST221_31B representing Sequence Type ST19 and 650 (ST152) SNPs were detected within 13 Kentucky genomes including SK222_32B representing Sequence Type ST152. In addition to serovar-specific conserved coding sequences, the genomes of ST221_31B and SK222_32B harbor several genomic regions with significant genetic differences. These included phage and phage-like elements, carbon utilization or transport operons, fimbriae operons, putative membrane associated protein-encoding genes, antibiotic resistance genes, siderophore operons, and numerous hypothetical protein-encoding genes. Phenotype microarray results demonstrated that ST221_31B is capable of utilizing certain carbon compounds more efficiently as compared to SK222_3B; namely, 1,2-propanediol, M-inositol, L-threonine, α-D-lactose, D-tagatose, adonitol, formic acid, acetoacetic acid, and L-tartaric acid. ST221_31B survived for 48 h in macrophages, while SK222_32B was mostly eliminated. Further, a 3-fold growth of ST221_31B was observed at 24 hours post-infection in chicken granulosa cells while SK222_32B was unable to replicate in these cells. These results suggest that Salmonella Typhimurium can survive host defenses better and could be more invasive than Salmonella Kentucky and provide some insights into the genomic determinants responsible for these differences.
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Affiliation(s)
- Rizwana Tasmin
- Agriculture, Food and Resource Sciences, University of Maryland, Eastern Shore, Princess Anne, Maryland, United States of America
| | - Nur A. Hasan
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America
- CosmosID Inc., Rockville, Maryland, United States of America
| | - Christopher J. Grim
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Ar’Quette Grant
- Agriculture, Food and Resource Sciences, University of Maryland, Eastern Shore, Princess Anne, Maryland, United States of America
| | - Seon Young Choi
- CosmosID Inc., Rockville, Maryland, United States of America
| | - M. Samiul Alam
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Rebecca Bell
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, United States of America
| | - Christopher Cavanaugh
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Kannan V. Balan
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Uma S. Babu
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, Laurel, Maryland, United States of America
| | - Salina Parveen
- Agriculture, Food and Resource Sciences, University of Maryland, Eastern Shore, Princess Anne, Maryland, United States of America
- * E-mail:
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Oliva M, Monno R, D'Addabbo P, Pesole G, Dionisi AM, Scrascia M, Chiara M, Horner DS, Manzari C, Luzzi I, Calia C, D'Erchia AM, Pazzani C. A novel group of IncQ1 plasmids conferring multidrug resistance. Plasmid 2016; 89:22-26. [PMID: 27916622 DOI: 10.1016/j.plasmid.2016.11.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 11/28/2022]
Abstract
The IncQ is a group of non-conjugative but mobilisable plasmids that are found and stably maintained in a wide range of bacteria contributing to the spread of antimicrobial resistance genes and to the insurgence of multidrug resistant bacteria. Here we report the identification, in clinical Salmonella Typhimurium strains, of an IncQ1 plasmid (pNUC) which confers resistance to sulfamethoxazole, streptomycin and tetracycline through the presence of sul2, strAB and tetA genes, respectively. pNUC was detected in five multidrug resistant S. Typhimurium strains collected in Southern Italy from various hospitals and years of isolation. Bioinformatics analyses highlighted the presence of pNUC-like plasmids in pathogenic bacteria of various Enterobacteriaceae genera or species. Taken as a whole, these plasmids constitute a novel group of IncQ1 plasmids that might have originated through recombination events between a tetR-tetA gene cluster (possibly derived from a Tn1721) and a recipient IncQ1 plasmid related to RSF1010. Our findings raise concerns regarding the possible contribution of the newly identified group of IncQ1 plasmids to the spread of tetracycline resistance.
