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Kenneally C, Murphy CP, Sleator RD, Culligan EP. Genotypic and phenotypic characterisation of asymptomatic bacteriuria (ABU) isolates displaying bacterial interference against multi-drug resistant uropathogenic E. Coli. Arch Microbiol 2024; 206:394. [PMID: 39245770 PMCID: PMC11381485 DOI: 10.1007/s00203-024-04114-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/19/2024] [Accepted: 08/22/2024] [Indexed: 09/10/2024]
Abstract
Escherichia coli can colonise the urogenital tract of individuals without causing symptoms of infection, in a condition referred to as asymptomatic bacteriuria (ABU). ABU isolates can protect the host against symptomatic urinary tract infections (UTIs) by bacterial interference against uropathogenic E. coli (UPEC). The aim of this study was to investigate the genotypic and phenotypic characteristics of five ABU isolates from midstream urine samples of adults. Comparative genomic and phenotypic analysis was conducted including an antibiotic resistance profile, pangenome analysis, and a putative virulence profile. Based on the genome analysis, the isolates consisted of one from phylogroup A, three from phylogroup B2, and one from phylogroup D. Two of the isolates, PUTS 58 and SK-106-1, were noted for their lack of antibiotic resistance and virulence genes compared to the prototypic ABU strain E. coli 83,972. This study provides insights into the genotypic and phenotypic profiles of uncharacterised ABU isolates, and how relevant fitness and virulence traits can impact their potential suitability for therapeutic bacterial interference.
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Affiliation(s)
- Ciara Kenneally
- Department of Biological Sciences, Munster Technological University, Cork, T12 P928, Bishopstown, Ireland
| | - Craig P Murphy
- Department of Biological Sciences, Munster Technological University, Cork, T12 P928, Bishopstown, Ireland
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Cork, T12 P928, Bishopstown, Ireland
| | - Eamonn P Culligan
- Department of Biological Sciences, Munster Technological University, Cork, T12 P928, Bishopstown, Ireland.
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Kenneally C, Murphy CP, Sleator RD, Culligan EP. Turbidimetric bioassays: A solution to antimicrobial activity detection in asymptomatic bacteriuria isolates against uropathogenic Escherichia coli. Microbiologyopen 2024; 13:e1411. [PMID: 38706434 PMCID: PMC11070844 DOI: 10.1002/mbo3.1411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Traditional bacteriocin screening methods often face limitations due to diffusion-related challenges in agar matrices, which can prevent the peptides from reaching their target organism. Turbidimetric techniques offer a solution to these issues, eliminating diffusion-related problems and providing an initial quantification of bacteriocin efficacy in producer organisms. This study involved screening the cell-free supernatant (CFS) from eight uncharacterized asymptomatic bacteriuria (ABU) isolates and Escherichia coli 83972 for antimicrobial activity against clinical uropathogenic E. coli (UPEC) strains using turbidimetric growth methods. ABU isolates exhibiting activity against five or more UPEC strains were further characterized (PUTS 37, PUTS 58, PUTS 59, S-07-4, and SK-106-1). The inhibition of the CFS by proteinase K suggested that the antimicrobial activity was proteinaceous in nature, potentially bacteriocins. The activity of E. coli PUTS 58 and SK-106-1 was enhanced in an artificial urine medium, with both inhibiting all eight UPECs. A putative microcin H47 operon was identified in E. coli SK-106-1, along with a previously identified microcin V and colicin E7 in E. coli PUTS 37 and PUTS 58, respectively. These findings indicate that ABU bacteriocin-producers could serve as viable prophylactics and therapeutics in the face of increasing antibiotic resistance among uropathogens.
