Dr Piklu Roy Chowdhury (nee: Piklu Bhattacharya) is a Senior Research Associate and Ausgem Fellow at the i3 institute within the Faculty of Science, University of Technology Sydney. Her expertise lies in the characterisation of “mobilomes” of Gram-negative bacteria, with a particular focus on laterally mobile regions of pathogen genomes that have clustered drug resistance genes and contribute to the rapid evolution of resistance phenotypes and dispersal of resistance genes within bacterial populations.
- 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
Although a molecular biologist by training, my major interest in science lies in studying the molecular mechanisms that better equip bacterial pathogens to successfully establish, adapt and survive while in contact with their hosts. My career is focused on the characterisation of mobile regions in pathogenic microorganisms and in the elucidation of the mechanism(s) by which multiple-drug resistance evolves rapidly within clinically important bacteria.
My passion lies in functional genomics and in interpreting how bacteria rapidly evolve multi-drug resistant and pan-resistant phenotypes. I primarily focus on the integron gene-cassette recombination and expression system, which is just one example of the dynamic, Darwinian process that drives evolution of resistant genomes via horizontal gene transfer.
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.
My key areas of expertise can be listed as:
(1) Detailed characterisation of complex drug resistant loci in Gram-negative bacteria
(2) Determining the genealogy of complex mobile loci that drive genome plasticity in bacteria
(3) Comparative Bioinformatics analysis of the genomes of large cohorts of drug resistant pathogens
(4) Developing molecular diagnostic tools for tracking the lateral movement of drug resistance regions within pathogen genomes
(5) Molecular characterisation of novel genes within pathogen genomes.
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
Bogema, DR, McKinnon, J, Liu, M, Hitchick, N, Miller, N, Venturini, C, Iredell, J, Darling, AE, Roy Chowdury, P & Djordjevic, SP 2019, 'Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups.', Microbial Genomics, vol. 5, pp. 1-18.View/Download from: UTS OPUS or Publisher's site
Sequence type (ST)73 has emerged as one of the most frequently isolated extraintestinal pathogenic Escherichia coli. To examine the localized diversity of ST73 clonal groups, including their mobile genetic element profile, we sequenced the genomes of 16 multiple-drug resistant ST73 isolates from patients with urinary tract infection from a single hospital in Sydney, Australia, between 2009 and 2011. Genome sequences were used to generate a SNP-based phylogenetic tree to determine the relationship of these isolates in a global context with ST73 sequences (n=210) from public databases. There was no evidence of a dominant outbreak strain of ST73 in patients from this hospital, rather we identified at least eight separate groups, several of which reoccurred, over a 2 year period. The inferred phylogeny of all ST73 strains (n=226) including the ST73 clone D i2 reference genome shows high bootstrap support and clusters into four major groups that correlate with serotype. The Sydney ST73 strains carry a wide variety of virulence-associated genes, but the presence of iss, pic and several iron-acquisition operons was notable.
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: UTS OPUS or 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: UTS OPUS or 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.
Wyrsch, ER, Reid, CJ, DeMaere, MZ, Liu, MY, Chapman, TA, Roy Chowdhury, P & Djordjevic, SP 2019, 'Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia', Frontiers in Sustainable Food Systems, vol. 3.View/Download from: UTS OPUS or Publisher's site
Cummins, ML, Reid, CJ, Roy Chowdhury, P, Bushell, RN, Esbert, N, Tivendale, KA, Noormohammadi, AH, Islam, S, Marenda, MS, Browning, GF, Markham, PF & Djordjevic, SP 2019, 'Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene.', Microbial genomics, vol. 5, no. 2.View/Download from: UTS OPUS or Publisher's site
Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum β-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the trimethoprim resistance gene cassettes dfrA5 (48/95, 50 %) and dfrA1 (25/95, 27 %), the tetracycline resistance determinant tet(A) (51/95, 55 %) and the ampicillin resistance genes blaTEM-1A/B/C (48/95, 52 %) was common. IS26 (77/95, 81 %), an insertion element known to capture and mobilize a wide spectrum of antimicrobial resistance genes, was also frequently identified. These studies provide a baseline snapshot of drug-resistant APEC in Australia and their role in the carriage of ColV-like virulence plasmids.
Cummins, ML, Roy Chowdhury, P, Marenda, MS, Browning, GF & Djordjevic, SP 2019, 'Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate.', mSphere, vol. 4, no. 3.View/Download from: UTS OPUS or Publisher's site
Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry bla NDM-1, bla VEB-6, and bla CTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3' end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023.IMPORTANCE 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 ...
