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Dr Maurizio Labbate

Biography

In 1997, Dr Maurizio Labbate completed a B. Sc (Hons 1) in Microbiology from the University of New South Wales (UNSW) and subsequently started his PhD in 1998 under the supervision of Prof. S. Kjelleberg at UNSW. During that time, he developed a project on the identification of genes involved in adhesion and infection by the pathogen Serratia marcescens. His research investigated genes involved in adhesion to abiotic surfaces and adhesion/infection of the human cornea by S. marcescens.

In February 2005, Dr Labbate commenced a Postdoctoral position with Prof. Hatch Stokes at Macquarie University managing projects dealing with lateral gene transfer (LGT) in human pathogens and commensals with an emphasis on integrons and antibiotic resistance.

In November 2008, Dr Labbate moved to the ithree Institute at the University of Technology and was awarded an ithree Institute Fellowship in 2010. In March 2013, he initiated a new role as Senior Lecturer in Microbiology in the Department of Medical and Molecular Biosciences (MMB) at UTS.

For information of Dr Labbate’s current research interests and programs, please visit his laboratory homepage (opens an external site)

Professional

Professional activities:
Member of the University of Technology, Sydney Biosafety Research Ethics Committee.
Member of the Australian Society for Microbiology (ASM).
Member of the International Society for Microbial Ecology (ISME).

Expertise:
Microbial physiology
Lateral gene transfer
Molecular biology techniques
Vibrio genetics
Antibiotic resistance

Image of Maurizio Labbate
Senior Lecturer, School of Life Sciences
Associate Member, ithree - Institute of Infection, Immunity and Innovation
B Sc (Honours Class 1), Ph D
 
Phone
+61 2 9514 4064

Research Interests

For information on Dr Maurizio Labbate's research interests - please visit his laboratory homepage (opens an external site)

Can supervise: Yes
Registered at Level 1 Student: Rita Rapa (PhD) "Mobile genetic elements and Vibrio evolution". Student: Chris Allen (PhD) "Evolution of pathogenic Vibrio cholerae".

General Microbiology 91314 - Autumn Semester

Books

Labbate, M., Seymour, J.R., Lauro, F. & Brown, M.V. 2016, Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments, Frontiers Media SA, Lausanne, Switzerland.
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Aquatic ecosystems are currently experiencing unprecedented levels of impact from human activities including over-exploitation of resources, habitat destruction, pollution and the influence of climate change. The impacts of these activities on the microbial ecology of aquatic environments are only now beginning to be defined. One of the many implications of environmental degradation and climate change is the geographical expansion of disease- causing microbes such as those from the Vibrio genus. Elevating sea surface temperatures correlate with increasing Vibrio numbers and disease in marine animals (e.g. corals) and humans. Contamination of aquatic environments with heavy metals and other pollutants affects microbial ecology with downstream effects on biogeochemical cycles and nutrient turnover. Also of importance is the pollution of aquatic environments with antibiotics, resistance genes and the mobile genetic elements that house resistance genes from human and animal waste. Such contaminated environments act as a source of resistance genes long after an antibiotic has ceased being used in the community. Environments contaminated with mobile genetic elements that are adapted to human commensals and pathogens function to capture new resistance genes for potential reintroduction back into clinical environments. This research topic encompasses these diverse topics and describes the affect(s) of human activity on the microbial ecology and function in aquatic environments and, describes methods of restoration and for modelling disturbances.

Chapters

Roy Chowdhury, P., Stokes, H. & Labbate, M. 2013, 'Integrons: antibiotic resistance evolution and beyond' in Roberts, A.P. & Mullany, P. (eds), Bacterial Integrative Mobile Genetic Elements, Landes Bioscience, Austin, Texas USA, pp. 53-69.
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Labbate, M., Case, R.J. & Stokes, H. 2009, 'The integron/gene cassette system: an active player in bacterial adaptation' in Gogarten, M., Gogarten, P. & Olendzenski, L. (eds), Horizontal Gene Transfer, Humana Press, New York, pp. 103-125.
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The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir of antibiotic-resistance genes. Integrons are now known to be ancient structures that are phylogenetically diverse and, to date, have been found in approximately 9 % of sequenced bacterial genomes. Overall, gene diversity in cassettes is extraordinarily high suggesting that the integron/gene cassette system has a broad role in adaptation rather than being confined to simply conferring resistance to antibiotics. In this chapter, we provide a review of the integron/gene cassette system highlighting characteristics associated with this system, diversity of elements contained within it and their importance in driving bacterial evolution and consequently adaptation. Ideas on the evolution of gene cassettes and gene cassette arrays are discussed.