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Affiliation(s)
- Ciara Kenneally
- Department of Biological SciencesMunster Technological University, BishopstownCorkIreland
| | - Craig P. Murphy
- Department of Biological SciencesMunster Technological University, BishopstownCorkIreland
| | - Roy D. Sleator
- Department of Biological SciencesMunster Technological University, BishopstownCorkIreland
| | - Eamonn P. Culligan
- Department of Biological SciencesMunster Technological University, BishopstownCorkIreland
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3
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Chagneau CV, Payros D, Goman A, Goursat C, David L, Okuno M, Bordignon PJ, Séguy C, Massip C, Branchu P, Ogura Y, Nougayrède JP, Marenda M, Oswald E. HlyF, an underestimated virulence factor of uropathogenic Escherichia coli. Clin Microbiol Infect 2023; 29:1449.e1-1449.e9. [PMID: 37532127 DOI: 10.1016/j.cmi.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVES Urinary tract infections (UTIs) are primarily caused by uropathogenic Escherichia coli (UPEC). This study aims to elucidate the role of the virulence factor HlyF in the epidemiology and pathophysiology of UTIs and investigate the dissemination of plasmids carrying the hlyF gene. METHODS An epidemiological analysis was conducted on a representative collection of 225 UPEC strains isolated from community-acquired infections. Selected hlyF+ strains were fully sequenced using a combination of Illumina and Nanopore technologies. To investigate the impact of HlyF, a murine model of UTI was utilized to compare clinical signs, bacterial loads in the bladder, kidney, and spleen, onset of bacteraemia, and inflammation through cytokine quantification among wild-type hlyF+ strains, isogenic mutants, and complemented mutants. RESULTS Our findings demonstrate that 20% of UPEC encode the HlyF protein. These hlyF+ UPEC strains exhibited enhanced virulence, frequently leading to pyelonephritis accompanied by bloodstream infections. Unlike typical UPEC strains, hlyF+ UPEC strains demonstrate a broader phylogroup distribution and possess a unique array of virulence factors and antimicrobial resistance genes, primarily carried by ColV-like plasmids. In the murine UTI model, expression of HlyF was linked to the UPECs' capacity to induce urosepsis and elicit an exacerbated inflammatory response, setting them apart from typical UPEC strains. DISCUSSION Overall, our results strongly support the notion that HlyF serves as a significant virulence factor for UPECs, and the dissemination of ColV-like plasmids encoding HlyF warrants further investigation.
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Affiliation(s)
- Camille V Chagneau
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France; Service de Bactériologie-Hygiène, Univerity Hospital of Toulouse, Hôpital Purpan, Toulouse, France
| | - Delphine Payros
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Audrey Goman
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Cécile Goursat
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Laure David
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Pierre-Jean Bordignon
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Carine Séguy
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Clémence Massip
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France; Service de Bactériologie-Hygiène, Univerity Hospital of Toulouse, Hôpital Purpan, Toulouse, France
| | - Priscilla Branchu
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Jean-Philippe Nougayrède
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Marc Marenda
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Eric Oswald
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France; Service de Bactériologie-Hygiène, Univerity Hospital of Toulouse, Hôpital Purpan, Toulouse, France.
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Cave R, Ter-Stepanyan MM, Mkrtchyan HV. Short- and Long-Read Sequencing Reveals the Presence and Evolution of an IncF Plasmid Harboring blaCTX-M-15 and blaCTX-M-27 Genes in Escherichia coli ST131. Microbiol Spectr 2023; 11:e0035623. [PMID: 37466446 PMCID: PMC10433869 DOI: 10.1128/spectrum.00356-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Escherichia coli sequence type 131 (ST131) has contributed to the spread of extended-spectrum beta-lactamase (ESBL) and has emerged as the dominant cause of hospital- and community-acquired urinary tract infections. Here, we report for the first time an in-depth analysis of whole-genome sequencing (WGS) of 4 ESBL-producing E. coli ST131 isolates recovered from patients in two hospitals in Armenia using Illumina short-read sequencing for accurate base calling to determine their genotype and to infer their phylogeny and using Oxford Nanopore Technologies long-read sequencing to resolve plasmid and chromosomal genetic elements. Genotypically, the four Armenian isolates were identified as part of the H30Rx/clade C2 (n = 2) and H41/clade A (n = 2) lineages and were phylogenetically closely related to isolates from the European Nucleotide Archive (ENA) database previously recovered from patients in the United States, Australia, and New Zealand. The Armenian isolates recovered in this study had chromosomal integration of the blaCTX-M-15 gene in the H30Rx isolates and a high number of virulence genes found in the H41 isolates associated with the carriage of a rare genomic island (in the context of E. coli ST131) containing the S fimbrial, salmochelin siderophore, and microcin H47 virulence genes. Furthermore, our data show the evolution of the IncF[2:A2:B20] plasmid harboring both blaCTX-M-15 and blaCTX-M-27 genes, derived from the recombination of genes from an IncF[F2:A-:B-] blaCTX-M-15-associated plasmid into the IncF[F1:A2:B20] blaCTX-M-27-associated plasmid backbone seen in two genetically closely related H41 Armenian isolates. IMPORTANCE Combining short and long reads from whole-genome sequencing analysis provided a genetic context for uncommon genes of clinical importance to better understand transmission and evolutionary features of ESBL-producing uropathogenic E. coli (UPEC) ST131 isolates recovered in Armenia. Using hybrid genome assembly in countries lacking genomic surveillance studies can inform us about new lineages not seen in other countries with genes encoding high virulence and antibiotic resistance harbored on mobile genetic elements.