Roy Chowdhury, P, McKinnon, J, Liu, M & Djordjevic, SP 2019, 'Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS26 Transposon in a Unique Chromosomal Location.', Frontiers in microbiology, vol. 9, no. Jan, pp. 3212-3212.View/Download from: UTS OPUS or Publisher's site
Escherichia coli ST405 is an emerging urosepsis pathogen, noted for carriage of bla CTX-M, bla NDM, and a repertoire of virulence genes comparable with O25b:H4-ST131. Extraintestinal and multidrug resistant E. coli ST405 are poorly studied in Australia. Here we determined the genome sequence of a uropathogenic, multiple drug resistant E. coli ST405 (strain 2009-27) from the mid-stream urine of a hospital patient in Sydney, Australia, using a combination of Illumina and SMRT sequencing. The genome of strain 2009-27 assembled into two unitigs; a chromosome comprising 5,287,472 bp and an IncB/O plasmid, pSDJ2009-27, of 89,176 bp. In silico and phenotypic analyses showed that strain 2009-27 is a serotype O102:H6, phylogroup D ST405 resistant to ampicillin, azithromycin, kanamycin, streptomycin, trimethoprim, and sulphafurazole. The genes encoding resistance to these antibiotics reside within a novel, mobile IS26-flanked transposon, identified here as Tn6242, in the chromosomal gene yjdA. Tn6242 comprises four modules that each carries resistance genes flanked by IS26, including a class 1 integron with dfrA17 and aadA5 gene cassettes, a variant of Tn6029, and mphA. We exploited unique genetic signatures located within Tn6242 to identify strains of ST405 from Danish patients that also carry the transposon in the same chromosomal location. The acquisition of Tn6242 into yjdA in ST405 is significant because it (i) is vertically inheritable; (ii) represents a reservoir of resistance genes that can transpose onto resident/circulating plasmids; and (iii) is a site for the capture of further IS26-associated resistance gene cargo.
McKinnon, J, Roy Chowdhury, P & Djordjevic, SP 2018, 'Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis.', International journal of antimicrobial agents, vol. 52, no. 3, pp. 430-435.View/Download from: UTS OPUS or Publisher's site
Sequence type 58 (ST58) phylogroup B1 Escherichia coli have been isolated from a wide variety of mammalian and avian hosts but are not noted for their ability to cause serious disease in humans or animals. Here we determined the genome sequences of two multidrug-resistant E. coli ST58 strains from urine and blood of one patient using a combination of Illumina and Single Molecule, Real-Time (SMRT) sequencing. Both ST58 strains were clonal and were characterised as serotype O8:H25, phylogroup B1 and carried a complex resistance locus/loci (CRL) that featured an atypical class 1 integron with a dfrA5 (trimethoprim resistance) gene cassette followed by only 24 bp of the 3'-CS. CRL that carry this particular integron have been described previously in E. coli from cattle, pigs and humans in Australia. The integron abuts a copy of Tn6029, an IS26-flanked composite transposon encoding blaTEM, sul2 and strAB genes that confer resistance to ampicillin, sulfathiazole and streptomycin, respectively. The CRL resides within a novel Tn2610-like hybrid Tn1721/Tn21 transposon on an IncF, ColV plasmid (pSDJ2009-52F) of 138 553 bp that encodes virulence associated genes implicated in life-threatening extraintestinal pathogenic E. coli (ExPEC) infections. Notably, pSDJ2009-52F shares high sequence identity with pSF-088-1, a plasmid reported in an E. coli ST95 strain from a patient with blood sepsis from a hospital in San Francisco. These data suggest that extraintestinal infections caused by E. coli carrying ColV-like plasmids, irrespective of their phylogroup or ST, may pose a potential threat to human health, particularly to the elderly and immunocompromised.
Rychener, L, In-Albon, S, Djordjevic, SP, Chowdhury, PR, Nicholson, P, Ziech, RE, de Vargas, AC, Frey, J & Falquet, L 2018, 'Corrigendum: Clostridium chauvoei, an Evolutionary Dead-End Pathogen.', Frontiers in Microbiology, vol. 9.View/Download from: UTS OPUS or Publisher's site
[This corrects the article on p. 1054 in vol. 8, PMID: 28649238.].
