Dr Nico Petty is a Senior Lecturer and group leader in Microbial Genomics at the ithree institute, University of Technology Sydney (UTS).
Following a degree in Biochemistry with Medical Biosciences at the University of Kent, Nico worked as a Pharmacologist in the pharmaceutical company Pfizer for a few years. A passion for bacteriophages and fighting infectious diseases led her to return to academia and pursue a PhD in Molecular Microbiology at the University of Cambridge, where she studied transducing phages of several bacterial pathogens. After postdoctoral positions at the Sanger Institute and University of Queensland (UQ), where she worked on the genomic analysis of pathogenic bacteria and the development of new bioinformatics tools, Nico was appointed Australian Infectious Diseases Research Fellow in the Australian Infectious Diseases Research Centre at UQ.
Nico joined the ithree institute in 2013 and leads the Microbial Genomics research group, using genomics, bioinformatics and molecular microbiology to investigate emerging pathogens, with a focus on their mobile genetic elements.
Australian Society for Microbiology (MASM)
Society for General Microbiology (UK)
American Society for Microbiology
International Society for Viruses of Microorganisms
Biennial Evergreen International Phage Meeting Organising Committee
Australian Society for Microbiology NSW-ACT Branch Committee
Dr Nico Petty investigates the evolution and spread of clinically important microbial pathogens and their viruses (bacteriophages) using approaches such as genomic epidemiology and comparative genomics as well as molecular microbiology techniques, with the aim of developing new strategies for the diagnosis, treatment and prevention of infectious diseases. Her research focuses on the contribution of phages and other mobile genetic elements to the emergence of new pathogens and antibiotic resistance. Nico is also interested in the development of new bioinformatics tools to enable easier and quicker analyses of microbial genome data, particularly by the growing number of clinicians and biologists wanting to use new sequencing technologies.
Current research areas include:
• Genome evolution in emerging bacterial pathogens
• Interactions and horizontal gene transfer between bacteriophages and their bacterial hosts
• Development of new bioinformatics tools for analysis of microbial genome data
• Exploitation of viruses to combat bacterial disease
Adriaenssens, EM, Sullivan, MB, Knezevic, P, van Zyl, LJ, Sarkar, BL, Dutilh, BE, Alfenas-Zerbini, P, Lobocka, M, Tong, Y, Brister, JR, Switt, AI, Klumpp, J, Aziz, RK, Barylski, J, Uchiyama, J, Edwards, RA, Kropinski, AM, Petty, NK, Clokie, MRJ, Kushkina, AI, Morozova, VV, Duffy, S, Gillis, A, Rumnieks, J, Kurtboke, I, Chanishvili, N, Goodridge, L, Wittmann, J, Lavigne, R, Jang, HB, Prangishvili, D, Enault, F, Turner, D, Poranen, MM, Oksanen, HM & Krupovic, M 2020, 'Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee', ARCHIVES OF VIROLOGY, vol. 165, no. 5, pp. 1253-1260.View/Download from: Publisher's site
Adriaenssens, EM, Wittmann, J, Kuhn, JH, Turner, D, Sullivan, MB, Dutilh, BE, Jang, HB, van Zyl, LJ, Klumpp, J, Lobocka, M, Moreno Switt, AI, Rumnieks, J, Edwards, RA, Uchiyama, J, Alfenas-Zerbini, P, Petty, NK, Kropinski, AM, Barylski, J, Gillis, A, Clokie, MRC, Prangishvili, D, Lavigne, R, Aziz, RK, Duffy, S, Krupovic, M, Poranen, MM, Knezevic, P, Enault, F, Tong, Y, Oksanen, HM & Rodney Brister, J 2018, 'Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.', Archives of virology, vol. 163, no. 4, pp. 1125-1129.View/Download from: Publisher's site
Aziz, RK, Ackermann, H-W, Petty, NK & Kropinski, AM 2018, 'Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis.', Methods in molecular biology (Clifton, N.J.), vol. 1681, pp. 197-215.View/Download from: Publisher's site
Because of the rise in antimicrobial resistance there has been a significant increase in interest in phages for therapeutic use. Furthermore, the cost of sequencing phage genomes has decreased to the point where it is being used as a teaching tool for genomics. Unfortunately, the quality of the descriptions of the phage and its annotation frequently are substandard. The following chapter is designed to help people working on phages, particularly those new to the field, to accurately describe their newly isolated viruses.
