Antibiotic Resistance And Horizontal DNA Transfer

(Jain, Rivera et al. 1999; Syvanen 2002; Wolska 2003; Beiko, Harlow et al. 2005; Breitbart and Rohwer 2005; Edwards and Rohwer 2005; Garcia Martin, Ivanova et al. 2006; Gill, Pop et al. 2006; Koonin 2006; Simoes-Barbosa, Arganaraz et al. 2006; Bench, Hanson et al. 2007; Casas and Rohwer 2007; Choi and Kim 2007; Juhas, Crook et al. 2007; Rogers, Patron et al. 2007; Rusch, Halpern et al. 2007; Desnues, Rodriguez-Brito et al. 2008; Gaillard, Pernet et al. 2008; Minoia, Gaillard et al. 2008; Tamames and Moya 2008; Tumapa, Holden et al. 2008; Williamson, Rusch et al. 2008; Abedon 2009; Aklujkar, Krushkal et al. 2009; Alsmark, Sicheritz-Ponten et al. 2009; Brakhage, Thon et al. 2009; Chan, Beiko et al. 2009; Coombs 2009; Heidelberg, Nelson et al. 2009; Ho Sui, Fedynak et al. 2009; Iwasaki and Takagi 2009; Keeling 2009; Labonte, Reid et al. 2009; Lechner, Schmitt et al. 2009; Novo, Bigey et al. 2009; Pasic, Rodriguez-Mueller et al. 2009; Penn, Jenkins et al. 2009; Putze, Hennequin et al. 2009; Sentchilo, Czechowska et al. 2009; Webb, Fisher et al. 2009; Bittner, Halary et al. 2010; Boto 2010; Danchin, Rosso et al. 2010; Hecht, Nitz et al. 2010; Lundin, Gribaldo et al. 2010; Moliner, Fournier et al. 2010; Paz and Espinosa 2010; Smillie, Garcillan-Barcia et al. 2010; Snir and Trifonov 2010; Thomas, Schaack et al. 2010; Aminov 2011; Andam, Fournier et al. 2011; Andam and Gogarten 2011; Andam and Gogarten 2011; Anderson and Seifert 2011; Creevey, Doerks et al. 2011; D'Costa, King et al. 2011; Kloesges, Popa et al. 2011; Petrova, Gorlenko et al. 2011; Smillie, Smith et al. 2011; Treangen and Rocha 2011; Treangen and Rocha 2011; Vogan and Higgs 2011; Wang, Wong et al. 2011; Wiedenbeck and Cohan 2011; Grassi, Grilli et al. 2012; Menigaud, Mallet et al. 2012)

Evolutionary Lessons From Superbugs Posted January 8, 2012   http://www.huffingtonpost.com/james-a-shapiro/bacterial-antibiotic-resistance_b_1192507.html

(Watanabe 1963; Watanabe 1967; Watanabe 1967; Clowes 1973; Davies 1979; Novick 1980; Chilton 1983; Sonea and Panisset 1983; Heinemann and Sprague 1989; Heinemann and Sprague 1991; Sprague 1991; Levy 1998; Miller 1998; Mazel and Davies 1999; Fauci 2001; Hacker and Carniel 2001; Mattick 2002; Morens, Folkers et al. 2004; Bhavsar, Guttman et al. 2007; Juhas, Crook et al. 2007; Juhas, Crook et al. 2008; Juhas, van der Meer et al. 2009; Tseng, Tyler et al. 2009; Filloux 2010; Gilbert and Dupont 2011)

The Distinct Roles of Selection, Horizontal Transfer and Natural Genetic Engineering in Dangerous Superbug Evolution  Posted: 08/29/2012 http://www.huffingtonpost.com/james-a-shapiro/the-distinct-roles-of-sel_b_1831996.html

(Watanabe 1963; Watanabe 1967; Watanabe 1967; Hayes 1968; Hedges and Jacob 1974; Bukhari 1977; Cohen and Shapiro 1980; Novick 1980; Hall and Stokes 1993; Hall and Collis 1995; Hall 2012)

The Evolutionary Importance of Horizontal DNA Transfer into Animal Germ Lines

Posted: 10/03/2012 http://www.huffingtonpost.com/james-a-shapiro/the-evolutionary-importan_b_1936059.html

