Joshua P Ramsay

Joshua P Ramsay
Curtin University · School of Biomedical Sciences

PhD (Genetics)

About

69
Publications
9,180
Reads
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1,733
Citations
Additional affiliations
June 2017 - present
Curtin University
Position
  • Fellow
June 2013 - June 2017
Curtin University
Position
  • Lecturer
October 2011 - May 2013
University of Otago
Position
  • Fellow

Publications

Publications (69)
Article
Full-text available
Tripartite integrative and conjugative elements (ICE³) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp.. Prior to conjugative transfer the three ICE³ regions of M. ciceri WSM1271 ICEMcSym¹²⁷¹ combine and excise to form a single circular element. This assembly requires three coordin...
Article
Conjugation is a dominant mechanism of horizontal gene transfer and substantially contributes to the plasticity and evolvability of prokaryotic genomes. The impact of conjugation on genetic flux extends well beyond self-transmissible conjugative elements, because non-conjugative 'mobilizable elements' utilize other elements' conjugative apparatus f...
Article
Full-text available
Integrative and conjugative elements (ICEs) are ubiquitous mobile genetic elements present as "genomic islands" within bacterial chromosomes. Symbiosis islands are ICEs that convert nonsymbiotic mesorhizobia into symbionts of legumes. Here we report the discovery of symbiosis ICEs that exist as three separate chromosomal regions when integrated in...
Article
Symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. Excision of the Mesorhizobium loti symbiosis island ICEMlSym(R7A) is indirectly activated by quorum sensing through TraR-dependent activation of the excisionase gene rdfS. Here we show tha...
Article
Full-text available
Staphylococcus aureus is a common cause of hospital, community and livestock-associated infections and is increasingly resistant to multiple antimicrobials. A significant proportion of antimicrobial-resistance genes are plasmid-borne, but only a minority of S. aureus plasmids encode proteins required for conjugative transfer or Mob relaxase protein...
Article
Full-text available
Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state term...
Article
Full-text available
Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the c...
Article
Full-text available
Initially reported in Western Australia in the 1980s, community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a major cause of S. aureus infections globally. We report the complete genome sequences of three of the earliest CA-MRSA strains isolated from remote Australian Indigenous communities in the Kimberley region of...
Article
Full-text available
Sequence type 1 (ST1) methicillin-resistant Staphylococcus aureus (MRSA) type IV[2B] has become one of the most common community-associated MRSA clones in Australia. We report the complete genome sequence of one of the earliest isolated Australian S. aureus ST1-MRSA-IV strains, WBG8287, isolated from an Indigenous Australian patient living in the r...
Article
Burn injuries can cause traumatic and debilitating physical trauma, with burn wounds prone to bacterial infection. This study examined in vitro the effectiveness of the silver nanoparticle based antimicrobial dressing, Acticoat™, in combination with a range of antimicrobial compounds against Staphylococcus aureus and Pseudomonas aeruginosa and inve...
Article
Full-text available
In Staphylococcus aureus, most multiresistance plasmids lack conjugation or mobilization genes for horizontal transfer. However, most are mobilizable due to carriage of origin-of-transfer (oriT) sequences mimicking those of conjugative plasmids related to pWBG749. pWBG749-family plasmids have diverged to carry five distinct oriT subtypes and non-co...
Article
Full-text available
Antimicrobial resistance poses a significant threat to modern healthcare as it limits treatment options for bacterial infections, particularly impacting those with chronic conditions such as cystic fibrosis (CF). Viscous mucus accumulation in the lungs of individuals genetically predisposed to CF leads to recurrent bacterial infections, necessitati...
Article
Full-text available
Rhizobia are soil bacteria capable of forming N2-fixing symbioses with legumes, with highly effective strains often selected in agriculture as inoculants to maximize symbiotic N2 fixation. When rhizobia in the genus Mesorhizobium have been introduced with exotic legumes into farming systems, horizontal transfer of symbiosis integrative and conjugat...
Article
Mesorhizobium is a genus of soil bacteria, some isolates of which form an endosymbiotic relationship with diverse legumes of the Loteae tribe. The symbiotic genes of these mesorhizobia are generally carried on integrative and conjugative elements termed symbiosis islands (ICESyms). Mesorhizobium strains that nodulate Lotus spp. have been divided in...
Article
Of 1,033 E. coli urinary tract infection isolates collected from females >12 years of age in Australia, in 2019, only two isolates were resistant to fosfomycin with an MIC >256 mg/L. Despite having different multilocus sequence types, the two isolates harboured an identical plasmid-encoded fosA4 gene. The fosA4 gene has previously been identified i...