Journal articles

Siboni, N., Balaraju, V., Carney, R., Labbate, M. & Seymour, J.R. 2016, 'Spatiotemporal Dynamics of Vibrio spp. within the Sydny harbour Estuary', FRONTIERS IN MICROBIOLOGY, vol. 7.
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Labbate, M., Seymour, J.R., Lauro, F. & Brown, M.V. 2016, 'Editorial: Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments.', Frontiers in microbiology, vol. 7, p. 1044.
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Sartelli, M., Weber, D.G., Ruppé, E., Bassetti, M., Wright, B.J., Ansaloni, L., Catena, F., Coccolini, F., Abu-Zidan, F.M., Coimbra, R., Moore, E.E., Moore, F.A., Maier, R.V., De Waele, J.J., Kirkpatrick, A.W., Griffiths, E.A., Eckmann, C., Brink, A.J., Mazuski, J.E., May, A.K., Sawyer, R.G., Mertz, D., Montravers, P., Kumar, A., Roberts, J.A., Vincent, J.L., Watkins, R.R., Lowman, W., Spellberg, B., Abbott, I.J., Adesunkanmi, A.K., Al-Dahir, S., Al-Hasan, M.N., Agresta, F., Althani, A.A., Ansari, S., Ansumana, R., Augustin, G., Bala, M., Balogh, Z.J., Baraket, O., Bhangu, A., Beltrán, M.A., Bernhard, M., Biffl, W.L., Boermeester, M.A., Brecher, S.M., Cherry-Bukowiec, J.R., Buyne, O.R., Cainzos, M.A., Cairns, K.A., Camacho-Ortiz, A., Chandy, S.J., Che Jusoh, A., Chichom-Mefire, A., Colijn, C., Corcione, F., Cui, Y., Curcio, D., Delibegovic, S., Demetrashvili, Z., De Simone, B., Dhingra, S., Diaz, J.J., Di Carlo, I., Dillip, A., Di Saverio, S., Doyle, M.P., Dorj, G., Dogjani, A., Dupont, H., Eachempati, S.R., Enani, M.A., Egiev, V.N., Elmangory, M.M., Ferrada, P., Fitchett, J.R., Fraga, G.P., Guessennd, N., Giamarellou, H., Ghnnam, W., Gkiokas, G., Goldberg, S.R., Gomes, C.A., Gomi, H., Guzmán-Blanco, M., Haque, M., Hansen, S., Hecker, A., Heizmann, W.R., Herzog, T., Hodonou, A.M., Hong, S.K., Kafka-Ritsch, R., Kaplan, L.J., Kapoor, G., Karamarkovic, A., Kees, M.G., Kenig, J. & Kiguba, R. 2016, 'Antimicrobials: A global alliance for optimizing their rational use in intra-abdominal infections (AGORA)', World Journal of Emergency Surgery, vol. 11, no. 1.
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© 2016 The Author(s).Intra-abdominal infections (IAI) are an important cause of morbidity and are frequently associated with poor prognosis, particularly in high-risk patients. The cornerstones in the management of complicated IAIs are timely effective source control with appropriate antimicrobial therapy. Empiric antimicrobial therapy is important in the management of intra-abdominal infections and must be broad enough to cover all likely organisms because inappropriate initial antimicrobial therapy is associated with poor patient outcomes and the development of bacterial resistance. The overuse of antimicrobials is widely accepted as a major driver of some emerging infections (such as C. difficile), the selection of resistant pathogens in individual patients, and for the continued development of antimicrobial resistance globally. The growing emergence of multi-drug resistant organisms and the limited development of new agents available to counteract them have caused an impending crisis with alarming implications, especially with regards to Gram-negative bacteria. An international task force from 79 different countries has joined this project by sharing a document on the rational use of antimicrobials for patients with IAIs. The project has been termed AGORA (Antimicrobials: A Global Alliance for Optimizing their Rational Use in Intra-Abdominal Infections). The authors hope that AGORA, involving many of the world's leading experts, can actively raise awareness in health workers and can improve prescribing behavior in treating IAIs.
Labbate, M., Orata, F.D., Petty, N.K., Jayatilleke, N.D., King, W.L., Kirchberger, P.C., Allen, C., Mann, G., Mutreja, A., Thomson, N.R., Boucher, Y. & Charles, I.G. 2016, 'A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules.', Sci Rep, vol. 6, p. 36891.
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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.
Michael, C.A., Franks, A.E. & Labbate, M. 2016, 'The antimicrobial resistance crisis: management through gene monitoring.', Open Biol, vol. 6, no. 11.
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Antimicrobial resistance (AMR) is an acknowledged crisis for humanity. Its genetic origins and dire potential outcomes are increasingly well understood. However, diagnostic techniques for monitoring the crisis are currently largely limited to enumerating the increasing incidence of resistant pathogens. Being the end-stage of the evolutionary process that produces antimicrobial resistant pathogens, these measurements, while diagnostic, are not prognostic, and so are not optimal in managing this crisis. A better test is required. Here, using insights from an understanding of evolutionary processes ruling the changing abundance of genes under selective pressure, we suggest a predictive framework for the AMR crisis. We then discuss the likely progression of resistance for both existing and prospective antimicrobial therapies. Finally, we suggest that by the environmental monitoring of resistance gene frequency, resistance may be detected and tracked presumptively, and how this tool may be used to guide decision-making in the local and global use of antimicrobials.
Labbate, M., Islam, A., Monahan, L.G., Charles, I.G. & Stokes, H.W. 2015, 'A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage', Environmental Microbiology.
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Dominey-Howes, D., Bajorek, B., Michael, C.A., Betteridge, B., Iredell, J. & Labbate, M. 2015, 'Applying the emergency risk management process to tackle the crisis of antibiotic resistance', FRONTIERS IN MICROBIOLOGY, vol. 6.
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Laczka, O.F., Labbate, M. & Doblin, M.A. 2014, 'Application of an ELISA-type amperometric assay to the detection of Vibrio species with screenprinted electrodes', Analytical Methods, vol. 6, pp. 2020-2023.
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Laczka, O.F., Labbate, M., Seymour, J.R., Bourne, D.G., Fielder, S.S. & Doblin, M.A. 2014, 'Surface Immuno-Functionalisation for the Capture and Detection of Vibrio Species in the Marine Environment: A New Management Tool for Industrial Facilities', PLOS ONE, vol. 9, no. 10.
