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Martin CL, Hill JH, Aller SG. Host Tropism and Structural Biology of ABC Toxin Complexes. Toxins (Basel) 2024; 16:406. [PMID: 39330864 PMCID: PMC11435725 DOI: 10.3390/toxins16090406] [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: 08/21/2024] [Revised: 09/12/2024] [Accepted: 09/17/2024] [Indexed: 09/28/2024] Open
Abstract
ABC toxin complexes are a class of protein toxin translocases comprised of a multimeric assembly of protein subunits. Each subunit displays a unique composition, contributing to the formation of a syringe-like nano-machine with natural cargo carrying, targeting, and translocation capabilities. Many of these toxins are insecticidal, drawing increasing interest in agriculture for use as biological pesticides. The A subunit (TcA) is the largest subunit of the complex and contains domains associated with membrane permeation and targeting. The B and C subunits, TcB and TcC, respectively, package into a cocoon-like structure that contains a toxic peptide and are coupled to TcA to form a continuous channel upon final assembly. In this review, we outline the current understanding and gaps in the knowledge pertaining to ABC toxins, highlighting seven published structures of TcAs and how these structures have led to a better understanding of the mechanism of host tropism and toxin translocation. We also highlight similarities and differences between homologues that contribute to variations in host specificity and conformational change. Lastly, we review the biotechnological potential of ABC toxins as both pesticides and cargo-carrying shuttles that enable the transport of peptides into cells.
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Affiliation(s)
- Cole L Martin
- Graduate Biomedical Sciences Pathobiology, Physiology and Pharmacology Theme, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - John H Hill
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephen G Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Chen L, Wu MY, Chen SL, Hu R, Wang Y, Zeng W, Feng S, Ke M, Wang L, Chen S, Gu M. The Guardian of Vision: Intelligent Bacteriophage-Based Eyedrops for Clinical Multidrug-Resistant Ocular Surface Infections. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2407268. [PMID: 39091071 DOI: 10.1002/adma.202407268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Clinical multidrug-resistant Pseudomonas aeruginosa (MDR-PA) is the leading cause of refractory bacterial keratitis (BK). However, the reported BK treatment methods lack biosecurity and bioavailability, which usually causes irreversible visual impairment and even blindness. Herein, for BK caused by clinically isolated MDR-PA infection, armed phages are modularized with the type I photosensitizer (PS) ACR-DMT, and an intelligent phage eyedrop is developed for combined phagotherapy and photodynamic therapy (PDT). These eyedrops maximize the advantages of bacteriophages and ACR-DMT, enabling more robust and specific targeting killing of MDR-PA under low oxygen-dependence, penetrating and disrupting biofilms, and efficiently preventing biofilm reformation. Altering the biofilm and immune microenvironments alleviates inflammation noninvasively, promotes corneal healing without scar formation, protects ocular tissues, restores visual function, and prevents long-term discomfort and pain. This strategy exhibits strong scalability, enables at-home treatment of ocular surface infections with great patient compliance and a favorable prognosis, and has significant potential for clinical application.
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Affiliation(s)
- Luojia Chen
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ming-Yu Wu
- College of Biomedical Engineering, Sichuan University, Chengdu, 610065, China
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China
| | - Si-Ling Chen
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rui Hu
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yifei Wang
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Weijuan Zeng
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Shun Feng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, 610031, China
| | - Min Ke
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518026, China
| | - Shi Chen
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Department of Burn and Plastic Surgery, Shenzhen Key Laboratory of Microbiology in Genomic Modification & Editing and Application, Shenzhen Institute of Translational Medicine, Shenzhen University Medical School, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Meijia Gu
- Department of Ophthalmology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, TaiKang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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Riva F, Dechesne A, Eckert EM, Riva V, Borin S, Mapelli F, Smets BF, Crotti E. Conjugal plasmid transfer in the plant rhizosphere in the One Health context. Front Microbiol 2024; 15:1457854. [PMID: 39268528 PMCID: PMC11390587 DOI: 10.3389/fmicb.2024.1457854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 08/12/2024] [Indexed: 09/15/2024] Open
Abstract
Introduction Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is one of the primary routes of antimicrobial resistance (AMR) dissemination. In the One Health context, tracking the spread of mobile genetic elements (MGEs) carrying ARGs in agri-food ecosystems is pivotal in understanding AMR diffusion and estimating potential risks for human health. So far, little attention has been devoted to plant niches; hence, this study aimed to evaluate the conjugal transfer of ARGs to the bacterial community associated with the plant rhizosphere, a hotspot for microbial abundance and activity in the soil. We simulated a source of AMR determinants that could enter the food chain via plants through irrigation. Methods Among the bacterial strains isolated from treated wastewater, the strain Klebsiella variicola EEF15 was selected as an ARG donor because of the relevance of Enterobacteriaceae in the AMR context and the One Health framework. The strain ability to recolonize lettuce, chosen as a model for vegetables that were consumed raw, was assessed by a rifampicin resistant mutant. K. variicola EEF15 was genetically manipulated to track the conjugal transfer of the broad host range plasmid pKJK5 containing a fluorescent marker gene to the natural rhizosphere microbiome obtained from lettuce plants. Transconjugants were sorted by fluorescent protein expression and identified through 16S rRNA gene amplicon sequencing. Results and discussion K. variicola EEF15 was able to colonize the lettuce rhizosphere and inhabit its leaf endosphere 7 days past bacterial administration. Fluorescence stereomicroscopy revealed plasmid transfer at a frequency of 10-3; cell sorting allowed the selection of the transconjugants. The conjugation rates and the strain's ability to colonize the plant rhizosphere and leaf endosphere make strain EEF15::lacIq-pLpp-mCherry-gmR with pKJK5::Plac::gfp an interesting candidate to study ARG spread in the agri-food ecosystem. Future studies taking advantage of additional environmental donor strains could provide a comprehensive snapshot of AMR spread in the One Health context.
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Affiliation(s)
- Francesco Riva
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ester M Eckert
- CNR - IRSA Water Research Institute, Molecular Ecology Group (MEG), Verbania, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Valentina Riva
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Biological and Chemical Engineering, Center for Water Technology, Aarhus University, Aarhus, Denmark
| | - Elena Crotti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Frick-Cheng AE, Shea AE, Roberts JR, Smith SN, Ohi MD, Mobley HLT. Iron limitation induces motility in uropathogenic E. coli CFT073 partially through action of LpdA. mBio 2024; 15:e0104824. [PMID: 38874412 PMCID: PMC11253704 DOI: 10.1128/mbio.01048-24] [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: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024] Open
Abstract
More than half of women will experience a urinary tract infection (UTI) with most cases caused by uropathogenic Escherichia coli (UPEC). Bacterial swimming motility enhances UPEC pathogenicity, resulting in more severe disease outcomes including kidney infection. Surprisingly, the connection between motility and iron limitation is mostly unexplored despite the lack of free iron available in the host. We sought to investigate a potential connection between iron restriction and regulation of motility in UPEC. We cultured E. coli CFT073, a prototypical UPEC strain, under iron limitation and observed that CFT073 had elevated fliC (flagella) promoter activity, and this iron-specific response was repressed by the addition of exogenous iron. We confirmed increased flagellar expression in CFT073 by measuring fliC transcript, FliC protein, and surface-expressed flagella under iron-limited conditions. Interestingly, known motility regulator flhDC did not have altered transcription under these conditions. To define the regulatory mechanism of this response, we constructed single knockouts of eight master regulators and found the iron-regulated response was lost in crp, arcA, and fis mutants. Thus, we focused on the five genes regulated by all three regulators. Of the five genes knocked out, the iron-regulated motility response was most strongly dysregulated in the lpdA mutant, which also resulted in significantly lowered fitness in the murine model of ascending UTI, both against the WT and a non-motile fliC mutant. Collectively, we demonstrated that iron-mediated motility in CFT073 is partially regulated by lpdA, which contributes to the understanding of how uropathogens differentially regulate motility mechanisms in the iron-restricted host. IMPORTANCE Urinary tract infections (UTIs) are ubiquitous and responsible for over five billion dollars in associated health care costs annually. Both iron acquisition and motility are highly studied virulence factors associated with uropathogenic Escherichia coli (UPEC), the main causative agent of uncomplicated UTI. This work is innovative by providing mechanistic insight into the synergistic relationship between these two critical virulence properties. Here, we demonstrate that iron limitation has pleiotropic effects with consequences that extend beyond metabolism and impact other virulence mechanisms. Indeed, targeting iron acquisition as a therapy may lead to an undesirable enhancement of UPEC pathogenesis through increased motility. It is vital to understand the full breadth of UPEC pathogenesis to adequately respond to this common infection, especially with the increase of antibiotic-resistant pathogens.
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Affiliation(s)
- A. E. Frick-Cheng
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - A. E. Shea
- Department of Microbiology and Immunology, University of South Alabama Medical School, Mobile, Alabama, USA
| | - J. R. Roberts
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - S. N. Smith
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - M. D. Ohi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - H. L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Andrade AD, Almeida PGC, Mariani NAP, Santos NCM, Camargo IA, Martini PV, Kushima H, Ai D, Avellar MCW, Meinhardt A, Pleuger C, Silva EJR. Regional modulation of toll-like receptor signaling pathway genes in acute epididymitis in mice. Andrology 2024; 12:1024-1037. [PMID: 38497291 DOI: 10.1111/andr.13630] [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: 11/23/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Region-specific immune environments in the epididymis influence the immune responses to uropathogenic Escherichia coli (UPEC) infection, a relevant cause of epididymitis in men. Toll-like receptors (TLRs) are essential to orchestrate immune responses against bacterial infections. The epididymis displays region-specific inflammatory responses to bacterial-derived TLR agonists, such as lipopolysaccharide (LPS; TLR4 agonist) and lipoteichoic acid (LTA; TLR2/TLR6 agonist), suggesting that TLR-associated signaling pathways could influence the magnitude of inflammatory responses in epididymitis. OBJECTIVES To investigate the expression and regulation of key genes associated with TLR4 and TLR2/TLR6 signaling pathways during epididymitis induced by UPEC, LPS, and LTA in mice. MATERIAL AND METHODS Epididymitis was induced in mice using UPEC, ultrapure LPS, or LTA, injected into the interstitial space of the initial segment or the lumen of the vas deferens close to the cauda epididymidis. Samples were harvested after 1, 5, and 10 days for UPEC-treated animals and 6 and 24 h for LPS-/LTA-treated animals. Ex vivo epididymitis was induced by incubating epididymal regions from naive mice with LPS or LTA. RT-qPCR and Western blot assays were conducted. RESULTS UPEC infection up-regulated Tlr2, Tlr4, and Tlr6 transcripts and their associated signaling molecules Cd14, Ticam1, and Traf6 in the cauda epididymidis but not in the initial segment. In these epididymal regions, LPS and LTA differentially modulated Tlr2, Tlr4, Tlr6, Cd14, Myd88, Ticam1, Traf3, and Traf6 expression levels. NFKB and AP1 activation was required for LPS- and LTA-induced up-regulation of TLR-associated signaling transcripts in the cauda epididymidis and initial segment, respectively. CONCLUSION The dynamic modulation of TLR4 and TLR2/TLR6 signaling pathways gene expression during epididymitis indicates bacterial-derived antigens elicit an increased tissue sensitivity to combat microbial infection in a spatial manner in the epididymis. Differential activation of TLR-associated signaling pathways may contribute to fine-tuning inflammatory responses along the epididymis.
