Dr Leigh Monahan has over ten years of research experience in microbiology and molecular biology. His work has focused on fundamental aspects of bacterial physiology, as well understanding how bacteria adapt to changes in their environment and evade treatment with antibiotics. More broadly, Leigh is also interested in developing molecular techniques that help drive research forward in these areas.
In 2015, Leigh took up a research position in a newly formed, venture capital-funded biotechnology start-up based at UTS. His current work aims to develop, and ultimately commercialise, novel tools to maximise the useful information generated from next-generation DNA sequencing experiments. This will have wide-ranging applications, from basic microbiology through to clinical genomics.
Previously, Leigh obtained a B. Sc (Hons I) in biochemistry from the University of Sydney, and a PhD in molecular microbiology from the University of Technology Sydney.
Can supervise: YES
Leigh is interested in how bacteria grow and multiply, how they adapt to different environments, and how they are able to resist treatment with antibiotics. He is an expert in next-generation DNA sequencing platforms, including those from Illumina and Oxford Nanopore, and is currently working on the development and commercialisation of novel sequencing-based technologies. In addition, Leigh has expertise in molecular genetics and cell biology of bacteria, fluorescence microscopy and protein chemistry.
Yasir, M, Keith Turner, A, Bastkowski, S, Baker, D, Page, AJ, Telatin, A, Phan, MD, Monahan, L, Savva, GM, Darling, A, Webber, MA & Charles, IG 2020, 'TRADIS-XPress: A high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance', Genome Research, vol. 30, no. 2, pp. 239-249.View/Download from: Publisher's site
© 2020 Yasir et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. Understanding the genetic basis for a phenotype is a central goal in biological research. Much has been learnt about bacterial genomes by creating large mutant libraries and looking for conditionally important genes. However, current genome-wide methods are largely unable to assay essential genes which are not amenable to disruption. To overcome this limitation, we developed a new version of “TraDIS” (transposon directed insertion-site sequencing) that we term “TraDIS-Xpress” that combines an inducible promoter into the transposon cassette. This allows controlled overexpression and repression of all genes owing to saturation of inserts adjacent to all open reading frames as well as conventional inactivation. We applied TraDIS-Xpress to identify responses to the biocide triclosan across a range of concentrations. Triclosan is endemic in modern life, but there is uncertainty about its mode of action with a concentration-dependent switch from bacteriostatic to bactericidal action unexplained. Our results show a concentration-dependent response to triclosan with different genes important in survival between static and cidal exposures. These genes include those previously reported to have a role in triclosan resistance as well as a new set of genes, including essential genes. Novel genes identified as being sensitive to triclosan exposure include those involved in barrier function, small molecule uptake, and integrity of transcription and translation. We anticipate the approach we show here, by allowing comparisons across multiple experimental conditions of TraDIS data, and including essential genes, will be a starting point for future work examining how different drug conditions impact bacterial survival mechanisms.
DeMaere, MZ, Liu, MYZ, Lin, E, Djordjevic, SP, Charles, IG, Worden, P, Burke, CM, Monahan, LG, Gardiner, M, Borody, TJ & Darling, AE 2020, 'Metagenomic Hi-C of a healthy human fecal microbiome transplant donor', Microbiology Resource Announcements, vol. 9, no. 6.View/Download from: Publisher's site
Copyright © 2020 DeMaere et al. This is an open-access article distributed under the term of the Creative Commons Attribution 4.0 International license. We report the availability of a high-quality metagenomic Hi-C data set generated from a fecal sample taken from a healthy fecal microbiome transplant donor subject. We report on basic features of the data to evaluate their quality.
Monahan, LG, DeMaere, MZ, Cummins, ML, Djordjevic, SP, Roy Chowdhury, P & Darling, AE 2019, 'High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei.', Gut pathogens, vol. 11, no. 1.View/Download from: Publisher's site
Background:Enterobacter hormaechei is an important emerging pathogen and a key member of the highly diverse Enterobacter cloacae complex. E. hormaechei strains can persist and spread in nosocomial environments, and often exhibit resistance to multiple clinically important antibiotics. However, the genomic regions that harbour resistance determinants are typically highly repetitive and impossible to resolve with standard short-read sequencing technologies. Results:Here we used both short- and long-read methods to sequence the genome of a multidrug-resistant hospital isolate (C15117), which we identified as E. hormaechei. Hybrid assembly generated a complete circular chromosome of 4,739,272 bp and a fully resolved plasmid of 339,920 bp containing several antibiotic resistance genes. The strain also harboured a 34,857 bp repeat encoding copper resistance, which was present in both the chromosome and plasmid. Long reads that unambiguously spanned this repeat were required to resolve the chromosome and plasmid into separate replicons. Conclusion:This study provides important insights into the evolution and potential spread of antimicrobial resistance in a nosocomial E. hormaechei strain. More broadly, it further exemplifies the power of long-read sequencing technologies, particularly the Oxford Nanopore platform, for the characterisation of bacteria with complex resistance loci and large repeat elements.