Marquez Ortiz, A, Haggerty, L, Sim, EM, Duarte, C, Castro-Cardozo, BE, Beltran, M, Saavedra, S, Vanegas, N, Escobar-Perez, J & Petty, NK 2017, 'First Complete Providencia rettgeri Genome Sequence, the NDM-1-Producing Clinical Strain RB151.', Genome Announcements, vol. 5, no. 3, pp. 1-2.View/Download from: Publisher's site
Providencia rettgeri is an opportunistic bacterial pathogen of clinical significance due to its association with urinary tract infections and multidrug resistance. Here, we report the first complete genome sequence of P. rettgeri The genome of strain RB151 consists of a 4.8-Mbp chromosome and a 108-kbp blaNDM-1-positive plasmid.
Marquez-Ortiz, RA, Haggerty, L, Olarte, N, Duarte, C, Garza-Ramos, U, Silva-Sanchez, J, Castro, BE, Sim, EM, Beltran, M, Moncada, MV, Valderrama, A, Castellanos, JE, Charles, IG, Vanegas, N, Escobar-Perez, J & Petty, NK 2017, 'Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance.', Genome biology and evolution, vol. 9, no. 6, pp. 1725-1741.View/Download from: Publisher's site
Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes.
Labbate, M, Orata, FD, Petty, NK, Jayatilleke, ND, King, WL, Kirchberger, PC, Allen, C, Mann, G, Mutreja, A, Thomson, NR, Boucher, Y & Charles, IG 2016, 'A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules.', Scientific Reports, vol. 6, pp. 1-7.View/Download from: Publisher's site
Cholera is a devastating diarrhoeal disease caused by certain strains of serogroup O1/O139 Vibrio cholerae. Mobile genetic elements such as genomic islands (GIs) have been pivotal in the evolution of O1/O139 V. cholerae. Perhaps the most important GI involved in cholera disease is the V. cholerae pathogenicity island 1 (VPI-1). This GI contains the toxin-coregulated pilus (TCP) gene cluster that is necessary for colonization of the human intestine as well as being the receptor for infection by the cholera-toxin bearing CTX phage. In this study, we report a GI (designated GIVchS12) from a non-O1/O139 strain of V. cholerae that is present in the same chromosomal location as VPI-1, contains an integrase gene with 94% nucleotide and 100% protein identity to the VPI-1 integrase, and attachment (att) sites 100% identical to those found in VPI-1. However, instead of TCP and the other accessory genes present in VPI-1, GIVchS12 contains a CRISPR-Cas element and a type VI secretion system (T6SS). GIs similar to GIVchS12 were identified in other V. cholerae genomes, also containing CRISPR-Cas elements and/or T6SS's. This study highlights the diversity of GIs circulating in natural V. cholerae populations and identifies GIs with VPI-1 recombination characteristics as a propagator of CRISPR-Cas and T6SS modules.
