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Saenkham-Huntsinger P, Ritter M, Donati GL, Mitchell AM, Subashchandrabose S. The inner membrane protein YhiM links copper and CpxAR envelope stress responses in uropathogenic E. coli. mBio 2024; 15:e0352223. [PMID: 38470052 PMCID: PMC11005409 DOI: 10.1128/mbio.03522-23] [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: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Urinary tract infection (UTI) is a ubiquitous infectious condition, and uropathogenic Escherichia coli (UPEC) is the predominant causative agent of UTI. Copper (Cu) is implicated in innate immunity, including against UPEC. Cu is a trace element utilized as a co-factor, but excess Cu is toxic due to mismetalation of non-cognate proteins. E. coli precisely regulates Cu homeostasis via efflux systems. However, Cu import mechanisms into the bacterial cell are not clear. We hypothesized that Cu import defective mutants would exhibit increased resistance to Cu. This hypothesis was tested in a forward genetic screen with transposon (Tn5) insertion mutants in UPEC strain CFT073, and we identified 32 unique Cu-resistant mutants. Transposon and defined mutants lacking yhiM, which encodes a hypothetical inner membrane protein, were more resistant to Cu than parental strain. Loss of YhiM led to decreased cellular Cu content and increased expression of copA, encoding a Cu efflux pump. The CpxAR envelope stress response system was activated in the ΔyhiM mutant as indicated by increased expression of cpxP. Transcription of yhiM was regulated by CueR and CpxR, and the CpxAR system was essential for increased Cu resistance in the ΔyhiM mutant. Importantly, activation of CpxAR system in the ΔyhiM mutant was independent of NlpE, a known activator of this system. YhiM was required for optimal fitness of UPEC in a mouse model of UTI. Our findings demonstrate that YhiM is a critical mediator of Cu homeostasis and links bacterial adaptation to Cu stress with the CpxAR-dependent envelope stress response in UPEC.IMPORTANCEUPEC is a common bacterial infection. Bacterial pathogens are exposed to host-derived Cu during infection, including UTI. Here, we describe detection of genes involved in Cu homeostasis in UPEC. A UPEC mutant lacking YhiM, a membrane protein, exhibited dramatic increase in resistance to Cu. Our study demonstrates YhiM as a nexus between Cu stress and the CpxAR-dependent envelope stress response system. Importantly, our findings establish NlpE-independent activation of CpxAR system during Cu stress in UPEC. Collectively, YhiM emerges as a critical mediator of Cu homeostasis in UPEC and highlights the interlinked nature of bacterial adaptation to survival during Cu and envelope stress.
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Affiliation(s)
- Panatda Saenkham-Huntsinger
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Matthew Ritter
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - George L. Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Angela M. Mitchell
- Department of Biology, College of Science, Texas A&M University, College Station, Texas, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the phylogenetic diversity of human bladder bacterial isolates. Genome Biol 2024; 25:75. [PMID: 38515176 PMCID: PMC10958879 DOI: 10.1186/s13059-024-03216-8] [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: 10/02/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. RESULTS To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches. CONCLUSIONS This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Present address: Division of Nutritional Science, Cornell University, Ithaca, NY, 14850, USA
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Baylie R Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Alan J Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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Westcott MM, Morse AE, Troy G, Blevins M, Wierzba T, Sanders JW. Photochemical inactivation as an alternative method to produce a whole-cell vaccine for uropathogenic Escherichia coli (UPEC). Microbiol Spectr 2024; 12:e0366123. [PMID: 38315025 PMCID: PMC10913755 DOI: 10.1128/spectrum.03661-23] [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: 10/20/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the primary causative agent of lower urinary tract infection (UTI). UTI presents a serious health risk and has considerable secondary implications including economic burden, recurring episodes, and overuse of antibiotics. A safe and effective vaccine would address this widespread health problem and emerging antibiotic resistance. Killed, whole-cell vaccines have shown limited efficacy to prevent recurrent UTI in human trials. We explored photochemical inactivation with psoralen drugs and UVA light (PUVA), which crosslinks nucleic acid, as an alternative to protein-damaging methods of inactivation to improve whole-cell UTI vaccines. Exposure of UPEC to the psoralen drug AMT and UVA light resulted in a killed but metabolically active (KBMA) state, as reported previously for other PUVA-inactivated bacteria. The immunogenicity of PUVA-UPEC as compared to formalin-inactivated UPEC was compared in mice. Both generated high UPEC-specific serum IgG titers after intramuscular delivery. However, using functional adherence as a measure of surface protein integrity, we found differences in the properties of PUVA- and formalin-inactivated UPEC. Adhesion mediated by Type-1 and P-fimbriae was severely compromised by formalin but was unaffected by PUVA, indicating that PUVA preserved the functional conformation of fimbrial proteins, which are targets of protective immune responses. In vitro assays indicated that although they retained metabolic activity, PUVA-UPEC lost virulence properties that could negatively impact vaccine safety. Our results imply the potential for PUVA to improve killed, whole-cell UTI vaccines by generating bacteria that more closely resemble their live, infectious counterparts relative to vaccines generated with protein-damaging methods. IMPORTANCE Lower urinary tract infection (UTI), caused primarily by uropathogenic Escherichia coli, represents a significant health burden, accounting for 7 million primary care and 1 million emergency room visits annually in the United States. Women and the elderly are especially susceptible and recurrent infection (rUTI) is common in those populations. Lower UTI can lead to life-threatening systemic infection. UTI burden is manifested by healthcare dollars spent (1.5 billion annually), quality of life impact, and resistant strains emerging from antibiotic overuse. A safe and effective vaccine to prevent rUTI would address a substantial healthcare issue. Vaccines comprised of inactivated uropathogenic bacteria have yielded encouraging results in clinical trials but improvements that enhance vaccine performance are needed. To that end, we focused on inactivation methodology and provided data to support photochemical inactivation, which targets nucleic acid, as a promising alternative to conventional protein-damaging inactivation methods to improve whole-cell UTI vaccines.