(Palmer and Logsdon 1991; Andersson, Sjogren et al. 2003; Bergthorsson, Adams et al. 2003; Bergthorsson, Richardson et al. 2004; Andersson 2005; Richards, Dacks et al. 2006; Dunning Hotopp, Clark et al. 2007; Richardson and Palmer 2007; Belbahri, Calmin et al. 2008; Keeling and Palmer 2008; Andersson 2009; Andersson 2009; Hao, Richardson et al. 2010; Lundin, Gribaldo et al. 2010; Mower, Stefanovic et al. 2010; Schaack, Gilbert et al. 2010; Andersson 2011; Dunning Hotopp 2011; Li, Shen et al. 2011; Zhu, Lou et al. 2011; Andersson 2012; Arias, Danchin et al. 2012; Bertelli and Greub 2012; Sloan, Alverson et al. 2012; Sloan, Alverson et al. 2012; Stegemann, Keuthe et al. 2012)

 

Inter-Kingdom Horizontal DNA Transfer in all directions: Infectious bacteria evolve by acquiring protein domains from eukaryotic hosts  Posted: 11/06/2012 http://www.huffingtonpost.com/james-a-shapiro/interkingdom-horizontal-d_b_2081420.html  

(Stone and Kwaik 1999; Sexton and Vogel 2004; Borella, Guerrieri et al. 2005; de Felipe, Pampou et al. 2005; Albert-Weissenberger, Cazalet et al. 2007; Charpentier, Faucher et al. 2008; de Felipe, Glover et al. 2008; Habyarimana, Al-Khodor et al. 2008; Burstein, Zusman et al. 2009; Chong, Lima et al. 2009; Degtyar, Zusman et al. 2009; Franco, Shuman et al. 2009; Gomez-Valero, Rusniok et al. 2009; Price, Al-Khodor et al. 2009; Al-Khodor, Price et al. 2010; Cazalet, Gomez-Valero et al. 2010; D'Auria, Jimenez-Hernandez et al. 2010; Gasparich 2010; Habyarimana, Price et al. 2010; Hubber and Roy 2010; Kozak, Buss et al. 2010; Lurie-Weinberger, Gomez-Valero et al. 2010; Newton, Ang et al. 2010; Price, Al-Khodor et al. 2010; Price, Al-Quadan et al. 2010; Price, Jones et al. 2010; Price and Kwaik 2010; Schroeder, Petty et al. 2010; Al-Quadan and Kwaik 2011; Charpentier, Kay et al. 2011; Cui and Shao 2011; Fontana, Banga et al. 2011; Ge and Shao 2011; Gomez-Valero, Rusniok et al. 2011; Gomez-Valero, Rusniok et al. 2011; Hervet, Charpentier et al. 2011; Magori and Citovsky 2011; Meresse 2011; Nagai and Kubori 2011; O'Connor, Adepoju et al. 2011; Voth 2011; Al-Quadan, Price et al. 2012; Amaro, Gilbert et al. 2012; Arias, Danchin et al. 2012; Bertelli and Greub 2012; Durmus Tekir, Cakir et al. 2012; Kessler, Schell et al. 2012; Luo 2012; Tiaden and Hilbi 2012; Voth, Broederdorf et al. 2012)