McAllister, LJ, Bent, SJ, Petty, NK, Skippington, E, Beatson, SA, Paton, JC & Paton, AW 2016, 'Genomic Comparison of Two O111:H- Enterohemorrhagic Escherichia coli Isolates from a Historic Hemolytic-Uremic Syndrome Outbreak in Australia', INFECTION AND IMMUNITY, vol. 84, no. 3, pp. 775-781.View/Download from: Publisher's site
Turnbull, L, Toyofuku, M, Hynen, AL, Kurosawa, M, Pessi, G, Petty, NK, Osvath, SR, Carcamo-Oyarce, G, Gloag, ES, Shimoni, R, Omasits, U, Ito, S, Yap, X, Monahan, LG, Cavaliere, R, Ahrens, CH, Charles, IG, Nomura, N, Eberl, L & Whitchurch, CB 2016, 'Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms', NATURE COMMUNICATIONS, vol. 7.View/Download from: Publisher's site
Wailan, AM, Sidjabat, HE, Yam, WK, Alikhan, N-F, Petty, NK, Sartor, AL, Williamson, DA, Forde, BM, Schembri, MA, Beatson, SA, Paterson, DL, Walsh, TR & Partridge, SR 2016, 'Mechanisms Involved in Acquisition of bla(NDM) Genes by IncA/C-2 and IncFII(Y) Plasmids', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 60, no. 7, pp. 4082-4088.View/Download from: Publisher's site
Baker, KS, Dallman, TJ, Ashton, PM, Day, M, Hughes, G, Crook, PD, Gilbart, VL, Zittermann, S, Allen, VG, Howden, BP, Tomita, T, Valcanis, M, Harris, SR, Connor, TR, Sintchenko, V, Howard, P, Brown, JD, Petty, NK, Gouali, M, Duy, PT, Keddy, KH, Smith, AM, Talukder, KA, Faruque, SM, Parkhill, J, Baker, S, Weill, F-X, Jenkins, C & Thomson, NR 2015, 'Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study', LANCET INFECTIOUS DISEASES, vol. 15, no. 8, pp. 913-921.View/Download from: Publisher's site
Beatson, SA, Ben Zakour, NL, Totsika, M, Forde, BM, Watts, RE, Mabbett, AN, Szubert, JM, Sarkar, S, Phan, M-D, Peters, KM, Petty, NK, Alikhan, N-F, Sullivan, MJ, Gawthorne, JA, Stanton-Cook, M, Nguyen, TKN, Chong, TM, Yin, W-F, Chan, K-G, Hancock, V, Ussery, DW, Ulett, GC & Schembri, MA 2015, 'Molecular Analysis of Asymptomatic Bacteriuria Escherichia coli Strain VR50 Reveals Adaptation to the Urinary Tract by Gene Acquisition', INFECTION AND IMMUNITY, vol. 83, no. 5, pp. 1749-1764.View/Download from: Publisher's site
Tan, A, Petty, NK, Hocking, D, Bennett-Wood, V, Wakefield, M, Praszkier, J, Tauschek, M, Yang, J & Robins-Browne, R 2015, 'Evolutionary Adaptation of an AraC-Like Regulatory Protein in Citrobacter rodentium and Escherichia Species', INFECTION AND IMMUNITY, vol. 83, no. 4, pp. 1384-1395.View/Download from: Publisher's site
Bachmann, N, Petty, N, Ben Zakour, NL, Szubert, JM, Savill, J & Beatson, SA 2014, 'Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow.', BMC Genomics, vol. 15.View/Download from: Publisher's site
Background Salmonella enterica subsp. enterica serovar Virchow has been recognized as a significant health burden in Asia, Australia and Europe. In addition to its global distribution, S. Virchow is clinically significant due to the frequency at which it causes invasive infections and its association with outbreaks arising from food-borne transmission. Here, we examine the genome of an invasive isolate of S. Virchow SVQ1 (phage type 8) from an outbreak in southeast Queensland, Australia. In addition to identifying new potential genotyping targets that could be used for discriminating between S. Virchow strains in outbreak scenarios, we also aimed to carry out a comprehensive comparative analysis of the S. Virchow genomes. Results Genome comparisons between S. Virchow SVQ1 and S. Virchow SL491, a previously published strain, identified a high degree of genomic similarity between the two strains with fewer than 200 single nucleotide differences. Clustered Regularly Interspaced Palindromic Repeats (CRISPR) regions were identified as a highly variable region that could be used to discriminate between S. Virchow isolates. We amplified and sequenced the CRISPR regions of fifteen S. Virchow isolates collected from seven different outbreaks across Australia. We observed three allelic types of the CRISPR region from these isolates based on the presence/absence of the spacers and were able to discriminate S. Virchow phage type 8 isolates originating from different outbreaks. A comparison with 27 published Salmonella genomes found that the S. Virchow SVQ1 genome encodes 11 previously described Salmonella Pathogenicity Islands (SPI), as well as additional genomic islands including a remnant integrative conjugative element that is distinct from SPI-7. In addition, the S. Virchow genome possesses a novel prophage that encodes the Type III secretion system effector protein SopE, a key Salmonella virulence factor. The prophage shares very little similarity to the SopE prophages...