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Affiliation(s)
- Marlena M. Westcott
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston Salem, North Carolina, USA
| | - Alexis E. Morse
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston Salem, North Carolina, USA
| | - Gavin Troy
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston Salem, North Carolina, USA
| | - Maria Blevins
- Department of Internal Medicine, Infectious Diseases Section, Wake Forest University School of Medicine, Winston Salem, North Carolina, USA
| | - Thomas Wierzba
- Department of Internal Medicine, Infectious Diseases Section, Wake Forest University School of Medicine, Winston Salem, North Carolina, USA
| | - John W. Sanders
- Department of Internal Medicine, Infectious Diseases Section, Wake Forest University School of Medicine, Winston Salem, North Carolina, USA
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Jiang L, Wang H, Luo L, Pang X, Liu T, Sun L, Zhang G. Urogenital microbiota-driven virulence factor genes associated with recurrent urinary tract infection. Front Microbiol 2024; 15:1344716. [PMID: 38384270 PMCID: PMC10879396 DOI: 10.3389/fmicb.2024.1344716] [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: 11/27/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024] Open
Abstract
Urinary tract infections (UTIs) are a common health issue affecting individuals worldwide. Recurrent urinary tract infections (rUTI) pose a significant clinical challenge, with limited understanding of the underlying mechanisms. Recent research suggests that the urobiome, the microbial community residing in the urinary tract, may play a crucial role in the development and recurrence of urinary tract infections. However, the specific virulence factor genes (VFGs) driven by urobiome contributing to infection recurrence remain poorly understood. Our study aimed to investigate the relationship between urobiome driven VFGs and recurrent urinary tract infections. By analyzing the VFGs composition of the urinary microbiome in patients with rUTI compared to a control group, we found higher alpha diversity in rUTI patients compared with healthy control. And then, we sought to identify specific VFGs features associated with infection recurrence. Specifically, we observed an increased abundance of certain VGFs in the recurrent infection group. We also associated VFGs and clinical data. We then developed a diagnostic model based on the levels of these VFGs using random forest and support vector machine analysis to distinguish healthy control and rUIT, rUTI relapse and rUTI remission. The diagnostic accuracy of the model was assessed using receiver operating characteristic curve analysis, and the area under the ROC curve were 0.83 and 0.75. These findings provide valuable insights into the complex interplay between the VFGs of urobiome and recurrent urinary tract infections, highlighting potential targets for therapeutic interventions to prevent infection recurrence.
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Affiliation(s)
| | | | | | | | | | - Lijiang Sun
- Department of Urology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guiming Zhang
- Department of Urology, Affiliated Hospital of Qingdao University, Qingdao, China
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Fatima S, Akbar A, Irfan M, Shafee M, Ali A, Ishaq Z, Raza SK, Samad A, Alshahrani MY, Hassan SS. Virulence Factors and Antimicrobial Resistance of Uropathogenic Escherichia coli EQ101 UPEC Isolated from UTI Patient in Quetta, Balochistan, Pakistan. BIOMED RESEARCH INTERNATIONAL 2023; 2023:7278070. [PMID: 37727279 PMCID: PMC10506881 DOI: 10.1155/2023/7278070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 03/31/2023] [Accepted: 07/11/2023] [Indexed: 09/21/2023]
Abstract
Infectious diseases have been tremendously increasing as the organisms of even normal flora become opportunistic and cause an infection, and Escherichia coli (E. coli EQ101) is one of them. Urinary tract infections are caused by various microorganisms, but Escherichia coli is the primary cause of almost 70%-90% of all UTIs. It has multiple strains, possessing diverse virulence factors, contributing to its pathogenicity. Furthermore, these virulent strains also can cause overlapping pathogenesis by sharing resistance and virulence factors among each other. The current study is aimed at analyzing the genetic variants associated with multi-drug-resistant (MDR) E. coli using the whole genome sequencing platform. The study includes 100 uropathogenic Escherichia coli (UPEC) microorganisms obtained from urine samples out of which 44% were multi-drug-resistant (MDR) E. coli. Bacteria have been isolated and antimicrobial susceptibility test (AST) was determined by disk diffusion method on the Mueller-Hinton agar plate as recommended by the Clinical and Laboratory Standards Institute (CLSI) 2020, and one isolate has been selected which shows resistance to most of the antibiotics, and that isolate has been analyzed by whole genome sequencing (WGS), accompanied by data and phylogenetic analysis, respectively. Organisms were showing resistance against ampicillin (10 μg), cefixime (5 μg), ceftriaxone (30 μg), nalidixic acid (30 μg), ciprofloxacin (5 μg), and ofloxacin (5 μg) on antimicrobial susceptibility test. WGS were done on selected isolate which identified 25 virulence genes (air, astA, chuA, fyuA, gad, hra, iha, irp2, iss, iucC, iutA, kpsE, kpsMII_K1, lpfA, mchF, ompT, papA_F43, sat, senB, sitA, terC, traT, usp, vat, and yfcV) and seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA). Among resistance genes, seven genes (TolC, emrR, evgA, qacEdelta1, H-NS, cpxA, and mdtM) were identified to be involved in antibiotic efflux, three AMR genes (aadA5, mphA, and CTX-M-15) were involved in antibiotic inactivation, and two genes (sul1 and dfrA14) were found to be involved in antibiotic drug replacement. Our data identified antibiotic resistance and virulence genes of the isolate. We suggest further research work to establish region-based resistance profile in comparison with the global resistance pattern.
