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Dr Piklu Roy Chowdhury

Biography

Dr Piklu Roy Chowdhury (nee: Piklu Bhattacharya) is a Senior Research Associate at the i3 institute, within the Faculty of Science of the University of Technology Sydney. Her expertise lies in the characterisation of “mobilomes” of Gram-negative bacteria, with a particular focus on genomic regions that are rich in drug resistance genes.

Professional

  • Member of the Australian Society of Microbiology.
  • Member of the American Society for Microbiology
  • Member of the Australian Society for Antimicrobials
  • Member of the International Society for Plasmid Biology
Image of Piklu Roy Chowdhury
Postdoctoral Research Fellow, The ithree Institute
Core Member, ithree - Institute of Infection, Immunity and Innovation
PHILOSOPHY, Ph D
Member, Australian Society for Microbiology
 
Phone
+61 2 9514 4129

Research Interests

A molecular biologist by training, my passion is in the Bioinformatics analysis of pathogen genomes and linking them back to phenotypes. My major interest in science lies in studying host pathogen relationships. My research therefore focuses on two aspects of such interactions.

  • Firstly, studying the evolving molecular mechanisms that better equip bacterial pathogens to successfully establish, adapt and survive within and interact with hosts.
  • Secondly, bioinformatics analysis of pathogen genomes and looking at unique candidate gene/s that have the capacity of providing competitive advantage to the pathogen.

The integron gene recombination and expression system is one such genetic system that enables pathogen to evolve resistance to multiple drugs rapidly by a mechanism called horizontal gene transfer; and has been the major focus of my work in the past five years. Presently I am actively involved in mining genomic and proteomic data on a global collection of drug resistance ESKAPE pathogens to develop a holistic understanding of multiple drug resistant mobilomes.

Can supervise: Yes
Yes

Bacterial Pathogenesis

Lateral Gene transfer

Evolution of Complex Drug-resistant locus in Gram negative pathogens

Comparative Genomics of Bacterial Pathogens

Bio-informatics analysis of Drug resistant Pathogen  Genomes

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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Martinez, E., Djordjevic, S.P., Stokes, H. & Roy Chowdhury, P. 2013, 'Mobilized Integrons: Team Players in the Spread of Antibiotic Resistance Genes' in Uri Gophna (ed), Lateral Gene Transfer in Evolution, Springer, New York, pp. 79-103.
Martinez Diaz, M.E., Djordjevic, S.P., Stokes, H. & Roy Chowdhury, P. 2013, 'Mobilized Integrons: Team Players in the Spread of Antibiotic Resistance Genes' in Uri Gophna (ed), Lateral Gene Transfer in Evolution, Springer, New York, pp. 79-103.
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Integrons possess a site-specific recombination system and comprise a family of elements that are broadly distributed amongst the Proteobacteria. The units of capture into these elements are gene cassettes, which normally comprise of only a single gene along with an attachment site recognized by the recombination system. The class 1 integron has at least two features that distinguishes it from most other members of the integron family of integrase elements. The first of these is that they are located on mobile elements as opposed to being fixed in the chromosome and the second is that most of the associated gene cassettes include genes that encode antibiotic resistance. The linkage of the class 1 integron to mobile elements was an important step since it has meant that diverse molecular processes act cooperatively to disseminate resistance genes in Gram-negative bacteria. The selection for resistance in the antibiotic era has now led to an enormous diversity of elements that in many cases has resulted in conjugation, transposition, and site-specific recombination processes combining to spread large clusters of resistance genes. All these processes existed in nature prior to the antibiotic era but the level and extent of cooperation did not. Here we discuss how some of these complex class 1-associated mobile resistance regions evolved and their ramifications for the management of the antibiotic resistance problem.