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Affiliation(s)
- M Oliva
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - R Monno
- Department of Basic Medical Sciences Neurosciences and Sense Organs Medical Faculty, University of Bari Piazza G. Cesare Policlinico, 70124 Bari, Italy
| | - P D'Addabbo
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - G Pesole
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - A M Dionisi
- Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
| | - M Scrascia
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - M Chiara
- Department of Biosciences, University of Milano, via Celoria 26, 20131 Milano, Italy
| | - D S Horner
- Department of Biosciences, University of Milano, via Celoria 26, 20131 Milano, Italy
| | - C Manzari
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy
| | - I Luzzi
- Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome 00161, Italy
| | - C Calia
- Department of Basic Medical Sciences Neurosciences and Sense Organs Medical Faculty, University of Bari Piazza G. Cesare Policlinico, 70124 Bari, Italy
| | - A M D'Erchia
- Institute of Biomembranes and Bioenergetics, National Research Council, via Amendola 165A, 70125 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, via Orabona, 4, 70125 Bari, Italy
| | - C Pazzani
- Department of Biology, University of Bari, via Orabona, 4, 70125 Bari, Italy.
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Hanon JB, Jaspers S, Butaye P, Wattiau P, Méroc E, Aerts M, Imberechts H, Vermeersch K, Van der Stede Y. A trend analysis of antimicrobial resistance in commensal Escherichia coli from several livestock species in Belgium (2011-2014). Prev Vet Med 2015; 122:443-52. [PMID: 26423778 DOI: 10.1016/j.prevetmed.2015.09.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 08/30/2015] [Accepted: 09/01/2015] [Indexed: 12/26/2022]
Abstract
A temporal trend analysis was performed on antimicrobial resistance data collected over 4 consecutive years (2011-2014) in the official Belgian antimicrobial resistance monitoring programme. Commensal Escherichia coli strains were isolated from faecal samples of four livestock categories (veal calves, young beef cattle, broiler chickens and slaughter pigs) and the trends of resistance profiles were analysed. The resistance prevalence remained high (>50%) during the study period for ampicillin in veal calves and chickens, for ciprofloxacin and nalidixic acid in chickens, for sulfamethoxazole in veal calves, chickens and pigs and for tetracycline in veal calves. Using logistic regression and Generalized Estimating Equation and after p value adjustment for multiple testing (Linear step-up method), statistically significant decreasing temporal trends were observed for several of the 11 tested antimicrobials in several livestock categories: in veal calves (10/11), in chickens (6/11) and in pigs (5/11). A significant increasing trend was observed for the prevalence of resistance to ciprofloxacin in chickens. Multi-resistance, considered as the resistance to at least three antimicrobials of different antibiotic classes, was observed in the four livestock categories but was significantly decreasing in veal calves, chickens and pigs. Overall, the prevalence of resistance and of multi-resistance was lowest in the beef cattle livestock category and highest in broiler chickens. These decreasing temporal trends of antimicrobial resistance might be due to a decrease of the total antimicrobial consumption for veterinary use in Belgium which was reported for the period between 2010 and 2013. The methodology and statistical tools developed in this study provide outputs which can detect shifts in resistance levels or resistance trends associated with particular antimicrobial classes and livestock categories. Such outputs can be used as objective evidence to evaluate the possible efficacy of measures taken by animal health authorities and stakeholders in the livestock sector to limit antimicrobial resistance occurrence.
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Affiliation(s)
- Jean-Baptiste Hanon
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Groeselenberg 99, 1180 Brussels, Belgium.
| | - Stijn Jaspers
- Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Patrick Butaye
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Groeselenberg 99, 1180 Brussels, Belgium; Ghent University, Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Salisburylaan 133, 9820 Merelbeke, Belgium; Ross University, Department of Biosciences, Basseterre, Saint Kitts and Nevis
| | - Pierre Wattiau
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Groeselenberg 99, 1180 Brussels, Belgium
| | - Estelle Méroc
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Groeselenberg 99, 1180 Brussels, Belgium
| | - Marc Aerts
- Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BioStat), Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Hein Imberechts
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Groeselenberg 99, 1180 Brussels, Belgium
| | - Katie Vermeersch
- Federal Agency for the Safety of the Food Chain (FASFC), Food Safety Centre, Boulevard du Jardin Botanique 55, 1000 Brussels, Belgium
| | - Yves Van der Stede
- Veterinary and Agrochemical Research Centre (CODA-CERVA), Groeselenberg 99, 1180 Brussels, Belgium; Ghent University, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Salisburylaan 133, 9820 Merelbeke, Belgium
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