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Affiliation(s)
- Rory Cave
- School of Biomedical Sciences, University of West London, London, United Kingdom
| | - Mary M. Ter-Stepanyan
- Yerevan State Medical University after M. Heratsi, Faculty of Public Health, Department of Epidemiology, Yerevan, Republic of Armenia
- Research Center of Maternal and Child Health Protection, Yerevan, Armenia
| | - Hermine V. Mkrtchyan
- School of Biomedical Sciences, University of West London, London, United Kingdom
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Volpe MR, Velilla JA, Daniel-Ivad M, Yao JJ, Stornetta A, Villalta PW, Huang HC, Bachovchin DA, Balbo S, Gaudet R, Balskus EP. A small molecule inhibitor prevents gut bacterial genotoxin production. Nat Chem Biol 2023; 19:159-167. [PMID: 36253549 PMCID: PMC9889270 DOI: 10.1038/s41589-022-01147-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/19/2022] [Indexed: 02/04/2023]
Abstract
The human gut bacterial genotoxin colibactin is a possible key driver of colorectal cancer (CRC) development. Understanding colibactin's biological effects remains difficult owing to the instability of the proposed active species and the complexity of the gut microbiota. Here, we report small molecule boronic acid inhibitors of colibactin biosynthesis. Designed to mimic the biosynthetic precursor precolibactin, these compounds potently inhibit the colibactin-activating peptidase ClbP. Using biochemical assays and crystallography, we show that they engage the ClbP binding pocket, forming a covalent bond with the catalytic serine. These inhibitors reproduce the phenotypes observed in a clbP deletion mutant and block the genotoxic effects of colibactin on eukaryotic cells. The availability of ClbP inhibitors will allow precise, temporal control over colibactin production, enabling further study of its contributions to CRC. Finally, application of our inhibitors to related peptidase-encoding pathways highlights the power of chemical tools to probe natural product biosynthesis.
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Affiliation(s)
- Matthew R. Volpe
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - José A. Velilla
- grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA USA
| | - Martin Daniel-Ivad
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - Jenny J. Yao
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA
| | - Alessia Stornetta
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA
| | - Peter W. Villalta
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ,grid.17635.360000000419368657Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN USA
| | - Hsin-Che Huang
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Daniel A. Bachovchin
- grid.51462.340000 0001 2171 9952Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Silvia Balbo
- grid.17635.360000000419368657Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ,grid.17635.360000000419368657Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN USA
| | - Rachelle Gaudet
- grid.38142.3c000000041936754XDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA USA
| | - Emily P. Balskus
- grid.38142.3c000000041936754XDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XHoward Hughes Medical Institute, Harvard University, Cambridge, MA USA
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Kenneally C, Murphy CP, Sleator RD, Culligan EP. The Urinary Microbiome and Biological Therapeutics: Novel Therapies For Urinary Tract Infections. Microbiol Res 2022; 259:127010. [DOI: 10.1016/j.micres.2022.127010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/12/2022]
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Jones CV, Jarboe BG, Majer HM, Ma AT, Beld J. Escherichia coli Nissle 1917 secondary metabolism: aryl polyene biosynthesis and phosphopantetheinyl transferase crosstalk. Appl Microbiol Biotechnol 2021; 105:7785-7799. [PMID: 34546406 DOI: 10.1007/s00253-021-11546-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
Escherichia coli Nissle 1917 (EcN) is a Gram-negative bacterium that is used to treat inflammatory bowel diseases. The probiotic character of EcN is not well-understood, but its ability to produce secondary metabolites plays an important role in its activity. The EcN genome encodes for an aryl polyene (APE) biosynthetic gene cluster (BGC), and APE products have a role in biofilm formation. We show here that this unusual polyketide assembly line synthase produces four APE molecules which are likely cis/trans isomers. Within the APE BGC, two acyl carrier proteins are involved in biosynthesis. Acyl carrier proteins require activation by post-translational modification with a phosphopantetheinyl transferase (PPTase). Through analysis of single, double, and triple mutants of three PPTases, the PPTase-BGC crosstalk relationship in EcN was characterized. Understanding PPTase-BGC crosstalk is important for the engineering of secondary metabolite production hosts and for targeting of PPTases with new antibiotics. KEY POINTS: • Escherichia coli Nissle 1917 biosynthesizes four aryl polyene isoforms. • Phosphopantetheinyl transferase crosstalk is important for biosynthesis.