Frampton, RA, Taylor, C, Holguín Moreno, AV, Visnovsky, SB, Petty, N, Pitman, AR & Fineran, PC 2014, 'Identification of bacteriophages for the biocontrol of the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae', Applied and Environmental Microbiology, vol. 80, no. 7, pp. 2216-2228.View/Download from: Publisher's site
Pseudomonas syringae pv. actinidiae is a re-emerging pathogen, which causes bacterial canker of kiwifruit (Actinidia sp.). Since 2008, a global outbreak of P. syringae pv. actinidiae has occurred, and in 2010 this pathogen was detected in New Zealand. The economic impact, and the development of resistance in P. syringae pv. actinidiae and other pathovars against antibiotics and copper sprays, has led to a search for alternative management strategies. We isolated 275 phages, 258 active against P. syringae pv. actinidiae. Extensive host range testing on P. syringae pv. actinidiae, other pseudomonads and bacteria isolated from kiwifruit orchards, showed that most phages have a narrow host range. Twenty four were analyzed by electron microscopy, pulse-field gel electrophoresis and restriction digestion. Their suitability for biocontrol was tested by assessing stability and the absence of lysogeny and transduction. A detailed host-range was performed and phage resistant bacteria were isolated and resistance to other phages examined. The phages were Caudovirales and were analyzed based on morphology and genome size, with representatives of Myoviridae, Podoviridae and Siphoviridae. Twenty one Myoviridae have similar morphology and genome size, yet differ in restriction patterns, host range and resistance, indicating a closely related group. Nine of these Myoviridae were sequenced and each was unique. The most closely related sequenced phages were a group infecting Pseudomonas aeruginosa and characterized by JG004 and PAK_P1. In summary, this study reports the isolation and characterization of P. syringae pv. actinidiae phages and provides a framework for the intelligent formulation of phage biocontrol agents against kiwifruit bacterial canker.
Gomez-Valero, L, Rusniok, C, Rolando, M, Neou, M, Dervins-Ravault, D, Demirtas, J, Rouy, Z, Moore, RJ, Chen, H, Petty, NK, Jarraud, S, Etienne, J, Steinert, M, Heuner, K, Gribaldo, S, Médigue, C, Glöckner, G, Hartland, EL & Buchrieser, C 2014, 'Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease', Genome Biology, vol. 15, no. 11, pp. 505-505.View/Download from: Publisher's site
Petty, NK, Ben Zakour, NL, Stanton-Cook, M, Skippington, E, Totsika, M, Forde, BM, Phan, M, Gomes Moriel, D, Peters, KM, Davies, M, Rogers, BA, Dougan, G, Rodriguez-Baño, J, Pascual, A, Pitout, JD, Upton, M, Paterson, DL, Walsh, TR, Schembri, MA & Beatson, SA 2014, 'Global dissemination of a multidrug resistant Escherichia coli clone', Proceedings of The National Academy of Sciences of the United States of America, vol. 111, no. 15, pp. 5694-5699.View/Download from: Publisher's site
Escherichia coli sequence type 131 (ST131) is a globally disseminated, multidrug resistant (MDR) clone responsible for a high proportion of urinary tract and bloodstream infections. The rapid emergence and successful spread of E. coli ST131 is strongly associated with several factors, including resistance to fluoroquinolones, high virulence gene content, the possession of the type 1 fimbriae FimH30 allele, and the production of the CTX-M-15 extended spectrum ß-lactamase (ESBL). Here, we used genome sequencing to examine the molecular epidemiology of a collection of E. coli ST131 strains isolated from six distinct geographical locations across the world spanning 20002011. The global phylogeny of E. coli ST131, determined from whole-genome sequence data, revealed a single lineage of E. coli ST131 distinct from other extraintestinal E. coli strains within