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Michael, C.A., Dominey-Howes, D. & Labbate, M. 2014, 'The antimicrobial resistance crisis: causes, consequences, and management.', Frontiers in public health, vol. 2, p. 145.
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The antimicrobial resistance (AMR) crisis is the increasing global incidence of infectious diseases affecting the human population, which are untreatable with any known antimicrobial agent. This crisis will have a devastating cost on human society as both debilitating and lethal diseases increase in frequency and scope. Three major factors determine this crisis: (1) the increasing frequency of AMR phenotypes among microbes is an evolutionary response to the widespread use of antimicrobials; (2) the large and globally connected human population allows pathogens in any environment access to all of humanity; and (3) the extensive and often unnecessary use of antimicrobials by humanity provides the strong selective pressure that is driving the evolutionary response in the microbial world. Of these factors, the size of the human population is least amenable to rapid change. In contrast, the remaining two factors may be affected, so offering a means of managing the crisis: the rate at which AMR, as well as virulence factors evolve in microbial world may be slowed by reducing the applied selective pressure. This may be accomplished by radically reducing the global use of current and prospective antimicrobials. Current management measures to legislate the use of antimicrobials and to educate the healthcare world in the issues, while useful, have not comprehensively addressed the problem of achieving an overall reduction in the human use of antimicrobials. We propose that in addition to current measures and increased research into new antimicrobials and diagnostics, a comprehensive education program will be required to change the public paradigm of antimicrobial usage from that of a first line treatment to that of a last resort when all other therapeutic options have failed.
Dominey-Howes, D., Michael, C. & Labbate, M. 2014, 'Why emergency management should be interested in the emergence of antibiotic resistance', The Australian Journal of Emergency Management, vol. 29, no. 3, pp. 11-15.
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Bacterial epidemics and pandemics are biological risks to life every bit as significant as floods, fires, storms and earthquakes. Antibiotics have been a significant tool in the management of epidemics and pandemics (as well as for fighting general infections) since their discovery in the 1930s. Due to the development of antibiotic resistance by bacteria, we are now approaching a post- antibiotic era where our capacity to manage infectious disease, particularly bacterial epidemics and pandemics, is compromised. Despite considerable efforts by global heath organisations, we need new ways of thinking and acting on the global risk of antibiotic resistance. We argue for a rebranding of the issue to one of a disaster risk and suggest the use of the risk management process and expertise of emergency management to present a new way of thinking about this globally significant risk to life.
Islam, M.A., Labbate, M., Djordjevic, S.P., Alam, M., Darling, A.E., Melvold, J.A., Holmes, A.J., Johura, F.T., Cravioto, A., Charles, I.G. & Stokes, H. 2013, 'Indigenous Vibrio cholerae strains from a non-endemic region are pathogenic', Open Biology, vol. 3, p. 120181.
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Of the 200þ serogroups of Vibrio cholerae, only O1 or O139 strains are reported to cause cholera, and mostly in endemic regions. Cholera outbreaks elsewhere are considered to be via importation of pathogenic strains. Using established animal models, we show that diverse V. cholerae strains indigenous to a nonendemic environment (Sydney, Australia), including non-O1/O139 serogroup strains, are able to both colonize the intestine and result in fluid accumulation despite lacking virulence factors believed to be important. Most strains lacked the type three secretion system considered a mediator of diarrhoea in nonO1/O13 V. cholerae. Multi-locus sequence typing (MLST) showed that the Sydney isolates did not form a single clade and were distinct from O1/O139 toxigenic strains. There was no correlation between genetic relatedness and the profile of virulence-associated factors. Current analyses of diseases mediated by V. cholerae focus on endemic regions, with only those strains that possess particular virulence factors considered pathogenic. Our data suggest that factors other than those previously well described are of potential importance in influencing disease outbreaks.
Rapa, R.A. & Labbate, M. 2013, 'The function of integron-associated gene cassettes in Vibrio species: the tip of the iceberg', Frontiers in Microbiology, vol. 4, no. 385, pp. 1-4.
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The integron is a genetic element that incorporates mobile genes termed gene cassettes into a reserved genetic site via site-specific recombination. It is best known for its role in antibiotic resistance with one type of integron, the class 1 integron, a major player in the dissemination of antibiotic resistance genes across Gram negative pathogens and commensals. However, integrons are ancient structures with over 100 classes (including class 1) present in bacteria from the broader environment. While, the class 1 integron is only one example of an integron being mobilized into the clinical environment, it is by far the most successful. Unlike clinical class 1 integrons which are largely found on plasmids, other integron classes are found on the chromosomes of bacteria and carry diverse gene cassettes indicating a non-antibiotic resistance role(s). However, there is very limited knowledge on what these alternative roles are. This is particularly relevant to Vibrio species where gene cassettes make up approximately 13% of their entire genome. In this review, we discuss how emphasis on class 1 integron research has resulted in a limited understanding by the wider research community on the role of integrons in the broader environment. This has the capacity to be counterproductive in solving or improving the antibiotic resistance problem into the future. Furthermore, there is still a significant lack of knowledge on how gene cassettes in Vibrio species drive adaptation and evolution. From research in Vibrio rotiferianus DAT722, new insight into how gene cassettes affect cellular physiology offers new alternative roles for the gene cassette resource. At least a subset of gene cassettes are involved in host surface polysaccharide modification suggesting that gene cassettes may be important in processes such as bacteriophage resistance, adhesion/biofilm formation, protection from grazers and bacterial aggregation.