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Affiliation(s)
- Sareen Fatima
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
| | - Ali Akbar
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, 19120 Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Muhammad Shafee
- Center for Advanced Studies in Vaccinology & Biotechnology (CASVAB), University of Balochistan, Quetta, Balochistan, Pakistan
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Zaara Ishaq
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | | | - Abdul Samad
- Center for Advanced Studies in Vaccinology & Biotechnology (CASVAB), University of Balochistan, Quetta, Balochistan, Pakistan
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 9088, Saudi Arabia
| | - Syed Shah Hassan
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
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6
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541916. [PMID: 37292924 PMCID: PMC10245883 DOI: 10.1101/2023.05.23.541916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2 % of the genera found when we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder E. coli isolates and 387 gut E. coli isolates supports the hypothesis that phylogroup distribution and functions of E. coli strains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Baylie R. Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
- Department of Biology, Loyola University Chicago, Chicago, IL 60660
| | - Alan J. Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
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Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2022; 15:pharmaceutics15010152. [PMID: 36678781 PMCID: PMC9863128 DOI: 10.3390/pharmaceutics15010152] [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] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.
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Affiliation(s)
- Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence: (M.A.K.); or (H.K.)
| | - Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong, China
| | - Amin Ullah
- Molecular Virology Laboratory, Department of Microbiology and Biotechnology, Abasyn University, Peshawar 25000, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Khyber Shinwari
- Institute of Chemical Engineering, Department Immuno-Chemistry, Ural Federal University, Yekaterinbiurg 620002, Russia
| | - Yaseen Hussain
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Khalaf F. Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Haroon Khan
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (M.A.K.); or (H.K.)
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8
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Torres-Puig S, García V, Stærk K, Andersen TE, Møller-Jensen J, Olsen JE, Herrero-Fresno A. “Omics” Technologies - What Have They Told Us About Uropathogenic Escherichia coli Fitness and Virulence During Urinary Tract Infection? Front Cell Infect Microbiol 2022; 12:824039. [PMID: 35237532 PMCID: PMC8882828 DOI: 10.3389/fcimb.2022.824039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infection (UTI), a widespread infectious disease of great impact on human health. This is further emphasized by the rapidly increase in antimicrobial resistance in UPEC, which compromises UTI treatment. UPEC biology is highly complex since uropathogens must adopt extracellular and intracellular lifestyles and adapt to different niches in the host. In this context, the implementation of forefront ‘omics’ technologies has provided substantial insight into the understanding of UPEC pathogenesis, which has opened the doors for new therapeutics and prophylactics discovery programs. Thus, ‘omics’ technologies applied to studies of UPEC during UTI, or in models of UTI, have revealed extensive lists of factors that are important for the ability of UPEC to cause disease. The multitude of large ‘omics’ datasets that have been generated calls for scrutinized analysis of specific factors that may be of interest for further development of novel treatment strategies. In this review, we describe main UPEC determinants involved in UTI as estimated by ‘omics’ studies, and we compare prediction of factors across the different ‘omics’ technologies, with a focus on those that have been confirmed to be relevant under UTI-related conditions. We also discuss current challenges and future perspectives regarding analysis of data to provide an overview and better understanding of UPEC mechanisms involved in pathogenesis which should assist in the selection of target sites for future prophylaxis and treatment.