the B2 phylogroup. Three closely related E. coli ST131 sublineages were identified, with little association to geographic origin. The majority of single-nucleotide variants associated with each of the sublineages were due to recombination in regions adjacent to mobile genetic elements (MGEs). The most prevalent sublineage of ST131 strains was characterized by fluoroquinolone resistance, and a distinct virulence factor and MGE profile. Four different variants of the CTX-M ESBLresistance gene were identified in our ST131 strains, with acquisition of CTX-M-15 representing a defining feature of a discrete but geographically dispersed ST131 sublineage. This study confirms the global dispersal of a single E. coli ST131 clone and demonstrates the role of MGEs and recombination in the evolution of this important MDR pathogen. http://www.pnas.org/content/111/15/5694.full
Reuter, S, Connor, TR, Barquist, L, Walker, D, Harris, SH, Fookes, M, Hall, ME, Petty, N, Fuchs, TM, Corander, J, Dofour, M, Ringwood, T, Savin, C, Bouchier, C, Martin, L, Miettinen, M, Shubin, M, Riehm, JM, Laukkanen-Ninios, R, Sihvoven, LM, Siitonen, A, Skurnik, M, Pfrimer Falcão, J, Fukushima, H, Scholz, HC, Prentice, MB, Wren, BW, Parkhill, J, Carniel, E, Achtman, M, McNally, A & Thomson, NR 2014, 'Parallel independent evolution of pathogenicity within the genus Yersinia', Proceedings of The National Academy of Sciences of the United States of America, vol. 111, no. 18, pp. 6768-6773.View/Download from: Publisher's site
The genus Yersinia has been used as a model system to study pathogen evolution. Using whole-genome sequencing of all Yersinia species, we delineate the gene complement of the whole genus and define patterns of virulence evolution. Multiple distinct ecological specializations appear to have split pathogenic strains from environmental, nonpathogenic lineages. This split demonstrates that contrary to hypotheses that all pathogenic Yersinia species share a recent common pathogenic ancestor, they have evolved independently but followed parallel evolutionary paths in acquiring the same virulence determinants as well as becoming progressively more limited metabolically. Shared virulence determinants are limited to the virulence plasmid pYV and the attachment invasion locus ail. These acquisitions, together with genomic variations in metabolic pathways, have resulted in the parallel emergence of related pathogens displaying an increasingly specialized lifestyle with a spectrum of virulence potential, an emerging theme in the evolution of other important human pathogens.
Toribio, AL, Pickard, D, Cerdeño-Tárraga, AM, Petty, N, Thomson, N, Salmond, GP & Dougan, G 2014, 'Complete Genome Sequences of Two Citrobacter rodentium Bacteriophages, CR8 and CR44b', Genome Announcements, vol. 2, no. 3.View/Download from: Publisher's site
The complete genomes of two virulent phages infecting Citrobacter rodentium are reported here for the first time. Both bacteriophages were isolated from local sewage treatment plant effluents. Genome analyses revealed a close relationship between both phages and allowed their classification as members of the Autographivirinae subfamily in the T7-like genus.
Wee, BA, Woolfit, M, Beatson, SA & Petty, NK 2013, 'A Distinct and Divergent Lineage of Genomic Island-Associated Type IV Secretion Systems in Legionella', PLOS ONE, vol. 8, no. 12.View/Download from: Publisher's site
Chaperone-usher (CU) fimbriae are adhesive surface organelles common to many Gram-negative bacteria. Escherichia coli genomes contain a large variety of characterised and putative CU fimbrial operons, however, the classification and annotation of individ
Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. RESULTS: BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically. CONCLUSIONS: There is a ...