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Affiliation(s)
- Alexandre D Andrade
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Priscila G C Almeida
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Noemia A P Mariani
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Natalia C M Santos
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Isabela A Camargo
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Poliana V Martini
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Helio Kushima
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Dingding Ai
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Maria Christina W Avellar
- Department of Pharmacology, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
| | - Andreas Meinhardt
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
- Centre of Reproductive Health, Hudson Institute of Medical Research, Clayton, Australia
| | - Christiane Pleuger
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Erick J R Silva
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
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Khawaja T, Mäklin T, Kallonen T, Gladstone RA, Pöntinen AK, Mero S, Thorpe HA, Samuelsen Ø, Parkhill J, Izhar M, Akhtar MW, Corander J, Kantele A. Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nat Commun 2024; 15:5196. [PMID: 38890378 PMCID: PMC11189469 DOI: 10.1038/s41467-024-49591-5] [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: 02/14/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Multi-drug resistant (MDR) E. coli constitute a major public health burden globally, reaching the highest prevalence in the global south yet frequently flowing with travellers to other regions. However, our comprehension of the entire genetic diversity of E. coli colonising local populations remains limited. We quantified this diversity, its associated antimicrobial resistance (AMR), and assessed the impact of antibiotic use by recruiting 494 outpatients and 423 community dwellers in the Punjab province, Pakistan. Rectal swab and stool samples were cultured on CLED agar and DNA extracted from plate sweeps was sequenced en masse to capture both the genetic and AMR diversity of E. coli. We assembled 5,247 E. coli genomes from 1,411 samples, displaying marked genetic diversity in gut colonisation. Compared with high income countries, the Punjabi population generally showed a markedly different distribution of genetic lineages and AMR determinants, while use of antibiotics elevated the prevalence of well-known globally circulating MDR clinical strains. These findings implicate that longitudinal multi-regional genomics-based surveillance of both colonisation and infections is a prerequisite for developing mechanistic understanding of the interplay between ecology and evolution in the maintenance and dissemination of (MDR) E. coli.
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Affiliation(s)
- Tamim Khawaja
- Meilahti Infectious Diseases and Vaccine Research Center (MeiVac), Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland
| | - Tommi Mäklin
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | | | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Sointu Mero
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland
| | - Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Mateen Izhar
- Department of Microbiology, Shaikh Zayed Post-Graduate Medical Institute, Lahore, Pakistan
| | - M Waheed Akhtar
- School of Biological Science, University of the Punjab, Lahore, Pakistan
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
- Department of Biostatistics, University of Oslo, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.
| | - Anu Kantele
- Meilahti Infectious Diseases and Vaccine Research Center (MeiVac), Helsinki University Hospital and University of Helsinki, Helsinki, Finland.
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland.
- Multidiciplinary Center of Excellence in Antimicrobial Resistance Research, FIMAR, Medical Faculty, University of Helsinki, Helsinki, Finland.
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Fernández-Yáñez V, Suazo P, Hormazábal C, Ibaceta V, Arenas-Salinas M, Vidal RM, Silva-Ojeda F, Arellano C, Muñoz I, Del Canto F. Distribution of papA and papG Variants among Escherichia coli Genotypes: Association with Major Extraintestinal Pathogenic Lineages. Int J Mol Sci 2024; 25:6657. [PMID: 38928363 PMCID: PMC11203468 DOI: 10.3390/ijms25126657] [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: 04/24/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The pyelonephritis-associated fimbria (P fimbria) is one of the most recognized adhesion determinants of extraintestinal pathogenic Escherichia coli strains (ExPECs). Twelve variants have been described for the gene encoding the P fimbria major structural subunit PapA and three variants for the gene encoding the adhesin subunit PapG. However, their distribution among the ExPEC diversity has not been comprehensively addressed. A complete landscape of that distribution might be valuable for delineating basic studies about the pathogenicity mechanisms of ExPECs and following up on the evolution of ExPEC lineages, particularly those most epidemiologically relevant. Therefore, we performed a massive descriptive study to detect the papA and papG variants along different E. coli genotypes represented by genomic sequences contained in the NCBI Assembly Refseq database. The most common papA variants were F11, F10, F48, F16, F12, and F7-2, which were found in significant association with the most relevant ExPEC genotypes, the phylogroups B2 and D, and the sequence types ST95, ST131, ST127, ST69, ST12, and ST73. On the other hand, the papGII variant was by far the most common followed by papGIII, and both were also found to have a significant association with common ExPEC genotypes. We noticed the presence of genomes, mainly belonging to the sequence type ST12, harboring two or three papA variants and two papG variants. Furthermore, the most common papA and papG variants were also detected in records representing strains isolated from humans and animals such as poultry, bovine, and dogs, supporting previous hypotheses of potential cross-transmission. Finally, we characterized a set of 17 genomes from Chilean uropathogenic E. coli strains and found that ST12 and ST73 were the predominant sequence types. Variants F7-1, F7-2, F8, F9, F11, F13, F14, F16, and F48 were detected for papA, and papGII and papGIII variants were detected for papG. Significant associations with the sequence types observed in the analysis of genomes contained in the NCBI Assembly Refseq database were also found in this collection in 16 of 19 cases for papA variants and 7 of 9 cases for the papG variants. This comprehensive characterization might support future basic studies about P fimbria-mediated ExPEC adherence and future typing or epidemiological studies to monitor the evolution of ExPECs producing P fimbria.
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Affiliation(s)
- Valentina Fernández-Yáñez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Santiago 9170022, Chile; (V.F.-Y.)
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Patricio Suazo
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Claudia Hormazábal
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Santiago 9170022, Chile; (V.F.-Y.)
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Valentina Ibaceta
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Mauricio Arenas-Salinas
- Centro de Bioinformática Simulación y Modelado, Facultad de Ingeniería, Universidad de Talca, Av. Lircay s/n, Talca 3460787, Chile
| | - Roberto M. Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Francisco Silva-Ojeda
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Av. Dr. Carlos Lorca Tobar 999, Santiago 8380453, Chile
| | - Carolina Arellano
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Ignacio Muñoz
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
| | - Felipe Del Canto
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile
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8
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Amoura A, Pistien C, Chaligné C, Dion S, Magnan M, Bridier-Nahmias A, Baron A, Chau F, Bourgogne E, Le M, Denamur E, Ingersoll MA, Fantin B, Lefort A, El Meouche I. Variability in cell division among anatomical sites shapes Escherichia coli antibiotic survival in a urinary tract infection mouse model. Cell Host Microbe 2024; 32:900-912.e4. [PMID: 38759643 DOI: 10.1016/j.chom.2024.04.015] [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: 08/14/2023] [Revised: 04/06/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
Urinary tract infection (UTI), mainly caused by Escherichia coli, are frequent and have a recurrent nature even after antibiotic treatment. Potential bacterial escape mechanisms include growth defects, but probing bacterial division in vivo and establishing its relation to the antibiotic response remain challenging. Using a synthetic reporter of cell division, we follow the temporal dynamics of cell division for different E. coli clinical strains in a UTI mouse model with and without antibiotics. We show that more bacteria are actively dividing in the kidneys and urine compared with the bladder. Bacteria that survive antibiotic treatment are consistently non-dividing in three sites of infection. Additionally, we demonstrate how both the strain in vitro persistence profile and the microenvironment impact infection and treatment dynamics. Understanding the relative contribution of the host environment, growth heterogeneity, non-dividing bacteria, and antibiotic persistence is crucial to improve therapies for recurrent infections.
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Affiliation(s)
- Ariane Amoura
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France
| | - Claire Pistien
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France
| | - Camille Chaligné
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France
| | - Sara Dion
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France
| | - Mélanie Magnan
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France
| | | | - Alexandra Baron
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France
| | - Françoise Chau
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France
| | - Emmanuel Bourgogne
- AP-HP, Hôpital Bichat, Laboratoire de Toxicologie Pharmacocinétique, 75018 Paris, France; Université Paris Cité, Faculté de Santé, Pharmacie, Laboratoire de Toxicologie, 75018 Paris, France
| | - Minh Le
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Toxicologie Pharmacocinétique, 75018 Paris, France
| | - Erick Denamur
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, 75018 Paris, France
| | - Molly A Ingersoll
- Université Paris Cité, CNRS, Inserm, Institut Cochin, 75014 Paris, France; Department of Immunology, Institut Pasteur, 75015 Paris, France
| | - Bruno Fantin
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France
| | - Agnès Lefort
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France; AP-HP, Hôpital Beaujon, Service de Médecine Interne, 92110 Clichy, France
| | - Imane El Meouche
- Université Paris Cité, Université Sorbonne Paris Nord, Inserm, IAME, 75018 Paris, France.
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9
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Suarez SA, Martiny AC. Intraspecific variation in antibiotic resistance potential within E. coli. Microbiol Spectr 2024; 12:e0316223. [PMID: 38661581 PMCID: PMC11237723 DOI: 10.1128/spectrum.03162-23] [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: 08/22/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024] Open
Abstract
Intraspecific genomic diversity brings the potential for an unreported and diverse reservoir of cryptic antibiotic resistance genes in pathogens, as cryptic resistance can occur without major mutations and horizontal transmission. Here, we predicted the differences in the types of antibiotics and genes that induce cryptic and latent resistance between micro-diverse Escherichia coli strains. For example, we hypothesize that known resistance genes will be the culprit of latent resistance within clinical strains. We used a modified functional metagenomics method to induce expression in eight E. coli strains. We found a total of 66 individual genes conferring phenotypic resistance to 11 out of 16 antibiotics. A total of 14 known antibiotic resistance genes comprised 21% of total identified genes, whereas the majority (52 genes) were unclassified cryptic resistance genes. Between the eight strains, 1.2% of core orthologous genes were positive (conferred resistance in at least one strain). Sixty-four percent of positive orthologous genes conferred resistance to only one strain, demonstrating high intraspecific variability of latent resistance genes. Cryptic resistance genes comprised most resistance genes among laboratory and clinical strains as well as natural, semisynthetic, and synthetic antibiotics. Known antibiotic resistance genes primarily conferred resistance to multiple antibiotics from varying origins and within multiple strains. Hence, it is uncommon for E. coli to develop cross-cryptic resistance to antibiotics from multiple origins or within multiple strains. We have uncovered prospective and previously unknown resistance genes as well as antibiotics that have the potential to trigger latent antibiotic resistance in E. coli strains from varying origins.IMPORTANCEIntraspecific genomic diversity may be a driving force in the emergence of adaptive antibiotic resistance. Adaptive antibiotic resistance enables sensitive bacterial cells to acquire temporary antibiotic resistance, creating an optimal window for the development of permanent mutational resistance. In this study, we investigate cryptic resistance, an adaptive resistance mechanism, and unveil novel (cryptic) antibiotic resistance genes that confer resistance when amplified within eight E. coli strains derived from clinical and laboratory origins. We identify the potential of cryptic resistance genes to confer cross-resistance to antibiotics from varying origins and within multiple strains. We discern antibiotic characteristics that promote latent resistance in multiple strains, considering intraspecific diversity. This study may help detect novel resistance genes and functional genes that could become responsible for cryptic resistance among diverse strains and antibiotics, thus also identifying potential novel antibiotic targets and mechanisms.
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Affiliation(s)
- Stacy A. Suarez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Adam C. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
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10
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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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11
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Dewar AE, Hao C, Belcher LJ, Ghoul M, West SA. Bacterial lifestyle shapes pangenomes. Proc Natl Acad Sci U S A 2024; 121:e2320170121. [PMID: 38743630 PMCID: PMC11126918 DOI: 10.1073/pnas.2320170121] [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: 11/16/2023] [Accepted: 04/06/2024] [Indexed: 05/16/2024] Open
Abstract
Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.
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Affiliation(s)
- Anna E. Dewar
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | | | - Melanie Ghoul
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Stuart A. West
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
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12
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Xing Y, Clark JR, Chang JD, Zulk JJ, Chirman DM, Piedra FA, Vaughan EE, Hernandez Santos HJ, Patras KA, Maresso AW. Progress toward a vaccine for extraintestinal pathogenic E. coli (ExPEC) II: efficacy of a toxin-autotransporter dual antigen approach. Infect Immun 2024; 92:e0044023. [PMID: 38591882 PMCID: PMC11075464 DOI: 10.1128/iai.00440-23] [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: 11/01/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of worldwide morbidity and mortality, the top cause of antimicrobial-resistant (AMR) infections, and the most frequent cause of life-threatening sepsis and urinary tract infections (UTI) in adults. The development of an effective and universal vaccine is complicated by this pathogen's pan-genome, its ability to mix and match virulence factors and AMR genes via horizontal gene transfer, an inability to decipher commensal from pathogens, and its intimate association and co-evolution with mammals. Using a pan virulome analysis of >20,000 sequenced E. coli strains, we identified the secreted cytolysin α-hemolysin (HlyA) as a high priority target for vaccine exploration studies. We demonstrate that a catalytically inactive pure form of HlyA, expressed in an autologous host using its own secretion system, is highly immunogenic in a murine host, protects against several forms of ExPEC infection (including lethal bacteremia), and significantly lowers bacterial burdens in multiple organ systems. Interestingly, the combination of a previously reported autotransporter (SinH) with HlyA was notably effective, inducing near complete protection against lethal challenge, including commonly used infection strains ST73 (CFT073) and ST95 (UTI89), as well as a mixture of 10 of the most highly virulent sequence types and strains from our clinical collection. Both HlyA and HlyA-SinH combinations also afforded some protection against UTI89 colonization in a murine UTI model. These findings suggest recombinant, inactive hemolysin and/or its combination with SinH warrant investigation in the development of an E. coli vaccine against invasive disease.
