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Casiano González A, Pacheco Villanueva A, Castro-Alarcón N, Méndez J, Oropeza R, Martínez-Santos VI. A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026. PeerJ 2024; 12:e17336. [PMID: 38784397 PMCID: PMC11114119 DOI: 10.7717/peerj.17336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Background Urinary tract infections (UTIs) are very common worldwide. According to their symptomatology, these infections are classified as pyelonephritis, cystitis, or asymptomatic bacteriuria (AB). Approximately 75-95% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which is an extraintestinal bacterium that possesses virulence factors for bacterial adherence and invasion in the urinary tract. In addition, UPEC possesses type 6 secretion systems (T6SS) as virulence mechanisms that can participate in bacterial competition and in bacterial pathogenicity. UPEC UMN026 carries three genes, namely, ECUMN_0231, ECUMN_0232, and ECUMN_0233, which encode three uncharacterized proteins related to the T6SS that are conserved in strains from phylogroups B2 and D and have been proposed as biomarkers of UTIs. Aim To analyze the frequency of the ECUMN_0231, ECUMN_0232, ECUMN_0233, and vgrG genes in UTI isolates, as well as their expression in Luria Bertani (LB) medium and urine; to determine whether these genes are related to UTI symptoms or bacterial competence and to identify functional domains on the putative proteins. Methods The frequency of the ECUMN and vgrG genes in 99 clinical isolates from UPEC was determined by endpoint PCR. The relationship between gene presence and UTI symptomatology was determined using the chi2 test, with p < 0.05 considered to indicate statistical significance. The expression of the three ECUMN genes and vgrG was analyzed by RT-PCR. The antibacterial activity of strain UMN026 was determined by bacterial competence assays. The identification of functional domains and the docking were performed using bioinformatic tools. Results The ECUMN genes are conserved in 33.3% of clinical isolates from patients with symptomatic and asymptomatic UTIs and have no relationship with UTI symptomatology. Of the ECUMN+ isolates, only five (15.15%, 5/33) had the three ECUMN and vgrG genes. These genes were expressed in LB broth and urine in UPEC UMN026 but not in all the clinical isolates. Strain UMN026 had antibacterial activity against UPEC clinical isolate 4014 (ECUMN-) and E. faecalis but not against isolate 4012 (ECUMN+). Bioinformatics analysis suggested that the ECUMN genes encode a chaperone/effector/immunity system. Conclusions The ECUMN genes are conserved in clinical isolates from symptomatic and asymptomatic patients and are not related to UTI symptoms. However, these genes encode a putative chaperone/effector/immunity system that seems to be involved in the antibacterial activity of strain UMN026.
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Affiliation(s)
- América Casiano González
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Arantxa Pacheco Villanueva
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Natividad Castro-Alarcón
- Microbiology Research Laboratory, Faculty of Chemical Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Julio Méndez
- Department of Molecular Microbiology, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ricardo Oropeza
- Department of Molecular Microbiology, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Damborg P, Pirolo M, Schøn Poulsen L, Frimodt-Møller N, Guardabassi L. Dogs Can Be Reservoirs of Escherichia coli Strains Causing Urinary Tract Infection in Human Household Contacts. Antibiotics (Basel) 2023; 12:1269. [PMID: 37627689 PMCID: PMC10451620 DOI: 10.3390/antibiotics12081269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/06/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
This study aimed to investigate the role played by pets as reservoirs of Escherichia coli strains causing human urinary tract infections (UTIs) in household contacts. Among 119 patients with community-acquired E. coli UTIs, we recruited 19 patients who lived with a dog or a cat. Fecal swabs from the household pet(s) were screened by antimicrobial selective culture to detect E. coli displaying the resistance profile of the human strain causing UTI. Two dogs shed E. coli isolates indistinguishable from the UTI strain by pulsed-field gel electrophoresis. Ten months later, new feces from these dogs and their owners were screened selectively and quantitatively for the presence of the UTI strain, followed by core-genome phylogenetic analysis of all isolates. In one pair, the resistance phenotype of the UTI strain occurred more frequently in human (108 CFU/g) than in canine feces (104 CFU/g), and human fecal isolates were more similar (2-7 SNPs) to the UTI strain than canine isolates (83-86 SNPs). In the other pair, isolates genetically related to the UTI strain (23-40 SNPs) were only detected in canine feces (105 CFU/g). These results show that dogs can be long-term carriers of E. coli strains causing UTIs in human household contacts.
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Affiliation(s)
- Peter Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (P.D.); (M.P.); (L.S.P.)
| | - Mattia Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (P.D.); (M.P.); (L.S.P.)
| | - Laura Schøn Poulsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (P.D.); (M.P.); (L.S.P.)
| | | | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (P.D.); (M.P.); (L.S.P.)