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Affiliation(s)
- Sergi Torres-Puig
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Kristian Stærk
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Thomas E. Andersen
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- *Correspondence: Ana Herrero-Fresno,
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9
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Yang W, Liu P, Chen Y, Lv Q, Wang Z, Huang W, Jiang H, Zheng Y, Jiang Y, Sun L. Dictamnine Inhibits the Adhesion to and Invasion of Uropathogenic Escherichia Coli (UPEC) to Urothelial Cells. Molecules 2022; 27:molecules27010272. [PMID: 35011504 PMCID: PMC8746591 DOI: 10.3390/molecules27010272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/25/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common pathogenic bacteria associated with urinary tract infection (UTI). UPEC can cause UTI by adhering to and invading uroepithelial cells. Fimbriae is the most important virulence factor of UPEC, and a potentially promising target in developing novel antibacterial treatments. In this study, the antibacterial properties and effects of the compound dictamnine, extracted from the traditional Chinese medicine Cortex Dictamni, on the bacterial morphology, cell adhesion, and invasion of UPEC were studied. Dictamnine exhibited no obvious antibacterial activity against UPEC, but significantly impeded the ability of UPEC to adhere to and invade uroepithelial cells. RT-qPCR analysis showed that treatment downregulated the expression of type 1 fimbriae, P fimbriae, and curli fimbriae adhesion genes, and also downregulated adhesion-related receptor genes of uroepithelial cells. Transmission electron microscopy showed that dictamnine destroyed the structure of the fimbriae and the surface of the bacteria became smooth. These results suggest that dictamnine may help to prevent UTI by simultaneously targeting UPEC fimbriae and urothelial adhesin receptors, and may have a potential use as a new anti-UPEC drug.
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Affiliation(s)
- Wenbo Yang
- College of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China; (W.Y.); (Z.W.)
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (P.L.); (Q.L.); (W.H.); (H.J.); (Y.Z.)
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (P.L.); (Q.L.); (W.H.); (H.J.); (Y.Z.)
| | - Ying Chen
- School of Light Industry, Beijing Technology and Business University (BTBU), Beijing 100048, China;
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (P.L.); (Q.L.); (W.H.); (H.J.); (Y.Z.)
| | - Zhongtian Wang
- College of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China; (W.Y.); (Z.W.)
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (P.L.); (Q.L.); (W.H.); (H.J.); (Y.Z.)
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (P.L.); (Q.L.); (W.H.); (H.J.); (Y.Z.)
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (P.L.); (Q.L.); (W.H.); (H.J.); (Y.Z.)
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (P.L.); (Q.L.); (W.H.); (H.J.); (Y.Z.)
- Correspondence: (Y.J.); (L.S.)
| | - Liping Sun
- College of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China; (W.Y.); (Z.W.)
- Correspondence: (Y.J.); (L.S.)
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10
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Panunzio A, Tafuri A, Princiotta A, Gentile I, Mazzucato G, Trabacchin N, Antonelli A, Cerruto MA. Omics in urology: An overview on concepts, current status and future perspectives. Urologia 2021; 88:270-279. [PMID: 34169788 DOI: 10.1177/03915603211022960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent technological advances in molecular biology have led to great progress in the knowledge of structure and function of cells and their main constituents. In this setting, 'omics' is standing out in order to significantly improve the understanding of etiopathogenetic mechanisms of disease and contribute to the development of new biochemical diagnostics and therapeutic tools. 'Omics' indicates the scientific branches investigating every aspect of cell's biology, including structures, functions and dynamics pathways. The main 'omics' are genomics, epigenomics, proteomics, transcriptomics, metabolomics and radiomics. Their diffusion, success and proliferation, addressed to many research fields, has led to many important acquisitions, even in Urology. Aim of this narrative review is to define the state of art of 'omics' application in Urology, describing the most recent and relevant findings, in both oncological and non-oncological diseases, focusing the attention on urinary tract infectious, interstitial cystitis, urolithiasis, prostate cancer, bladder cancer and renal cell carcinoma. In Urology the majority of 'omics' applications regard the pathogenesis and diagnosis of the investigated diseases. In future, its role should be implemented in order to develop specific predictors and tailored treatments.
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Affiliation(s)
- Andrea Panunzio
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Alessandro Tafuri
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy.,Department of Neuroscience, Imaging and Clinical Science, Physiology and Physiopathology division, "G. D'Annunzio" University, Chieti, Italy
| | - Alessandro Princiotta
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Ilaria Gentile
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Giovanni Mazzucato
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Nicolò Trabacchin
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Alessandro Antonelli
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Maria Angela Cerruto
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
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11
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Vieira KCDO, Silva HRAD, Rocha IPM, Barboza E, Eller LKW. Foodborne pathogens in the omics era. Crit Rev Food Sci Nutr 2021; 62:6726-6741. [PMID: 33783282 DOI: 10.1080/10408398.2021.1905603] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.
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Affiliation(s)
| | | | | | - Emmanuel Barboza
- Health Sciences Faculty, University of Western Sao Paulo, Presidente Prudente, Sao Paulo, Brazil
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12
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Sharma A, Sanduja P, Anand A, Mahajan P, Guzman CA, Yadav P, Awasthi A, Hanski E, Dua M, Johri AK. Advanced strategies for development of vaccines against human bacterial pathogens. World J Microbiol Biotechnol 2021; 37:67. [PMID: 33748926 PMCID: PMC7982316 DOI: 10.1007/s11274-021-03021-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 02/17/2021] [Indexed: 12/18/2022]
Abstract
Infectious diseases are one of the main grounds of death and disabilities in human beings globally. Lack of effective treatment and immunization for many deadly infectious diseases and emerging drug resistance in pathogens underlines the need to either develop new vaccines or sufficiently improve the effectiveness of currently available drugs and vaccines. In this review, we discuss the application of advanced tools like bioinformatics, genomics, proteomics and associated techniques for a rational vaccine design.