Reid, C, Wyrsch, E, Chowdhury, PR, Zingali, T, Liu, M, Darling, A, Chapman, T & Djordjevic, S 2017, 'Porcine commensal Escherichia coli: A reservoir for class 1 integrons associated with IS26'.View/Download from: UTS OPUS or Publisher's site
Abstract Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial resistance and virulence-associated genes (VAGs) and the zoonotic potential of commensal Escherichia coli from swine is largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilisation of antimicrobial resistance genes between food animals and the environment. Here, we report whole genome sequence analysis of 141 E. coli from the faeces of healthy pigs. Most strains belonged to phylogroups A and B1 and carried i) a class 1 integron; ii) VAGs linked with extraintestinal infection in humans; iii) antimicrobial resistance genes bla TEM , aphAl, cmlA, strAB, tet(A) A, dfrA12, dfrA5, sul1, sul2, sul3 ; iv) IS26; and v) heavy metal resistance genes ( merA, cusA, terA ). Carriage of the sulphonamide resistance gene sul3 was notable in this study. The 141 strains belonged to 42 multilocus sequence types, but clonal complex 10 featured prominently. Structurally diverse class 1 integrons that were frequently associated with IS26 carried unique genetic features that were also identified in extraintestinal pathogenic E. coli (ExPEC) from humans. This study provides the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin, facilitating tracking of specific lineages and the mobile resistance genes they carry. Conflict of Interest Statement None to declare.
Reid, CJ, Wyrsch, ER, Roy Chowdhury, P, Zingali, T, Liu, M, Darling, AE, Chapman, TA & Djordjevic, SP 2017, 'Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26.', Microbial Genomics, vol. 3, no. 12, pp. 1-13.View/Download from: UTS OPUS or Publisher's site
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.
Roy Chowdhury, P, Scott, M & Djordjevic, SP 2017, '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.View/Download from: UTS OPUS or Publisher's site
Rychener, L, InAlbon, S, Djordjevic, SP, Chowdhury, PR, Ziech, RE, de Vargas, AC, Frey, J & Falquet, L 2017, 'Clostridium chauvoei, an Evolutionary Dead-End Pathogen', FRONTIERS IN MICROBIOLOGY, vol. 8.View/Download from: UTS OPUS or Publisher's site
Chowdhury, PR, DeMaere, M, Chapman, T, Worden, P, Charles, IG, Darling, AE & Djordjevic, SP 2016, 'Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease', BMC MICROBIOLOGY, vol. 16.View/Download from: UTS OPUS or Publisher's site
Wyrsch, E, Roy Chowdhury, P, Chapman, TA, Charles, IG, Hammond, JM & Djordjevic, SP 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.View/Download from: UTS OPUS or Publisher's site
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', Open Biology, vol. 6, pp. 1-12.View/Download from: UTS OPUS or Publisher's site
Pseudomonas aeruginosa are noscomially acquired, opportunistic pathogens that pose a major threat to the health of burns patients and the immunocompromised. We sequenced the genomes of P. aeruginosa isolates RNS_PA1, RNS_PA46 and RNS_PAE05, which displayed resistance to almost all frontline antibiotics, including gentamicin, piperacillin, timentin, meropenem, ceftazidime and colistin. We provide evidence that the isolates are representatives of P. aeruginosa sequence type (ST) 235 and carry Tn6162 and Tn6163 in genomic islands 1 (GI1) and 2 (GI2), respectively. GI1 disrupts the endA gene at precisely the same chromosomal location as in P. aeruginosa strain VR-143/97, of unknown ST, creating an identical CA direct repeat. The class 1 integron associated with Tn6163 in GI2 carries a blaGES-5–aacA4–gcuE15–aphA15 cassette array conferring resistance to carbapenems and aminoglycosides. GI2 is flanked by a 12 nt direct repeat motif, abuts a tRNA-gly gene, and encodes proteins with putative roles in integration, conjugative transfer as well as integrative conjugative element-specific proteins. This suggests that GI2 may have evolved from a novel integrative conjugative element. Our data provide further support to the hypothesis that genomic islands play an important role in de novo evolution of multiple antibiotic resistance phenotypes in P. aeruginosa.
Wyrsch, E, Roy Chowdhury, P, Abraham, S, Santos, J, Darling, AE, Charles, IG, Chapman, TA & Djordjevic, SP 2015, 'Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs.', BMC Genomics, vol. 16, pp. 1-11.View/Download from: UTS OPUS or Publisher's site
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, CJ, Roy Chowdhury, P & Djordjevic, SP 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.View/Download from: UTS OPUS or Publisher's site
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.
Chowdhury, PR, Charles, IG & Djordjevic, SP 2015, 'Correction: 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. 4.View/Download from: UTS OPUS or Publisher's site
Roy Chowdhury, P, Charles, IG & Djordjevic, SP 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, pp. 1-15.View/Download from: UTS OPUS or Publisher's site
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.