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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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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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Heltveit-Olsen SR, Sundvall PD, Gunnarsson R, Snaebjörnsson Arnljots E, Kowalczyk A, Godycki-Cwirko M, Platteel TN, Koning HAM, Groen WG, Åhrén C, Grude N, Verheij TJM, Hertogh CMPM, Lindbaek M, Hoye S. Methenamine hippurate to prevent recurrent urinary tract infections in older women: protocol for a randomised, placebo-controlled trial (ImpresU). BMJ Open 2022; 12:e065217. [PMID: 36319057 PMCID: PMC10098264 DOI: 10.1136/bmjopen-2022-065217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
INTRODUCTION Methenamine hippurate is a urinary antiseptic used as preventive treatment for recurrent urinary tract infections (UTIs) in some Scandinavian countries. However, the scientific evidence for the preventive effect and safety for longer-term use is limited. The aim of this study is to assess whether methenamine hippurate can reduce the incidence of UTIs in older women with recurrent UTIs. METHODS AND ANALYSIS The ImpresU consortium is a collaboration between Norway, Sweden, Poland and the Netherlands. The study is a randomised, controlled, triple-blind phase IV clinical trial. Women ≥70 years with recurrent UTIs are screened for eligibility in a general practice setting. We aim to include 400 women in total, with 100 recruited from each collaborating country. The participants are randomised to treatment with methenamine hippurate 1 g or placebo tablets two times per day for a treatment period of 6 months, followed by a drug-free follow-up period of 6 months. The primary outcome is number of antibiotic treatments for UTIs during the treatment period. The secondary outcomes include number of antibiotic treatments for UTIs during the follow-up period and self-reported symptom of severity and duration of UTI episodes. Differences in complications between the treatment groups are measured as safety outcomes. We also aim to investigate whether strain characteristics or phylogenetic subgroups of Escherichia coli present in the urine culture at inclusion have a modifying effect on the outcomes. ETHICS AND DISSEMINATION Ethical approvals are obtained in all participating countries. The results will be communicated in peer-reviewed journals and at scientific conferences. TRIAL REGISTRATION NUMBER ClinicalTrials.gov Registry (NCT04077580); EudraCT: 2018-002235-15.
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Affiliation(s)
- Silje Rebekka Heltveit-Olsen
- Antibiotic Centre for Primary Care, Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Pär-Daniel Sundvall
- General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Research, Education, Development & Innovation, Primary Health Care, Region Västra Götaland, Borås, Sweden
| | - Ronny Gunnarsson
- General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Research, Education, Development & Innovation, Primary Health Care, Region Västra Götaland, Borås, Sweden
| | - Egill Snaebjörnsson Arnljots
- General Practice/Family Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Research, Education, Development & Innovation, Primary Health Care, Region Västra Götaland, Borås, Sweden
| | - Anna Kowalczyk
- Centre for Family and Community Medicine, Faculty of Health Sciences, Medical University of Lodz, Lodz, Poland
| | - Maciek Godycki-Cwirko
- Centre for Family and Community Medicine, Faculty of Health Sciences, Medical University of Lodz, Lodz, Poland
| | - Tamara N Platteel
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hilde A M Koning
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Wim G Groen
- Department of Medicine for Older People, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Aging & Later Life, Amsterdam, The Netherlands
| | - Christina Åhrén
- Institute of Biomedicine, Department of Infectious Diseases and Centrum for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Swedish Strategic Program against Antimicrobial Resistance (Strama), Region Västra Götaland, Gothenburg, Sweden
| | - Nils Grude
- Antibiotic Centre for Primary Care, Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Theo J M Verheij
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Cees M P M Hertogh
- Department of Medicine for Older People, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Aging & Later Life, Amsterdam, The Netherlands
| | - Morten Lindbaek
- Antibiotic Centre for Primary Care, Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Sigurd Hoye
- Antibiotic Centre for Primary Care, Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