Roy Chowdhury, P, Fourment, M, DeMaere, MZ, Monahan, L, Merlino, J, Gottlieb, T, Darling, AE & Djordjevic, SP 2019, 'Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids.', Plasmid, vol. 102, pp. 56-61.View/Download from: Publisher's site
IncHI2-ST1 plasmids play an important role in co-mobilizing genes conferring resistance to critically important antibiotics and heavy metals. Here we present the identification and analysis of IncHI2-ST1 plasmid pSPRC-Echo1, isolated from an Enterobacter hormaechei strain from a Sydney hospital, which predates other multi-drug resistant IncHI2-ST1 plasmids reported from Australia. Our time-resolved phylogeny analysis indicates pSPRC-Echo1 represents a new lineage of IncHI2-ST1 plasmids and show how their diversification relates to the era of antibiotics.
ABSTRACT We developed Hackflex, a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 11 times more libraries for high-throughput Illumina sequencing to be generated at a fixed cost. We call this new method Hackflex. Quality of library preparation was tested by constructing libraries from E. coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. We demonstrated that Hackflex can produce high quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. Using Hackflex, we were able to achieve a per sample reagent cost of library prep of A$8.66, which is 8.23 times lower than the Standard Nextera Flex protocol at advertised retail price. An additional simple modification to the protocol enables a further price reduction of up to 11 fold or about A$6.50/sample. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programs where sequencing large numbers of libraries is beneficial.
Lee, AS, White, E, Monahan, LG, Jensen, SO, Chan, R & van Hal, SJ 2018, 'Defining the Role of the Environment in the Emergence and Persistence of vanA Vancomycin-Resistant Enterococcus (VRE) in an Intensive Care Unit: A Molecular Epidemiological Study.', Infection control and hospital epidemiology, vol. 39, no. 6, pp. 668-675.View/Download from: Publisher's site
OBJECTIVETo describe the transmission dynamics of the emergence and persistence of vanA vancomycin-resistant enterococcus (VRE) in an intensive care unit (ICU) using whole-genome sequencing of patient and environmental isolates.DESIGNRetrospective cohort study.SETTINGICU in a tertiary referral center.PARTICIPANTSPatients admitted to the ICU over an 11-month period.METHODS VanA VRE isolated from patients (n=31) were sequenced using the Illumina MiSeq platform. Environmental samples from bed spaces, equipment, and waste rooms were collected. All vanA VRE-positive environmental samples (n=14) were also sequenced. Data were collected regarding patient ward and bed movements.RESULTSThe 31 patient vanA VRE isolates were from screening (n=19), urine (n=4), bloodstream (n=3), skin/wound (n=3), and intra-abdominal (n=2) sources. The phylogeny from sequencing data confirmed several VRE clusters, with 1 group accounting for 38 of 45 isolates (84%). Within this cluster, cross-transmission was extensive and complex across the ICU. Directionality indicated that colonized patients contaminated environmental sites. Similarly, environmental sources not only led to patient colonization but also to infection. Notably, shared equipment acted as a conduit for transmission between different ICU areas. Infected patients, however, were not linked to further VRE transmission.CONCLUSIONSGenomic sequencing confirmed a predominantly clonal outbreak of VRE with complex transmission dynamics. The environmental reservoir, particularly from shared equipment, played a key role in ongoing VRE spread. This study provides evidence to support the use of multifaceted strategies, with an emphasis on measures to reduce bacterial burden in the environment, for successful VRE control.Infect Control Hosp Epidemiol 2018;39:668-675.
Darling, AE, Liu, M, Worden, P, Monahan, L, Demaere, M, Burke, C, Djordjevic, S & Charles, I 2017, 'Evaluation of ddRADseq for reduced representation metagenome sequencing', PeerJ, vol. 5.View/Download from: Publisher's site
'Who is doing what' is the ultimate open question in microbiome study. Shotgun metagenomics is often applied to gain knowledge of functional roles for bacteria in microbial communities, where the data can be used to predict protein encoding genes and enzymatic pathways present in the community, sometimes leading to testable hypotheses for microbial
function. We describe a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. This technique takes advantage of the sequence
specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can
be tuned by size selection.