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Affiliation(s)
- Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, USA
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, USA
| | - James D. Chang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, USA
| | - Jacob J. Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, USA
| | - Dylan M. Chirman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, USA
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ellen E. Vaughan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Haroldo J. Hernandez Santos
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, USA
| | - Kathryn A. Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, USA
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13
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Forte J, Maurizi L, Fabiano MG, Conte AL, Conte MP, Ammendolia MG, D'Intino E, Catizone A, Gesualdi L, Rinaldi F, Carafa M, Marianecci C, Longhi C. Gentamicin loaded niosomes against intracellular uropathogenic Escherichia coli strains. Sci Rep 2024; 14:10196. [PMID: 38702355 PMCID: PMC11068731 DOI: 10.1038/s41598-024-59144-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: 09/26/2023] [Accepted: 04/08/2024] [Indexed: 05/06/2024] Open
Abstract
Urinary tract infections (UTIs) are the most common bacterial infections and uropathogenic Escherichia coli (UPEC) is the main etiological agent of UTIs. UPEC can persist in bladder cells protected by immunological defenses and antibiotics and intracellular behavior leads to difficulty in eradicating the infection. The aim of this paper is to design, prepare and characterize surfactant-based nanocarriers (niosomes) able to entrap antimicrobial drug and potentially to delivery and release antibiotics into UPEC-infected cells. In order to validate the proposed drug delivery system, gentamicin, was chosen as "active model drug" due to its poor cellular penetration. The niosomes physical-chemical characterization was performed combining different techniques: Dynamic Light Scattering Fluorescence Spectroscopy, Transmission Electron Microscopy. Empty and loaded niosomes were characterized in terms of size, ζ-potential, bilayer features and stability. Moreover, Gentamicin entrapped amount was evaluated, and the release study was also carried out. In addition, the effect of empty and loaded niosomes was studied on the invasion ability of UPEC strains in T24 bladder cell monolayers by Gentamicin Protection Assay and Confocal Microscopy. The observed decrease in UPEC invasion rate leads us to hypothesize a release of antibiotic from niosomes inside the cells. The optimization of the proposed drug delivery system could represent a promising strategy to significatively enhance the internalization of antimicrobial drugs.
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Affiliation(s)
- Jacopo Forte
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
| | - Linda Maurizi
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
| | - Maria Gioia Fabiano
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
| | - Antonietta Lucia Conte
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
| | - Maria Pia Conte
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
| | - Maria Grazia Ammendolia
- Centro Nazionale Tecnologie Innovative in Sanità Pubblica, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy.
| | - Eleonora D'Intino
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
| | - Angela Catizone
- Dipartimento Scienze Anatomiche, Istologiche, Medico Legali e Dell'Apparato Locomotore, Sapienza Università di Roma, Via Scarpa, 16, 00161, Rome, Italy
| | - Luisa Gesualdi
- Dipartimento Scienze Anatomiche, Istologiche, Medico Legali e Dell'Apparato Locomotore, Sapienza Università di Roma, Via Scarpa, 16, 00161, Rome, Italy
| | - Federica Rinaldi
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy.
| | - Maria Carafa
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
| | - Carlotta Marianecci
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
| | - Catia Longhi
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
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14
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Yazlık MO, Müştak İB, Özkan H, Vural SA, Kaya U, Özöner Ö, Mutluer İ, Altınbaş YF, Soylu MS, Vural MR. The presence of virulence factor genes downregulates uterine AQP3 and alters glutathione peroxidase activity and uterine histopathology in canine pyometra. Reprod Domest Anim 2024; 59:e14615. [PMID: 38798181 DOI: 10.1111/rda.14615] [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: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Present study was designed to evaluate the role of virulence factor genes (papG, cnf1 and hylA) in the pathogenesis of canine pyometra. Antimicrobial susceptibility test and detection of virulence genes were performed Escherichia coli (E. coli) detected in uterine swab samples. Animals were divided into two groups based on the presence (VF+, n:14) or absence (VF-, n:7) of the virulence factor genes papG, cnf1 and hylA. Blood and tissue glutathione peroxidase activity, uterine histopathologic analysis and AQP3, ESR1, PGR, OXTR gene expressions were determined in both groups. Statistical analyses were performed using Stata version 15.1. All E. coli isolates were susceptible to amikacin, whereas resistant to ampicillin, amoxicillin/clavulanic acid and lincomycin. None of the isolates were susceptible to cefotaxime. E. coli isolates had at least one virulence gene. The most prevalent gene was fimH (100%), followed by fyuA (95.8%), usp (83.3%), sfa (75%), cnf1 and hlyA (70.8%) genes. Blood GPx activity was greater in VF+ animals. On the other hand, uterine tissue GPx activity was lower in VF+ group compared to the control group. Expression levels of AQP3 were upregulated more than fivefold in VF-dogs compared to the control group. In addition, AQP3 expression levels were found approximately threefold higher in VF (-) than VF (+) group (p < .05). Varying degree of inflammation noted for all animals with pyometra, but the presence of bacteria noted only in VF+ animals. In conclusion, the presence of virulence factor genes does not play a role in the histopathological degree of inflammation, the presence of bacteria was found to vary. Serum GPx activity increased in VF+ animals. While the hormone receptor expressions were similar, AQP expression was upregulated in the absence of virulence factor genes.
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Affiliation(s)
- Murat Onur Yazlık
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - İnci Başak Müştak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - Hüseyin Özkan
- Department of Genetics, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Sevil Atalay Vural
- Department of Pathology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - Ufuk Kaya
- Department of Biostatistics, Faculty of Veterinary Medicine, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Özgür Özöner
- Department of Pathology, Faculty of Veterinary Medicine, Siirt University, Siirt, Turkey
| | - İpek Mutluer
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
- Ankara University Graduate School of Health Sciences, Ankara, Turkey
| | - Yunus Furkan Altınbaş
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
- Ankara University Graduate School of Health Sciences, Ankara, Turkey
| | - Miray Sevde Soylu
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
- Ankara University Graduate School of Health Sciences, Ankara, Turkey
| | - Mehmet Rıfat Vural
- Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
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15
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Sato Y, Takita A, Suzue K, Hashimoto Y, Hiramoto S, Murakami M, Tomita H, Hirakawa H. TusDCB, a sulfur transferase complex involved in tRNA modification, contributes to UPEC pathogenicity. Sci Rep 2024; 14:8978. [PMID: 38637685 PMCID: PMC11026471 DOI: 10.1038/s41598-024-59614-2] [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: 12/19/2023] [Accepted: 04/12/2024] [Indexed: 04/20/2024] Open
Abstract
tRNA modifications play a crucial role in ensuring accurate codon recognition and optimizing translation levels. While the significance of these modifications in eukaryotic cells for maintaining cellular homeostasis and physiological functions is well-established, their physiological roles in bacterial cells, particularly in pathogenesis, remain relatively unexplored. The TusDCB protein complex, conserved in γ-proteobacteria like Escherichia coli, is involved in sulfur modification of specific tRNAs. This study focused on the role of TusDCB in the virulence of uropathogenic E. coli (UPEC), a bacterium causing urinary tract infections. The findings indicate that TusDCB is essential for optimal production of UPEC's virulence factors, including type 1 fimbriae and flagellum, impacting the bacterium's ability to aggregate in bladder epithelial cells. Deletion of tusDCB resulted in decreased virulence against urinary tract infection mice. Moreover, mutant TusDCB lacking sulfur transfer activity and tusE- and mnmA mutants revealed the indispensability of TusDCB's sulfur transfer activity for UPEC pathogenicity. The study extends its relevance to highly pathogenic, multidrug-resistant strains, where tusDCB deletion reduced virulence-associated bacterial aggregation. These insights not only deepen our understanding of the interplay between tRNA sulfur modification and bacterial pathogenesis but also highlight TusDCB as a potential therapeutic target against UPEC strains resistant to conventional antimicrobial agents.
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Affiliation(s)
- Yumika Sato
- Department of Bacteriology, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Ayako Takita
- Department of Bacteriology, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kazutomo Suzue
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Yusuke Hashimoto
- Department of Bacteriology, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Suguru Hiramoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Masami Murakami
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
- Laboratory of Bacterial Drug Resistance, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi Maebashi, Gunma, 371-8511, Japan
| | - Hidetada Hirakawa
- Department of Bacteriology, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
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16
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Shea AE, Forsyth VS, Stocki JA, Mitchell TJ, Frick-Cheng AE, Smith SN, Hardy SL, Mobley HLT. Emerging roles for ABC transporters as virulence factors in uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 2024; 121:e2310693121. [PMID: 38607934 PMCID: PMC11032443 DOI: 10.1073/pnas.2310693121] [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: 06/28/2023] [Accepted: 03/07/2024] [Indexed: 04/14/2024] Open
Abstract
Urinary tract infections (UTI) account for a substantial financial burden globally. Over 75% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which have demonstrated an extraordinarily rapid growth rate in vivo. This rapid growth rate appears paradoxical given that urine and the human urinary tract are relatively nutrient-restricted. Thus, we lack a fundamental understanding of how uropathogens propel growth in the host to fuel pathogenesis. Here, we used large in silico, in vivo, and in vitro screens to better understand the role of UPEC transport mechanisms and their contributions to uropathogenesis. In silico analysis of annotated transport systems indicated that the ATP-binding cassette (ABC) family of transporters was most conserved among uropathogenic bacterial species, suggesting their importance. Consistent with in silico predictions, we determined that the ABC family contributed significantly to fitness and virulence in the urinary tract: these were overrepresented as fitness factors in vivo (37.2%), liquid media (52.3%), and organ agar (66.2%). We characterized 12 transport systems that were most frequently defective in screening experiments by generating in-frame deletions. These mutant constructs were tested in urovirulence phenotypic assays and produced differences in motility and growth rate. However, deletion of multiple transport systems was required to achieve substantial fitness defects in the cochallenge murine model. This is likely due to genetic compensation among transport systems, highlighting the centrality of ABC transporters in these organisms. Therefore, these nutrient uptake systems play a concerted, critical role in pathogenesis and are broadly applicable candidate targets for therapeutic intervention.
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Affiliation(s)
- Allyson E. Shea
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Valerie S. Forsyth
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Jolie A. Stocki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Taylor J. Mitchell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Arwen E. Frick-Cheng
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Sara N. Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Sicily L. Hardy
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL36688
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
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17
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Brannon JR, Reasoner SA, Bermudez TA, Comer SL, Wiebe MA, Dunigan TL, Beebout CJ, Ross T, Bamidele A, Hadjifrangiskou M. Mapping niche-specific two-component system requirements in uropathogenic Escherichia coli. Microbiol Spectr 2024; 12:e0223623. [PMID: 38385738 PMCID: PMC10986536 DOI: 10.1128/spectrum.02236-23] [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: 05/26/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Sensory systems allow pathogens to differentiate between different niches and respond to stimuli within them. A major mechanism through which bacteria sense and respond to stimuli in their surroundings is two-component systems (TCSs). TCSs allow for the detection of multiple stimuli to lead to a highly controlled and rapid change in gene expression. Here, we provide a comprehensive list of TCSs important for the pathogenesis of uropathogenic Escherichia coli (UPEC). UPEC accounts for >75% of urinary tract infections (UTIs) worldwide. UTIs are most prevalent among people assigned female at birth, with the vagina becoming colonized by UPEC in addition to the gut and the bladder. In the bladder, adherence to the urothelium triggers E. coli invasion of bladder cells and an intracellular pathogenic cascade. Intracellular E. coli are safely hidden from host neutrophils, competition from the microbiota, and antibiotics that kill extracellular E. coli. To survive in these intimately connected, yet physiologically diverse niches E. coli must rapidly coordinate metabolic and virulence systems in response to the distinct stimuli encountered in each environment. We hypothesized that specific TCSs allow UPEC to sense these diverse environments encountered during infection with built-in redundant safeguards. Here, we created a library of isogenic TCS deletion mutants that we leveraged to map distinct TCS contributions to infection. We identify-for the first time-a comprehensive panel of UPEC TCSs that are critical for infection of the genitourinary tract and report that the TCSs mediating colonization of the bladder, kidneys, or vagina are distinct.IMPORTANCEWhile two-component system (TCS) signaling has been investigated at depth in model strains of Escherichia coli, there have been no studies to elucidate-at a systems level-which TCSs are important during infection by pathogenic Escherichia coli. Here, we report the generation of a markerless TCS deletion library in a uropathogenic E. coli (UPEC) isolate that can be leveraged for dissecting the role of TCS signaling in different aspects of pathogenesis. We use this library to demonstrate, for the first time in UPEC, that niche-specific colonization is guided by distinct TCS groups.