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Roussel C, Chabaud S, Lessard-Lord J, Cattero V, Pellerin FA, Feutry P, Bochard V, Bolduc S, Desjardins Y. UPEC Colonic-Virulence and Urovirulence Are Blunted by Proanthocyanidins-Rich Cranberry Extract Microbial Metabolites in a Gut Model and a 3D Tissue-Engineered Urothelium. Microbiol Spectr 2022; 10:e0243221. [PMID: 35972287 PMCID: PMC9603664 DOI: 10.1128/spectrum.02432-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/27/2022] [Indexed: 01/04/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) ecology-pathophysiology from the gut reservoir to its urothelium infection site is poorly understood, resulting in equivocal benefits in the use of cranberry as prophylaxis against urinary tract infections. To add further understanding from the previous findings on PAC antiadhesive properties against UPEC, we assessed in this study the effects of proanthocyanidins (PAC) rich cranberry extract microbial metabolites on UTI89 virulence and fitness in contrasting ecological UPEC's environments. For this purpose, we developed an original model combining a colonic fermentation system (SHIME) with a dialysis cassette device enclosing UPEC and a 3D tissue-engineered urothelium. Two healthy fecal donors inoculated the colons. Dialysis cassettes containing 7log10 CFU/mL UTI89 were immersed for 2h in the SHIME colons to assess the effect of untreated (7-day control diet)/treated (14-day PAC-rich extract) metabolomes on UPEC behavior. Engineered urothelium were then infected with dialysates containing UPEC for 6 h. This work demonstrated for the first time that in the control fecal microbiota condition without added PAC, the UPEC virulence genes were activated upstream the infection site, in the gut. However, PAC microbial-derived cranberry metabolites displayed a remarkable propensity to blunt activation of genes encoding toxin, adhesin/invasins in the gut and on the urothelium, in a donor-dependent manner. Variability in subjects' gut microbiota and ensuing contrasting cranberry PAC metabolism affects UPEC virulence and should be taken into consideration when designing cranberry efficacy clinical trials. IMPORTANCE Uropathogenic Escherichia coli (UPEC) are the primary cause of recurrent urinary tract infections (UTI). The poor understanding of UPEC ecology-pathophysiology from its reservoir-the gut, to its infection site-the urothelium, partly explains the inadequate and abusive use of antibiotics to treat UTI, which leads to a dramatic upsurge in antibiotic-resistance cases. In this context, we evaluated the effect of a cranberry proanthocyanidins (PAC)-rich extract on the UPEC survival and virulence in a bipartite model of a gut microbial environment and a 3D urothelium model. We demonstrated that PAC-rich cranberry extract microbial metabolites significantly blunt activation of UPEC virulence genes at an early stage in the gut reservoir. We also showed that altered virulence in the gut affects infectivity on the urothelium in a microbiota-dependent manner. Among the possible mechanisms, we surmise that specific microbial PAC metabolites may attenuate UPEC virulence, thereby explaining the preventative, yet contentious properties of cranberry against UTI.
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Affiliation(s)
- Charlène Roussel
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Stéphane Chabaud
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Jacob Lessard-Lord
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Valentina Cattero
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | - Félix-Antoine Pellerin
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Perrine Feutry
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
| | | | - Stéphane Bolduc
- Centre de Recherche en Organogenèse Expérimentale de l Université Laval/LOEX, Centre de Recherche du CHU de Québec‐Université Laval, Axe Médecine Régénératrice, Québec, Quebec, Canada
| | - Yves Desjardins
- Institute of Nutrition and Functional Foods (INAF), Faculty of Agriculture and Food Sciences, Laval University, Québec, Quebec, Canada
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Kudinha T, Kong F. Distribution of papG alleles among uropathogenic Escherichia coli from reproductive age women. J Biomed Sci 2022; 29:66. [PMID: 36068602 PMCID: PMC9450305 DOI: 10.1186/s12929-022-00848-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Extraintestinal Escherichia coli (E. coli) causing urinary tract infections (UTIs), and often referred to as uropathogenic E. coli (UPEC), are a major contributor to the morbidity of UTIs and associated healthcare costs. UPEC possess several virulence factors (VFs) for infecting and injuring the host. We studied the papG allele distribution, and its association with other VF genes and phylogenetic groups, amongst 836 UPEC and fecal isolates from reproductive age women. RESULTS The papGII gene was highly prevalent amongst pyelonephritis isolates (68%), whilst the majority, albeit smaller proportion, of cystitis isolates (31%) harboured the papGIII gene. Among the pyelonephritis and cystitis isolates, papG positive isolates on average had higher VF gene scores, and were more likely to belong to phylogenetic group B2, than their negative counterparts. This was mostly due to the contribution of papGII isolates, which on average contained more VF genes than their papGIII counterparts, irrespective of the uro-clinical syndrome. However, the papGII isolates from the pyelonephritis cohort had higher VF gene scores than the cystitis ones, suggesting presence of possible papGII clones with differing inferred virulence potential. Furthermore, papGII isolates were more likely to possess an intact pap gene operon than their papGIII counterparts. Also of note was the high proportion of isolates with the papGI allele which was not associated with other pap operon genes; and this finding has not been described before. CONCLUSIONS The association of the papGII gene with several VF genes compared to the papGIII gene, appears to explain the abundance of these genes in pyelonephritis and cystitis isolates, respectively.