We assessed the performance of the metagenomic ddRADseq approach by applying the method to human stool samples and generating sequence data. We evaluate the extent to which ddRADseq data provides an unbiased reduced representation for microbiome profiling.
Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.
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
Fluctuations in nutrient availability are a fact of life for bacterial cells in the 'wild'. To survive and compete, bacteria must rapidly modulate cell-cycle processes to accommodate changing nutritional conditions and concomitant changes in cell growth. Our understanding of how this is achieved has been transformed in recent years, with cellular metabolism emerging as a central player. Several metabolic enzymes, in addition to their normal catalytic functions, have been shown to directly modulate cell-cycle processes in response to changing nutrient levels. Here we focus on cell division, the final event in the bacterial cell cycle, and discuss recent compelling evidence connecting division regulation to nutritional status and metabolic activity.
Labbate, M, Islam, A, Monahan, LG, Stokes, HW, Rapa, R, Mutreja, A, Thomson, N & Charles, IG 2015, 'A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage', Environmental Microbiology.View/Download from: Publisher's site
Monahan, LG, Turnbull, L, Osvath, SR, Birch, D, Charles, IG & Whitchurch, CB 2014, 'Rapid conversion of Pseudomonas aeruginosa to a spherical cell morphotype facilitates tolerance to carbapenems and penicillins but increases susceptibility to antimicrobial peptides', Antimicrobial Agents and Chemotherapy, vol. 58, no. 4, pp. 1956-1962.View/Download from: Publisher's site
The Gram negative human pathogen Pseudomonas aeruginosa is able to tolerate high concentrations of ß-lactam antibiotics. Despite inhibiting the growth of the organism, these cell wall-targeting drugs exhibit remarkably little bactericidal activity. However, the mechanisms underlying ß-lactam tolerance are currently unclear. Here we show that P. aeruginosa undergoes a rapid en masse transition from normal rod shaped cells to viable, cell wall defective spherical cells when treated with ß-lactams from the widely used carbapenem and penicillin classes. When the antibiotic is removed, the entire population of spherical cells quickly converts back to the normal bacillary form. Our results demonstrate that these rapid population-wide cell morphotype transitions function as a strategy to survive antibiotic exposure. Taking advantage of these findings, we have developed a novel approach to efficiently kill P. aeruginosa by using carbapenem treatment to induce en masse transition to the spherical cell morphotype and then exploiting the relative fragility and sensitivity of these cells to killing by antimicrobial peptides (AMPs) that are relatively inactive against P. aeruginosa bacillary cells. This approach could broaden the repertoire of antimicrobial compounds used to treat P. aeruginosa and serve as a basis for developing new therapeutics to combat bacterial infections.
Monahan, LG, Liew, AT, Bottomley, AL & Harry, L 2014, 'Division site positioning in bacteria: one size does not fit all', Frontiers in Microbiology, vol. 5, no. 19.View/Download from: Publisher's site
Spatial regulation of cell division in bacteria has been a focus of research for decades. It has been well studied in two model rod-shaped organisms, Escherichia coli and Bacillus subtilis, with the general belief that division site positioning occurs as a result of the combination of two negative regulatory systems, Min and nucleoid occlusion. These systems influence division by preventing the cytokinetic Z ring from forming anywhere other than midcell. However, evidence is accumulating for the existence of additional mechanisms that are involved in controlling Z ring positioning both in these organisms and in several other bacteria. In some cases the decision of where to divide is solved by variations on a common evolutionary theme, and in others completely different proteins and mechanisms are involved. Here we review the different ways bacteria solve the problem of finding the right place to divide. It appears that a one-size-fits-all model does not apply, and that individual species have adapted a division-site positioning mechanism that best suits their lifestyle, environmental niche and mode of growth to ensure equal partitioning of DNA for survival of the next generation.