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Affiliation(s)
- Abhinay Sharma
- School of Life Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Vaccinology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research, Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Pooja Sanduja
- School of Life Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Aparna Anand
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research, Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Pooja Mahajan
- School of Life Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Carlos A Guzman
- Department of Vaccinology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendragarh, Harayana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad-Gurgaon Expressway, PO box #04, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121001, India
| | - Emanuel Hanski
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research, Israel-Canada (IMRIC), Faculty of Medicine, The Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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13
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Adaptation of Arginine Synthesis among Uropathogenic Branches of the Escherichia coli Phylogeny Reveals Adjustment to the Urinary Tract Habitat. mBio 2020; 11:mBio.02318-20. [PMID: 32994329 PMCID: PMC7527732 DOI: 10.1128/mbio.02318-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common cause of human urinary tract infection (UTI). Population bottlenecks during early stages of UTI make high-throughput screens impractical for understanding clinically important later stages of UTI, such as persistence and recurrence. As UPEC is hypothesized to be adapted to these later pathogenic stages, we previously identified 29 genes evolving under positive selection in UPEC. Here, we found that 8 of these genes, including argI (which is involved in arginine biosynthesis), are important for persistence in a mouse model of UTI. Deletion of argI and other arginine synthesis genes resulted in (i) arginine auxotrophy and (ii) defects in persistent UTI. Replacement of a B2 clade argI with a non-B2 clade argI complemented arginine auxotrophy, but the resulting strain remained attenuated in its ability to cause persistent bacteriuria. Thus, argI may have a second function during UTI that is not related to simple arginine synthesis. This study demonstrates how variation in metabolic genes can impact virulence and provides insight into the mechanisms and evolution of bacterial virulence. Urinary tract infections (UTIs) are predominantly caused by uropathogenic Escherichia coli (UPEC). UPEC pathogenesis requires passage through a severe population bottleneck involving intracellular bacterial communities (IBCs) that are clonal expansions of a single invading UPEC bacterium in a urothelial superficial facet cell. IBCs occur only during acute pathogenesis. The bacteria in IBCs form the founder population that develops into persistent extracellular infections. Only a small fraction of UPEC organisms proceed through the IBC cycle, regardless of the inoculum size. This dramatic reduction in population size precludes the utility of genomic mutagenesis technologies for identifying genes important for persistence. To circumvent this bottleneck, we previously identified 29 positively selected genes (PSGs) within UPEC and hypothesized that they contribute to virulence. Here, we show that 8 of these 29 PSGs are required for fitness during persistent bacteriuria. Conversely, 7/8 of these PSG mutants showed essentially no phenotype in acute UTI. Deletion of the PSG argI leads to arginine auxotrophy. Relative to the other arg genes, argI in the B2 clade (which comprises most UPEC strains) of E. coli has diverged from argI in other E. coli clades. Replacement of argI in a UPEC strain with a non-UPEC argI allele complemented the arginine auxotrophy but not the persistent bacteriuria defect, showing that the UPEC argI allele contributes to persistent infection. These results highlight the complex roles of metabolic pathways during infection and demonstrate that evolutionary approaches can identify infection-specific gene functions downstream of population bottlenecks, shedding light on virulence and the genetic evolution of pathogenesis.
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14
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Garretto A, Miller-Ensminger T, Ene A, Merchant Z, Shah A, Gerodias A, Biancofiori A, Canchola S, Canchola S, Castillo E, Chowdhury T, Gandhi N, Hamilton S, Hatton K, Hyder S, Krull K, Lagios D, Lam T, Mitchell K, Mortensen C, Murphy A, Richburg J, Rokas M, Ryclik S, Sulit P, Szwajnos T, Widuch M, Willis J, Woloszyn M, Brassil B, Johnson G, Mormando R, Maskeri L, Batrich M, Stark N, Shapiro JW, Montelongo Hernandez C, Banerjee S, Wolfe AJ, Putonti C. Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms. Front Microbiol 2020; 11:2094. [PMID: 33013764 PMCID: PMC7500147 DOI: 10.3389/fmicb.2020.02094] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/10/2020] [Indexed: 01/19/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant's symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition.