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Affiliation(s)
- John R. Brannon
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seth A. Reasoner
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tomas A. Bermudez
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Sarah L. Comer
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michelle A. Wiebe
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Taryn L. Dunigan
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Connor J. Beebout
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tamia Ross
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Adebisi Bamidele
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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18
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Goh KJ, Stubenrauch CJ, Lithgow T. The TAM, a Translocation and Assembly Module for protein assembly and potential conduit for phospholipid transfer. EMBO Rep 2024; 25:1711-1720. [PMID: 38467907 PMCID: PMC11014939 DOI: 10.1038/s44319-024-00111-y] [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: 09/18/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The assembly of β-barrel proteins into the bacterial outer membrane is an essential process enabling the colonization of new environmental niches. The TAM was discovered as a module of the β-barrel protein assembly machinery; it is a heterodimeric complex composed of an outer membrane protein (TamA) bound to an inner membrane protein (TamB). The TAM spans the periplasm, providing a scaffold through the peptidoglycan layer and catalyzing the translocation and assembly of β-barrel proteins into the outer membrane. Recently, studies on another membrane protein (YhdP) have suggested that TamB might play a role in phospholipid transport to the outer membrane. Here we review and re-evaluate the literature covering the experimental studies on the TAM over the past decade, to reconcile what appear to be conflicting claims on the function of the TAM.
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Affiliation(s)
- Kwok Jian Goh
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christopher J Stubenrauch
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia.
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
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19
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Domingo-Sananes MR, Meehan CJ. The population genetics of prokaryotic pangenomes. Nat Ecol Evol 2024; 8:190-191. [PMID: 38177691 DOI: 10.1038/s41559-023-02276-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Affiliation(s)
| | - Conor J Meehan
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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20
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Flores-Oropeza MA, Ochoa SA, Cruz-Córdova A, Chavez-Tepecano R, Martínez-Peñafiel E, Rembao-Bojórquez D, Zavala-Vega S, Hernández-Castro R, Flores-Encarnacion M, Arellano-Galindo J, Vélez D, Xicohtencatl-Cortes J. Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection. Front Microbiol 2024; 14:1340427. [PMID: 38328583 PMCID: PMC10848155 DOI: 10.3389/fmicb.2023.1340427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Recurrent urinary tract infections (RUTIs) caused by uropathogenic Escherichia coli are costly public health problems impacting patients' quality of life. Aim In this work, a comparative genomics analysis of three clinical RUTI strains isolated from bladder biopsy specimens was performed. Materials and methods One hundred seventy-two whole genomes of urinary tract E. coli strains were selected from the NCBI database. The search for virulence factors, fitness genes, regions of interest, and genetic elements associated with resistance was manually carried out. The phenotypic characterization of antibiotic resistance, haemolysis, motility, and biofilm formation was performed. Moreover, adherence and invasion assays with human bladder HTB-5 cells, and transmission electron microscopy (TEM) were performed. Results The UTI-1_774U and UTI-3_455U/ST1193 strains were associated with the extraintestinal pathotypes, and the UTI-2_245U/ST295 strain was associated with the intestinal pathotype, according to a phylogenetic analysis of 172 E. coli urinary strains. The three RUTI strains were of clinical, epidemiological, and zoonotic relevance. Several resistance genes were found within the plasmids of these strains, and a multidrug resistance phenotype was revealed. Other virulence genes associated with CFT073 were not identified in the three RUTI strains (genes for type 1 and P fimbriae, haemolysin hlyA, and sat toxin). Quantitative adherence analysis showed that UTI-1_774U was significantly (p < 0.0001) more adherent to human bladder HTB-5 cells. Quantitative invasion analysis showed that UTI-2_245U was significantly more invasive than the control strains. No haemolysis or biofilm activity was detected in the three RUTI strains. The TEM micrographs showed the presence of short and thin fimbriae only in the UTI-2_245U strain. Conclusion The high variability and genetic diversity of the RUTI strains indicate that are a mosaic of virulence, resistance, and fitness genes that could promote recurrence in susceptible patients.
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Affiliation(s)
- Marco A. Flores-Oropeza
- Posgrado en Ciencias Biomédicas, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Sara A. Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Eva Martínez-Peñafiel
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Daniel Rembao-Bojórquez
- Departamento de Patología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
| | - Sergio Zavala-Vega
- Departamento de Patología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
- Laboratorio Clínico y Banco de Sangre, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
| | - Rigoberto Hernández-Castro
- Departmento de Ecología de Agentes Patógenos, Hospital General “Dr. Manuel Gea González”, Mexico City, Mexico
| | - Marcos Flores-Encarnacion
- Laboratorio de Microbiología Molecular y Celular, Biomedicina, Facultad de Medicina, BUAP, Puebla, Mexico
| | - José Arellano-Galindo
- Laboratorio de Virología Clínica y Experimental, Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Daniel Vélez
- Hospital Militar de Especialidades de la Mujer y Neonatología, Mexico City, Mexico
- Unidad Médica de Alta Especialidad, Hospital de Ginecología y Obstetricia No. 3 IMSS, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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21
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Beavan A, Domingo-Sananes MR, McInerney JO. Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome. Proc Natl Acad Sci U S A 2024; 121:e2304934120. [PMID: 38147560 PMCID: PMC10769857 DOI: 10.1073/pnas.2304934120] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/05/2023] [Indexed: 12/28/2023] Open
Abstract
Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem's set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene-gene relationships across the pangenome.
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Affiliation(s)
- Alan Beavan
- School of Life Sciences, The University of Nottingham, NottinghamNG7 2UH, United Kingdom
| | - Maria Rosa Domingo-Sananes
- School of Life Sciences, The University of Nottingham, NottinghamNG7 2UH, United Kingdom
- School of Science and Technology, Nottingham Trent University, NottinghamNG1 4FQ, United Kingdom
| | - James O. McInerney
- School of Life Sciences, The University of Nottingham, NottinghamNG7 2UH, United Kingdom
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22
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Carhuaricra-Huaman D, Setubal JC. Step-by-Step Bacterial Genome Comparison. Methods Mol Biol 2024; 2802:107-134. [PMID: 38819558 DOI: 10.1007/978-1-0716-3838-5_5] [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] [Indexed: 06/01/2024]
Abstract
Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their own genome datasets.
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Affiliation(s)
- Dennis Carhuaricra-Huaman
- Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, Sao Paulo, SP, Brazil
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima, Peru
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
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23
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Hullahalli K, Dailey KG, Hasegawa Y, Torres E, Suzuki M, Zhang H, Threadgill DW, Navarro VM, Waldor MK. Genetic and immune determinants of E. coli liver abscess formation. Proc Natl Acad Sci U S A 2023; 120:e2310053120. [PMID: 38096412 PMCID: PMC10743367 DOI: 10.1073/pnas.2310053120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Systemic infections can yield distinct outcomes in different tissues. In mice, intravenous inoculation of Escherichia coli leads to bacterial replication within liver abscesses, while other organs such as the spleen clear the pathogen. Abscesses are macroscopic necrotic regions that comprise the vast majority of the bacterial burden in the animal, yet little is known about the processes underlying their formation. Here, we characterize E. coli liver abscesses and identify host determinants of abscess susceptibility. Spatial transcriptomics revealed that liver abscesses are associated with heterogenous immune cell clusters comprised of macrophages, neutrophils, dendritic cells, innate lymphoid cells, and T-cells that surround necrotic regions of the liver. Abscess susceptibility is heightened in the C57BL lineage, particularly in C57BL/6N females. Backcross analyses demonstrated that abscess susceptibility is a polygenic trait inherited in a sex-dependent manner without direct linkage to sex chromosomes. As early as 1 d post infection, the magnitude of E. coli replication in the liver distinguishes abscess-susceptible and abscess-resistant strains of mice, suggesting that the immune pathways that regulate abscess formation are induced within hours. We characterized the early hepatic response with single-cell RNA sequencing and found that mice with reduced activation of early inflammatory responses, such as those lacking the LPS receptor TLR4 (Toll-like receptor 4), are resistant to abscess formation. Experiments with barcoded E. coli revealed that TLR4 mediates a tradeoff between abscess formation and bacterial clearance. Together, our findings define hallmarks of E. coli liver abscess formation and suggest that hyperactivation of the hepatic innate immune response drives liver abscess susceptibility.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Katherine G. Dailey
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Yuko Hasegawa
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Encarnacion Torres
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
| | - Masataka Suzuki
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - Hailong Zhang
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
| | - David W. Threadgill
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX76549
- Department of Nutrition, Texas A&M University, College Station, TX76549
| | - Victor M. Navarro
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02115
| | - Matthew K. Waldor
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- Division of Infectious Diseases, Brigham & Women’s Hospital, Boston, MA02115
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24
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Konstantinidis KT. Sequence-discrete species for prokaryotes and other microbes: A historical perspective and pending issues. MLIFE 2023; 2:341-349. [PMID: 38818268 PMCID: PMC10989153 DOI: 10.1002/mlf2.12088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/04/2023] [Accepted: 10/08/2023] [Indexed: 06/01/2024]
Abstract
Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter "intermediate" organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often-but not always-appears to be around 85%-95% genome-average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.
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Affiliation(s)
- Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA
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25
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Alberto S, Ordonez AA, Arjun C, Aulakh GK, Beziere N, Dadachova E, Ebenhan T, Granados U, Korde A, Jalilian A, Lestari W, Mukherjee A, Petrik M, Sakr T, Cuevas CLS, Welling MM, Zeevaart JR, Jain SK, Wilson DM. The Development and Validation of Radiopharmaceuticals Targeting Bacterial Infection. J Nucl Med 2023; 64:1676-1682. [PMID: 37770110 PMCID: PMC10626374 DOI: 10.2967/jnumed.123.265906] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/18/2023] [Indexed: 10/03/2023] Open
Abstract
The International Atomic Energy Agency organized a technical meeting at its headquarters in Vienna, Austria, in 2022 that included 17 experts representing 12 countries, whose research spanned the development and use of radiolabeled agents for imaging infection. The meeting focused largely on bacterial pathogens. The group discussed and evaluated the advantages and disadvantages of several radiopharmaceuticals, as well as the science driving various imaging approaches. The main objective was to understand why few infection-targeted radiotracers are used in clinical practice despite the urgent need to better characterize bacterial infections. This article summarizes the resulting consensus, at least among the included scientists and countries, on the current status of radiopharmaceutical development for infection imaging. Also included are opinions and recommendations regarding current research standards in this area. This and future International Atomic Energy Agency-sponsored collaborations will advance the goal of providing the medical community with innovative, practical tools for the specific image-based diagnosis of infection.