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Affiliation(s)
- Timothy Kudinha
- NSW Health Pathology, Regional and Rural, Orange Base Hospital, Orange, NSW, 2800, Australia. .,School of Biomedical Sciences, Charles Sturt University, Orange Campus, 346 Leeds Parade, Orange, NSW, 2800, Australia.
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Westmead Hospital, Westmead, NSW, 2145, Australia
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Rui L, Lindbaek M, Gjelstad S. Preventive effect of methenamine in women with recurrent urinary tract infections - a case-control study. Scand J Prim Health Care 2022; 40:331-338. [PMID: 36369890 PMCID: PMC9848284 DOI: 10.1080/02813432.2022.2139363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Urinary tract infection (UTI) is the most common bacterial infection in women. In Norwegian general practice, methenamine has been prescribed for many years as long-term prevention and accounted for 20% of the total antibiotic prescribing in 2015, as measured in defined daily dosages (DDDs). The efficacy of methenamine is unknown. If shown to be effective, this drug may become an important preventive against UTI. OBJECTIVE To examine whether methenamine is preventive against recurrent UTI in women. DESIGN Data for all antibiotics used for UTIs dispensed from all pharmacies from 2005 to 2015 were collected from the Norwegian prescription database (NorPD). SUBJECTS Women aged ≥ 40 years with recurrent UTI, defined as ≥3 courses of UTI antibiotic/year, were included. MAIN OUTCOME MEASURES Patients using methenamine (cases) and those not using methenamine (controls) were compared. The numbers of UTI prescriptions during the 2 years before and after inclusion were analysed. Results: The yearly prevalence for recurrent UTI was 2.4% in women ≥ 40 years. The change in antibiotic use from 2 years before to 2 years after inclusion in the study differed significantly between groups: 44.6 and 34.9% reductions in the number of antibiotic prescriptions for UTI in the methenamine and control groups, respectively. The decrease in UTI antibiotic prescriptions (58.9%) was greater in patients with a higher consumption of antibiotics before starting methenamine. CONCLUSIONS Methenamine seems to be effective against recurrent UTI over the time span studied. The effect seems to be greater in patients with the highest number of recurrent UTIs. Key pointsMethenamine has been used for many years for prevention of recurrent UTI, but no studies have demonstrated a significant preventive effect of long time use.This study shows that methenamine seems to be effective for prevention in patients having recurrent UTI over 2 years or more.The effect seems to be larger in patients with a high number of UTIs over 2 years.
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Affiliation(s)
- Linda Rui
- Department of General Practice, Antibiotic Centre for Primary Care, Institute for Health and Society, University of Oslo, Oslo, Norway
| | - Morten Lindbaek
- Department of General Practice, Antibiotic Centre for Primary Care, Institute for Health and Society, University of Oslo, Oslo, Norway
- CONTACT Morten Lindbaek Department of General Practice, Antibiotic Centre for Primary Care, Institute for Health and Society, University of Oslo, Oslo, Norway
| | - Svein Gjelstad
- Department of General Practice, Antibiotic Centre for Primary Care, Institute for Health and Society, University of Oslo, Oslo, Norway
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The impact of the ST131 clone on recurrent ESBL-producing E. coli urinary tract infection: a prospective comparative study. Sci Rep 2022; 12:10048. [PMID: 35710924 PMCID: PMC9203711 DOI: 10.1038/s41598-022-14177-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/02/2022] [Indexed: 11/24/2022] Open
Abstract
The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is of great concern. Almost one third of patients with UTI, develop recurrent UTI (RUTI). We followed 297 patients for one year after their first episode of UTI due to ESBL-E. coli. Our aim was to evaluate the impact of the globally dominant sequence type (ST)131 clone and its clades, on the risk of subsequent recurrences with ESBL-E. coli. Isolates from patients developing RUTI (68/297) were compared with those from patients with sporadic UTI (SUTI, 229/297). No association was found between RUTI and the two most prevalent phylogroups B2 and D, blaCTX-M genes, or resistance profile. Half of the patients with RUTI were infected with ST131 isolates. Clade C2 were in dominance (50/119) among ST131 isolates. They were more common in patients with RUTI than SUTI (28% vs 13%) and multivariate analysis showed an increased odds-ratio (OR = 2.21, p = 0.033) for recurrences in patients infected with these isolates as compared to non-ST131 isolates. Detecting specific biomarkers, as ST131 clade C2, in ESBL-E. coli UTI isolates may aid in prediction of RUTI and improve diagnostics and care of patients with a risk of ESBL-E. coli recurrences.