Article
Full-text available
Horizontal transfer of plasmids encoding antimicrobial-resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s the first CA-MRSA isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline...
Article
Staphylococcus aureus is a serious human and animal pathogen. Multilocus sequence type 612 (ST612) is the dominant methicillin-resistant S. aureus (MRSA) clone in certain South African hospitals and is sporadically isolated from horses and horse-associated veterinarians in Australia. Colonisation and infection by ST612-MRSA is increasing in Western...
Article
Integrative and conjugative elements (ICEs) are chromosomally-integrated mobile genetic elements that excise from their host chromosome and transfer to other bacteria via conjugation. ICEMlSym R7A is the prototypical member of a large family of “symbiosis ICEs” which confer upon their hosts the ability to form a nitrogen-fixing symbiosis with a var...
Article
The resurgence of whooping cough reflects novel genetic variants of Bordetella pertussis and inadequate protection conferred by current acellular vaccines (aP). Biofilm is a source of novel vaccine candidates, including membrane protein assembly factor (BamB) and lipopolysaccharide assembly protein (LptD). Responses of BALB/c mice to candidate vacc...
Article
Staphylococcal Plasmids, Transposable and Integrative Elements, Page 1 of 2 Abstract Strains of Staphylococcus aureus, and to a lesser extent other staphylococcal species, are a significant cause of morbidity and mortality. An important factor in the notoriety of these organisms stems from their frequent resistance to many antimicrobial agents us...
Article
Full-text available
We report here the complete genome sequence of Stenotrophomonas maltophilia AB550, a multidrug- and solar radiation-resistant strain isolated from the effluents of an urban wastewater treatment plant in Western Australia. The genome consists of a single 4.9-Mb chromosome.
Article
Full-text available
Staphylococcus aureus is a serious pathogen of humans and animals. Multilocus sequence type 612 is dominant and highly virulent in South African hospitals but relatively uncommon elsewhere. We present the complete genome sequence of methicillin-resistant Staphylococcus aureus strain SVH7513, isolated from a horse at a veterinary clinic in New South...
Article
Urban wastewater treatment plant effluents represent one of the major emission sources of antibiotic-resistant bacteria (ARB) in natural aquatic environments. In this study, the effect of artificial solar radiation on total culturable heterotrophic bacteria and ARB (including amoxicillin-resistant, ciprofloxacin-resistant, rifampicin-resistant, sul...
Data
Predicted secondary structures of RdfG, RdfM, and RdfS. Secondary structures were predicted using Jpred(v4) [64]. α-helices are highlighted in yellow, β-sheets are highlighted in blue. All three proteins carry a predicted two stranded MerR-family winged helix-turn-helix motif characteristic of RDFs [25]. (TIF)
Data
Production of AHLs by TraI1. The C. violaceum CV026 biosensor strain [29] was used to detect the production of AHLs in (A) E. coli DH10B or (B) M. loti R7ANS either constitutively expressing ICEMcSym1271-derived traI1 from the plasmid pPR3-traI1, or carry the empty vector pPR3. Production of a purple violacein halo indicated production of C4-C8 AHL...
Data
TPM values and DESeq2 output for differential gene expression analysis. (XLSX)
Data
TraI1-dependent activation of the traI1 promoter by TraR1 and TraR2. β-galactosidase assays [67] were performed on a set of R7ANS strains carrying the same traI1 promoter-lacZ fusion on either pSDz, pSDz-traR1, or pSDz-traR2. These strains were induced for expression of traR1/traR2 with 1 μM IPTG, and also carried either a constitutively expressed...
Data
RNA-Seq mapping of the transcriptional start sites for traI1, traI2, and rdfS. The promoter regions of traI1 (A), traI2 (B), and rdfS genes (C) from WSM1271 were identified based on similarity with homologous regions in R7A. Nucleotide alignments were performed using the T-Coffee multiple sequence aligner [63]. Transcriptional start sites for R7A g...
Data
Alignment of traI2 promoter regions and TraI2 protein sequences in diverse Mesorhizobium spp. (A) The nucleotide sequence of traI2 promoters and (B) the TraI2 amino acid sequences from six Mesorhizobium strains were aligned using the T-coffee multiple sequence aligner [63]. (TIF)
Data
Possible evolution of QS loci on ICEMlSymR7A and ICEMcSym1271. On ICEMlSymR7A, traR is encoded upstream of an operon encoding the likely non-functional AHL-synthase gene traI2, msi172-msi171 and qseM-qseC. The functional AHL synthase TraI1 is encoded at a separate location. ICEMcSym1271 carries traR2 upstream of qseM-qseC, however, the traI2-msi172...
Data
Oligonucleotides used in this study. (PDF)
Data
Supplementary materials and methods. (DOCX)
Article
Full-text available
The currently widespread and increasing prevalence of resistant bacterial pathogens is a significant medical problem. In clinical strains of staphylococci, the genetic determinants that confer resistance to antimicrobial agents are often located on mobile elements, such as plasmids. Many of these resistance plasmids are capable of horizontal transm...