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Affiliation(s)
- Signore Alberto
- Nuclear Medicine Unit, Department of Medical-Surgical Sciences and Translational Medicine, Faculty of Medicine and Psychology, University of Rome "Sapienza," Rome, Italy
| | - Alvaro A Ordonez
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chanda Arjun
- Radiopharmaceutical Program, Board of Radiation and Isotope Technology, Mumbai, India
| | - Gurpreet Kaur Aulakh
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Nicolas Beziere
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Ekaterina Dadachova
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Thomas Ebenhan
- Nuclear Medicine, University of Pretoria, and Radiochemistry, Applied Radiation, South African Nuclear Energy Corporation, Pelindaba, South Africa
| | - Ulises Granados
- Department of Nuclear Medicine, Hospital Internacional de Colombia-Fundación Cardiovascular de Colombia, Piedecuesta, Colombia
| | - Aruna Korde
- Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Amirreza Jalilian
- Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - Wening Lestari
- National Nuclear Energy Agency, South Tangerang, Indonesia
| | - Archana Mukherjee
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Milos Petrik
- Institute of Molecular and Translational Medicine and Czech Advanced Technology and Research Institute, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Tamer Sakr
- Radioactive Isotopes and Generator Department, Hot Labs Center, Egyptian Atomic Energy Authority, Cairo, Egypt
| | | | - Mick M Welling
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands; and
| | - Jan Rijn Zeevaart
- Nuclear Medicine, University of Pretoria, and Radiochemistry, Applied Radiation, South African Nuclear Energy Corporation, Pelindaba, South Africa
| | - Sanjay K Jain
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David M Wilson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
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26
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Brown AN, Anderson MT, Smith SN, Bachman MA, Mobley HLT. Conserved metabolic regulator ArcA responds to oxygen availability, iron limitation, and cell envelope perturbations during bacteremia. mBio 2023; 14:e0144823. [PMID: 37681955 PMCID: PMC10653796 DOI: 10.1128/mbio.01448-23] [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: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023] Open
Abstract
IMPORTANCE Infections of the bloodstream are life-threatening and can result in sepsis. Gram-negative bacteria cause a significant portion of bloodstream infections, which is also referred to as bacteremia. The long-term goal of our work is to understand how such bacteria establish and maintain infection during bacteremia. We have previously identified the transcription factor ArcA, which promotes fermentation in bacteria, as a likely contributor to the growth and survival of bacteria in this environment. Here, we study ArcA in the Gram-negative species Citrobacter freundii, Klebsiella pneumoniae, and Serratia marcescens. Our findings aid in determining how these bacteria sense their environment, utilize nutrients, and generate energy while countering the host immune system. This information is critical for developing better models of infection to inform future therapeutic development.
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Affiliation(s)
- Aric N. Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mark T. Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sara N. Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Michael A. Bachman
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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27
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Ustick LJ, Larkin AA, Martiny AC. Global scale phylogeography of functional traits and microdiversity in Prochlorococcus. THE ISME JOURNAL 2023; 17:1671-1679. [PMID: 37454234 PMCID: PMC10504305 DOI: 10.1038/s41396-023-01469-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.
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Affiliation(s)
- Lucas J Ustick
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alyse A Larkin
- Department of Earth System Science, University of California Irvine, Irvine, CA, 92697, USA
- Global Ocean Monitoring and Observing, National Oceanic and Atmospheric Administration, Washington, DC, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
- Department of Earth System Science, University of California Irvine, Irvine, CA, 92697, USA.
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Frick-Cheng AE, Shea AE, Roberts JR, Smith SN, Ohi MD, Mobley HLT. Altered motility in response to iron-limitation is regulated by lpdA in uropathogenic E. coli CFT073. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559868. [PMID: 37808639 PMCID: PMC10557643 DOI: 10.1101/2023.09.27.559868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
More than half of all women will experience a urinary tract infection (UTI) in their lifetime with most cases caused by uropathogenic Escherichia coli (UPEC). Bacterial motility enhances UPEC pathogenicity, resulting in more severe disease outcomes including kidney infection. Surprisingly, the connection between motility and iron limitation is mostly unexplored, despite the lack of free iron available in the host. Therefore, we sought to explore the potential connection between iron restriction and regulation of motility in UPEC. We cultured E. coli CFT073, a prototypical UPEC strain, in media containing an iron chelator. Under iron limitation, CFT073 had elevated fliC (flagella) promoter activity, driving motility on the leading edge of the colony. Furthermore, this iron-specific response was repressed by the addition of exogenous iron. We confirmed increased flagella expression in CFT073 by measuring fliC transcript, FliC protein, and surface-expressed flagella under iron-limited conditions. To define the regulatory mechanism, we constructed single knockouts of eight master regulators. The iron-regulated response was lost in crp, arcA, and fis mutants. Thus, we focused on the five genes regulated by all three transcription factors. Of the five genes knocked out, the iron-regulated motility response was most strongly dysregulated in an lpdA mutant, which also resulted in significantly lowered fitness in the murine model of ascending UTI. Collectively, we demonstrated that iron-mediated motility in CFT073 is regulated by lpdA , which contributes to the understanding of how uropathogens differentially regulate motility mechanisms in the iron-restricted host. Importance Urinary tract infections (UTIs) are ubiquitous and responsible for over five billion dollars in associated health care costs annually. Both iron acquisition and motility are highly studied virulence factors associated with uropathogenic E. coli (UPEC), the main causative agent of uncomplicated UTI. This work is innovative by providing mechanistic insight into the synergistic relationship between these two critical virulence properties. Here, we demonstrate that iron limitation has pleiotropic effects with consequences that extend beyond metabolism, and impact other virulence mechanisms. Indeed, targeting iron acquisition as a therapy may lead to an undesirable enhancement of UPEC pathogenesis through increased motility. It is vital to understand the full breadth of UPEC pathogenesis to adequately respond to this common infection, especially with the increase of antibiotic resistant pathogens.
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Hirakawa H, Shimokawa M, Noguchi K, Tago M, Matsuda H, Takita A, Suzue K, Tajima H, Kawagishi I, Tomita H. The PapB/FocB family protein TosR acts as a positive regulator of flagellar expression and is required for optimal virulence of uropathogenic Escherichia coli. Front Microbiol 2023; 14:1185804. [PMID: 37533835 PMCID: PMC10392849 DOI: 10.3389/fmicb.2023.1185804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/30/2023] [Indexed: 08/04/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is a major causative agent of urinary tract infections. The bacteria internalize into the uroepithelial cells, where aggregate and form microcolonies. UPEC fimbriae and flagella are important for the formation of microcolonies in uroepithelial cells. PapB/FocB family proteins are small DNA-binding transcriptional regulators consisting of approximately 100 amino acids that have been reported to regulate the expression of various fimbriae, including P, F1C, and type 1 fimbriae, and adhesins. In this study, we show that TosR, a member of the PapB/FocB family is the activator of flagellar expression. The tosR mutant had similar expression levels of type 1, P and F1C fimbriae as the parent strain, but flagellar production was markedly lower than in the parent strain. Flagellin is a major component of flagella. The gene encoding flagellin, fliC, is transcriptionally activated by the sigma factor FliA. The fliA expression is induced by the flagellar master regulator FlhDC. The flhD and flhC genes form an operon. The promoter activity of fliC, fliA and flhD in the tosR mutant was significantly lower than in the parent strain. The purified recombinant TosR does not bind to fliC and fliA but to the upstream region of the flhD gene. TosR is known to bind to an AT-rich DNA sequence consisting of 29 nucleotides. The characteristic AT-rich sequence exists 550-578 bases upstream of the flhD gene. The DNA fragment lacking this sequence did not bind TosR. Furthermore, loss of the tosR gene reduced motility and the aggregation ability of UPEC in urothelial cells. These results indicate that TosR is a transcriptional activator that increases expression of the flhDC operon genes, contributing to flagellar expression and optimal virulence.
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Affiliation(s)
- Hidetada Hirakawa
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Mizuki Shimokawa
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Koshi Noguchi
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Minori Tago
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Hiroshi Matsuda
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Ayako Takita
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Kazutomo Suzue
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
| | - Hirotaka Tajima
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
| | - Ikuro Kawagishi
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
- Laboratory of Bacterial Drug Resistance, Graduate School of Medicine, Gunma University, Maebashi, Gunma, Japan
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Deipenbrock M, Scotti F, Mo B, Heinrich M, Hensel A. Seven-day Oral Intake of Orthosiphon stamineus Leaves Infusion Exerts Antiadhesive Ex Vivo Activity Against Uropathogenic E. coli in Urine Samples. PLANTA MEDICA 2023; 89:778-789. [PMID: 34521130 DOI: 10.1055/a-1585-6322] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Orthosiphon stamineus leaves (Java tea) extract is traditionally used for the treatment of urinary tract infections. According to recent in vitro data, animal infection studies, and transcriptomic investigations, polymethoxylated flavones from Java tea exert antiadhesive activity against uropathogenic Escherichia coli (UPEC). This antiadhesive activity has been shown to reduce bladder and kidney lesion in a mice infection model. As no data on the antivirulent activity of Java tea intake on humans are available, a biomedical study was performed on 20 healthy volunteers who self-administered Orthosiphon infusion (4 × 3 g per day, orally) for 7 days. The herbal material used for the study conformed to the specification of the European Pharmacopoeia, and ultra high-performance liquid chromatography (UHPLC) of the infusion showed rosmarinic acid, caffeic acid, and cichoric acid to be the main compounds aside from polymethoxylated flavones. Rosmarinic acid was quantified in the tea preparations with 243 ± 22 µg/mL, indicating sufficient reproducibility of the preparation of the infusion. Urine samples were obtained during the biomedical study on day 1 (control urine, prior to Java tea intake), 3, 6 and 8. Antiadhesive activity of the urine samples was quantified by flowcytometric assay using pre-treated UPEC NU14 and human T24 bladder cells. Pooled urine samples indicated significant inhibition of bacterial adhesion on day 3, 6 and 8. The urine samples had no influence on the invasion of UPEC into host cells. Bacterial proliferation was slightly reduced after 24 h incubation with the urine samples. Gene expression analysis (qPCR) revealed strong induction of fitness and motility gene fliC and downregulation of hemin uptake system chuT. These data correlate with previously reported datasets from in vitro transcriptomic analysis. Increased bacterial motility was monitored using a motility assay in soft agar with UPEC UTI89. The intake of Java tea had no effect on the concentration of Tamm-Horsfall Protein in the urine samples. The present study explains the antiadhesive and anti-infective effect of the plant extract by triggering UPEC from a sessile lifestyle into a motile bacterial form, with reduced adhesive capacity.