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Non-antibiotic Approaches to Preventing Pediatric UTIs: a Role for D-Mannose, Cranberry, and Probiotics? Curr Urol Rep 2022; 23:113-127. [PMID: 35441976 DOI: 10.1007/s11934-022-01094-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW While antibiotics have been a staple in the management and even prevention of urinary tract infections (UTIs), it is not without significant consequences due to intolerance and development of antibiotic resistant bacteria. These concerns necessitate alternatives to antibiotic use in the management of pediatric UTIs. This review seeks to evaluate non-antibiotic means of preventing UTI in the pediatric population. RECENT FINDINGS The search for preventative alternatives to antibiotics has included D-mannose, cranberry, and probiotics. These products similarly work through competitive inhibition of uropathogens in the urinary tract. Pediatric studies exist highlighting the use of cranberry extract/juice and probiotics in UTI prevention, although significant heterogeneity amongst studies have limited overarching recommendations for their use. Data of D-mannose use is extrapolated from adult literature. More studies are required in the utility of each treatment, with some emphasis on larger sample sizes and clarifications regarding dosing and formulation.
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Kondo T, Sakamoto K, Morinaga Y, Miyata Y, Yanagihara K, Sakai H. Escherichia coli ST131 isolated from urological patients can acquire plasmid-mediated extended spectrum β-lactamase from other bacteria with high frequency. Int J Urol 2022; 29:587-594. [PMID: 35288997 DOI: 10.1111/iju.14845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/20/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To investigate the prevalence of the clonal group Escherichia coli ST131 in urologic patients, and to clarify the mechanisms underlying the high prevalence of the antimicrobial resistant genes in ST131. METHODS We used 65 Escherichia coli strains collected from the Department of Urology, Nagasaki University Hospital, between January 2018 and December 2018. All of them underwent multilocus sequence typing and were analyzed for genes associated with quinolone resistance and extended-spectrum β-lactamases. To compare ST131 and non-ST131 strains, bacterial conjugation experiments and intestinal colonization evaluations were performed. RESULTS ST131 was the most dominant among all the strains, along with levofloxacin resistant strains, and extended-spectrum β-lactamases positive strains (32%, 63%, and 73%, respectively). 12 out of 15 extended-spectrum β-lactamases-producing Escherichia coli strains harbored CTX-M-9. In particular, all extended-spectrum β-lactamases-producing ST131 strains possessed CTX-M-9. The proportions of ST131 strains with or without quinolone resistance-determining region mutations were significantly higher and lower, respectively, than that of non-ST131 strains (P = 0.0002 and P < 0.0001, respectively). When Klebsiella pneumoniae was used as a donor, three ST131 strains acquired extended-spectrum β-lactamases a total of 16 times (six, four, and six times each), which was significantly more than that in one of the non-ST131 strains (two times). The amount of bacteria was significantly lower in the ST131 strains than in the non-ST131 strains administered to mice. Both the ST131 and non-ST131 strains increased again after the administration of vancomycin, even after the colony was not detected. CONCLUSIONS These results support the mechanisms underlying the prevalence of ST131 strains in hospitals, particularly in urologic patients.
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Affiliation(s)
- Tsubasa Kondo
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kei Sakamoto
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yasuyoshi Miyata
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hideki Sakai
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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12
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Kenneally C, Murphy CP, Sleator RD, Culligan EP. The Urinary Microbiome and Biological Therapeutics: Novel Therapies For Urinary Tract Infections. Microbiol Res 2022; 259:127010. [DOI: 10.1016/j.micres.2022.127010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/12/2022]
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13
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Molecular Epidemiology of Multidrug-Resistant Uropathogenic Escherichia coli O25b Strains Associated with Complicated Urinary Tract Infection in Children. Microorganisms 2021; 9:microorganisms9112299. [PMID: 34835425 PMCID: PMC8623209 DOI: 10.3390/microorganisms9112299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Uropathogenic Escherichia coli (UPEC) has increased the incidence of urinary tract infection (UTI). It is the cause of more than 80% of community-acquired cystitis cases and more than 70% of uncomplicated acute pyelonephritis cases. Aim: The present study describes the molecular epidemiology of UPEC O25b clinical strains based on their resistance profiles, virulence genes, and genetic diversity. Methods: Resistance profiles were identified using the Kirby–Bauer method, including the phenotypic production of extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs). The UPEC serogroups, phylogenetic groups, virulence genes, and integrons were determined via multiplex PCR. Genetic diversity was established using pulsed-field gel electrophoresis (PFGE), and sequence type (ST) was determined via multilocus sequence typing (MLST). Results: UPEC strains (n = 126) from hospitalized children with complicated UTIs (cUTIs) were identified as O25b, of which 41.27% were multidrug resistant (MDR) and 15.87% were extensively drug resistant (XDR). The O25b strains harbored the fimH (95.23%), csgA (91.26%), papGII (80.95%), chuA (95.23%), iutD (88.09%), satA (84.92%), and intl1 (47.61%) genes. Moreover, 64.28% were producers of ESBLs and had high genetic diversity. ST131 (63.63%) was associated primarily with phylogenetic group B2, and ST69 (100%) was associated primarily with phylogenetic group D. Conclusion: UPEC O25b/ST131 harbors a wide genetic diversity of virulence and resistance genes, which contribute to cUTIs in pediatrics.