Journal articles

Rychener, L., InAlbon, S., Djordjevic, S.P., Chowdhury, P.R., Ziech, R.E., de Vargas, A.C., Frey, J. & Falquet, L. 2017, 'Clostridium chauvoei, an Evolutionary Dead-End Pathogen.', Front Microbiol, vol. 8, p. 1054.
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Full genome sequences of 20 strains of Clostridium chauvoei, the etiological agent of blackleg of cattle and sheep, isolated from four different continents over a period of 64 years (1951-2015) were determined and analyzed. The study reveals that the genome of the species C. chauvoei is highly homogeneous compared to the closely related species C. perfringens, a widespread pathogen that affects human and many animal species. Analysis of the CRISPR locus is sufficient to differentiate most C. chauvoei strains and is the most heterogenous region in the genome, containing in total 187 different spacer elements that are distributed as 30 - 77 copies in the various strains. Some genetic differences are found in the 3 allelic variants of fliC1, fliC2 and fliC3 genes that encode structural flagellin proteins, and certain strains do only contain one or two alleles. However, the major virulence genes including the highly toxic C.chauvoei toxin A, the sialidase and the two hyaluronidases are fully conserved as are the metabolic and structural genes of C. chauvoei. These data indicate that C. chauvoei is a strict ruminant-associated pathogen that has reached a dead end in its evolution.
Chowdhury, P.R., DeMaere, M., Chapman, T., Worden, P., Charles, I.G., Darling, A.E. & Djordjevic, S.P. 2016, 'Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease', BMC MICROBIOLOGY, vol. 16.
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Roy Chowdhury, P., Scott, M., Worden, P., Huntington, P., Hudson, B., Karagiannis, T., Charles, I. & Djordjevic, S. 2016, 'Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa', OpenBiology, vol. 6.
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Wyrsch, E., Roy Chowdhury, P., Chapman, T.A., Charles, I.G., Hammond, J.M. & Djordjevic, S.P. 2016, 'Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis', Frontiers in Microbiology, vol. 7, no. 843.
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Wyrsch, E., Roy Chowdhury, P., Chapman, T.A., Charles, I.G., Hammond, J.M. & Djordjevic, S.P. 2016, 'Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis', Frontiers in Microbiology, vol. 7, no. 843.
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Roy Chowdhury, P., Scott, M. & Djordjevic, S.P. 2016, 'Genomic islands 1 and 2 carry multiple antibiotic resistance genes in Pseudomonas aeruginosa ST235, ST253, ST111 and ST175 and are globally dispersed', Journal of Antimicrobial Chemotherapy, vol. 72, no. 2, pp. 620-622.
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Roy Chowdhury, P., Charles, I.G. & Djordjevic, S.P. 2015, 'A role for Tn6029 in the evolution of the complex antibiotic resistance gene loci in genomic island 3 in enteroaggregative hemorrhagic Escherichia coli O104:H4.', PloS one, vol. 10, no. 2, p. e0115781.
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In enteroaggregative hemorrhagic Escherichia coli (EAHEC) O104 the complex antibiotic resistance gene loci (CRL) found in the region of divergence 1 (RD1) within E. coli genomic island 3 (GI3) contains blaTEM-1, strAB, sul2, tet(A)A, and dfrA7 genes encoding resistance to ampicillin, streptomycin, sulfamethoxazole, tetracycline and trimethoprim respectively. The precise arrangement of antibiotic resistance genes and the role of mobile elements that drove the evolutionary events and created the CRL have not been investigated. We used a combination of bioinformatics and iterative BLASTn searches to determine the micro-evolutionary events that likely led to the formation of the CRL in GI3 using the closed genome sequences of EAHEC O104:H4 strains 2011C-3493 and 2009EL-2050 and high quality draft genomes of EAHEC E. coli O104:H4 isolates from sporadic cases not associated with the initial outbreak. Our analyses indicate that the CRL in GI3 evolved from a progenitor structure that contained an In2-derived class 1 integron in a Tn21/Tn1721 hybrid backbone. Within the hybrid backbone, a Tn6029-family transposon, identified here as Tn6029C abuts the sul1 gene in the 3'-Conserved Segment (-CS) of a class 1 integron generating a unique molecular signature that has only previously been observed in pASL01a, a small plasmid found in commensal E. coli in West Africa. From this common progenitor, independent IS26-mediated events created two novel transposons identified here as Tn6029D and Tn6222 in 2011C-3493 and 2009EL-2050 respectively. Analysis of RD1 within GI3 reveals IS26 has played a crucial role in the assembly of regions within the CRL.
Wyrsch, E., Roy Chowdhury, P., Abraham, S., Santos, J., Darling, A.E., Charles, I.G., Chapman, T.A. & Djordjevic, S.P. 2015, 'Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs.', BMC genomics, vol. 16, pp. 165-165.