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Affiliation(s)
- Melanie Deipenbrock
- University of Münster, Institute of Pharmaceutical Biology and Phytochemistry, Münster, Germany
| | - Francesca Scotti
- Pharmacognosy and Phytotherapy, UCL School of Pharmacy, London, United Kingdom
| | - Boris Mo
- University of Münster, Institute of Pharmaceutical Biology and Phytochemistry, Münster, Germany
| | - Michael Heinrich
- Pharmacognosy and Phytotherapy, UCL School of Pharmacy, London, United Kingdom
| | - Andreas Hensel
- University of Münster, Institute of Pharmaceutical Biology and Phytochemistry, Münster, Germany
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31
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Hullahalli K, Dailey KG, Hasegawa Y, Suzuki M, Zhang H, Threadgill DW, Waldor MK. Genetic and immune determinants of E. coli liver abscess formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.543319. [PMID: 37398354 PMCID: PMC10312621 DOI: 10.1101/2023.06.11.543319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Systemic infections can yield distinct outcomes in different tissues. In mice, intravenous inoculation of E. coli leads to bacterial replication within liver abscesses while other organs such as the spleen largely clear the pathogen. Abscesses are macroscopic necrotic regions that comprise the vast majority of the bacterial burden in the animal, yet little is known about the processes underlying their formation. Here, we characterize E. coli liver abscesses and identify host determinants of abscess susceptibility. Spatial transcriptomics revealed that liver abscesses are associated with heterogenous immune cell clusters comprised of macrophages, neutrophils, dendritic cells, innate lymphoid cells, and T-cells that surround necrotic regions of the liver. Susceptibility to liver abscesses is heightened in the C57BL/6 lineage, particularly in C57BL/6N females. Backcross analyses demonstrated that abscess susceptibility is a polygenic trait inherited in a sex-dependent manner without direct linkage to sex chromosomes. As early as one day post infection, the magnitude of E. coli replication in the liver distinguishes abscess-susceptible and abscess-resistant strains of mice, suggesting that the immune pathways that regulate abscess formation are induced within hours. We characterized the early hepatic response with single-cell RNA sequencing and found that mice with reduced activation of early inflammatory responses, such as those lacking the LPS receptor TLR4, are resistant to abscess formation. Experiments with barcoded E. coli revealed that TLR4 mediates a tradeoff between abscess formation and bacterial clearance. Together, our findings define hallmarks of E. coli liver abscess formation and suggest that hyperactivation of the hepatic innate immune response drives liver abscess susceptibility.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
| | - Katherine G Dailey
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
| | - Yuko Hasegawa
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
| | - Masataka Suzuki
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
| | - Hailong Zhang
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
| | - David W Threadgill
- Department of Cell Biology and Genetics and Department of Nutrition, Texas A&M University, College Station, TX 76549, USA
| | - Matthew K Waldor
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
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Hullahalli K, Dailey KG, Waldor MK. Innate immune responses yield tissue-specific bottlenecks that scale with pathogen dose. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.543079. [PMID: 37333208 PMCID: PMC10274871 DOI: 10.1101/2023.06.09.543079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
To cause infection, pathogens must overcome bottlenecks imposed by the host immune system. These bottlenecks restrict the inoculum and largely determine whether pathogen exposure results in disease. Infection bottlenecks therefore quantify the effectiveness of immune barriers. Here, using a model of Escherichia coli systemic infection, we identify bottlenecks that tighten or widen with higher inoculum sizes, revealing that the efficacy of innate immune responses can increase or decrease with pathogen dose. We term this concept "dose scaling". During E. coli systemic infection, dose scaling is tissue specific, dependent on the LPS receptor TLR4, and can be recapitulated by mimicking high doses with killed bacteria. Scaling is therefore due to sensing of pathogen molecules rather than interactions between the host and live bacteria. We propose that dose scaling quantitatively links innate immunity with infection bottlenecks and is a valuable framework for understanding how the inoculum size governs the outcome of pathogen exposure.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
| | - Katherine G Dailey
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
| | - Matthew K Waldor
- Department of Microbiology, Harvard Medical School, Boston, MA 02115; Division of Infectious Diseases, Brigham & Women's Hospital, Boston, MA 02115
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Brannon JR, Reasoner SA, Bermudez TA, Dunigan TL, Wiebe MA, Beebout CJ, Ross T, Bamidele A, Hadjifrangiskou M. Mapping Niche-specific Two-Component System Requirements in Uropathogenic Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541942. [PMID: 37292752 PMCID: PMC10245908 DOI: 10.1101/2023.05.23.541942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sensory systems allow pathogens to differentiate between different niches and respond to stimuli within them. A major mechanism through which bacteria sense and respond to stimuli in their surroundings is two-component systems (TCSs). TCSs allow for the detection of multiple stimuli to lead to a highly controlled and rapid change in gene expression. Here, we provide a comprehensive list of TCSs important for the pathogenesis of uropathogenic Escherichia coli (UPEC). UPEC accounts for >75% of urinary tract infections (UTIs) worldwide. UTIs are most prevalent among people assigned female at birth, with the vagina becoming colonized by UPEC in addition to the gut and the bladder. In the bladder, adherence to the urothelium triggers E. coli invasion of bladder cells and an intracellular pathogenic cascade. Intracellular E. coli are safely hidden from host neutrophils, competition from the microbiota, and antibiotics that kill extracellular E. coli. To survive in these intimately connected, yet physiologically diverse niches E. coli must rapidly coordinate metabolic and virulence systems in response to the distinct stimuli encountered in each environment. We hypothesized that specific TCSs allow UPEC to sense these diverse environments encountered during infection with built-in redundant safeguards. Here, we created a library of isogenic TCS deletion mutants that we leveraged to map distinct TCS contributions to infection. We identify - for the first time - a comprehensive panel of UPEC TCSs that are critical for infection of the genitourinary tract and report that the TCSs mediating colonization of the bladder, kidneys, or vagina are distinct.
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Affiliation(s)
- John R. Brannon
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth A. Reasoner
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tomas A. Bermudez
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Taryn L. Dunigan
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michelle A. Wiebe
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Connor J. Beebout
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tamia Ross
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adebisi Bamidele
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology & Immunology, Division of Molecular Pathogenesis, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
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Dickson K, Scott C, White H, Zhou J, Kelly M, Lehmann C. Antibacterial and Analgesic Properties of Beta-Caryophyllene in a Murine Urinary Tract Infection Model. Molecules 2023; 28:molecules28104144. [PMID: 37241885 DOI: 10.3390/molecules28104144] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Beta-caryophyllene has demonstrated anti-inflammatory effects in a variety of conditions, including interstitial cystitis. These effects are mediated primarily via the activation of the cannabinoid type 2 receptor. Additional antibacterial properties have recently been suggested, leading to our investigation of the effects of beta-caryophyllene in a murine model of urinary tract infection (UTI). Female BALB/c mice were intravesically inoculated with uropathogenic Escherichia coli CFT073. The mice received either beta-caryophyllene, antibiotic treatment using fosfomycin, or combination therapy. After 6, 24, or 72 h, the mice were evaluated for bacterial burden in the bladder and changes in pain and behavioral responses using von Frey esthesiometry. In the 24 h model, the anti-inflammatory effects of beta-caryophyllene were also assessed using intravital microscopy. The mice established a robust UTI by 24 h. Altered behavioral responses persisted 72 h post infection. Treatment with beta-caryophyllene resulted in a significant reduction in the bacterial burden in urine and bladder tissues 24 h post UTI induction and significant improvements in behavioral responses and intravital microscopy parameters, representing reduced inflammation in the bladder. This study demonstrates the utility of beta-caryophyllene as a new adjunct therapy for the management of UTI.
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Affiliation(s)
- Kayle Dickson
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Cassidy Scott
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Hannah White
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Juan Zhou
- Department of Anesthesiology, Pain Management and Perioperative Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Melanie Kelly
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Christian Lehmann
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Anesthesiology, Pain Management and Perioperative Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Tang Y, Wu Z, Zhang Y, Wang C, Ma X, Zhang K, Pan R, Cao Y, Zhou X. Cultivation-dependent and cultivation-independent investigation of O-methylated pollutant-producing bacteria in three drinking water treatment plants. WATER RESEARCH 2023; 231:119618. [PMID: 36706470 DOI: 10.1016/j.watres.2023.119618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
O-methylated pollutants (OMPs) are emerging contaminants in drinking water and mainly produced through bacterial O-methylation. However, the information of OMP-producing bacteria (OMPPB) in drinking water treatment plant (DWTP) is largely unknown so far. In this study, the OMPPB in water samples from three DWTPs (XL, JX and NX) were investigated by using cultivation-dependent and cultivation-independent technologies. Four OMPs were detected and their odor and toxicity risks were assessed. Formation potentials (FPs) of 2,4,6-trichloanisole, 2,3,6-trichloanisole, 2,4,6-tribromoanisole, pentachloroanisole and diclofenac methyl ester were determined in water samples and their values shifted significantly among DWTPs. A most probable number (MPN) method was established to quantify OMPPB numbers and the relationships between total haloanisole FPs (HAFPs) (y) and OMPPB numbers (x) in three DWTPs could be described by the following functions: y = 0.496×0.373 (XL), y = 0.041×0.465 (JX) and y = 0.218×0.237 (NX). Several genera like Bacillus, Ralstonia, Brevundimonas, etc. were newly found OMPPB among the cultivable bacteria, and their OMP products were evaluated in terms of quantity and environment risks (odor, toxicity and bioaccumulation). High-throughput sequencing revealed treatment process was the main driving factor to shape the OMPPB community structures and Mantel test showed HAFP profile was significantly influenced by Mycobacterium and Pelomonas. PICURSt2 analysis discovered four phenolic O-methyltransferases (OMTs) and four carboxylic OMTs which might be responsible for OMP formation. Several strategies were recommended to assess risk and control contamination brought by OMPPB in DWTPs.
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Affiliation(s)
- Yiran Tang
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Zhixuan Wu
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Yanfen Zhang
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Chuanxuan Wang
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Xuelian Ma
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Kejia Zhang
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Renjie Pan
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yucheng Cao
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China
| | - Xinyan Zhou
- College of Environment and Resources, College of Carbon Neutral, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang 311300, China.
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Pokharel P, Dhakal S, Dozois CM. The Diversity of Escherichia coli Pathotypes and Vaccination Strategies against This Versatile Bacterial Pathogen. Microorganisms 2023; 11:344. [PMID: 36838308 PMCID: PMC9965155 DOI: 10.3390/microorganisms11020344] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Escherichia coli (E. coli) is a gram-negative bacillus and resident of the normal intestinal microbiota. However, some E. coli strains can cause diseases in humans, other mammals and birds ranging from intestinal infections, for example, diarrhea and dysentery, to extraintestinal infections, such as urinary tract infections, respiratory tract infections, meningitis, and sepsis. In terms of morbidity and mortality, pathogenic E. coli has a great impact on public health, with an economic cost of several billion dollars annually worldwide. Antibiotics are not usually used as first-line treatment for diarrheal illness caused by E. coli and in the case of bloody diarrhea, antibiotics are avoided due to the increased risk of hemolytic uremic syndrome. On the other hand, extraintestinal infections are treated with various antibiotics depending on the site of infection and susceptibility testing. Several alarming papers concerning the rising antibiotic resistance rates in E. coli strains have been published. The silent pandemic of multidrug-resistant bacteria including pathogenic E. coli that have become more difficult to treat favored prophylactic approaches such as E. coli vaccines. This review provides an overview of the pathogenesis of different pathotypes of E. coli, the virulence factors involved and updates on the major aspects of vaccine development against different E. coli pathotypes.
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Affiliation(s)
- Pravil Pokharel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Sabin Dhakal
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Charles M. Dozois
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
- Pasteur Network, Laval, QC H7V 1B7, Canada
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Ustick LJ, Larkin AA, Martiny AC. Global scale phylogeography of functional traits and microdiversity in Prochlorococcus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525399. [PMID: 36747826 PMCID: PMC9900765 DOI: 10.1101/2023.01.24.525399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenomically assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenomically assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype’s phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus .
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Pmorf0222, a Virulence Factor in Pasteurella multocida, Activates Nuclear Factor Kappa B and Mitogen-Activated Protein Kinase via Toll-Like Receptor 1/2. Infect Immun 2023; 91:e0019322. [PMID: 36541752 PMCID: PMC9872710 DOI: 10.1128/iai.00193-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pasteurella multocida primarily causes hemorrhagic septicemia and pneumonia in poultry and livestock. Identification of the relevant virulence factors is therefore essential for understanding its pathogenicity. Pmorf0222, encoding the PM0222 protein, is located on a specific prophage island of the pathogenic strain C48-1 of P. multocida. Its role in the pathogenesis of P. multocida infection is still unknown. The proinflammatory cytokine plays an important role in P. multocida infection; therefore, murine peritoneal exudate macrophages were treated with the purified recombinant PM0222, which induced the secretion of tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β) via the Toll-like receptor 1/2 (TLR1/2)-nuclear factor kappa B (NF-κB)/mitogen-activated protein kinase (MAPK) signaling and inflammasome activation. Additionally, the mutant strain and complemented strain were evaluated in the mouse model with P. multocida infection, and PM0222 was identified as a virulence factor, which was secreted by outer membrane vesicles of P. multocida. Further results revealed that Pmorf0222 affected the synthesis of the capsule, adhesion, serum sensitivity, and biofilm formation. Thus, we identified Pmorf0222 as a novel virulence factor in the C48-1 strain of P. multocida, explaining the high pathogenicity of this pathogenic strain.
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Guillaume D, Racha B, Sandrine B, Etienne R, Laurent G, Virginie B, Pierre SS, Amine G, Vincent G, Nicolas B, Julien D, Richard B. Genes mcr improve the intestinal fitness of pathogenic E. coli and balance their lifestyle to commensalism. MICROBIOME 2023; 11:12. [PMID: 36670449 PMCID: PMC9863213 DOI: 10.1186/s40168-022-01457-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 12/22/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND The plasmid-mediated resistance gene mcr-1 confers colistin resistance in Escherichia coli and paves the way for the evolution to pan-drug resistance. We investigated the impact of mcr-1 in gut colonization in the absence of antibiotics using isogenic E. coli strains transformed with a plasmid encoding or devoid of mcr-1. RESULTS In gnotobiotic and conventional mice, mcr-1 significantly enhanced intestinal anchoring of E. coli but impaired their lethal effect. This improvement of intestinal fitness was associated with a downregulation of intestinal inflammatory markers and the preservation of intestinal microbiota composition. The mcr-1 gene mediated a cross-resistance to antimicrobial peptides secreted by the microbiota and intestinal epithelial cells (IECs), enhanced E. coli adhesion to IECs, and decreased the proinflammatory activity of both E. coli and its lipopolysaccharides. CONCLUSION Overall, mcr-1 changed multiple facets of bacterial behaviour and appeared as a factor enhancing commensal lifestyle and persistence in the gut even in the absence of antibiotics. Video Abstract.