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14
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Singh PK, Johnston BD, Johnson JR, Donnenberg MS. Draft genome sequences of concurrent Escherichia coli blood and fecal isolates from a patient with bacteremia and diarrhea belie BioFire-based detection of fecal enteropathogenic E. coli. Pathog Dis 2021; 78:5913320. [PMID: 32997108 DOI: 10.1093/femspd/ftaa058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/27/2020] [Indexed: 11/12/2022] Open
Abstract
The BioFire FilmArray® Gastrointestinal panel is a multiplex PCR assay widely used to determine the etiology of infectious gastroenteritis directly from stool specimens. Recently a positive BioFire result for fecal enteropathogenic Escherichia coli (EPEC) was reported by a clinical microbiology laboratory for an adult patient with diarrhea and bacteremia. Since EPEC infrequently infects adults and rarely causes bacteremia, we isolated fecal E. coli and characterized the patient's blood and fecal E. coli isolates. Draft genome sequencing using a combination of methods indicated that the blood and fecal strains are virtually identical, are from sequence type 963 (phylogroup D) and exhibit neither the virulence genes characteristic of EPEC and extraintestinal pathogenic E. coli (ExPEC) nor classic EPEC-associated phenotypes. These findings support a gut source for the patient's bacteremia but exclude EPEC as the causative organism, and suggest that results of multiplex PCR assays from complex samples can be misleading, and should be interpreted with caution when they are discordant with clinical information. BioProject accession numbers for strains MVAST5574 and MVAST5635 genomes are PRJNA611789 and PRJNA611804, respectively.
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Affiliation(s)
- Pradip Kumar Singh
- Virginia Commonwealth University, 1101 East Marshall Street, Sanger Hall Room 1-055C, Richmond, VA 23298, USA
| | - Brian D Johnston
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota, 420 Delaware Street SE, MMC 250, Minneapolis, MN 55455, USA.,Infectious Diseases (111F), Minneapolis VA Medical Center, 1 Veterans Drive, Minneapolis, MN 55417, USA
| | - James R Johnson
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota, 420 Delaware Street SE, MMC 250, Minneapolis, MN 55455, USA.,Infectious Diseases (111F), Minneapolis VA Medical Center, 1 Veterans Drive, Minneapolis, MN 55417, USA
| | - Michael S Donnenberg
- Virginia Commonwealth University, 1101 East Marshall Street, Sanger Hall Room 1-055C, Richmond, VA 23298, USA
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15
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Jones-Freeman B, Chonwerawong M, Marcelino VR, Deshpande AV, Forster SC, Starkey MR. The microbiome and host mucosal interactions in urinary tract diseases. Mucosal Immunol 2021; 14:779-792. [PMID: 33542492 DOI: 10.1038/s41385-020-00372-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of waste products and maintaining systemic homeostasis. In this capacity, the urinary tract is impacted by its interactions with other mucosal sites, including the genitourinary and gastrointestinal systems. Each of these sites harbors diverse ecosystems of microbes termed the microbiota, that regulates complex interactions with the local and systemic immune system. It remains unclear whether changes in the microbiota and associated metabolites may be a consequence or a driver of urinary tract diseases. Here, we review the current literature, investigating the impact of the microbiota on the urinary tract in homeostasis and disease including urinary stones, acute kidney injury, chronic kidney disease, and urinary tract infection. We propose new avenues for exploration of the urinary microbiome using emerging technology and discuss the potential of microbiome-based medicine for urinary tract conditions.
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Affiliation(s)
- Bernadette Jones-Freeman
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Aniruddh V Deshpande
- Priority Research Centre GrowUpWell, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia.,Department of Pediatric Urology and Surgery, John Hunter Children's Hospital, New Lambton Heights, NSW, Australia.,Urology Unit, Department of Pediatric Surgery, Children's Hospital at Westmead, Sydney Children's Hospital Network, Westmead, NSW, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Malcolm R Starkey
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia. .,Priority Research Centre GrowUpWell, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia.