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Affiliation(s)
- Courtney V Jones
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
| | - Brianna G Jarboe
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
| | - Haley M Majer
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
| | - Amy T Ma
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Center for Advanced Microbial Processing and Center for Genomics Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA.
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Auvray F, Perrat A, Arimizu Y, Chagneau CV, Bossuet-Greif N, Massip C, Brugère H, Nougayrède JP, Hayashi T, Branchu P, Ogura Y, Oswald E. Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population. Microb Genom 2021; 7:000579. [PMID: 33961542 PMCID: PMC8209727 DOI: 10.1099/mgen.0.000579] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/11/2021] [Indexed: 01/19/2023] Open
Abstract
The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of Escherichia coli strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine E. coli isolates, we identified 109 strains carrying a highly conserved pks island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of pks acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, pks was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the asnW tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, pks inserted at the asnU or asnV tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, pks was acquired, independently of the HPI, at a non-tRNA locus. All the pks-positive strains except 18 produced colibactin. Sixteen strains contained mutations in clbB or clbD, or a fusion of clbJ and clbK and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the pks island. One strain was fully metabolically inactive without pks alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the pks island is not restricted to human pathogenic B2 strains and is more widely distributed in the E. coli population, while preserving its functionality.
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Affiliation(s)
- Frédéric Auvray
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | - Alexandre Perrat
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | - Yoko Arimizu
- Department of Bacteriology, Kyushu University, Fukuoka, Japan
| | | | | | - Clémence Massip
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Hubert Brugère
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | | | - Tetsuya Hayashi
- Department of Bacteriology, Kyushu University, Fukuoka, Japan
| | - Priscilla Branchu
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Eric Oswald
- IRSD, INSERM, Université de Toulouse, INRAE, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
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Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase ( pks) Island. mBio 2021; 12:mBio.03634-20. [PMID: 33653937 PMCID: PMC8545132 DOI: 10.1128/mbio.03634-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The genotoxin colibactin is a secondary metabolite produced by the polyketide synthase (pks) island harbored by extraintestinal pathogenic E. coli (ExPEC) and other members of the Enterobacteriaceae that has been increasingly reported to have critical implications in human health. The present study entails a high-throughput whole-genome comparison and phylogenetic analysis of such pathogenic E. coli isolates to gain insights into the patterns of distribution, horizontal transmission, and evolution of the island. For the current study, 23 pks-positive ExPEC genomes were newly sequenced, and their virulome and resistome profiles indicated a preponderance of virulence encoding genes and a reduced number of genes for antimicrobial resistance. In addition, 4,090 E. coli genomes from the public domain were also analyzed for large-scale screening for pks-positive genomes, out of which a total of 530 pks-positive genomes were studied to understand the subtype-based distribution pattern(s). The pks island showed a significant association with the B2 phylogroup (82.2%) and a high prevalence in sequence type 73 (ST73; n = 179) and ST95 (n = 110) and the O6:H1 (n = 110) serotype. Maximum-likelihood (ML) phylogeny of the core genome and intergenic regions (IGRs) of the ST95 model data set, which was selected because it had both pks-positive and pks-negative genomes, displayed clustering in relation to their carriage of the pks island. Prevalence patterns of genes encoding RM systems in the pks-positive and pks-negative genomes were also analyzed to determine their potential role in pks island acquisition and the maintenance capability of the genomes. Further, the maximum-likelihood phylogeny based on the core genome and pks island sequences from 247 genomes with an intact pks island demonstrated horizontal gene transfer of the island across sequence types and serotypes, with few exceptions. This study vitally contributes to understanding of the lineages and subtypes that have a higher propensity to harbor the pks island-encoded genotoxin with possible clinical implications.