Robinson, M.W., Buchtmann, K.A., Jenkins, C., Tacchi, J.L., Raymond, B.B.A., To, J., Chowdhury, P.R., Woolley, L.K., Labbate, M., Turnbull, L., Whitchurch, C.B., Padula, M.P. & Djordjevic, S.P. 2013, 'MHJ_0125 is an M42 glutamyl aminopeptidase that moonlights as a multifunctional adhesin on the surface of Mycoplasma hyopneumoniae', OPEN BIOLOGY, vol. 3.
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Rapa, R.A., Shimmon, R., Djordjevic, S.P., Stokes, H.W. & Labbate, M. 2013, 'Deletion of Integron-Associated Gene Cassettes Impact on the Surface Properties of Vibrio rotiferianus DAT722', PLOS ONE, vol. 8, no. 3.
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Labbate, M., Boucher, Y., Luu, I., Roy Chowdhury, P. & Stokes, H. 2012, 'Integron associated mobile genes: Just a collection of plug in apps or essential components of cell network hardware?', Mobile Genetic Elements, vol. 2, no. 1, pp. 13-18.
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Lateral gene transfer (LGT) impacts on the evolution of prokaryotes in both the short and long-term. The short-term impacts of mobilized genes are a concern to humans since LGT explains the global rise of multi drug resistant pathogens seen in the past 70 years. However, LGT has been a feature of prokaryotes from the earliest days of their existence and the concept of a bifurcating tree of life is not entirely applicable to prokaryotes since most genes in extant prokaryotic genomes have probably been acquired from other lineages. Successful transfer and maintenance of a gene in a new host is understandable if it acts independently of cell networks and confers an advantage. Antibiotic resistance provides an example of this whereby a gene can be advantageous in virtually any cell across broad species backgrounds. In a longer evolutionary context however laterally transferred genes can be assimilated into even essential cell networks. How this happens is not well understood and we discuss recent work that identifies a mobile gene, unique to a cell lineage, which is detrimental to the cell when lost. We also present some additional data and believe our emerging model will be helpful in understanding how mobile genes integrate into cell networks.
Scott, N.E., Nothaft, H., Edwards, A.V., Labbate, M., Djordjevic, S.P., Larsen, M.R., Szymanski, C.M. & Cordwell, S.J. 2012, 'Modification Of The Campylobacter Jejuni N-linked Glycan By EptC Protein-mediated Addition Of Phosphoethanolamine', Journal Of Biological Chemistry, vol. 287, no. 35, pp. 29384-29396.
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Campylobacter jejuni is the major worldwide cause of bacterial gastroenteritis. C. jejuni possesses an extensive repertoire of carbohydrate structures that decorate both protein and nonprotein surface-exposed structures. An N-linked glycosylation system
Deshpande, C.N., Harrop, S.J., Boucher, Y., Hassan, K.A., Di Leo, R., Xu, X., Cui, H., Savchenko, A., Chang, C., Labbate, M., Paulsen, I.T., Stokes, H., Curmi, P.M. & Mabbutt, B.C. 2011, 'Crystal structure of an integron gene cassette- associated protein from Vibrio cholerae identifies a cationic drug-binding module', PLoS ONE, vol. 6, no. 3, p. e16934.
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Background: The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes. Methodology/Principal Findings: We report the 1.8 A° crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effectorbinding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators. Conclusions/Significance: Genetic analysis identifies Cass2 to be representative of a larger family of independent effectorbinding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.
Sajjad, A., Holley, M.P., Labbate, M., Stokes, H. & Gillings, M.R. 2011, 'Preclinical class 1 integron with a complete Tn402-like transposition module', Applied and Environmental Microbiology, vol. 77, no. 1, pp. 335-337.
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The presence of integrons was assessed in gut bacteria isolated from wild-caught prawns. A pseudomonad was recovered that contained a Tn402-like class 1 integron with a complete transposition module and two gene cassettes. One cassette was identical to a previously described cassette from a chromosomal class 3 integron in Delftia tsuruhatensis.
Roy Chowdhury, P., Boucher, Y., Hassan, K.A., Paulsen, I.T., Stokes, H. & Labbate, M. 2011, 'Genome sequence of Vibrio rotiferianus Strain DAT722', Journal Of Bacteriology, vol. 193, no. 13, pp. 3381-3382.
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Vibrio rotiferianus is a marine pathogen capable of causing disease in various aquatic organisms. We announce the genome sequence of V. rotiferianus DAT722, which has a large chromosomal integron containing 116 gene cassettes and is a model organism for studying the role of this system in vibrio evolution.
Labbate, M., Boucher, Y., Roy Chowdhury, P. & Stokes, H. 2011, 'Integration of a laterally acquired gene into a cell network important for growth in a strain of Vibrio rotiferianus', BMC Microbiology, vol. 11, no. 253, p. 253.