Article
Successful process development for the bioleaching of mineral ores, particularly the refractory copper sulfide ore chalcopyrite, remains a challenge in regions where freshwater is scarce and source water contains high concentrations of chloride ion. In this study, a pure isolate of Acidihalobacter prosperus strain F5 was characterized for its abili...
Article
Full-text available
We report here the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1497, the efficient nitrogen-fixing microsymbiont and commercial inoculant in Australia of the forage legume Biserrula pelecinus . The genome consists of 7.2 Mb distributed across a single chromosome (6.67 Mb) and a single plasmid (0.53 Mb).
Article
Full-text available
Background Statins are a class of therapeutics used to regulate serum cholesterol and reduce the risk of heart disease. Although statins are highly effective in removing cholesterol from the blood, their consumption has been linked to potential adverse effects in some individuals. The most common events associated with statin intolerance are myopat...
Article
Integrative and conjugative elements (ICEs) are generally regarded as regions of contiguous DNA integrated within a bacterial genome that are capable of excision and horizontal transfer via conjugation. We recently characterized a unique group of ICEs present in Mesorhizobium spp., which exist as three entirely separate but inextricably linked chro...
Article
Full-text available
The use of halotolerant acidophiles for bioleaching provides a biotechnical approach for the extraction of metals from regions where high salinity exists in the ores and source water. Here, we describe the first draft genome of a new species of a halotolerant and iron- and sulfur-oxidizing acidophile, Acidihalobacter ferrooxidans DSM 14175 (strain...
Article
Full-text available
The principal genomic features of Acidihalobacter prosperus DSM 14174 (strain V6) are presented here. This is a mesophilic, halotolerant, and iron/sulfur-oxidizing acidophile that was isolated from seawater at Vulcano, Italy. It has potential for use in biomining applications in regions where high salinity exists in the source water and ores.
Article
Methicillin resistance in the clinically important bacterium Staphylococcus aureus (MRSA) has evolved in multiple S. aureus lineages through acquisition of chromosomally integrating mobile genetic elements named SCCmec. Now Rice and colleagues show that the conserved SCCmec cch gene encodes an active DNA helicase, thus suggesting that extrachromoso...
Article
Full-text available
The horizontal gene transfer facilitated by mobile genetic elements impacts almost all areas of bacterial evolution, including the accretion and dissemination of antimicrobial-resistance genes in the human and animal pathogen Staphylococcus aureus. Genome surveys of staphylococcal plasmids have revealed an unexpected paucity of conjugation and mobi...
Article
Full-text available
We report the complete genome sequence of Mesorhizobium ciceri strain CC1192, an efficient nitrogen-fixing microsymbiont of Cicer arietinum (chickpea). The genome consists of 6.94 Mb distributed between a single chromosome (6.29 Mb) and a plasmid (0.65 Mb).
Article
Full-text available
We report the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284, a nitrogen-fixing microsymbiont of the pasture legume Biserrula pelecinus . The genome consists of 6.88 Mb distributed between a single chromosome (6.33 Mb) and a single plasmid (0.55 Mb).
Article
Aspiration of bile into the cystic fibrosis (CF) lung has emerged as a prognostic factor for reduced microbial lung biodiversity and the establishment of often fatal, chronic pathogen infections. Staphylococcus aureus is one of the earliest pathogens detected in the lungs of children with CF, and once established as a chronic infection, strategies...
Article
Full-text available
Different modes of bacterial taxis play important roles in environmental adaptation, survival, colonization and the dissemination of disease. One mode of taxis is flotation due to the production of gas vesicles. Gas vesicles are proteinaceous intracellular organelles, permeable only to gas, that enable flotation in aquatic niches. Gene clusters for...
Article
Importance: Understanding the mechanism of antimicrobial resistance transfer in bacteria such as Staphylococcus aureus is an important step toward potentially slowing the spread of antimicrobial resistant infections. This work establishes protein-DNA interactions essential for the transfer of the Staphylococcus aureus multiresistance plasmid pSK41...
Article
Full-text available
Random transposon mutagenesis is a powerful technique used to generate libraries of genetic insertions in many different bacterial strains. Here we develop a system facilitating random transposon mutagenesis in a range of different Gram-negative bacterial strains, including Pectobacterium atrosepticum, Citrobacter rodentium, Serratia sp. ATCC39006,...
Article
Full-text available
Mobile genetic elements run an evolutionary gauntlet to maintain their mobility in the face of selection against their selfish dissemination but, paradoxically, they can accelerate the adaptability of bacteria through the gene-transfer events that they facilitate. These temporally conflicting evolutionary forces have shaped exquisite regulation sys...