Fookes, M, Schroeder, G, Langridge, G, Blondel, C, Mammina, C, Connor, T, Seth-smith, H, Vernikos, G, Robinson, KS, Sanders, M, Petty, N, Kingsley, R, Baumler, A, Nuccio, S, Contreras, I, Santiviago, C, Maskell, D, Barrow, P, Humphrey, T, Nastasi, A, Roberts, M, Frankel, G, Parkhill, J, Dougan, G & Thomson, NR 2011, 'Salmonella bongori Provides Insights into the Evolution of the Salmonellae', PLoS Pathogens, vol. 7, no. 8, pp. 1-16.View/Download from: Publisher's site
The genus Salmonella contains two species, S. bongori and S. enterica. Compared to the well-studied S. enterica there is a marked lack of information regarding the genetic makeup and diversity of S. bongori. S. bongori has been found predominantly associ
Petty, N, Feltwell, T, Pickard, D, Clare, S, Toribio, A, Fookes, M, Roberts, K, Monson, R, Nair, S, Kingsley, R, Bulgin, R, Wiles, S, Goulding, D, Keane, T, Corton, C, Lennard, N, Harris, D, Willey, D, Rance, R, Yu, L, Choudhary, J, Churcher, C, Quail, M, Parkhill, J, Frankel, G, Dougan, G, Salmond, GP & Thomson, NR 2011, 'Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux', PLoS Pathogens, vol. 7, no. 4, pp. 1-15.View/Download from: Publisher's site
Citrobacter rodentium is a natural mouse pathogen that causes attaching and effacing (A/E) lesions. It shares a common virulence strategy with the clinically significant human A/E pathogens enteropathogenic E. coli (EPEC) and enterohaemorrhagic E. coli (
Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, c
Totsika, M, Beatson, SA, Sarkar, S, Phan, M, Petty, N, Bachmann, N, Szubert, M, Sidjabat, H, Paterson, D, Upton, M & Schembri, MA 2011, 'Insights Into A Multidrug Resistant Escherichia coli Pathogen Of The Globally Disseminated ST131 Lineage: Genome Analysis and Virulence Mechanisms', PLoS One, vol. 6, no. 10, pp. 1-11.View/Download from: Publisher's site
Escherichia coli strains causing urinary tract infection (UTI) are increasingly recognized as belonging to specific clones. E. coli clone O25b:H4-ST131 has recently emerged globally as a leading multi-drug resistant pathogen causing urinary tract and blo
Crossman, L, Chaudhuri, R, Beatson, SA, Wells, T, Desvaux, M, Cunningham, AF, Petty, N, Mahon, V, Brinkley, C, Hobman, J, Savarino, S, Turner, S, Pallen, M, Penn, C, Parkhill, J, Turner, A, Johnson, T, Thomson, N, Smith, S & Henderson, I 2010, 'A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407', Journal of Bacteriology, vol. 192, no. 21, pp. 5822-5831.View/Download from: Publisher's site
In most cases, Escherichia coli exists as a harmless commensal organism, but it may on occasion cause intestinal and/or extraintestinal disease. Enterotoxigenic E. coli (ETEC) is the predominant cause of E. coli-mediated diarrhea in the developing world
Following on from last months discussion of sequence assembly and correction, this months Genome Watch examines genome annotation in the context of advances in second-generation sequencing.