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Background Lateral Gene Transfer (LGT) is a major contributor to bacterial evolution and up to 25% of a bacterium's genome may have been acquired by this process over evolutionary periods of time. Successful LGT requires both the physical transfer of DNA and its successful incorporation into the host cell. One system that contributes to this latter step by site-specific recombination is the integron. Integrons are found in many diverse bacterial Genera and is a genetic system ubiquitous in vibrios that captures mobile DNA at a dedicated site. The presence of integron-associated genes, contained within units of mobile DNA called gene cassettes makes up a substantial component of the vibrio genome (1-3%). Little is known about the role of this system since the vast majority of genes in vibrio arrays are highly novel and functions cannot be ascribed. It is generally regarded that strain-specific mobile genes cannot be readily integrated into the cellular machinery since any perturbation of core metabolism is likely to result in a loss of fitness. Results In this study, at least one mobile gene contained within the Vibrio rotiferianus strain DAT722, but lacking close relatives elsewhere, is shown to greatly reduce host fitness when deleted and tested in growth assays. The precise role of the mobile gene product is unknown but impacts on the regulation of outermembrane porins. This demonstrates that strain specific laterally acquired mobile DNA can be integrated rapidly into bacterial networks such that it becomes advantageous for survival and adaptation in changing environments.
Michael, C.A. & Labbate, M. 2010, 'Gene Cassette Transcription In A Large Integron-Associated Array', BMC Genetics, vol. 11, pp. 1-13.
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Background: The integron/gene cassette system is a diverse and effective adaptive resource for prokaryotes. Short cassette arrays, with less than 10 cassettes adjacent to an integron, provide this resource through the expression of cassette-associated ge
Joss, M.J., Koenig, J.E., Labbate, M., Polz, M.F., Gillings, M., Stokes, H., Doolittle, W.F. & Boucher, Y. 2009, 'ACID: annotation of cassette and integron data', BMC Bioinformatics, vol. 10, no. 118, pp. 1-9.
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Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms.
Gillings, M., Labbate, M., Sajjad, A., Giguère, N., Holley, M.P. & Stokes, H. 2009, 'Mobilization of a Tn402-Like Class 1 Integron with a Novel Cassette Array via Flanking Miniature Inverted-Repeat Transposable Element-Like Structures', Applied and Environmental Microbiology, vol. 75, no. 18, pp. 6002-6004.
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A Tn402-like class 1 integron was recovered from a prawn-associated bacterium. One of its cassettes included methionine sulfoxide reductase genes, the first example of such genes being captured by an integron. The integron was flanked by direct repeats that resemble miniature inverted-repeat transposable element equences. Excision of the integron by homologous ecombination through these sequences was demonstrated.
Roy Chowdhury, P., Merlino, J., Labbate, M., Cheong, E.Y., Gottlieb, T. & Stokes, H. 2009, 'Tn6060, a Transposon from a Genomic Island in a Pseudomonas aeruginosa Clinical Isolate That Includes Two Class 1 Integrons', Antimicrobial agents and chemotherapy, vol. 53, no. 12, pp. 5294-5296.
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A 25,441-bp transposon was recovered from a Pseudomonas aeruginosa clinical isolate. While the transposition module was >99% identical to sequence of Tn1403, the element had been subject to rearrangements, with two In70.2-like class 1 integrons inserted into it in an unusual "tail-to-tail" configuration. One cassette array was the same as that in In70.2; however, the second was different, generating a transposon that collectively includes six resistance cassettes.
Joss, M.J., Koenig, J.E., Labbate, M., Polz, M.F., Gillings, M.R., Stokes, H.W., Doolittle, W.F. & Boucher, Y. 2009, 'ACID: annotation of cassette and integron data.', BMC bioinformatics, vol. 10, p. 118.
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BACKGROUND: Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in public databases. These genetic elements have been overlooked in comparison to other vectors that facilitate lateral gene transfer between microorganisms. DESCRIPTION: By automating the identification of integron integrase genes and of the non-coding cassette-associated attC recombination sites, we were able to assemble a database containing all publicly available sequence information regarding these genetic elements. Specialists manually curated the database and this information was used to improve the automated detection and annotation of integrons and their encoded gene cassettes. ACID (annotation of cassette and integron data) can be searched using a range of queries and the data can be downloaded in a number of formats. Users can readily annotate their own data and integrate it into ACID using the tools provided. CONCLUSION: ACID is a community resource providing easy access to annotations of integrons and making tools available to detect them in novel sequence data. ACID also hosts a forum to prompt integron-related discussion, which can hopefully lead to a more universal definition of this genetic element.
Labbate, M., Case, R.J. & Stokes, H.W. 2009, 'The integron/gene cassette system: an active player in bacterial adaptation.', Methods in molecular biology (Clifton, N.J.), vol. 532, pp. 103-125.
The integron includes a site-specific recombination system capable of integrating and expressing genes contained in structures called mobile gene cassettes. Integrons were originally identified on mobile elements from pathogenic bacteria and were found to be a major reservoir of antibiotic-resistance genes. Integrons are now known to be ancient structures that are phylogenetically diverse and, to date, have been found in approximately 9% of sequenced bacterial genomes. Overall, gene diversity in cassettes is extraordinarily high, suggesting that the integron/gene cassette system has a broad role in adaptation rather than being confined to simply conferring resistance to antibiotics. In this chapter, we provide a review of the integron/gene cassette system highlighting characteristics associated with this system, diversity of elements contained within it, and their importance in driving bacterial evolution and consequently adaptation. Ideas on the evolution of gene cassettes and gene cassette arrays are discussed.