Chapter
The Mesorhizobium loti symbiosis island (ICEMlSymR7A) is a 500-kb mobile integrative and conjugative element (ICE) that converts non-symbiotic mesorhizobia into strains capable of forming a symbiosis with Lotus corniculatus. ICEMlSymR7A chromosomal excision and conjugative transfer is stimulated by the quorum-sensing regulator TraR. Quorum sensing...
Article
Full-text available
To describe a family of conjugative plasmids isolated from colonizing community Staphylococcus aureus and determine their ability to mobilize unrelated antimicrobial resistance/virulence plasmids, not encoding mobilization functions. Plasmid pWBG749 was labelled with Tn551 (pWBG749e) to enable laboratory manipulation. Plasmid pWBG749e was conjugate...
Article
Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial signalling molecule produced by diguanylate cyclases of the GGDEF-domain family. Elevated c-di-GMP levels or increased GGDEF protein expression is frequently associated with the onset of sessility and biofilm formation in numerous bacterial species. Conversely,...
Chapter
A symbiosis island is a genomic island that confers upon the bacterium carrying it the ability to form a mutualistic relationship with a eukaryotic host. The symbiosis island of Mesorhizobium loti strain R7A is a 501.8-kb chromosomally integrated element that is able to excise and transfer by conjugation to nonsymbiotic mesorhizobia in the environm...
Article
Full-text available
Serratia sp. ATCC 39006 (S39006) is a Gram-negative enterobacterium that is virulent in plant and animal models. It produces a red-pigmented trypyrrole secondary metabolite, prodigiosin (Pig), and a carbapenem antibiotic (Car), as well as the exoenzymes, pectate lyase and cellulase. Secondary metabolite production in this strain is controlled by a...
Article
Full-text available
Serratia sp. strain ATCC 39006 is a Gram-negative bacterium and a member of the Enterobacteriaceae that produces various bioactive secondary metabolites, including the tripyrrole red pigment prodigiosin and the β-lactam antibiotic 1-carbapenen-2-em-3-carboxylic acid (a carbapenem). This strain is the only member of the Enterobacteriaceae known to n...
Article
ICEMlSym(R7A) of Mesorhizobium loti is an integrative and conjugative element (ICE) that confers the ability to form a nitrogen-fixing symbiosis with Lotus species. Horizontal transfer is activated by TraR and N-acyl-homoserine lactone (AHL), which can stimulate ICE excision in 100% of cells. However in wild-type cultures, the ICE is excised at low...
Article
Gas vesicles are gas-filled microcompartments produced by many cyanobacteria and haloarchaea to regulate buoyancy and control positioning in the water column. Recently we identified the first case of gas vesicle production by a member of the Enterobacteriaceae, Serratia sp ATCC39006. Gas vesicle production enabled colonisation of the air-liquid int...
Article
Gas vesicles are hollow intracellular proteinaceous organelles produced by aquatic Eubacteria and Archaea, including cyanobacteria and halobacteria. Gas vesicles increase buoyancy and allow taxis toward air-liquid interfaces, enabling subsequent niche colonization. Here we report a unique example of gas vesicle-mediated flotation in an enterobacter...
Article
Serratia sp. ATCC 39006 (S39006) is a Gram-negative bacterium that is virulent in plant (potato) and animal (Caenorhabditis elegans) models. It produces two secondary metabolite antibiotics, a prodigiosin and a carbapenem, and the exoenzymes, pectate lyase and cellulase. A complex regulatory network that includes quorum sensing (QS) controls produc...
Article
The symbiosis island ICEMlSym(R7A) of Mesorhizobium loti R7A is an integrative and conjugative element (ICE) that carries genes required for a nitrogen-fixing symbiosis with Lotus species. ICEMlSym(R7A) encodes homologues (TraR, TraI1 and TraI2) of proteins that regulate plasmid transfer by quorum sensing in rhizobia and agrobacteria. Introduction...
Article
The Mesorhizobium loti strain R7A symbiosis island is an Integrative Conjugative Element (ICE), herein termed ICEMlSymR7A, which integrates into a phetRNA gene. Integration reconstructs the phetRNA gene at one junction with the core chromosome, and a direct repeat of the 3-prime 17 bp of the gene is formed at the other junction. We show that the IC...
Article
The imprinted gene and parent-of-origin effect database (www.otago.ac.nz/IGC) consists of two sections. One section catalogues the current literature on imprinted genes in humans and animals. The second, and new, section catalogues current reports of parental origin of de novo mutations in humans alone. The addition of a catalogue of de novo mutati...
Article
Full-text available
Genomic imprinting, the parent-of-origin-specific silencing of a small proportion of genes, introduces a paradoxical vulnerability of hemizygosity into the diploid mammalian genome. To facilitate the evaluation of the biological and evolutionary significance of imprinting, we have collated a census of known imprinted genes, listing 83 transcription...

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Identify Bordetella pertussis biofilm associated vaccines