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16
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Nielsen KL, Stegger M, Kiil K, Lilje B, Ejrnæs K, Leihof RF, Skjøt-Rasmussen L, Godfrey P, Monsen T, Ferry S, Hammerum AM, Frimodt-Møller N. Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections. Microorganisms 2021; 9:microorganisms9071416. [PMID: 34209190 PMCID: PMC8303582 DOI: 10.3390/microorganisms9071416] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 01/04/2023] Open
Abstract
Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0-13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.
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Affiliation(s)
- Karen Leth Nielsen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.S.); (K.K.); (B.L.); (K.E.); (R.F.L.); (L.S.-R.); (A.M.H.)
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.S.); (K.K.); (B.L.); (K.E.); (R.F.L.); (L.S.-R.); (A.M.H.)
| | - Berit Lilje
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.S.); (K.K.); (B.L.); (K.E.); (R.F.L.); (L.S.-R.); (A.M.H.)
| | - Karen Ejrnæs
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.S.); (K.K.); (B.L.); (K.E.); (R.F.L.); (L.S.-R.); (A.M.H.)
- Department of Pathology, Herlev Hospital, 2730 Herlev, Denmark
| | - Rikke Fleron Leihof
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.S.); (K.K.); (B.L.); (K.E.); (R.F.L.); (L.S.-R.); (A.M.H.)
- Analytical Development, Novo Nordisk, 2880 Måløv, Denmark
| | - Line Skjøt-Rasmussen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.S.); (K.K.); (B.L.); (K.E.); (R.F.L.); (L.S.-R.); (A.M.H.)
- Animal Health Innovation, Chr. Hansen, 2970 Hørsholm, Denmark
| | - Paul Godfrey
- Genome Sequencing and Analysis Program, Institute of Technology, Broad Institute of Harvard and Massachusetts, Cambridge, MA 02142, USA;
| | - Tor Monsen
- Department of Clinical Microbiology, University of Umeå, 901 04 Umeå, Sweden; (T.M.); (S.F.)
| | - Sven Ferry
- Department of Clinical Microbiology, University of Umeå, 901 04 Umeå, Sweden; (T.M.); (S.F.)
| | - Anette M. Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.S.); (K.K.); (B.L.); (K.E.); (R.F.L.); (L.S.-R.); (A.M.H.)
| | - Niels Frimodt-Møller
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark;
- Correspondence: ; Tel.: +45-35457738
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17
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Verschuuren TD, van Hout D, Arredondo-Alonso S, Fluit AC, Reuland EA, Top J, Schürch AC, Bosch T, Bonten MJM, Kluytmans JAJW, Willems RJL. Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014-17). J Antimicrob Chemother 2021; 76:901-908. [PMID: 33428729 PMCID: PMC7953314 DOI: 10.1093/jac/dkaa534] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The human gut microbiota is an important reservoir of ESBL-producing Escherichia coli (ESBL-Ec). Community surveillance studies of ESBL-Ec to monitor circulating clones and ESBL genes are logistically challenging and costly. OBJECTIVES To evaluate if isolates obtained in routine clinical practice can be used as an alternative to monitor the distribution of clones and ESBL genes circulating in the community. METHODS WGS was performed on 451 Dutch ESBL-Ec isolates (2014-17), including 162 community faeces and 289 urine and blood isolates. We compared proportions of 10 most frequently identified STs, PopPUNK-based sequence clusters (SCs) and ESBL gene subtypes and the degree of similarity using Czekanowski's proportional similarity index (PSI). RESULTS Nine out of 10 most prevalent STs and SCs and 8/10 most prevalent ESBL genes in clinical ESBL-Ec were also the most common types in community faeces. The proportions of ST131 (39% versus 23%) and SC131 (40% versus 25%) were higher in clinical isolates than in community faeces (P < 0.01). Within ST131, H30Rx (C2) subclade was more prevalent among clinical isolates (55% versus 26%, P < 0.01). The proportion of ESBL gene blaCTX-M-1 was lower in clinical isolates (5% versus 18%, P < 0.01). Czekanowski's PSI confirmed that the differences in ESBL-Ec from community faeces and clinical isolates were limited. CONCLUSIONS Distributions of the 10 most prevalent clones and ESBL genes from ESBL-Ec community gut colonization and extra-intestinal infection overlapped in majority, indicating that isolates from routine clinical practice could be used to monitor ESBL-Ec clones and ESBL genes in the community.