Marquez, C., Labbate, M., Ingold, A.J., Roy Chowdhury, P., Ramirez, M.S., Centron, D., Borthagaray, G. & Stokes, H. 2008, 'Recovery of a functional class 2 integron from an Escherichia coli strain mediating a urinary tract infection', Antimicrobial Agents And Chemotherapy, vol. 52, no. 11, pp. 4153-4154.
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A class 2 integron was found in an Escherichia coli isolate mediating a urinary tract infection. Unlike other class 2 integrons from pathogens, the encoded IntI2 protein was functional. The integron possessed a dfrA14 cassette, and a second novel cassett
Case, R.J., Labbate, M. & Kjelleberg, S.L. 2008, 'AHL-driven quorum sensing circuits: their frequency and function among the Proteobacteria', ISME Journal, vol. 2, no. 4, pp. 345-349.
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It is now apparent that bacteria utilize regulatory systems called quorum sensing (QS) to sense their population density. Such systems are dependant on the production of signaling molecules that activate specific genes when the signal reaches a critical threshold concentration. Such QS-regulated genes produce phenotypes that require coordinate behavior to convey competitive advantage to the population (such as biofilm formation and pathogenesis). The best-characterized QS system is that driven by acylated homoserine lactone (AHL) molecules.
Labbate, M., Roy Chowdhury, P. & Stokes, H. 2008, 'A Class 1 Integron Present in a Human Commensal Has a Hybrid Transposition Module Compared to Tn402: Evidence of Interaction with Mobile DNA from Natural Environments', Journal Of Bacteriology, vol. 190, no. 15, pp. 5318-5327.
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In a survey of class 1 integrons from human stools, an unusual class 1 integron from a strain of Enterobacter cloacae was isolated and characterized in detail. Sequence analysis of a fosmid containing the class 1 integron revealed a complex set of transposons which included two Tn402-like transposons. One of these transposons, Tn6007, included a class 1 integron with two non-antibiotic-resistance-type gene cassettes and a complete transposition module. This tni module is a hybrid with a boundary within the res site compared to Tn402, implying that a site-specific recombination event generated either Tn6007 or Tn402. The second Tn402-like transposon, Tn6008, possesses neither a mer operon nor an integron, and most of its tni module has been deleted. Tn6007, Tn6008, and the 2,478 bases between them, collectively designated Tn6006, have transposed into a Tn5036/Tn3926-like transposon as a single unit. Tn6006, Tn6007, and Tn6008 could all transpose as discrete entities. Database analysis also revealed that a version of Tn6008 was present in the genome of Xanthomonas campestris pv. vesicatoria. Overall, the E. cloacae isolate further demonstrated that functional class 1 integrons/transposons are probably common in bacterial communities and have the potential to add substantially to the problem of multidrug-resistant nosocomial infections.
Marquez, C., Labbate, M., Raymondo, C., Fernandez, J., Gestal, A.M., Holley, M.P., Borthagaray, G. & Stokes, H. 2008, 'Urinary Tract Infections in a South American Population: Dynamic Spread of Class 1 Integrons and Multidrug Resistance by Homologous and Site-Specific Recombination', Journal Of Clinical Microbiology, vol. 46, no. 10, pp. 3417-3425.
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One hundred four bacterial strains mediating urinary tract infections in separate individuals from a Uruguayan community were isolated. Forty-six strains conferred a multidrug resistance phenotype. All 104 strains were examined for the presence of class 1, 2, and 3 integrons. Class 1 integrons were found in 21 isolates across four distinct bacterial genera. A large class 1 integron in a Klebsiella pneumoniae strain was fully sequenced and was 29,093 bp in length. This integron probably arose by homologous recombination since it was embedded in a hybrid Tn21-like transposon backbone which comprised a Tn5036-like tnp transposition module at the IRi integron end and a Tn21 mer module at the IRt integron end. The parent integron/transposon that contributed the Tn5036 module was not related to Tn1696 since the integron insertion points in the transposon backbones were 16 bases apart. Examination of the other 20 class 1 integron-containing strains revealed further evidence of genetic exchange. This included a strain that possessed a Tn5036 module at the IRt end but not at the IRi end and another that possessed a tnp module beyond IRi that was a hybrid of Tn21 and Tn5051 and that is presumed to have arisen by site-specific recombination. This study highlights the ability of different genetic elements to act cooperatively to spread and rearrange antibiotic resistance in a community.
Gillings, M., Boucher, Y., Labbate, M., Holmes, A.J., Krishnan, S., Holley, M.P. & Stokes, H. 2008, 'The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance', Journal Of Bacteriology, vol. 190, no. 14, pp. 5095-5100.
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Class 1 integrons are central players in the worldwide problem of antibiotic resistance, because they can capture and express diverse resistance genes. In addition, they are often embedded in promiscuous plasmids and transposons, facilitating their lateral transfer into a wide range of pathogens. Understanding the origin of these elements is important for the practical control of antibiotic resistance and for exploring how lateral gene transfer can seriously impact on, and be impacted by, human activities. We now show that class 1 integrons can be found on the chromosomes of nonpathogenic soil and freshwater Betaproteobacteria. Here they exhibit structural and sequence diversity, an absence of antibiotic resistance genes, and a phylogenetic signature of lateral transfer. Some examples are almost identical to the core of the class 1 integrons now found in pathogens, leading us to conclude that environmental Betaproteobacteria were the original source of these genetic elements. Because these elements appear to be readily mobilized, their lateral transfer into human commensals and pathogens was inevitable, especially given that Betaproteobacteria carrying class 1 integrons are common in natural environments that intersect with the human food chain. The strong selection pressure imposed by the human use of antimicrobial compounds then ensured their fixation and global spread into new species.
