Papers by Piklu Chowdhury
Antimicrobial Agents and Chemotherapy, Nov 1, 2008
'Cavity disease', defined as the rapid degradation of the sporocarps of white button mushrooms, i... more 'Cavity disease', defined as the rapid degradation of the sporocarps of white button mushrooms, is caused by Burkholderia gladioli pv. agaricicola, a member of Pseudomonaceae. The specific strain analysed in this thesis, BG 164, was isolated from New Zealand, but the disease has also been sporadically reported in Europe. Nine mutants that did not cause cavity symptoms ('no-cavity') were isolated by transposon mutagenesis of the BG 164 derivative, BG 164R. Eight mutants had altered flagella number, did not secrete protease, had a highly reduced capacity to secrete chitinase and did not degrade mushroom mycelia. All these eight mutations were clustered in the GSP (General Secretory ~athway) operon. A cosmid, carrying 23.4kb genomic DNA, pCosGSP, complemented all mutations, which along with mapping of the cosmid, confirms that the cosmid has most or all of the functional gsp operon.
Integrons: antibiotic resistance evolution and beyond
Landes Bioscience eBooks, 2013
ABSTRACT I ntegrons include a site‑specific recombination system that can capture gene cassettes.... more ABSTRACT I ntegrons include a site‑specific recombination system that can capture gene cassettes. Gene cassettes are the smallest known mobilizable units of DNA and normally only comprise a single gene and a recombination site essential for the site‑specific recombination event to occur. Although the site specific recombination reaction is catalyzed by an integrase protein that is a member of the tyrosine family of site specific recombinases, the biology and biochemistry of the system is unusual in a number of respects. Most notably, gene cassettes comprise a family of elements that are highly diverse both with respect to the genes and the recombination sites within them. Integrons first came to prominence as a consequence of their infiltrating pathogenic Gram negative bacteria. In this context integrons commonly possess multiple cassettes with the associ‑ ated genes conferring, collectively, resistance to a wide range of clinically important antibiotics. As a consequence they are one of the single biggest contributors to the evolution of antibiotic resistant bacteria. Integrons however are ancient structures that are widely distributed among the Proteobacteria. In the broader context, cassette associated genes are remarkably diverse and highly novel. This mobile cassette "metagenome" includes a pool of novel gene cassettes potentially available to whole microbial communities. While the function of most cassette genes in this pool remains unknown, it is clear that they are rich source of innovation and novelty.
Microbiology resource announcements, Mar 17, 2022
Here, we present the completely closed genome sequence of Pasteurella multocida 17BRD-035, a bovi... more Here, we present the completely closed genome sequence of Pasteurella multocida 17BRD-035, a bovine respiratory disease (BRD) pathogen from Queensland, Australia, with genes that confer resistance to b-lactams, tilmicosin, and tetracycline. It consists of a single 2,624,884-bp chromosome and an average GC content of 40.23% and belongs to the newly described Rural Industries Research and Development Corporation (RIRDC) sequence type 394. W e present a completely closed genome sequence of a recently catalogued multilocus sequence type (MLST) variant, sequence type 394 (ST394), of Pasteurella multocida (strain 17BRD-035) for the RefSeq database. The ST394 designation is based on housekeeping genes used for the P. multocida Rural Industries Research and Development Corporation (RIRDC) MLST scheme (1) available via pubMLST. Using the multihost sequence typing scheme developed for P. multocida (2), 17BRD-035 represents ST159. P. multocida is one of the most frequently isolated bacterial pathogens associated with bovine respiratory disease (BRD) and is increasingly associated with antimicrobial resistance in the feedlot cattle industry, both globally and within Australia (3). Strain 17BRD-035 was isolated from a diagnostic submission (lung swab from a BRDaffected animal collected postmortem) in Queensland, Australia, in 2017 (3). The strain was maintained on sheep blood agar for routine microbiological assays and grown in brain heart
Applied and Environmental Microbiology, May 1, 2006
Cavity disease in white button mushrooms is caused by Burkholderia gladioli pv. agaricicola. We d... more Cavity disease in white button mushrooms is caused by Burkholderia gladioli pv. agaricicola. We describe the isolation and characterization of six mutants of the strain BG164R that no longer cause this disease on mushrooms. The mutations were mapped to genes of the general secretory pathway (GSP). This is the first report of the association of the type II secretion pathway with a disease in mushrooms. Phenotypes of the six avirulent mutants were the following: an inability to degrade mushroom tissue, a highly reduced capacity to secrete chitinase and protease, and a reduced number of flagella. Using these mutants, we also made the novel observation that the factors causing mushroom tissue degradation, thereby leading to the expression of cavity disease, can be separated from mycelium inhibition because avirulent mutants continued to inhibit the growth of actively growing mushroom mycelia. The GSP locus of B. gladioli was subsequently cloned and mapped and compared to the same locus in closely related species, establishing that the genetic organization of the gsp operon of B. gladioli pv. agaricicola is consistent with that of other species of the genus. We also identify the most common indigenous bacterial population present in the mushroom fruit bodies from a New Zealand farm, one of which, Ewingella americana, was found to be an apparent antagonist of B. gladioli pv. agaricicola. While other investigators have reported enhanced disease symptoms due to interactions between endogenous and disease-causing bacteria in other mushroom diseases, to the best of our knowledge this is the first report of an antagonistic effect.