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Affiliation(s)
- Dalmasso Guillaume
- Université Clermont Auvergne, Inserm U1071, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, 28 place Henri Dunant, 63001 Clermont-Ferrand, France
| | - Beyrouthy Racha
- Université Clermont Auvergne, Inserm U1071, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, 28 place Henri Dunant, 63001 Clermont-Ferrand, France
- Centre de référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire, 58 place Montalembert, 63000 Clermont-Ferrand, France
| | - Brugiroux Sandrine
- Université Clermont Auvergne, Inserm U1071, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, 28 place Henri Dunant, 63001 Clermont-Ferrand, France
| | - Ruppé Etienne
- Université de Paris, IAME, INSERM, F-75018 Paris, France
- AP-HP, Hôpital Bichat, DEBRC, F-75018 Paris, France
| | - Guillouard Laurent
- Centre de référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire, 58 place Montalembert, 63000 Clermont-Ferrand, France
| | - Bonnin Virginie
- Université Clermont Auvergne, Inserm U1071, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, 28 place Henri Dunant, 63001 Clermont-Ferrand, France
| | - Saint-Sardos Pierre
- Université Clermont Auvergne, Inserm U1071, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, 28 place Henri Dunant, 63001 Clermont-Ferrand, France
| | - Ghozlane Amine
- Hub de Bioinformatique et Biostatistique—Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Gaumet Vincent
- IMOST, UMR 1240 Inserm, Université Clermont Auvergne, 58 Rue Montalembert, 63005 Clermont-Ferrand, France
| | - Barnich Nicolas
- Université Clermont Auvergne, Inserm U1071, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, 28 place Henri Dunant, 63001 Clermont-Ferrand, France
| | - Delmas Julien
- Université Clermont Auvergne, Inserm U1071, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, 28 place Henri Dunant, 63001 Clermont-Ferrand, France
| | - Bonnet Richard
- Université Clermont Auvergne, Inserm U1071, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, 28 place Henri Dunant, 63001 Clermont-Ferrand, France
- Centre de référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire, 58 place Montalembert, 63000 Clermont-Ferrand, France
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Goldman AD, Kaçar B. Very early evolution from the perspective of microbial ecology. Environ Microbiol 2023; 25:5-10. [PMID: 35944516 DOI: 10.1111/1462-2920.16144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/21/2023]
Abstract
The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.
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Affiliation(s)
- Aaron D Goldman
- Department of Biology, Oberlin College and Conservatory, Oberlin, Ohio, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Tan A, Alsenani Q, Lanz M, Birchall C, Drage LKL, Picton D, Mowbray C, Ali A, Harding C, Pickard RS, Hall J, Aldridge PD. Evasion of toll-like receptor recognition by Escherichia coli is mediated via population level regulation of flagellin production. Front Microbiol 2023; 14:1093922. [PMID: 37032848 PMCID: PMC10078357 DOI: 10.3389/fmicb.2023.1093922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Uropathogenic Escherichia coli is a major cause of urinary tract infections. Analysis of the innate immune response in immortalized urothelial cells suggests that the bacterial flagellar subunit, flagellin, is key in inducing host defenses. A panel of 48 clinical uro-associated E. coli isolates recovered from either cystitis, pyelonephritis asymptomatic bacteriuria (ABU) or UTI-associated bacteraemia infections were characterized for motility and their ability to induce an innate response in urothelial cells stably transfected with a NF-κB luciferase reporter. Thirty-two isolates (67%) were identified as motile with strains recovered from cystitis patients exhibiting an uneven motility distribution pattern; seven of the cystitis isolates were associated with a > 5-fold increase in NF-κB signaling. To explore whether the NF-κB signaling response reflected antigenic variation, flagellin was purified from 14 different isolates. Purified flagellin filaments generated comparable NF-κB signaling responses, irrespective of either the source of the isolate or H-serotype. These data argued against any variability between isolates being related to flagellin itself. Investigations also argued that neither TLR4 dependent recognition of bacterial lipopolysaccharide nor growth fitness of the isolates played key roles in leading to the variable host response. To determine the roles, if any, of flagellar abundance in inducing these variable responses, flagellar hook numbers of a range of cystitis and ABU isolates were quantified. Images suggested that up to 60% of the isolate population exhibited flagella with the numbers averaging between 1 and 2 flagella per bacterial cell. These data suggest that selective pressures exist in the urinary tract that allow uro-associated E. coli strains to maintain motility, but exploit population heterogeneity, which together function to prevent host TLR5 recognition and bacterial killing.
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Affiliation(s)
- Aaron Tan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Qusai Alsenani
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marcello Lanz
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher Birchall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lauren K. L. Drage
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Picton
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine Mowbray
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ased Ali
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher Harding
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Urology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Robert S. Pickard
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Urology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Judith Hall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- *Correspondence: Judith Hall,
| | - Phillip D. Aldridge
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Phillip D. Aldridge,
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Conway C, Beckett MC, Dorman CJ. The DNA relaxation-dependent OFF-to-ON biasing of the type 1 fimbrial genetic switch requires the Fis nucleoid-associated protein. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001283. [PMID: 36748578 PMCID: PMC9993118 DOI: 10.1099/mic.0.001283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The structural genes expressing type 1 fimbriae in Escherichia coli alternate between expressed (phase ON) and non-expressed (phase OFF) states due to inversion of the 314 bp fimS genetic switch. The FimB tyrosine integrase inverts fimS by site-specific recombination, alternately connecting and disconnecting the fim operon, encoding the fimbrial subunit protein and its associated secretion and adhesin factors, to and from its transcriptional promoter within fimS. Site-specific recombination by the FimB recombinase becomes biased towards phase ON as DNA supercoiling is relaxed, a condition that occurs when bacteria approach the stationary phase of the growth cycle. This effect can be mimicked in exponential phase cultures by inhibiting the negative DNA supercoiling activity of DNA gyrase. We report that this bias towards phase ON depends on the presence of the Fis nucleoid-associated protein. We mapped the Fis binding to a site within the invertible fimS switch by DNase I footprinting. Disruption of this binding site by base substitution mutagenesis abolishes both Fis binding and the ability of the mutated switch to sustain its phase ON bias when DNA is relaxed, even in bacteria that produce the Fis protein. In addition, the Fis binding site overlaps one of the sites used by the Lrp protein, a known directionality determinant of fimS inversion that also contributes to phase ON bias. The Fis–Lrp relationship at fimS is reminiscent of that between Fis and Xis when promoting DNA relaxation-dependent excision of bacteriophage λ from the E. coli chromosome. However, unlike the co-binding mechanism used by Fis and Xis at λ attR, the Fis–Lrp relationship at fimS involves competitive binding. We discuss these findings in the context of the link between fimS inversion biasing and the physiological state of the bacterium.
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Affiliation(s)
- Colin Conway
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland.,Present address: Technical University of the Atlantic, Galway, Ireland
| | - Michael C Beckett
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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van ‘t Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA. High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinformatics 2022; 23:566. [PMID: 36585633 PMCID: PMC9801561 DOI: 10.1186/s12859-022-05108-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Escherichia coli Nissle 1917 (EcN) is a probiotic bacterium used to treat various gastrointestinal diseases. EcN is increasingly being used as a chassis for the engineering of advanced microbiome therapeutics. To aid in future engineering efforts, our aim was to construct an updated metabolic model of EcN with extended secondary metabolite representation. RESULTS An updated high-quality genome-scale metabolic model of EcN, iHM1533, was developed based on comparison with 55 E. coli/Shigella reference GEMs and manual curation, including expanded secondary metabolite pathways (enterobactin, salmochelins, aerobactin, yersiniabactin, and colibactin). The model was validated and improved using phenotype microarray data, resulting in an 82.3% accuracy in predicting growth phenotypes on various nutrition sources. Flux variability analysis with previously published 13C fluxomics data validated prediction of the internal central carbon fluxes. A standardised test suite called Memote assessed the quality of iHM1533 to have an overall score of 89%. The model was applied by using constraint-based flux analysis to predict targets for optimisation of secondary metabolite production. Modelling predicted design targets from across amino acid metabolism, carbon metabolism, and other subsystems that are common or unique for influencing the production of various secondary metabolites. CONCLUSION iHM1533 represents a well-annotated metabolic model of EcN with extended secondary metabolite representation. Phenotype characterisation and the iHM1533 model provide a better understanding of the metabolic capabilities of EcN and will help future metabolic engineering efforts.
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Affiliation(s)
- Max van ‘t Hof
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Omkar S. Mohite
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jonathan M. Monk
- grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Tilmann Weber
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Bernhard O. Palsson
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark ,grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Morten O. A. Sommer
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Kaur H, Singh V, Kalia M, Mohan B, Taneja N. Identification and functional annotation of hypothetical proteins of uropathogenic Escherichia coli strain CFT073 towards designing antimicrobial drug targets. J Biomol Struct Dyn 2022; 40:14084-14095. [PMID: 34751095 DOI: 10.1080/07391102.2021.2000499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Urinary tract infections are a serious health concern worldwide, especially in developing countries. Escherichia coli strain CFT073 is a highly virulent pathogenic bacterial strain. CFT073 proteome contains 4897 proteins, out of which 992 have been classified as hypothetical proteins. Identification and characterization of hypothetical proteins can aid in the selection of targets for drug design. In this study, we studied the hypothetical proteins from the UPEC strain CFT073 using various computational tools. By NCBI-CDD, 376 protein sequences showed conserved domains. Based on the functional motifs in their primary sequences, we classified these 376 hypothetical proteins into 7 functional categories. Further KEGG database was used to find the roles of these hypothetical proteins in several pathways. Protein interaction network analysis of hypothetical proteins identified 53 proteins as highly interacting metabolic proteins. Virulence factor analysis of the proteins identified 8 proteins as virulent. We conducted a non-homology search for the identified proteins of UPEC in the available human proteome. We observed that 35 proteins are non-homologous to humans and hence could be selected for drug designing targets. Qualitative characterization of the selected 35 non-homologous hypothetical proteins including essentiality analysis and evaluation of druggability by similarity search against drug bank database was performed. Out of these 35 proteins, three-dimensional structures of six proteins (NP_752562.1, NP_756345.1, NP_754893.1, NP_756600.2, NP_755264.1 and NP_752994.1) could be successfully modelled. These new annotations can help to better understand disease mechanisms at the molecular level, as well as provide new targets for drug development against the UPEC strain CFT073.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harpreet Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Vikram Singh
- Center of Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, India
| | - Manmohit Kalia
- Department of Biology, State University of New York, Binghamton, NY, USA
| | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Phenotypic Assessment of Clinical Escherichia coli Isolates as an Indicator for Uropathogenic Potential. mSystems 2022; 7:e0082722. [PMID: 36445110 PMCID: PMC9765037 DOI: 10.1128/msystems.00827-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
For women in the United States, urinary tract infections (UTIs) are the most frequent diagnosis in emergency departments, comprising 21.3% of total visits. Uropathogenic Escherichia coli (UPEC) causes ~80% of uncomplicated UTIs. To combat this public health issue, it is vital to characterize UPEC strains as well as to differentiate them from commensal strains to reduce the overuse of antibiotics. It has been challenging to determine a consistent genetic signature that clearly distinguishes UPEC from other E. coli strains. Therefore, we examined whether phenotypic data could be predictive of uropathogenic potential. We screened 13 clinical strains of UPEC, isolated from cases of uncomplicated UTI in young otherwise healthy women, in a series of microbiological phenotypic assays using UPEC prototype strain CFT073 and nonpathogenic E. coli strain MG1655 K-12 as controls. Phenotypes included adherence, iron acquisition, biofilm formation, human serum resistance, motility, and stress resistance. By use of a well-established experimental mouse model of UTI, these data were able to predict the severity of the bacterial burden in both the urine and bladders. Multiple linear regression using three different phenotypic assays, i.e., growth in minimal medium, siderophore production, and type 1 fimbrial expression, was predictive of bladder colonization (adjusted R2 = 0.6411). Growth in ex vivo human urine, hemagglutination of red blood cells, and motility modeled urine colonization (adjusted R2 = 0.4821). These results showcase the utility of phenotypic characterization to predict the severity of infection that these strains may cause. We predict that these methods will also be applicable to other complex, genetically redundant, pathogens. IMPORTANCE Urinary tract infections are the second leading infectious disease worldwide, occurring in over half of the female population during their lifetime. Most infections are caused by uropathogenic Escherichia coli (UPEC) strains. These strains can establish a reservoir in the gut, in which they do not cause disease but, upon introduction to the urinary tract, can infect the host and elicit pathogenesis. Clinically, it would be beneficial to screen patient E. coli strains to understand their pathogenic potential, which may lead to the administration of prophylactic antibiotic treatment for those with increased risk. Others have proposed the use of PCR-based genetic screening methods to detect UPEC strains and differentiate them from other E. coli pathotypes; however, this method has not yielded a consistent uropathogenic genetic signature. Here, we used phenotypic characteristics such as growth rate, siderophore production, and expression of fimbriae to better predict uropathogenic potential.