Monahan, LG, Hajduk, IV, Blaber, SP, Charles, IG & Harry, EJ 2014, 'Coordinating Bacterial Cell Division with Nutrient Availability: a Role for Glycolysis', MBIO, vol. 5, no. 3.View/Download from: Publisher's site
Turnbull, L, Strauss, MP, Liew, ATF, Monahan, LG, Whitchurch, CB & Harry, EJ 2014, 'Super-resolution Imaging of the Cytokinetic Z Ring in Live Bacteria Using Fast 3D-Structured Illumination Microscopy (f3D-SIM)', JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, no. 91.View/Download from: Publisher's site
Bacterial cell division begins with the polymerization of the FtsZ protein to form a Z ring at the division site. This ring subsequently recruits the division machinery to allow cytokinesis. How the Z ring is positioned correctly remains a challenging qu
Gloag, ES, Turnbull, L, Huang, A, Vallotton, P, Wang, H, Nolan, LM, Mililli, L, Hunt, C, Lu, J, Osvath, SR, Monahan, LG, Cavaliere, R, Charles, IG, Wand, M, Gee, M, Ranganathan, P & Whitchurch, CB 2013, 'Self-organization of bacterial biofilms is facilitated by extracellular DNA', Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 28, pp. 11541-11546.View/Download from: Publisher's site
Twitching motility-mediated biofilm expansion is a complex, multicellular behavior that enables the active colonization of surfaces by many species of bacteria. In this study we have explored the emergence of intricate network patterns of interconnected trails that form in actively expanding biofilms of Pseudomonas aeruginosa. We have used high-resolution, phase-contrast time-lapse microscopy and developed sophisticated computer vision algorithms to track and analyze individual cell movements during expansion of P. aeruginosa biofilms. We have also used atomic force microscopy to examine the topography of the substrate underneath the expanding biofilm. Our analyses reveal that at the leading edge of the biofilm, highly coherent groups of bacteria migrate across the surface of the semisolid media and in doing so create furrows along which following cells preferentially migrate. This leads to the emergence of a network of trails that guide mass transit toward the leading edges of the biofilm. We have also determined that extracellular DNA (eDNA) facilitates efficient traffic flow throughout the furrow network by maintaining coherent cell alignments, thereby avoiding traffic jams and ensuring an efficient supply of cells to the migrating front. Our analyses reveal that eDNA also coordinates the movements of cells in the leading edge vanguard rafts and is required for the assembly of cells into the bulldozer aggregates that forge the interconnecting furrows. Our observations have revealed that large-scale self-organization of cells in actively expanding biofilms of P. aeruginosa occurs through construction of an intricate network of furrows that is facilitated by eDNA
Strauss, M, Liew, AT, Turnbull, L, Whitchurch, CB, Monahan, LG & Harry, L 2012, '3D-SIM super resolution microscopy reveals a bead-like arrangement for FtsZ and the division machinery: implications for triggering cytokinesis', Plos Biology, vol. 10, no. 9, p. e1001389.View/Download from: Publisher's site
FtsZ is a tubulin-like GTPase that is the major cytoskeletal protein in bacterial cell division. It polymerizes into a ring, called the Z ring, at the division site and acts as a scaffold to recruit other division proteins to this site as well as providing a contractile force for cytokinesis. To understand how FtsZ performs these functions, the in vivo architecture of the Z ring needs to be established, as well as how this structure constricts to enable cytokinesis. Conventional wide-field fluorescence microscopy depicts the Z ring as a continuous structure of uniform density. Here we use a form of super resolution microscopy, known as 3D-structured illumination microscopy (3D-SIM), to examine the architecture of the Z ring in cells of two Gram-positive organisms that have different cell shapes: the rod-shaped Bacillus subtilis and the coccoid Staphylococcus aureus. We show that in both organisms the Z ring is composed of a heterogeneous distribution of FtsZ. In addition, gaps of fluorescence were evident, which suggest that it is a discontinuous structure. Time-lapse studies using an advanced form of fast live 3D-SIM (Blaze) support a model of FtsZ localization within the Z ring that is dynamic and remains distributed in a heterogeneous manner. However, FtsZ dynamics alone do not trigger the constriction of the Z ring to allow cytokinesis. Lastly, we visualize other components of the divisome and show that they also adopt a bead-like localization pattern at the future division site. Our data lead us to propose that FtsZ guides the divisome to adopt a similar localization pattern to ensure Z ring constriction only proceeds following the assembly of a mature divisome.
Peters, PC, Cox, G, Monahan, LG & Harry, L 2011, 'Super-resolution imaging of the bacterial cytokinetic protein FtsZ', Micron, vol. 42, no. 4 Special Issue, pp. 336-341.View/Download from: Publisher's site
The idea of a bacterial cytoskeleton arose just 10 years ago with the identification of the cell division protein, FtsZ, as a tubulin homolog. Fts,Z plays a pivotal role in bacterial division, and is present in virtually all prokaryotes and in some eukaryotic organelles. The earliest stage of bacterial cell division is the assembly of FtsZ into a Z ring at the -division site, which subsequently constricts during cytokinesis. FtsZ also assembles into dynamic helical structures along the bacterial ceil, which are thought to act as precursors to the Z fing via a cell-cycle-mediated FtsZ polymer remodelling. The fine structures of the FtsZ helix and ring are unknown but crucial for identifying the molecular details of Z ring assembly and its regulation. We now reveal, using STED microscopy that the FtsZ helical structure in cells of the gram positive bacterium, Bacillus subtilis, is a highly irregular and discontinuous helix of FtsZ; very different to the smooth cable-like appearance observed by conventional fluorescence optics. STED also identifies a novel FtsZ helical structure of smaJ!er pitch that is invisible to standard optical methods, identifying a possible third intermediate in the pathway to Z ring assembly, which commits bacterial cells to divide.