Petty, N, Bulgin, R, Crepin, V, Cerdeno-Tarraga, AM, Schroeder, G, Quail, M, Lennard, N, Corton, C, Barron, A, Clark, L, Toribio, A, Parkhill, J, Dougan, G, Frankel, G & Thomson, N 2010, 'The Citrobacter rodentium Genome Sequence Reveals Convergent Evolution with Human Pathogenic Escherichia coli', Journal Of Bacteriology, vol. 192, no. 2, pp. 525-538.View/Download from: Publisher's site
Citrobacter rodentium (formally Citrobacter freundii biotype 4280) is a highly infectious pathogen that causes colitis and transmissible colonic hyperplasia in mice. In common with enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, r
Pickard, D, Toribio, A, Petty, N, Van Tonder, A, Yu, L, Goulding, D, Barrell, B, Rance, R, Harris, D, Wetter, M, Wain, J, Choudhary, J, Thomson, N & Dougan, G 2010, 'A Conserved Acetyl Esterase Domain Targets Diverse Bacteriophages to the Vi Capsular Receptor of Salmonella enterica Serovar Typhi', Journal of Bacteriology, vol. 192, no. 21, pp. 5746-5754.View/Download from: Publisher's site
A number of bacteriophages have been identified that target the Vi capsular antigen of Salmonella enterica serovar Typhi. Here we show that these Vi phages represent a remarkably diverse set of phages belonging to three phage families, including Podoviri
Schroeder, G, Petty, N, Mousnier, A, Harding, C, Vogrin, A, Wee, B, Fry, N, Harrison, T, Newton, H, Thomson, N, Beatson, SA, Dougan, G, Hartland, E & Frankel, G 2010, 'Legionella pneumophila Strain 130b Possesses a Unique Combination of Type IV Secretion Systems and Novel Dot/Icm Secretion System Effector Proteins', Journal Of Bacteriology, vol. 192, no. 22, pp. 6001-6016.View/Download from: Publisher's site
Legionella pneumophila is a ubiquitous inhabitant of environmental water reservoirs. The bacteria infect a wide variety of protozoa and, after accidental inhalation, human alveolar macrophages, which can lead to severe pneumonia. The capability to thrive
Timms, A, Cambray-young, J, Scott, A, Petty, N, Connerton, P, Clarke, L, Seeger, K, Quail, M, Cummings, N, Maskell, D, Thomson, N & Connerton, I 2010, 'Evidence for a lineage of virulent bacteriophages that target Campylobacter', BMC Genomics, vol. 11, no. NA, pp. 1-10.View/Download from: Publisher's site
Background: Our understanding of the dynamics of genome stability versus gene flux within bacteriophage lineages is limited. Recently, there has been a renewed interest in the use of bacteriophages as 'therapeutic' agents; a prerequisite for their use in
This months Genome Watch discusses the genome sequences of pathogenic and commensal bacteria that are associated with plant crops and shows how analysis of such genomes can lead to new approaches to combat plant diseases
The experimentally amenable nature of phage and their use in testing fundamental biological questions have meant that phage research has had a profound effect on modern molecular biology. Phage research has also fuelled multiple biotechnological developm
Petty, N, Toribio, AL, Goulding, D, Foulds, IJ, Thomson, N, Dougan, G & Salmond, GP 2007, 'A generalized transducing phage for the murine pathogen Citrobacter rodentium', Microbiology, vol. 153, no. 9, pp. 2984-2988.View/Download from: Publisher's site
A virulent phage (phi CR1) capable of generalized transduction in Citrobacter rodentium was isolated from the environment and characterized. C. rodentium is a natural pathogen of mice, causing transmissible murine colonic hyperplasia. Sequencing of its g
Petty, NK, Foulds, IJ, Pradel, E, Ewbank, JJ & Salmond, GPC 2006, 'A generalized transducing phage (phi lF3) for the genomically sequenced Serratia marcescens strain Db11: a tool for functional genomics of an opportunistic human pathogen', MICROBIOLOGY-SGM, vol. 152, pp. 1701-1708.View/Download from: Publisher's site
Zuideveld, KP, Van der Graaf, PH, Newgreen, G, Thurlow, R, Petty, N, Jordan, P, Peletier, LA & Danhof, M 2004, 'Mechanism-based pharmacokinetic-pharmacodynamic modelling of 5-HT1A receptor agonists: estimation of in vivo affinity and intrinsic efficacy on body temperature in rats', Journal Of Pharmacology And Experimental Therapeutics, vol. 308, no. 3, pp. 1012-1020.View/Download from: Publisher's site
The pharmacokinetic-pharmacodynamic (PK-PD) correlations of seven prototypical 5-HT(1A) agonists were analyzed on the basis of a recently proposed semi-mechanistic PK-PD model for the effect on body temperature. The resulting concentration-effect relationships were subsequently analyzed on the basis of the operational model of agonism to estimate the operational affinity (pK(A)) and efficacy (log tau) at the 5-HT(1A) receptor in vivo. The values obtained in this manner were compared with estimates of the affinity (pK(i)) and intrinsic efficacy (log[agonist ratio]) in a receptor-binding assay. Between 5-HT(1A) agonists wide differences in in vivo affinity and efficacy were observed, with values of the pK(A) ranging from 5.67 for flesinoxan to 8.63 for WAY-100,635 [N-(2-(4-(2-methoxyphenyl)-1-piperazinyl)ethyl)-N-2-pyridinyl-cyclohexanecarboxamide] and of the log tau ranging from -1.27 for WAY-100,135 [N-(1,1-dimethylethyl)-4-(2-methoxyphenyl)-alpha-phenyl-1-piperazine-propanamide] to 0.62 for R-(+)-8-hydroxy-2-[di-n-propylamino)tetralin. Poor correlations were observed between the in vivo receptor affinity (pK(A)) and the affinity estimates in the in vitro receptor binding assay (pK(i); r(2) = 0.55, P > 0.05), which could in part be explained by differences in blood-brain distribution. In contrast, a highly significant correlation was observed between the efficacy parameters in vivo (log tau) and in vitro (log [agonist ratio]; r(2) = 0.76, P < 0.05). Thus by combining the previously proposed semi-mechanistic PK-PD model for the effect on body temperature with the operational model of agonism, a full mechanistic PK-PD model for 5-HT(1A) receptor agonists has been obtained, which is highly predictive of the in vivo intrinsic efficacy.