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BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) are a major economic threat to pig production globally, with serogroups O8, O9, O45, O101, O138, O139, O141, O149 and O157 implicated as the leading diarrhoeal pathogens affecting pigs below four weeks of age. A multiple antimicrobial resistant ETEC O157 (O157 SvETEC) representative of O157 isolates from a pig farm in New South Wales, Australia that experienced repeated bouts of pre- and post-weaning diarrhoea resulting in multiple fatalities was characterized here. Enterohaemorrhagic E. coli (EHEC) O157:H7 cause both sporadic and widespread outbreaks of foodborne disease, predominantly have a ruminant origin and belong to the ST11 clonal complex. Here, for the first time, we conducted comparative genomic analyses of two epidemiologically-unrelated porcine, disease-causing ETEC O157; E. coli O157 SvETEC and E. coli O157:K88 734/3, and examined their phylogenetic relationship with EHEC O157:H7. RESULTS: O157 SvETEC and O157:K88 734/3 belong to a novel sequence type (ST4245) that comprises part of the ST23 complex and are genetically distinct from EHEC O157. Comparative phylogenetic analysis using PhyloSift shows that E. coli O157 SvETEC and E. coli O157:K88 734/3 group into a single clade and are most similar to the extraintestinal avian pathogenic Escherichia coli (APEC) isolate O78 that clusters within the ST23 complex. Genome content was highly similar between E. coli O157 SvETEC, O157:K88 734/3 and APEC O78, with variability predominantly limited to laterally acquired elements, including prophages, plasmids and antimicrobial resistance gene loci. Putative ETEC virulence factors, including the toxins STb and LT and the K88 (F4) adhesin, were conserved between O157 SvETEC and O157:K88 734/3. The O157 SvETEC isolate also encoded the heat stable enterotoxin STa and a second allele of STb, whilst a prophage within O157:K88 734/3 encoded the serum survival gene bor. Both isolates harbor a large repertoire of antibi...
Reid, C.J., Roy Chowdhury, P. & Djordjevic, S.P. 2015, 'Tn6026 and Tn6029 are found in complex resistance regions mobilised by diverse plasmids and chromosomal islands in multiple antibiotic resistant Enterobacteriaceae.', Plasmid, vol. 80, pp. 127-137.
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Transposons flanked by direct copies of IS26 are important contributors to the evolution of multiple antibiotic resistance. Tn6029 and Tn6026 are examples of composite transposons that have become widely disseminated on small and large plasmids with different incompatibility markers in pathogenic and commensal Escherichia coli and various serovars of Salmonella enterica. Some of the plasmids that harbour these transposons also carry combinations of virulence genes. Recently, Tn6029 and Tn6026 and derivatives thereof have been found on chromosomal islands in both established and recently emerged pathogens. While Tn6029 and Tn6026 carry genes encoding resistance to older generation antibiotics, they also provide a scaffold for the introduction of genes encoding resistance to a wide variety of clinically relevant antibiotics that are mobilised by IS26. As a consequence, Tn6029 and Tn6026 or variants are likely to increasingly feature in complex resistance regions in multiple antibiotic resistant Enterobacteriaceae that threaten the health of humans and food production animals.
Darling, A.E., Worden, P.J., Chapman, T., Roy Chowdhury, P., Charles, I.G. & Djordjevic, S.P. 2014, 'The genome of Clostridium difficile 5.3', Gut Pathogens, vol. 6, no. 4.
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Background Clostridium difficile is the leading cause of infectious diarrhea in humans and responsible for large outbreaks of enteritis in neonatal pigs in both North America and Europe. Disease caused by C. difficile typically occurs during antibiotic therapy and its emergence over the past 40 years is linked with the widespread use of broad-spectrum antibiotics in both human and veterinary medicine. Results We sequenced the genome of Clostridium difficile 5.3 using the Illumina Nextera XT and MiSeq technologies. Assembly of the sequence data reconstructed a 4,009,318 bp genome in 27 scaffolds with an N50 of 786 kbp. The genome has extensive similarity to other sequenced C. difficile genomes, but also has several genes that are potentially related to virulence and pathogenicity that are not present in the reference C. difficile strain. Conclusion Genome sequencing of human and animal isolates is needed to understand the molecular events driving the emergence of C. difficile as a gastrointestinal pathogen of humans and food animals and to better define its zoonotic potential.
Roy Chowdhury, P. 2014, 'Genomic interplay in bacterial communities: implications for growth promoting practices in animal husbandry.', Frontiers in Microbiology, vol. 12, no. 5, pp. 394-394.
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Roy Chowdhury, P. 2014, 'A draft genome of Escherichia coli sequence type 127 strain 2009-46.', Gut Pathogens, vol. Sept 1, no. 6, pp. 32-32.
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Djordjevic, S.P., Stokes, H. & Roy Chowdhury, P. 2013, 'Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota', Frontiers in Microbiology, vol. 4, no. 86, pp. 1-12.