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Affiliation(s)
- Andrea Garretto
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | | | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Zubia Merchant
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Aashaka Shah
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Athina Gerodias
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Anthony Biancofiori
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Stacey Canchola
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Stephanie Canchola
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Emanuel Castillo
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Tasnim Chowdhury
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Nikita Gandhi
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Sarah Hamilton
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Kyla Hatton
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Syed Hyder
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Koty Krull
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Demetrios Lagios
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Thinh Lam
- Neuroscience Program, Loyola University Chicago, Chicago, IL, United States
| | - Kennedy Mitchell
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Christine Mortensen
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Amber Murphy
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Joseph Richburg
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Meghan Rokas
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Suzanne Ryclik
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Pauline Sulit
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Thomas Szwajnos
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Manuel Widuch
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Jessica Willis
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Mary Woloszyn
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Bridget Brassil
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Genevieve Johnson
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Rita Mormando
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Laura Maskeri
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Mary Batrich
- Niehoff School of Nursing, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Nicole Stark
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Jason W. Shapiro
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Swarnali Banerjee
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
- Department of Computer Science, Loyola University Chicago, Chicago, IL, United States
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15
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Soutourina O, Dubois T, Monot M, Shelyakin PV, Saujet L, Boudry P, Gelfand MS, Dupuy B, Martin-Verstraete I. Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile. Front Microbiol 2020; 11:1939. [PMID: 32903654 PMCID: PMC7438776 DOI: 10.3389/fmicb.2020.01939] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
The emerging human enteropathogen Clostridioides difficile is the main cause of diarrhea associated with antibiotherapy. Regulatory pathways underlying the adaptive responses remain understudied and the global view of C. difficile promoter structure is still missing. In the genome of C. difficile 630, 22 genes encoding sigma factors are present suggesting a complex pattern of transcription in this bacterium. We present here the first transcriptional map of the C. difficile genome resulting from the identification of transcriptional start sites (TSS), promoter motifs and operon structures. By 5′-end RNA-seq approach, we mapped more than 1000 TSS upstream of genes. In addition to these primary TSS, this analysis revealed complex structure of transcriptional units such as alternative and internal promoters, potential RNA processing events and 5′ untranslated regions. By following an in silico iterative strategy that used as an input previously published consensus sequences and transcriptomic analysis, we identified candidate promoters upstream of most of protein-coding and non-coding RNAs genes. This strategy also led to refine consensus sequences of promoters recognized by major sigma factors of C. difficile. Detailed analysis focuses on the transcription in the pathogenicity locus and regulatory genes, as well as regulons of transition phase and sporulation sigma factors as important components of C. difficile regulatory network governing toxin gene expression and spore formation. Among the still uncharacterized regulons of the major sigma factors of C. difficile, we defined the SigL regulon by combining transcriptome and in silico analyses. We showed that the SigL regulon is largely involved in amino-acid degradation, a metabolism crucial for C. difficile gut colonization. Finally, we combined our TSS mapping, in silico identification of promoters and RNA-seq data to improve gene annotation and to suggest operon organization in C. difficile. These data will considerably improve our knowledge of global regulatory circuits controlling gene expression in C. difficile and will serve as a useful rich resource for scientific community both for the detailed analysis of specific genes and systems biology studies.
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Affiliation(s)
- Olga Soutourina
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France.,Institut Universitaire de France, Paris, France.,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Thomas Dubois
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Marc Monot
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | | | - Laure Saujet
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Pierre Boudry
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems, Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Bruno Dupuy
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, Paris, France.,Institut Universitaire de France, Paris, France
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16
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Komesu YM, Dinwiddie DL, Richter HE, Lukacz ES, Sung VW, Siddiqui NY, Zyczynski HM, Ridgeway B, Rogers RG, Arya LA, Mazloomdoost D, Levy J, Carper B, Gantz MG. Defining the relationship between vaginal and urinary microbiomes. Am J Obstet Gynecol 2020; 222:154.e1-154.e10. [PMID: 31421123 DOI: 10.1016/j.ajog.2019.08.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/24/2019] [Accepted: 08/02/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Although the vaginal and urinary microbiomes have been increasingly well-characterized in health and disease, few have described the relationship between these neighboring environments. Elucidating this relationship has implications for understanding how manipulation of the vaginal microbiome may affect the urinary microbiome and treatment of common urinary conditions. OBJECTIVE To describe the relationship between urinary and vaginal microbiomes using 16S rRNA gene sequencing. We hypothesized that the composition of the urinary and vaginal microbiomes would be significantly associated, with similarities in predominant taxa. STUDY DESIGN This multicenter study collected vaginal swabs and catheterized urine samples from 186 women with mixed urinary incontinence enrolled in a parent study and 84 similarly aged controls. Investigators decided a priori that if vaginal and/or urinary microbiomes differed between continent and incontinent women, the groups would be analyzed separately; if similar, samples from continent and incontinent women would be pooled and analyzed together. A central laboratory sequenced variable regions 1-3 (v1-3) and characterized bacteria to the genus level. Operational taxonomic unit abundance was described for paired vaginal and urine samples. Pearson's correlation characterized the relationship between individual operational taxonomic units of paired samples. Canonical correlation analysis evaluated the association between clinical variables (including mixed urinary incontinence and control status) and vaginal and urinary operational taxonomic units, using the Canonical correlation analysis function in the Vegan package (R version 3.5). Linear discriminant analysis effect size was used to find taxa that discriminated between vaginal and urinary samples. RESULTS Urinary and vaginal samples were collected from 212 women (mean age 53±11 years) and results from 197 paired samples were available for analysis. As operational taxonomic units in mixed urinary incontinence and control samples were related in canonical correlation analysis and since taxa did not discriminate between mixed urinary incontinence or controls in either vagina or urine, mixed urinary incontinence and control samples were pooled for further analysis. Canonical correlation analysis of vaginal and urinary samples indicated that that 60 of the 100 most abundant operational taxonomic units in the samples largely overlapped. Lactobacillus was the most abundant genus in both urine and vagina (contributing on average 53% to an individual's urine sample and 64% to an individual's vaginal sample) (Pearson correlation r=0.53). Although less abundant than Lactobacillus, other bacteria with high Pearson correlation coefficients also commonly found in vagina and urine included: Gardnerella (r=0.70), Prevotella (r=0.64), and Ureaplasma (r=0.50). Linear discriminant analysis effect size analysis identified Tepidimonas and Flavobacterium as bacteria that distinguished the urinary environment for both mixed urinary incontinence and controls as these bacteria were absent in the vagina (Tepidimonas effect size 2.38, P<.001, Flavobacterium effect size 2.15, P<.001). Although Lactobacillus was the most abundant bacteria in both urine and vagina, it was more abundant in the vagina (linear discriminant analysis effect size effect size 2.72, P<.001). CONCLUSION Significant associations between vaginal and urinary microbiomes were demonstrated, with Lactobacillus being predominant in both urine and vagina. Abundance of other bacteria also correlated highly between the vagina and urine. This inter-relatedness has implications for studying manipulation of the urogenital microbiome in treating conditions such as urgency urinary incontinence and urinary tract infections.