Alikhan, N-F, Bachmann, NL, Zakour, NLB, Petty, NK, Stanton-Cook, M, Gawthorne, JA, Easton, DM, Mahony, TJ, Cobbold, R, Schembri, MA & Beatson, SA, 'Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli'.View/Download from: Publisher's site
AbstractBackgroundShiga toxigenic Escherichia coli (STEC) is an emerging global pathogen and remains a major cause of food-borne illness with more severe symptoms including hemorrhagic colitis and hemolytic-uremic syndrome. Since the characterization of the archetypal STEC serotype, E. coli O157:H7, more than 250 STEC serotypes have been defined. Many of these non-O157 STEC are associated with clinical cases of equal severity as O157. In this study, we utilize whole genome sequencing of 44 STEC strains from eight serogroups associated with human infection to establish their evolutionary relationships and contrast this with their virulence gene profiles and established typing methods.ResultsOur phylogenomic analysis delineated these STEC strains into seven distinct lineages, each with a characteristic repertoire of virulence factors. Some lineages included commensal or other E. coli pathotypes. Multiple independent acquisitions of the Locus for Enterocyte Effacement were identified, each associated with a distinct repertoire of effector genes. Lineages were inconsistent with O-antigen typing in several instances, consistent with lateral gene transfer within the O-antigen locus. STEC lineages could be defined by the conservation of clustered regularly interspaced short palindromic repeats (CRISPRs), however, no CRISPR profile could differentiate STEC from other E. coli strains. Six genomic regions (ranging from 500 bp - 10 kbp) were found to be conserved across all STEC in this dataset and may dictate interactions with Stx phage lysogeny.ConclusionsThe genomic analyses reported here present non-O157 STEC as a diverse group of pathogenic E. coli
Turner, D, Sutton, JM, Reynolds, DM, Sim, EM & Petty, NK 2018, 'Visualization of Phage Genomic Data: Comparative Genomics and Publication-Quality Diagrams.' in Bacteriophages, pp. 239-260.View/Download from: Publisher's site
The presentation of bacteriophage genomes as diagrams allows the location and organization of features to be communicated in a clear and effective manner. A wide range of software applications are available for the clear and accurate visualization of genomic data. Several of these applications incorporate comparative analysis tools, allowing for insertions, deletions, rearrangements and variations in syntenic regions to be visualized. In this chapter, freely available software and resources for the generation of high-quality graphical maps of bacteriophage genomes are listed and discussed.
Fineran, P, Petty, N & Salmond, GP 2009, 'Transduction: host DNA transfer by bacteriophages' in Schaechter, M (ed), Encyclopedia of Microbiology, Elsevier, Oxford, pp. 666-679.
Wellcome Trust Sanger Institute
Imperial College London
CSIRO Animal, Food and Health Sciences
University of Queensland
University of Otago
University of Melbourne
University of Cambridge