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Multiple antibiotic resistant pathogens represent a major clinical challenge in both human and veterinary context. It is now well-understood that the genes that encode resistance are context independent. That is, the same gene is commonly present in otherwise very disparate pathogens in both humans and production and companion animals, and among bacteria that proliferate in an agricultural context. This can be true even for pathogenic species or clonal types that are otherwise confined to a single host or ecological niche. It therefore follows that mechanisms of gene flow must exist to move genes from one part of the microbial biosphere to another. It is widely accepted that lateral (or horizontal) gene transfer (L(H)GT) drives this gene flow. LGT is relatively well-understood mechanistically but much of this knowledge is derived from a reductionist perspective. We believe that this is impeding our ability to deal with the medical ramifications of LGT. Resistance genes and the genetic scaffolds that mobilize them in multiply drug resistant bacteria of clinical significance are likely to have their origins in completely unrelated parts of the microbial biosphere.
Venturini, C., Hassan, K.A., Roy Chowdhury, P., Paulsen, I., Walker, M.J. & Djordjevic, S.P. 2013, 'Sequences of two related multiple antibiotic resistance virulence plasmids sharing a unique IS26-associated molecular signature isolated from different Escherichia coli pathovars from different hosts.', PLoS One, vol. 8, no. 11, pp. e78862-e78862.
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Enterohemorrhagic Escherichia coli (EHEC) and atypical enteropathogenic E. coli (aEPEC) are important zoonotic pathogens that increasingly are becoming resistant to multiple antibiotics. Here we describe two plasmids, pO26-CRL125 (125 kb) from a human O26:H- EHEC, and pO111-CRL115 (115kb) from a bovine O111 aEPEC, that impart resistance to ampicillin, kanamycin, neomycin, streptomycin, sulfathiazole, trimethoprim and tetracycline and both contain atypical class 1 integrons with an identical IS26-mediated deletion in their 3´-conserved segment. Complete sequence analysis showed that pO26-CRL125 and pO111-CRL115 are essentially identical except for a 9.7 kb fragment, present in the backbone of pO26-CRL125 but absent in pO111-CRL115, and several indels. The 9.7 kb fragment encodes IncI-associated genes involved in plasmid stability during conjugation, a putative transposase gene and three imperfect repeats. Contiguous sequence identical to regions within these pO26-CRL125 imperfect repeats was identified in pO111-CRL115 precisely where the 9.7 kb fragment is missing, suggesting it may be mobile. Sequences shared between the plasmids include a complete IncZ replicon, a unique toxin/antitoxin system, IncI stability and maintenance genes, a novel putative serine protease autotransporter, and an IncI1 transfer system including a unique shufflon. Both plasmids carry a derivate Tn21 transposon with an atypical class 1 integron comprising a dfrA5 gene cassette encoding resistance to trimethoprim, and 24 bp of the 3´-conserved segment followed by Tn6026, which encodes resistance to ampicillin, kanymycin, neomycin, streptomycin and sulfathiazole.
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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Martinez Diaz, M.E., Marquez, C., Ingold, A., Merlino, J., Djordjevic, S.P., Stokes, H. & Roy Chowdhury, P. 2012, 'Diverse mobilized class 1 integrons are common in the chromosomes of pathogenic Pseudomonas aeruginosa clinical isolates', Antimicrobial Agents and Chemotherapy, vol. 56, no. 4, pp. 2169-2172.
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Eleven clinical class 1 integron-containing Pseudomonas aeruginosa isolates from Australia and Uruguay were investigated for the genomic locations of these elements. Several novel class 1 integrons/transposons were found in at least four distinct locations in the chromosome, including genomic islands. These elements seem to be undergoing successful dispersal by lateral gene transfer since integrons were identified across several lineages and more than one clonal line.
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.
Stokes, H., Martinez Diaz, M.E., Roy Chowdhury, P. & Djordjevic, S.P. 2012, 'Class 1 integron-associated spread of resistance regions in Pseudomonas aeruginosa: plasmid or chromosomal platforms?', Journal of Antimicrobial Chemotherapy, vol. 67, no. 7, pp. 1799-1800.
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Multidrug-resistant Pseudomonas aeruginosa infections are a growing clinical problem. Of particular concern is the range of b-lactamase genes associated with this species. If the spread of resistance is to be controlled, it is critical that researchers have a good understanding of the mechanisms by which resistance genes are spread. In the Enterobacteriaceae, the role of plasmids in the lateral gene transfer (LGT) of resistance is extensive. However, many clinical isolates of Gram-negative bacteria also commonly carry additional syntenic blocks of DNA as part of the chromosome that are lineage specific within a species and are known as genomic islands.