Review in token-refereed journal on the bacterial cytoskeketon
Monahan, LG, Robinson, A & Harry, L 2009, 'Lateral Ftsz Association And The Assembly Of The Cytokinetic Z Ring In Bacteria', Molecular Microbiology, vol. 74, no. 4, pp. 1004-1017.View/Download from: Publisher's site
Cell division in bacteria is facilitated by a polymeric ring structure, the Z ring, composed of tubulin-like FtsZ protofilaments. Recently it has been shown that in Bacillus subtilis, the Z ring forms through the cell cycle-mediated remodelling of a helical FtsZ polymer. To investigate how this occurs in vivo, we have exploited a unique temperature-sensitive strain of B. subtilis expressing the mutant protein FtsZ(Ts1). FtsZ(Ts1) is unable to complete Z ring assembly at 49°C, becoming trapped at an intermediate stage in the helix-to-ring progression. To determine why this is the case, we used a combination of methods to identify the specific defect of the FtsZ(Ts1) protein in vivo. Our results indicate that while FtsZ(Ts1) is able to polymerize normally into protofilaments, it is defective in the ability to support lateral associations between these filaments at high temperatures. This strongly suggests that lateral FtsZ association plays a crucial role in the polymer transitions that lead to the formation of the Z ring in the cell. In addition, we show that the FtsZ-binding protein ZapA, when overproduced, can rescue the FtsZ(Ts1) defect in vivo. This suggests that ZapA functions to promote the helix-to-ring transition of FtsZ by stimulating lateral FtsZ association.
Michie, KA, Monahan, LG, Beech, PL & Harry, L 2006, 'Trapping of a spiral-like intermediate of the bacterial cytokinetic protein FtsZ', Journal Of Bacteriology, vol. 188, no. 5, pp. 1680-1690.View/Download from: Publisher's site
The earliest stage in bacterial cell division is the formation of a ring, composed of the tubulin-like protein FtsZ, at the division site. Tight spatial and temporal regulation of Z-ring formation is required to ensure that division occurs precisely at m
Monahan, LG, D'Elia, M & Harry, L 2011, 'Mining bacterial cell division for new antibacterial drugs' in Miller, AA & Miller, PF (eds), Emerging Trends in Antibacterial Discovery: Answering the Call to Arms, Caister Academic Press, United Kingdom, pp. 35-75.
As bacterial antibiotic resistance continues to exhaust our supply of effective antibiotics, a global public health disaster appears likely. Poor financial investment in antibiotic research has exacerbated the situation. A call to arms raised by several prestigious scientific organisations a few years ago rallied the scientific community, and now the scope of antibacterial research has broadened considerably. Multi-disciplinary approaches have yielded a wealth of new data on areas ranging from the identification of novel antibacterial targets to the use of biological agents for antibacterial therapy.
Harry, L, Monahan, LG & Thompson, L 2006, 'Bacterial cell division: the mechanism and its precision' in Jeon, KW (ed), International Review of Cytology: A Survey of Cell biology Volume 253, Elsevier, The netherlands, pp. 27-94.
The recent devlopment of cell biolofy technques for bacteria to allow visualisation of fundamental processes in time and space, and their use in synchronous populations of cells, has resulted in a dramatic increase in our understanding of cell division and it regulation in these tiny cells. The first stage of cell division is the formation of a Z ring, composed of apolymerised tubulin-like protein, FtZ,at the division site precisely at midcell. Several membrane-associated division proteins are then recruited to this ring to forma complex, the divisome, which causes invagination of the cell envelope layers to form a division septum. The z Ring marks the future division site, and the timing of assembly and positioning of this structure are important in determining where and when division will take place in the cell. Z ring assembly is controlled bnu many factors including negative regulatory mechanisms such as Min and nucleoid occlusion that influence Z ring positioning and FtZ accessory proteins that bind to FtZ directly and modulate its polymerisation behaviour. The replication status of the cell also influences the positionin of the Z ring,w hich may allow the tight coordination between DNA replication and cell division required toproduce two identical newborn cells.