Darling, AE, McKinnon, J, Santos, J, Charles, IG, Roy Chowdhury, P, Djordjevic, S & Worden, P 2014, 'A draft genome of Escherichia coli sequence type 127 strain 2009-46.', Gut Pathogens, vol. Sept 1, no. 6, pp. 32-32.View/Download from: UTS OPUS or Publisher's site
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, McKinnon, J, Wyrsch, E, Hammond, JM, Charles, I & Djordjevic, S 2014, 'Genomic interplay in bacterial communities: implications for growth promoting practices in animal husbandry.', Frontiers in Microbiology, vol. 12, no. 5, pp. 394-394.View/Download from: UTS OPUS or Publisher's site
Robinson, MW, Buchtmann, KA, Jenkins, C, Tacchi, JL, Raymond, BBA, To, J, Chowdhury, PR, Woolley, LK, Labbate, M, Turnbull, L, Whitchurch, CB, Padula, MP & Djordjevic, SP 2013, 'MHJ_0125 is an M42 glutamyl aminopeptidase that moonlights as a multifunctional adhesin on the surface of Mycoplasma hyopneumoniae', OPEN BIOLOGY, vol. 3.View/Download from: UTS OPUS or Publisher's site
Djordjevic, SP, 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.View/Download from: UTS OPUS or Publisher's site
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, KA, Roy Chowdhury, P, Paulsen, I, Walker, MJ & Djordjevic, SP 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.View/Download from: UTS OPUS or Publisher's site
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.
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.View/Download from: UTS OPUS
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.
Martinez Diaz, ME, Marquez, C, Ingold, A, Merlino, J, Djordjevic, SP, 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.View/Download from: UTS OPUS or Publisher's site
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.
Stokes, H, Martinez Diaz, ME, Roy Chowdhury, P & Djordjevic, SP 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.View/Download from: UTS OPUS or Publisher's site
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.
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.View/Download from: UTS OPUS or Publisher's site
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.
Price-Carter, M, Roy Chowdhury, P, Pope, C, Paine, S, de Lisle, G, Collins, D, Nicol, C & Carter, PE 2011, 'The evolution and distribution of phage ST160 within Salmonella enterica serotype Typhimurium', Epidemiology and Infection, vol. 139, no. 8, pp. 1262-1271.View/Download from: UTS OPUS or Publisher's site
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, KA, Paulsen, IT, Stokes, H & Labbate, M 2011, 'Genome sequence of Vibrio rotiferianus Strain DAT722', Journal Of Bacteriology, vol. 193, no. 13, pp. 3381-3382.View/Download from: UTS OPUS or Publisher's site
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.
Roy Chowdhury, P, Ingold, A, Vanegas-Gomez, N, Martinez Diaz, ME, Merlino, J, Merkier, AK, Castro, M, Rocha, GG, Borthagaray, G, Centron, D, Toledo, HB, Marquez, CM & 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.View/Download from: UTS OPUS or Publisher's site
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.
Roy Chowdhury, P, Merlino, J, Labbate, M, Cheong, EY, 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.View/Download from: UTS OPUS or Publisher's site
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.
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.View/Download from: UTS OPUS or Publisher's site
In a survey of class 1 integrons from human stools, an unusual class 1 integron from a strain of Enterobacter cloacae was isolated and characterized in detail. Sequence analysis of a fosmid containing the class 1 integron revealed a complex set of transposons which included two Tn402-like transposons. One of these transposons, Tn6007, included a class 1 integron with two non-antibiotic-resistance-type gene cassettes and a complete transposition module. This tni module is a hybrid with a boundary within the res site compared to Tn402, implying that a site-specific recombination event generated either Tn6007 or Tn402. The second Tn402-like transposon, Tn6008, possesses neither a mer operon nor an integron, and most of its tni module has been deleted. Tn6007, Tn6008, and the 2,478 bases between them, collectively designated Tn6006, have transposed into a Tn5036/Tn3926-like transposon as a single unit. Tn6006, Tn6007, and Tn6008 could all transpose as discrete entities. Database analysis also revealed that a version of Tn6008 was present in the genome of Xanthomonas campestris pv. vesicatoria. Overall, the E. cloacae isolate further demonstrated that functional class 1 integrons/transposons are probably common in bacterial communities and have the potential to add substantially to the problem of multidrug-resistant nosocomial infections.
Marquez, C, Labbate, M, Ingold, AJ, Roy Chowdhury, P, Ramirez, MS, 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.View/Download from: UTS OPUS or Publisher's site
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
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.View/Download from: UTS OPUS
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, JA 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.View/Download from: UTS OPUS or Publisher's site
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.
Martinez Diaz, ME, Djordjevic, SP, 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.View/Download from: UTS OPUS or Publisher's site
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.
The Department of Primary Industries of NSW