Table III.1. Examples of intercellular and interkingdom DNA transfer
Horizontal transfer mode	Documented transfers
Uptake of environmental and liposomal DNA	Bacteria – bacteria: (Averhoff and Friedrich 2003; Claverys, Prudhomme et al. 2006; Averhoff 2009) Archaea-archaea: (Bertani and Baresi 1987; Worrell, Nagle et al. 1988); (Cline, Schalkwyk et al. 1989; Patel, Nash et al. 1994; Metcalf, Zhang et al. 1997; Soppa 2006; Almeida, Leszczyniecka et al. 2008; Berkner and Lipps 2008; Soppa, Baumann et al. 2008) Algal transfection: (Walker, Purton et al. 2005). Plant – bacteria: (Kay, Vogel et al. 2002; de Vries, Herzfeld et al. 2004) Plastid transfection: (O'Neill, Horvath et al. 1993) Mammalian cell transfection: (Wolff and Budker 2005; Khalil, Kogure et al. 2006; Kim and Eberwine 2010) and lipofection: (Felgner 1987; Zuhorn, Kalicharan et al. 2002) Plant protoplasts: (Potrykus 1990; Davey, Anthony et al. 2005)
Conjugal transfer	Bacteria – bacteria: (Hayes 1968) Archaea – archaea: (Prangishvili, Albers et al. 1998) Bacteria – archaea: (Dodsworth, Li et al. 2010) Bacteria – yeast: (Heinemann and Sprague 1989; Heinemann and Sprague 1991) Bacteria – plant: (Winans 1992; Broothaerts, Mitchell et al. 2005)
Viral transduction and GTAs (gene transfer agents)	Bacteria – bacteria: (Stanton 2007; McDaniel, Young et al. 2010) Archaea -- archaea: (Meile, Abendschein et al. 1990; Bertani 1999); (Zillig, Prangishvilli et al. 1996; Eiserling, Pushkin et al. 1999; Prangishvili 2003; Snyder, Stedman et al. 2003; Prangishvili and Garrett 2005; Prangishvili, Forterre et al. 2006; Prangishvili, Garrett et al. 2006) Bacteria – plant: (Chung, Vaidya et al. 2006) Animal cell – animal cell: (El-Aneed 2004) Animal cell – virus: (Filee, Pouget et al. 2008)
direct fusion of cells or protoplasts that lack a rigid outer covering.	Bacteria -- bacteria: (Schaeffer, Cami et al. 1976; Hopwood, Wright et al. 1977; Patnaik, Louie et al. 2002; Dai, Ziesman et al. 2005) Mammal -- mammal: (Ramos, Bonenfant et al. 2002; Trontelj, Usaj et al. 2010; Yamanaka and Blau 2010) Plant -- plant: (Gamborg and Holl 1977; Binding, Krumbiegel-Schroeren et al. 1986; Nehls, Krumbiegel-Schroeren et al. 1986; Potrykus 1990; Fahleson and Glimelius 1999; Davey, Anthony et al. 2005; Poma, Limongi et al. 2006; Savitha, Sadhasivam et al. 2010)
Parasitic or endosymbiotic association	Plant – fern: (Davis, Anderson et al. 2005) Plant – plant: (Davis and Wurdack 2004) (Mower, Stefanovic et al. 2004) Bacteria – invertebrate: (Hotopp, Clark et al. 2007; Nikoh, Tanaka et al. 2008; Nikoh and Nakabachi 2009)
Undetermined mechanism	Archaea – Bacteria: (Woese, Olsen et al. 2000; Koonin, Makarova et al. 2001) Bacteria – fungus: (Belbahri, Calmin et al. 2008) Bacteria – protist: (Huang, Mullapudi et al. 2004; Stechmann, Baumgartner et al. 2006; Whitaker, McConkey et al. 2009) Archaea – protist: (Andersson, Sarchfield et al. 2005; Huang, Xu et al. 2005) Protist – protist: (Andersson 2005; Andersson, Sarchfield et al. 2005; Andersson, Hirt et al. 2006; Andersson, Sjogren et al. 2007; Andersson 2009; Andersson 2009)

 

Antibiotic resistance by mutation

(Woodford and Ellington 2007; Rosenthal and Elowitz 2011; Toprak, Veres et al. 2011)

Antibiotic resistance mechanisms encoded in the environment

(Wright 2007; Canton 2009; Andam, Fournier et al. 2011; Colomer-Lluch, Jofre et al. 2011; Yung, Burke et al. 2011)

Genomic Islands and Inserting Conjugative Elements (ICE)

(Hacker and Carniel 2001; van der Meer and Sentchilo 2003; Quirke, Reen et al. 2006; Juhas, Crook et al. 2007; Fedorova, Khaldi et al. 2008; Gaillard, Pernet et al. 2008; Lima, Paquola et al. 2008; Minoia, Gaillard et al. 2008; Tumapa, Holden et al. 2008; Ho Sui, Fedynak et al. 2009; Johnston, Lin et al. 2009; Juhas, van der Meer et al. 2009; Lechner, Schmitt et al. 2009; Lloyd, Henderson et al. 2009; Pasic, Rodriguez-Mueller et al. 2009; Penn, Jenkins et al. 2009; Putze, Hennequin et al. 2009; Sentchilo, Czechowska et al. 2009; Avrani, Wurtzel et al. 2011; Guglielmini, Quintais et al. 2011)