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Chagneau CV, Massip C, Bossuet-Greif N, Fremez C, Motta JP, Shima A, Besson C, Le Faouder P, Cénac N, Roth MP, Coppin H, Fontanié M, Martin P, Nougayrède JP, Oswald E. Uropathogenic E. coli induces DNA damage in the bladder. PLoS Pathog 2021; 17:e1009310. [PMID: 33630958 PMCID: PMC7906301 DOI: 10.1371/journal.ppat.1009310] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/13/2021] [Indexed: 01/19/2023] Open
Abstract
Urinary tract infections (UTIs) are among the most common outpatient infections, with a lifetime incidence of around 60% in women. We analysed urine samples from 223 patients with community-acquired UTIs and report the presence of the cleavage product released during the synthesis of colibactin, a bacterial genotoxin, in 55 of the samples examined. Uropathogenic Escherichia coli strains isolated from these patients, as well as the archetypal E. coli strain UTI89, were found to produce colibactin. In a murine model of UTI, the machinery producing colibactin was expressed during the early hours of the infection, when intracellular bacterial communities form. We observed extensive DNA damage both in umbrella and bladder progenitor cells. To the best of our knowledge this is the first report of colibactin production in UTIs in humans and its genotoxicity in bladder cells.
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Affiliation(s)
| | - Clémence Massip
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | | | | | - Jean-Paul Motta
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Ayaka Shima
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Céline Besson
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | | | - Nicolas Cénac
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Marie-Paule Roth
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | - Hélène Coppin
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
| | | | - Patricia Martin
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- VibioSphen, Prologue Biotech, Labège, France
| | | | - Eric Oswald
- IRSD, INSERM, Université de Toulouse, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
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Massip C, Oswald E. Siderophore-Microcins in Escherichia coli: Determinants of Digestive Colonization, the First Step Toward Virulence. Front Cell Infect Microbiol 2020; 10:381. [PMID: 32974212 PMCID: PMC7472721 DOI: 10.3389/fcimb.2020.00381] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Siderophore-microcins are antimicrobial peptides produced by enterobacteria, especially Escherichia coli and Klebsiella pneumoniae strains. The antibiotic peptide is post-translationally modified by the linkage of a siderophore moiety. Therefore, it can enter and kill phylogenetically related bacteria by a “Trojan Horse” stratagem, by mimicking the iron–siderophore complexes. Consequently, these antimicrobial peptides are key determinants of bacterial competition within the intestinal niche, which is the reservoir for pathogenic E. coli. The most frequent extraintestinal infections caused by E. coli are urinary tract infections. Uropathogenic E. coli (UPEC) can produce many virulence factors, including siderophore-microcins. Siderophore-microcins are chromosomally encoded by small genomic islands that exhibit conserved organization. In UPEC, the siderophore-microcin gene clusters and biosynthetic pathways differ from the “archetypal” models described in fecal strains. The gene cluster is shorter. Thus, active siderophore-microcin production requires proteins from two other genomic islands that also code for virulence factors. This functional and modular synergy confers a strong selective advantage for the domination of the colonic niche, which is the first step toward infection. This optimization of genetic resources might favor the selection of additional virulence factors, which are essential in the subsequent steps of pathogenesis in E. coli infection.
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Affiliation(s)
- Clémence Massip
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,Service de Bactériologie-Hygiène, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,Service de Bactériologie-Hygiène, Hôpital Purpan, CHU de Toulouse, Toulouse, France
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