Koh, K., Lam, K., Alhede, M., Queck, S., Labbate, M., Kjelleberg, S.L. & Rice, S.A. 2007, 'Phenotypic diversification and adaptation of Serratia marcescens MG1 biofilm-derived morphotypes', Journal Of Bacteriology, vol. 189, pp. 119-130.
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We report here the characterization of dispersal variants from microcolony-type biofilms of Serratia marcescens MG1. Biofilm formation proceeds through a reproducible process of attachment, aggregation, microcolony development, hollow colony formation, and dispersal. From the time when hollow colonies were observed in flow cell biofilms after 3 to 4 days, at least six different morphological colony variants were consistently isolated from the biofilm effluent. The timing and pattern of variant formation were found to follow a predictable sequence, where some variants, such as a smooth variant with a sticky colony texture (SSV), could be consistently isolated at the time when mature hollow colonies were observed, whereas a variant that produced copious amounts of capsular polysaccharide (SUMV) was always isolated at late stages of biofilm development and coincided with cell death and biofilm dispersal or sloughing. The morphological variants differed extensively from the wild type in attachment, biofilm formation, and cell ultrastructure properties. For example, SSV formed two- to threefold more biofilm biomass than the wild type in batch biofilm assays, despite having a similar growth rate and attachment capacity. Interestingly, the SUMV, and no other variants, was readily isolated from an established SSV biofilm, indicating that the SUMV is a second-generation genetic variant derived from SSV. Planktonic cultures showed significantly lower frequencies of variant formation than the biofilms (5.05 x 108 versus 4.83 x 106, respectively), suggesting that there is strong, diversifying selection occurring within biofilms and that biofilm dispersal involves phenotypic radiation with divergent phenotypes.
Labbate, M., Zhu, H., Thung, L., Bandara, R., Learsen, M.R., Willcox, M.D., Givskov, M., Rice, S.A. & Kjelleberg, S.L. 2007, 'Quorum sensing regulation of adhesion in Serratia marcescens is surface dependant', Journal Of Bacteriology, vol. 189, pp. 2702-2711.
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Serratia marcescens is an opportunistic pathogen and a major cause of ocular infections. In previous studies of S. marcescens MG1, we showed that biofilm maturation and sloughing were regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). Because of the importance of adhesion in initiating biofilm formation and infection, the primary goal of this study was to determine whether QS is important in adhesion to both abiotic and biotic surfaces, as assessed by determining the degree of attachment to hydrophilic tissue culture plates and human corneal epithelial (HCE) cells. Our results demonstrate that while adhesion to the abiotic surface was AHL regulated, adhesion to the HCE cell biotic surface was not. Type I fimbriae were identified as the critical adhesin for non-QS-mediated attachment to the biotic HCE cell surface but played no role in adhesion to the abiotic surface. While we were not able to identify a single QS-regulated adhesin essential for attachment to the abiotic surface, four AHL-regulated genes involved in adhesion to the abiotic surface were identified. Interestingly, two of these genes, bsmA and bsmB, were also shown to be involved in adhesion to the biotic surface in a non-QS-controlled fashion. Therefore, the expression of these two genes appears to be cocontrolled by regulators other than the QS system for mediation of attachment to HCE cells. We also found that QS in S. marcescens regulates other potential cell surface adhesins, including exopolysaccharide and the outer membrane protein OmpX. We concluded that S. marcescens MG1 utilizes different regulatory systems and adhesins in attachment to biotic and abiotic surfaces and that QS is a main regulatory pathway in adhesion to an abiotic surface but not in adhesion to a biotic surface.
Labbate, M., Boucher, Y., Joss, M.J., Michael, C.A., Gillings, M. & Stokes, H. 2007, 'Use of the chromosomal integron array as a phylogenetic typing system for Vibrio cholerae pandemic strains', Microbiology-uk, vol. 153, no. 5, pp. 1488-1498.
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Approximately 200 serogroups of Vibrio cholerae exist, with only two, O1 and O139, responsible for epidemic and pandemic cholera. Strains from these serogroups have evolved from a common progenitor, with lateral gene transfer largely driving their emergence. These strains are so closely related that separation using single- or multi-locus phylogeny has proven difficult. V. cholerae strains contain a genetic system called the integron that is located in the chromosome and that can integrate and excise DNA elements called mobile gene cassettes (MGCs) by site-specific recombination. Large arrays of MGCs are found in V. cholerae strains. For instance, the O1 El Tor strain N16961 contains 179 MGCs. Since integron arrays are dynamic through recombination and excision of MGCs, it was hypothesized that the MGC composition in a given V. cholerae pandemic strain would be useful as a phylogenetic typing system. To address this, a PCR-based method was used to rapidly characterize the MGC composition of V. cholerae arrays. The results showed that the MGC composition of pandemic V. cholerae cassette arrays is relatively conserved, providing further evidence that these strains have evolved from a common progenitor. Comparison of MGC composition between the V. cholerae pandemic strains was also able to resolve the evolution of O139 from a subgroup of O1 El Tor. This level of differentiation of closely related V. cholerae isolates was more sensitive than conventional single-gene phylogeny or multi-locus sequence analysis. Using this method, novel MGCs from an O1 classical strain and an Argentinian O139 isolate were also identified, and a major deletion in the MGC array in all pandemic O139 strains and a subset of O1 El Tor strains was identified. Analysis of sequenced V. cholerae integron arrays showed that their evolution can proceed by rearrangements and deletions/insertions of large portions of MGCs in addition to the insertion or excision of single MGCs.