Prophages and their phenotypic consequences

(Lazarevic 2001; Desiere, Lucchini et al. 2002; Canchaya, Fournous et al. 2004; Motro, La et al. 2009; Ronning, Losada et al. 2010; Colomer-Lluch, Jofre et al. 2011; Rasko, Webster et al. 2011)

Horizontal transfer in prokaryotes

(Matson, Thompson et al. 2005; Poggio, Abreu-Goodger et al. 2007; Stanton 2007; Davids and Zhang 2008; Price, Dehal et al. 2008; Coombs 2009; Lawrence and Retchless 2009; Brigulla and Wackernagel 2010; Aminov 2011; Treangen and Rocha 2011; Wiedenbeck and Cohan 2011; Tribble, Rigney et al. 2012)

Cyanobacteria: (Rogers, Patron et al. 2007; Yerrapragada, Siefert et al. 2009)

Symbionts and pathogens: (Sandstrom, Russell et al. 2001; Russell, Latorre et al. 2003; Russell and Moran 2005; Nogueira, Rankin et al. 2009) (Oliver, Degnan et al. 2010; Gomez-Valero, Rusniok et al. 2011)

Horizontal transfer in eukaryotes

(Fiebig, Hartmann et al. 2006; Holmes and Drummond 2007; Richardson and Palmer 2007; Fortune, Roulin et al. 2008; Keeling and Palmer 2008; Nedelcu, Miles et al. 2008; Parrish, Holmes et al. 2008; Rumpho, Worful et al. 2008; Andersson 2009; Andersson 2009; Bock 2009; Keeling 2009; Richards, Soanes et al. 2009; Bilewitch and Degnan 2011; Rodelsperger and Sommer 2011; Sanchez 2011; Zhang, Iyer et al. 2011; Zhu, Lou et al. 2011; Pierce, Fang et al. 2012; Xi, Bradley et al. 2012)

            Plastids and mitochondria: (Bergthorsson, Adams et al. 2003; Bergthorsson, Richardson et al. 2004; Alvarez, Benrey et al. 2006; Rogers, Patron et al. 2007; Sanchez-Puerta, Cho et al. 2008; Hao, Richardson et al. 2010; Mower, Stefanovic et al. 2010; Stegemann, Keuthe et al. 2012)

            Eukaryotic microbes: (Alsmark, Sicheritz-Ponten et al. 2009; Sorhannus 2011; Chan, Bhattacharya et al. 2012)

            Fungi and oomycetes: (Khaldi, Collemare et al. 2008; Morris, Schlosser et al. 2009; Richards, Soanes et al. 2009; Galeote, Novo et al. 2010; Mallet, Becq et al. 2010; Mehrabi, Bahkali et al. 2011; Richards, Soanes et al. 2011; Campbell, Rokas et al. 2012; Fitzpatrick 2012)

            Mobile genetic elements and viruses: (Daniels, Peterson et al. 1990; Kordis and Gubensek 1998; Dimcheff, Drovetski et al. 2000; Leaver 2001; Pinsker, Haring et al. 2001; Biedler, Shao et al. 2007; Bratke and McLysaght 2008; Pace, Gilbert et al. 2008; Gilbert, Schaack et al. 2010; Liu, Fu et al. 2010; Pagan, Smith et al. 2010; Schaack, Gilbert et al. 2010; Thomas, Schaack et al. 2010; Carareto 2011; Diao, Qi et al. 2011; Liu, Fu et al. 2011; Thomas, Sorourian et al. 2011; Liu, Fu et al. 2012)

Horizontal transfer between prokaryotes and eukaryotes

(Nielsen, Bones et al. 1998; Rogers, Patron et al. 2007; Fitzpatrick, Logue et al. 2008; Rumpho, Worful et al. 2008; Emiliani, Fondi et al. 2009; Mitreva, Smant et al. 2009; Pontiroli, Rizzi et al. 2009; McNulty, Foster et al. 2010; Roske, Foecking et al. 2010; Anderson and Seifert 2011; Danchin 2011; Dunning Hotopp 2011; Haegeman, Jones et al. 2011; Jackson 2011; Jackson, Macis et al. 2011; Li, Shen et al. 2011; Mayer, Schuster et al. 2011; Scholl and Bird 2011; Acuna, Padilla et al. 2012)

Horizontal RNA transfer

(Ramachandran and Palanisamy 2011; Zhang, Hou et al. 2011)

 

 

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