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17
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Fernandes TA, André V, Arol AS, França Â, Mikhalyonok S, Cerca N, Kirillov AM. New silver (thio)semicarbazide derivatives: synthesis, structural features, and antimicrobial activity. NEW J CHEM 2020. [DOI: 10.1039/d0nj02013c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
New silver(i) (thio)semicarbazide coordination compounds were prepared, fully characterized, and tested as antimicrobial and antibiofilm agents.
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Affiliation(s)
- Tiago A. Fernandes
- Centro de Química Estrutural and Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
| | - Vânia André
- Centro de Química Estrutural and Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
| | - Aliaksandr S. Arol
- Centro de Química Estrutural and Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
| | - Ângela França
- Centre of Biological Engineering
- University of Minho
- 4710-057 Braga
- Portugal
| | - Sergei Mikhalyonok
- Department of Organic Chemistry
- Belarusian State Technological University
- 220006 Minsk
- Belarus
| | - Nuno Cerca
- Centre of Biological Engineering
- University of Minho
- 4710-057 Braga
- Portugal
| | - Alexander M. Kirillov
- Centro de Química Estrutural and Departamento de Engenharia Química
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
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18
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Renouf MJ, Cho YH, McPhee JB. Emergent Behavior of IBD-Associated Escherichia coli During Disease. Inflamm Bowel Dis 2019; 25:33-44. [PMID: 30321333 DOI: 10.1093/ibd/izy312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel diseases are becoming increasingly common throughout the world, both in developed countries and increasingly in rapidly developing countries. Multiple lines of evidence point to a role for the microbial composition of the gastrointestinal tract in the etiology of IBD, but to date, attempts to define a specific microbial cause for IBD have proved unsuccessful. Microbial 16S rRNA profiling shows that IBD patients have elevated levels of Enterobacteriaceae, in particular Escherichia coli, and reduced levels of Faecalibacterium prausnitzii. The observed E. coli have been assigned to a specific pathovar, adherent-invasive E. coli (AIEC). Adherent-invasive E. coli are a genomically heterogenous group, and whereas many groups have attempted to identify specific genetic markers that differentiate AIEC from non-AIEC strains, very few concrete genetic associations have been uncovered. Here, we highlight the advantages of applying a phenotyping approach to the study of these organisms, rather than solely depending on a sequencing or genomic-based screening strategy because virulence-associated phenotypes exhibit behaviors of emergent systems. In this respect, attempts at genetic reductionism are prone to failure because there are numerous metabolic, regulatory or genetic paths that can underlie these virulence-associated behaviors. Here, we review these IBD-associated phenotypes in E. coli and make recommendations for experimental approaches to advance our understanding of IBD-associated bacteria more generally. With advances in high-throughput screening and nongenetically based metabolomic characterization of IBD-associated bacteria, we anticipate a fuller understanding of how altered microbial communities contribute to the development of IBD.
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Affiliation(s)
| | - Youn Hee Cho
- Department of Chemistry and Biology, Ryerson University, Toronto ON, Canada
| | - Joseph B McPhee
- Department of Chemistry and Biology, Ryerson University, Toronto ON, Canada
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Gutierrez DB, Gant-Branum RL, Romer CE, Farrow MA, Allen JL, Dahal N, Nei YW, Codreanu SG, Jordan AT, Palmer LD, Sherrod SD, McLean JA, Skaar EP, Norris JL, Caprioli RM. An Integrated, High-Throughput Strategy for Multiomic Systems Level Analysis. J Proteome Res 2018; 17:3396-3408. [PMID: 30114907 DOI: 10.1021/acs.jproteome.8b00302] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteomics, metabolomics, and transcriptomics generate comprehensive data sets, and current biocomputational capabilities allow their efficient integration for systems biology analysis. Published multiomics studies cover methodological advances as well as applications to biological questions. However, few studies have focused on the development of a high-throughput, unified sample preparation approach to complement high-throughput omic analytics. This report details the automation, benchmarking, and application of a strategy for transcriptomic, proteomic, and metabolomic analyses from a common sample. The approach, sample preparation for multi-omics technologies (SPOT), provides equivalent performance to typical individual omic preparation methods but greatly enhances throughput and minimizes the resources required for multiomic experiments. SPOT was applied to a multiomics time course experiment for zinc-treated HL-60 cells. The data reveal Zn effects on NRF2 antioxidant and NFkappaB signaling. High-throughput approaches such as these are critical for the acquisition of temporally resolved, multicondition, large multiomic data sets such as those necessary to assess complex clinical and biological concerns. Ultimately, this type of approach will provide an expanded understanding of challenging scientific questions across many fields.