Boucher, Y., Labbate, M., Koenig, J.E. & Stokes, H. 2007, 'Integrons: mobilizable platforms promoting genetic diversity in bacteria', Trends In Microbiology, vol. 15, no. 7, pp. 301-309.
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Integrons facilitate the capture of potentially adaptive exogenous genetic material by their host genomes. It is now clear that integrons are not limited to the clinical contexts in which they were originally discovered because not, vert, similar10% of bacterial genomes that have been partially or completely sequenced harbour this genetic element. This wealth of sequence information has revealed that integrons are not only much more phylogenetically diverse than previously thought but also more mobilizable, with many integrons having been subjected to frequent lateral gene transfer throughout their evolutionary history. This indicates that the genetic characteristics that make integrons such efficient vectors for the spread of antibiotic resistance genes have been associated with these elements since their earliest origins. Here, we give an overview of the structural and phylogenetic diversity of integrons and describe evolutionary events that have contributed to the success of these genetic elements.
Rice, S.A., Koh, K., Queck, S., Labbate, M., Lam, K. & Kjelleberg, S.L. 2005, 'Biofilm formation and sloughing in Serratia marcescens is controlled by quorum sensing and nutrient conditions', Journal Of Bacteriology, vol. 187, no. 10, pp. 3477-3485.
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We describe here a role for quorum sensing in the detachment, or sloughing, of Serratia marcescens filamentous biofilms, and we show that nutrient conditions affect the biofilm morphotype. Under reduced carbon or nitrogen conditions, S. marcescens formed a classical biofilm consisting of microcolonies. The filamentous biofilm could be converted to a microcolony-type biofilm by switching the medium after establishment of the biofilm. Similarly, when initially grown as a microcolony biofilm, S. marcescens could be converted back to a filamentous biofilm by increasing the nutrient composition. Under high-nutrient conditions, an N-acyl homoserine lactone quorum-sensing mutant formed biofilms that were indistinguishable from the wild-type biofilms. Similarly, other quorum-sensing-dependent behaviors, such as swarming motility, could be rendered quorum sensing independent by manipulating the growth medium. Quorum sensing was also found to be involved in the sloughing of the filamentous biofilm. The biofilm formed by the bacterium consistently sloughed from the substratum after approximately 75 to 80 h of development.
Labbate, M., Queck, S., Koh, K., Rice, S.A., Givskov, M. & Kjelleberg, S.L. 2004, 'Quorum sensing-controlled biofilm development in Serratia liquefaciens MG1', Journal Of Bacteriology, vol. 186, pp. 692-698.
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Serratia liquefaciens MG1 contains an N-acylhomoserine lactone-mediated quorum-sensing system that is known to regulate swarming motility colonization. In this study, we describe for S. liquefaciens MG1 the development of a novel biofilm consisting of cell aggregates and differentiated cell types, such as cell chains and long filamentous cells. Furthermore, quorum sensing is shown to be crucial for normal biofilm development and for elaborate differentiation. A mutant of S. liquefaciens MG1 that was incapable of synthesizing extracellular signal formed a thin and nonmature biofilm lacking cell aggregates and differentiated cell chains. Signal-based complementation of this mutant resulted in a biofilm with the wild-type architecture. Two quorum-sensing-regulated genes (bsmA and bsmB) involved in biofilm development were identified, and we propose that these genes are engaged in fine-tuning the formation of cell aggregates at a specific point in biofilm development.
Holden, M.T., Ram Chhabra, S., de Nys, R., Stead, P., Bainton, N.J., Hill, P.J., Manefield, M., Kumar, N., Labatte, M., England, D., Rice, S., Givskov, M., Salmond, G.P., Stewart, G.S., Bycroft, B.W., Kjelleberg, S. & Williams, P. 1999, 'Quorum-sensing cross talk: isolation and chemical characterization of cyclic dipeptides from Pseudomonas aeruginosa and other gram-negative bacteria.', Molecular microbiology, vol. 33, no. 6, pp. 1254-1266.
In cell-free Pseudomonas aeruginosa culture supernatants, we identified two compounds capable of activating an N-acylhomoserine lactone (AHL) biosensor. Mass spectrometry and NMR spectroscopy revealed that these compounds were not AHLs but the diketopiperazines (DKPs), cyclo(DeltaAla-L-Val) and cyclo(L-Pro-L-Tyr) respectively. These compounds were also found in cell-free supernatants from Proteus mirabilis, Citrobacter freundii and Enterobacter agglomerans [cyclo(DeltaAla-L-Val) only]. Although both DKPs were absent from Pseudomonas fluorescens and Pseudomonas alcaligenes, we isolated, from both pseudomonads, a third DKP, which was chemically characterized as cyclo(L-Phe-L-Pro). Dose-response curves using a LuxR-based AHL biosensor indicated that cyclo(DeltaAla-L-Val), cyclo(L-Pro-L-Tyr) and cyclo(L-Phe-L-Pro) activate the biosensor in a concentration-dependent manner, albeit at much higher concentrations than the natural activator N-(3-oxohexanoyl)-L-homoserine lactone (3-oxo-C6-HSL). Competition studies showed that cyclo(DeltaAla-L-Val), cyclo(L-Pro-L-Tyr) and cyclo(L-Phe-L-Pro) antagonize the 3-oxo-C6-HSL-mediated induction of bioluminescence, suggesting that these DKPs may compete for the same LuxR-binding site. Similarly, DKPs were found to be capable of activating or antagonizing other LuxR-based quorum-sensing systems, such as the N-butanoylhomoserine lactone-dependent swarming motility of Serratia liquefaciens. Although the physiological role of these DKPs has yet to be established, their activity suggests the existence of cross talk among bacterial signalling systems.