Genomic profiling of Pasteurella multocida isolated from feedlot cases of bovine respiratory disease
Veterinary Microbiology, Aug 1, 2023
Integrons
CRC Press eBooks, Feb 25, 2022
Isolation, identification and ecology of<i>Ewingella americana</i>(the causal agent of internal stipe necrosis) from cultivated mushrooms in New Zealand
Australasian Plant Pathology, 2007
Internal stipe necrosis of cultivated mushrooms (Agaricus bisporus) is caused by the bacterium Ew... more Internal stipe necrosis of cultivated mushrooms (Agaricus bisporus) is caused by the bacterium Ewingella americana, a member of the Enterobacteriaceae. Recently, E. americana was isolated from healthy cultivated button mushrooms grown in New Zealand and from mushrooms showing mild stipe browning. E. americana forms a part of the endogenous bacterial population present in mushroom sporocarp tissues. This is the first
Mobile genetic elements, 2012
BMC Microbiology, Nov 18, 2011
Background: Lateral Gene Transfer (LGT) is a major contributor to bacterial evolution and up to 2... more 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. Conclusions: Mobile genes that are highly strain specific are generally believed to act in isolation. This is because perturbation of existing cell machinery by the acquisition of a new gene by LGT is highly likely to lower fitness. In contrast, we show here that at least one mobile gene, apparently unique to a strain, encodes a product that has integrated into central cellular metabolic processes such that it greatly lowers fitness when lost under those conditions likely to be commonly encountered for the free living cell. This has ramifications for our understanding of the role mobile gene encoded products play in the cell from a systems biology perspective.
Molecular Analysis of an IncF ColV-Like Plasmid Lineage That Carries a Complex Resistance Locus with a Trackable Genetic Signature
Microbial Drug Resistance, Jul 1, 2020
IncF ColV plasmids are important plasmid incompatibility group that are currently restricted to t... more IncF ColV plasmids are important plasmid incompatibility group that are currently restricted to the Enterobacteriaceae. These plasmids carry an important repertoire of virulence-associated genes (VAGs) that contribute to the ability of avian pathogenic Escherichia coli to cause disease in poultry. VAGs found on ColV plasmids have also been linked to urosepsis and meningitis in humans but the mechanisms that elicit these disease conditions are not well understood. Recently we described the sequence of a ColV plasmid pSDJ2009-52F that carried the typical repertoire of VAGs and a complex resistance gene locus flanked by IS26, an insertion element that plays an important role in mobilizing antibiotic resistance genes on plasmids and genomic islands. We recovered complete ColV-like plasmid sequences from public databases that shared >80% sequence identity with pSDJ2009-52F in geographically diverse regions of the world over a 20-year timeframe. Previously we noted that pSDJ2009-52F carries a unique genetic signature in the class 1 integron within the complex resistance locus that was presumably created by the action of IS26. Here we show that most ColV-like plasmids that are closely related to pSDJ2009-52F also carry the same signature. Our studies provide insight into how these signature-bearing plasmids and the mobile genetic elements they carry traffic between E. coli sequence types over large geographic distances.
Nature Communications
Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic sh... more Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20–40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discover...