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RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS-StpA Nucleoprotein Filaments in Pathogenic Escherichia coli. mBio 2022; 13:e0266222. [PMID: 36264101 PMCID: PMC9765446 DOI: 10.1128/mbio.02662-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of virulence genes in pathogenic Escherichia coli is controlled in part by the transcription silencer H-NS and its paralogs (e.g., StpA), which sequester DNA in multi-kb nucleoprotein filaments to inhibit transcription initiation, elongation, or both. Some activators counter-silence initiation by displacing H-NS from promoters, but how H-NS inhibition of elongation is overcome is not understood. In uropathogenic E. coli (UPEC), elongation regulator RfaH aids expression of some H-NS-silenced pathogenicity operons (e.g., hlyCABD encoding hemolysin). RfaH associates with elongation complexes (ECs) via direct contacts to a transiently exposed, nontemplate DNA strand sequence called operon polarity suppressor (ops). RfaH-ops interactions establish long-lived RfaH-EC contacts that allow RfaH to recruit ribosomes to the nascent mRNA and to suppress transcriptional pausing and termination. Using ChIP-seq, we mapped the genome-scale distributions of RfaH, H-NS, StpA, RNA polymerase (RNAP), and σ70 in the UPEC strain CFT073. We identify eight RfaH-activated operons, all of which were bound by H-NS and StpA. Four are new additions to the RfaH regulon. Deletion of RfaH caused premature termination, whereas deletion of H-NS and StpA allowed elongation without RfaH. Thus, RfaH is an elongation counter-silencer of H-NS. Consistent with elongation counter-silencing, deletion of StpA alone decreased the effect of RfaH. StpA increases DNA bridging, which inhibits transcript elongation via topological constraints on RNAP. Residual RfaH effect when both H-NS and StpA were deleted was attributable to targeting of RfaH-regulated operons by a minor H-NS paralog, Hfp. These operons have evolved higher levels of H-NS-binding features, explaining minor-paralog targeting. IMPORTANCE Bacterial pathogens adapt to hosts and host defenses by reprogramming gene expression, including by H-NS counter-silencing. Counter-silencing turns on transcription initiation when regulators bind to promoters and rearrange repressive H-NS nucleoprotein filaments that ordinarily block transcription. The specialized NusG paralog RfaH also reprograms virulence genes but regulates transcription elongation. To understand how elongation regulators might affect genes silenced by H-NS, we mapped H-NS, StpA (an H-NS paralog), RfaH, σ70, and RNA polymerase (RNAP) locations on DNA in the uropathogenic E. coli strain CFT073. Although H-NS-StpA filaments bind only 18% of the CFT073 genome, all loci at which RfaH binds RNAP are also bound by H-NS-StpA and are silenced when RfaH is absent. Thus, RfaH represents a distinct class of counter-silencer that acts on elongating RNAP to enable transcription through repressive nucleoprotein filaments. Our findings define a new mechanism of elongation counter-silencing and explain how RfaH functions as a virulence regulator.
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Pleuger C, Ai D, Hoppe ML, Winter LT, Bohnert D, Karl D, Guenther S, Epelman S, Kantores C, Fijak M, Ravens S, Middendorff R, Mayer JU, Loveland KL, Hedger M, Bhushan S, Meinhardt A. The regional distribution of resident immune cells shapes distinct immunological environments along the murine epididymis. eLife 2022; 11:e82193. [PMID: 36515584 PMCID: PMC9750176 DOI: 10.7554/elife.82193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
The epididymis functions as transition zone for post-testicular sperm maturation and storage and faces contrasting immunological challenges, i.e. tolerance towards spermatozoa vs. reactivity against pathogens. Thus, normal organ function and integrity relies heavily on a tightly controlled immune balance. Previous studies described inflammation-associated tissue damage solely in the distal regions (corpus, cauda), but not in the proximal regions (initial segment, caput). To understand the observed region-specific immunity along the epididymal duct, we have used an acute bacterial epididymitis mouse model and analyzed the disease progression. Whole transcriptome analysis using RNAseq 10 days post infection showed a pro-inflammatory environment within the cauda, while the caput exhibited only minor transcriptional changes. High-dimensional flow cytometry analyses revealed drastic changes in the immune cell composition upon infection with uropathogenic Escherichia coli. A massive influx of neutrophils and monocytes was observed exclusively in distal regions and was associated with bacterial appearance and tissue alterations. In order to clarify the reasons for the region-specific differences in the intensity of immune responses, we investigated the heterogeneity of resident immune cell populations under physiological conditions by scRNASeq analysis of extravascular CD45+ cells. Twelve distinct immune cell subsets were identified, displaying substantial differences in distribution along the epididymis as further assessed by flow cytometry and immunofluorescence staining. Macrophages constituted the majority of resident immune cells and were further separated in distinct subgroups based on their transcriptional profile, tissue location and monocyte-dependence. Crucially, the proximal and distal regions showed striking differences in their immunological landscapes. These findings indicate that resident immune cells are strategically positioned along the epididymal duct, potentially providing different immunological environments required for addressing the contrasting immunological challenges and thus, preserving tissue integrity and organ function.
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Affiliation(s)
- Christiane Pleuger
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Dingding Ai
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Minea L Hoppe
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Laura T Winter
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Daniel Bohnert
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Dominik Karl
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Stefan Guenther
- ECCPS Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Slava Epelman
- Ted Rogers Center of Heart Research, Peter Munk Cardiac Centre, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Crystal Kantores
- Ted Rogers Center of Heart Research, Peter Munk Cardiac Centre, Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Monika Fijak
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Sarina Ravens
- Institute of Immunology, Hannover Medical School, Hanover, Germany
| | - Ralf Middendorff
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
- Institute of Anatomy and Cell Biology, Unit of Signal Transduction, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Johannes U Mayer
- Department of Dermatology and Allergology, Philipps-University of Marburg, Marburg, Germany
| | - Kate L Loveland
- Centre of Reproductive Health, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash Medical Centre, Monash University, Clayton, Australia
| | - Mark Hedger
- Centre of Reproductive Health, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash Medical Centre, Monash University, Clayton, Australia
| | - Sudhanshu Bhushan
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Andreas Meinhardt
- Institute of Anatomy and Cell Biology, Unit of Reproductive Biology, Justus-Liebig-University Giessen, Giessen, Germany
- Hessian Center of Reproductive Medicine, Justus-Liebig-University of Giessen, Giessen, Germany
- Centre of Reproductive Health, Hudson Institute of Medical Research, Clayton, Australia
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48
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Minadakis G, Tomazou M, Dietis N, Spyrou GM. Vir2Drug: a drug repurposing framework based on protein similarities between pathogens. Brief Bioinform 2022; 24:6895455. [PMID: 36513376 PMCID: PMC9851336 DOI: 10.1093/bib/bbac536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
We draw from the assumption that similarities between pathogens at both pathogen protein and host protein level, may provide the appropriate framework to identify and rank candidate drugs to be used against a specific pathogen. Vir2Drug is a drug repurposing tool that uses network-based approaches to identify and rank candidate drugs for a specific pathogen, combining information obtained from: (a) ranked pathogen-to-pathogen networks based on protein similarities between pathogens, (b) taxonomy distance between pathogens and (c) drugs targeting specific pathogen's and host proteins. The underlying pathogen networks are used to screen drugs by means of specific methodologies that account for either the host or pathogen's protein targets. Vir2Drug is a useful and yet informative tool for drug repurposing against known or unknown pathogens especially in periods where the emergence for repurposed drugs plays significant role in handling viral outbreaks, until reaching a vaccine. The web tool is available at: https://bioinformatics.cing.ac.cy/vir2drug, https://vir2drug.cing-big.hpcf.cyi.ac.cy.
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Affiliation(s)
- George Minadakis
- Corresponding author: George Minadakis, Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus. Tel.: +357-22-392852; Fax: +357-22-358238; E-mail:
| | - Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683 Nicosia, Cyprus,The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus
| | - Nikolas Dietis
- Medical School, University of Cyprus, Nicosia 1678, Cyprus
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683 Nicosia, Cyprus,The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, PO Box 23462, 1683 Nicosia, Cyprus
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49
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Dodd D, Cann I. Tutorial: Microbiome studies in drug metabolism. Clin Transl Sci 2022; 15:2812-2837. [PMID: 36099474 PMCID: PMC9747132 DOI: 10.1111/cts.13416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/20/2022] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
The human gastrointestinal tract is home to a dense population of microorganisms whose metabolism impacts human health and physiology. The gut microbiome encodes millions of genes, the products of which endow our bodies with unique biochemical activities. In the context of drug metabolism, microbial biochemistry in the gut influences humans in two major ways: (1) by producing small molecules that modulate expression and activity of human phase I and II pathways; and (2) by directly modifying drugs administered to humans to yield active, inactive, or toxic metabolites. Although the capacity of the microbiome to modulate drug metabolism has long been known, recent studies have explored these interactions on a much broader scale and have revealed an unprecedented scope of microbial drug metabolism. The implication of this work is that we might be able to predict the capacity of an individual's microbiome to metabolize drugs and use this information to avoid toxicity and inform proper dosing. Here, we provide a tutorial of how to study the microbiome in the context of drug metabolism, focusing on in vitro, rodent, and human studies. We then highlight some limitations and opportunities for the field.
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Affiliation(s)
- Dylan Dodd
- Department of PathologyStanford University School of MedicineStanfordCaliforniaUSA,Department of Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Isaac Cann
- Department of Animal ScienceUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme)University of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Division of Nutritional SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Center for East Asian & Pacific StudiesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
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50
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Qi Y, Gu S, Zhang Y, Guo L, Xu M, Cheng X, Wang O, Sun Y, Chen J, Fang X, Liu X, Deng L, Fan G. MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads. IMETA 2022; 1:e46. [PMID: 38867906 PMCID: PMC10989976 DOI: 10.1002/imt2.46] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 06/14/2024]
Abstract
Metagenomic evidence of great genetic diversity within the nonconserved regions of the human gut microbial genomes appeals for new methods to elucidate the species-level variability at high resolution. However, current approaches cannot satisfy this methodologically challenge. In this study, we proposed an efficient binning-first-and-assembly-later strategy, named MetaTrass, to recover high-quality species-resolved genomes based on public reference genomes and the single-tube long fragment read (stLFR) technology, which enables cobarcoding. MetaTrass can generate genomes with longer contiguity, higher completeness, and lower contamination than those produced by conventional assembly-first-and-binning-later strategies. From a simulation study on a mock microbial community, MetaTrass showed the potential to improve the contiguity of assembly from kb to Mb without accuracy loss, as compared to other methods based on the next-generation sequencing technology. From four human fecal samples, MetaTrass successfully retrieved 178 high-quality genomes, whereas only 58 ones were provided by the optimal performance of other conventional strategies. Most importantly, these high-quality genomes confirmed the high level of genetic diversity among different samples and unveiled much more. MetaTrass was designed to work with metagenomic reads sequenced by stLFR technology, but is also applicable to other types of cobarcoding libraries. With the high capability of assembling high-quality genomes of metagenomic data sets, MetaTrass seeks to facilitate the study of spatial characters and dynamics of complex microbial communities at enhanced resolution. The open-source code of MetaTrass is available at https://github.com/BGI-Qingdao/MetaTrass.
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Affiliation(s)
- Yanwei Qi
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
| | - Shengqiang Gu
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | - Lidong Guo
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Mengyang Xu
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
| | - Xiaofang Cheng
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
- MGIBGI‐ShenzhenShenzhenChina
| | - Ou Wang
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
- MGIBGI‐ShenzhenShenzhenChina
| | - Ying Sun
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
| | | | - Xiaodong Fang
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Xin Liu
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
| | - Li Deng
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
| | - Guangyi Fan
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
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