Roy Chowdhury, P., Ingold, A., Vanegas-Gomez, N., Martinez Diaz, M.E., Merlino, J., Merkier, A.K., Castro, M., Rocha, G.G., Borthagaray, G., Centron, D., Toledo, H.B., Marquez, C.M. & Stokes, H. 2011, 'Dissemination of multiple drug resistance genes by class 1 integrons in Klebsiella pneumoniae isolates from four countries: a comparative study', Antimicrobial agents and chemotherapy, vol. 55, no. 7, pp. 3140-3149.
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A comparative genetic analysis of 42 clinical Klebsiella pneumoniae isolates, resistant to two or more antibiotics belonging to the broad-spectrum -lactam group, sourced from Sydney, Australia, and three South American countries is presented. The study focuses on the genetic contexts of class 1 integrons, mobilizable genetic elements best known for their role in the rapid evolution of antibiotic resistance among Gram-negative pathogens. It was found that the class 1 integrons in this cohort were located in a number of different genetic contexts with clear regional differences. In Sydney, IS26-associated Tn21-like transposons on IncL/M plasmids contribute greatly to the dispersal of integron-associated multiple-drug-resistant (MDR) loci. In contrast, in the South American countries, Tn1696-like transposons on an IncA/C plasmid(s) appeared to be disseminating a characteristic MDR region. A range of mobile genetic elements is clearly being recruited by clinically important mobile class 1 integrons, and these elements appear to be becoming more common with time. This in turn is driving the evolution of complex and laterally mobile MDR units and may further complicate antibiotic therapy.
Price-Carter, M., Roy Chowdhury, P., Pope, C., Paine, S., de Lisle, G., Collins, D., Nicol, C. & Carter, P.E. 2011, 'The evolution and distribution of phage ST160 within Salmonella enterica serotype Typhimurium', Epidemiology and Infection, vol. 139, no. 8, pp. 1262-1271.
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Salmonellosis is an internationally important disease of mammals and birds. Unique epidemics in New Zealand in the recent past include two Salmonella serovars: Salmonella enterica subsp. enterica serovar Typhimurium definitive type (DT) 160 (S. Typhimurium DT160) and S. Brandenburg. Although not a major threat internationally, in New Zealand S. Typhimurium DT160 has been the most common serovar isolated from humans, and continues to cause significant losses in wildlife. We have identified DNA differences between the first New Zealand isolate of S. Typhimurium DT160 and the genome-sequenced strain, S. Typhimurium LT2. All the differences could be accounted for in one cryptic phage ST64B, and one novel P22-like phage, ST160. The majority of the ST160 genome is almost identical to phage SE1 but has two regions not found in SE1 which are identical to the P22-like phage ST64T, suggesting that ST160 evolved from SE1 via two recombination events with ST64T. All of the New Zealand isolates of DT160 were identical indicating the clonal spread of this particular Salmonella. Some overseas isolates of S. Typhimurium DT160 differed from the New Zealand strain and contained SE1 phage rather than ST160. ST160 was also identified in New Zealand isolates of S. Typhimurium DT74 and S. Typhimurium RDNC-April06 and in S. Typhimurium DT160 isolates from the USA. The emergence of S. Typhimurium DT160 as a significant pathogen in New Zealand is postulated to have occurred due to the sensitivity of the Salmonella strains to the ST160 phage when S. Typhimurium DT160 first arrived.
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.
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.
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
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.
Roy Chowdhury, P., Pay, J. & Braithwaite, M. 2007, 'Isolation, identification and ecology of Ewingella americana (the causal agent of internal stipe necrosis) from cultivated mushrooms in New Zealand', Australasian Plant Pathology, vol. 36, no. 5, pp. 424-428.
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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 time that E. americana has been isolated from a non-human host in New Zealand. Previously, the bacterium has been found associated with human blood and sputum samples. Presented here are the details of the identification methods used in providing evidence that this strain of E. americana has the capacity to induce typical symptoms of internal stipe necrosis. Ecological studies give a possible explanation as to why E. americana has previously been unnoticed in New Zealand.
Roy Chowdhury, P. & Heinemann, J.A. 2006, 'The General Secretory Pathway of Burkholderia gladioli pv. agaricicola BG164R Is Necessary for Cavity Disease in White Button Mushrooms', Applied and Environmental Microbiology, vol. 72, no. 5, pp. 3558-3565.
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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.
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