Characterisation of Verticillium dahliae by inter-simple sequence repeats identified a virulent subpopulation affecting Australian cotton
Australasian Plant Pathology
Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands
Microbial Genomics, 2020
Wildlife, and birds in particular, play an increasingly recognized role in the evolution and tran... more Wildlife, and birds in particular, play an increasingly recognized role in the evolution and transmission of Escherichia coli that pose a threat to humans. To characterize these lineages and their potential threat from an evolutionary perspective, we isolated and performed whole-genome sequencing on 11 sequence types (STs) of E. coli recovered from the desiccated faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands located in geographically different regions of New South Wales, Australia. Carriage of virulence-associated genes was limited, and no antimicrobial resistance genes were detected, but novel variants of an insertion element that plays an important role in capturing and mobilizing antibiotic resistance genes, IS26, were identified and characterized. The isolates belonged to phylogroups B1 and D, including types known to cause disease in humans and animals. Specifically, we found E. coli ST58, ST69, ST162, ST212, ST446, ST906, ST2520, ST6096 and ...
Genomic comparisons of Escherichia coli ST131 from Australia
Microbial Genomics, 2021
Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contrib... more Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by appr...
Microbial Genomics, 2020
The AB5 cytotoxins are important virulence factors in Escherichia coli . The most notable members... more The AB5 cytotoxins are important virulence factors in Escherichia coli . The most notable members of the AB5 toxin families include Shiga toxin families 1 (Stx1) and 2 (Stx2), which are associated with enterohaemorrhagic E. coli infections causing haemolytic uraemic syndrome and haemorrhagic colitis. The subAB toxins are the newest and least well understood members of the AB5 toxin gene family. The subtilase toxin genes are divided into a plasmid-based variant, subAB1, originally described in enterohaemorrhagic E. coli O113:H21, and distinct chromosomal variants, subAB2, that reside in pathogenicity islands encoding additional virulence effectors. Previously we identified a chromosomal subAB2 operon within an E. coli ST58 strain IBS28 (ONT:H25) taken from a wild ibis nest at an inland wetland in New South Wales, Australia. Here we show the subAB2 toxin operon comprised part of a 140 kb tRNA–Phe chromosomal island that co-hosted tia, encoding an outer-membrane protein that confers an...
Case Reports in Veterinary Medicine, 2020
We describe three cases of osteoarticular infection (OAI) in young thoroughbred horses in which t... more We describe three cases of osteoarticular infection (OAI) in young thoroughbred horses in which the causative organism was identified by MALDI-TOF as Kingella species. The pattern of OAI resembled that reported with Kingella infection in humans. Analysis by 16S rRNA PCR enabled construction of a phylogenetic tree that placed the isolates closer to Simonsiella and Alysiella species, rather than Kingella species. Average nucleotide identity (ANI) comparison between the new isolate and Kingella kingae and Alysiella crassa however revealed low probability that the new isolate belonged to either of these species. This preliminary analysis suggests the organism isolated is a previously unrecognised species.
mSphere, 2019
SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those confer... more SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii , and other members of the Enterobacteriaceae . SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3′ end of trmE . For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.
Plasmid, 2019
IncHI2-ST1 plasmids play an important role in co-mobilizing genes conferring resistance to critic... more 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 multidrug 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.
The Journal of antimicrobial chemotherapy, Feb 20, 2016
to that of the widely spread Tn1548-bearing plasmid pMDR-ZJ06 (Rep3 family), with the gene casset... more to that of the widely spread Tn1548-bearing plasmid pMDR-ZJ06 (Rep3 family), with the gene cassette aac(3 0)-II being replaced by aacA4 and catB8 (accession no. CP001938). The K. pneumoniae strain belongs to MLST sequence type 307 (ST307) and harboured a 20 kb plasmid (IncF) that was not investigated further. This study demonstrates that pan-aminoglycoside resistance may be acquired by P. aeruginosa following the transfer of Tn1548 on Pseudomonas-specific plasmids such as pOZ176. Whether the Tn1548 module was transmitted in vivo from K. pneumoniae or A. baumannii is unknown. However, the observation that a patient may be colonized with several phylogenetically different ArmA-producing bacteria highlights the diffusion potentials of Tn1548 among Gram-negative species and reinforces the need to screen for 16S rRNA methylases not only in Acinetobacter and Enterobacteriaceae species, but also in P. aeruginosa. A high resistance to arbekacin (MIC. 256 mg/L) may serve as an indicator of methylase production prior to the use of molecular biology methods.
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Papers by Piklu Chowdhury