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Kulchavenya E, Cherednichenko A. Urogenital tuberculosis, the cause of ineffective antibacterial therapy for urinary tract infections. Ther Adv Urol 2017; 10:95-101. [PMID: 29662539 DOI: 10.1177/1756287217745772] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 10/25/2017] [Indexed: 01/29/2023] Open
Abstract
Background Urogenital tuberculosis (UGTB) is one of the great imitators; it is commonly masked by urinary tract infections (UTIs). We aimed to estimate how many UGTB patients were among patients with a long history of UTIs. Material and Methods A total of 244 patients with recurrent UTIs and suspected UGTB were enrolled in an open, noncomparative prospective study. Their urine and expressed prostate secretion or ejaculate were cultured (a total of 1446 samples), and 421 isolates with growth of ⩾104 colony-forming units (CFU)/ml were investigated for drug resistance. Typically, UGTB diagnosis is made by individual case. Results All 244 patients had a long history of recurrent UTIs (on average, 7.9 ± 3.4 years); all received at least five courses of antibacterial therapy without good result. UGTB was diagnosed in 63 (25.8%), and in 41 of these (65.1%), there was comorbidity of UTI and UGTB. Of 1446 samples investigated, 421 (29.1%) were positive, and 1025 were negative. Escherichia coli was found in 57.3% of gram-negative microflora and in 29.0% only among all uropathogens. E. coli was resistant to amoxicillin/clavulanate in 51.5-57.1%, to cefotaxime in 50.0-52.0%, to gentamycin in 33.3-59.5%, to ciprofloxacin in 63.2-66.7%, to levofloxacin in 54.8-45.2%, and to nitrofurantoin in 23.5-20.8% in 2015 and 2016, respectively. If, in 2015, all isolates of E. coli were susceptible to imipenem, in 2016, 7.1% of strains were resistant to this antibiotic. Level of drug-resistance was higher in 2016, excluding only levofloxacin and nitrofurantoin. Conclusions Total prevalence of UGTB among UTI patients with poor results of antibacterial therapy was 25.8%. Comorbidity of UTI and UGTB was diagnosed in 65.1%.
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Affiliation(s)
- Ekaterina Kulchavenya
- Federal State Budgetary Institution 'The Novosibirsk Tuberculosis Research Institute (NTRI)' of the Ministry of Health of the Russian Federation, Novosibirsk Medical University, Russian Federation
| | - Andrey Cherednichenko
- Federal State Budgetary Institution 'The Novosibirsk Tuberculosis Research Institute (NTRI)' of the Ministry of Health of the Russian Federation, Russian Federation
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Terlizzi ME, Gribaudo G, Maffei ME. UroPathogenic Escherichia coli (UPEC) Infections: Virulence Factors, Bladder Responses, Antibiotic, and Non-antibiotic Antimicrobial Strategies. Front Microbiol 2017; 8:1566. [PMID: 28861072 PMCID: PMC5559502 DOI: 10.3389/fmicb.2017.01566] [Citation(s) in RCA: 333] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/02/2017] [Indexed: 12/21/2022] Open
Abstract
Urinary tract infections (UTIs) are one of the most common pathological conditions in both community and hospital settings. It has been estimated that about 150 million people worldwide develop UTI each year, with high social costs in terms of hospitalizations and medical expenses. Among the common uropathogens associated to UTIs development, UroPathogenic Escherichia coli (UPEC) is the primary cause. UPEC strains possess a plethora of both structural (as fimbriae, pili, curli, flagella) and secreted (toxins, iron-acquisition systems) virulence factors that contribute to their capacity to cause disease, although the ability to adhere to host epithelial cells in the urinary tract represents the most important determinant of pathogenicity. On the opposite side, the bladder epithelium shows a multifaceted array of host defenses including the urine flow and the secretion of antimicrobial substances, which represent useful tools to counteract bacterial infections. The fascinating and intricate dynamics between these players determine a complex interaction system that needs to be revealed. This review will focus on the most relevant components of UPEC arsenal of pathogenicity together with the major host responses to infection, the current approved treatment and the emergence of resistant UPEC strains, the vaccine strategies, the natural antimicrobial compounds along with innovative anti-adhesive and prophylactic approaches to prevent UTIs.
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Affiliation(s)
| | | | - Massimo E. Maffei
- Department of Life Sciences and Systems Biology, University of TurinTorino, Italy
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