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Affiliation(s)
- T D Verschuuren
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - D van Hout
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - S Arredondo-Alonso
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - E A Reuland
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Saltro Diagnostic Center for Primary Care, Utrecht, The Netherlands
- The Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J Top
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A C Schürch
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - T Bosch
- The Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - M J M Bonten
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - J A J W Kluytmans
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - R J L Willems
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
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18
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Leihof RF, Nielsen KL, Frimodt-Møller N. Asymptomatic Bacteriuria (ABU) in Elderly: Prevalence, Virulence, Phylogeny, Antibiotic Resistance and Complement C3 in Urine. Microorganisms 2021; 9:390. [PMID: 33672892 PMCID: PMC7918685 DOI: 10.3390/microorganisms9020390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/18/2022] Open
Abstract
Background: The incidence of asymptomatic bacteriuria (ABU) increases with age and is most common for persons 80 years of age and above and in elderly living in nursing homes. The distinction between ABU and urinary tract infection (UTI) is often difficult, especially in individuals, who are unable to communicate their symptoms, and there is a lack of objective methods to distinguish between the two entities. This can lead to overuse of antibiotics, which results in the selection and dissemination of antibiotic resistant isolates. Materials and methods: From voided midstream urine samples of 211 participants ≥60 years old from nursing homes, an activity center and a general practitioners clinic, we collected 19 ABU, 16 UTI and 22 control urine samples and compared them with respect to levels of complement component C3 in urine as determined by an ELISA assay relative to creatinine levels in the same urine samples, as measured by a creatinine assay. Further, we studied all Escherichia coli isolates for selected virulence genes by multiplex PCR, and by whole-genome sequencing (WGS) for genotypes and phylogenetic clustering. Antibiotic susceptibility was determined by microtiter broth dilution. Results: We identified a prevalence of ABU of 18.9% in nursing home residents, whereas ABU was only found in 4% of elderly living in the community (p < 0.001). E. coli from ABU patients were significantly more antibiotic resistant than E. coli from UTIs (p = 0.01). Prevalence of classical virulence genes, detected by multiplex PCR, was similar in E. coli isolates from ABU and UTI patients. Whole-genome sequencing of the E. coli isolates showed no specific clustering of ABU isolates compared to UTI isolates. Three isolates from three different individuals from one of the nursing homes showed signs of transmission. We demonstrated a significantly increased level of C3/creatinine ratio in ABU and UTI samples compared to healthy controls; however, there was no significant difference between the ABU and UTI group with respect to C3 level, or virulence factor genes. Conclusion: ABU was significantly more prevalent in the elderly residing in nursing homes than in the elderly living at home. Antibiotic resistance was more prevalent in E. coli from nursing homes than in UTI isolates, but there was no difference in prevalence of virulence associated genes between the two groups and no phylogenetic clustering, as determined by WGS relative to the two types of E. coli bacteriuria. The similar complement C3 response in ABU and UTI patients may indicate that ABU should be reconsidered as an infection albeit without symptoms.
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Affiliation(s)
- Rikke Fleron Leihof
- Department of Microbiology and Infection Control, Statens Serum Institut, 2200 Copenhagen, Denmark;
| | - Karen Leth Nielsen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark;
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19
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Riley LW. Distinguishing Pathovars from Nonpathovars: Escherichia coli. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0014-2020. [PMID: 33385193 PMCID: PMC10773148 DOI: 10.1128/microbiolspec.ame-0014-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
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Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
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20
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Biggel M, Xavier BB, Johnson JR, Nielsen KL, Frimodt-Møller N, Matheeussen V, Goossens H, Moons P, Van Puyvelde S. Horizontally acquired papGII-containing pathogenicity islands underlie the emergence of invasive uropathogenic Escherichia coli lineages. Nat Commun 2020; 11:5968. [PMID: 33235212 PMCID: PMC7686366 DOI: 10.1038/s41467-020-19714-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/27/2020] [Indexed: 12/29/2022] Open
Abstract
Escherichia coli is the leading cause of urinary tract infection, one of the most common bacterial infections in humans. Despite this, a genomic perspective is lacking regarding the phylogenetic distribution of isolates associated with different clinical syndromes. Here, we present a large-scale phylogenomic analysis of a spatiotemporally and clinically diverse set of 907 E. coli isolates, including 722 uropathogenic E. coli (UPEC) isolates. A genome-wide association approach identifies the (P-fimbriae-encoding) papGII locus as the key feature distinguishing invasive UPEC, defined as isolates associated with severe UTI, i.e., kidney infection (pyelonephritis) or urinary-source bacteremia, from non-invasive UPEC, defined as isolates associated with asymptomatic bacteriuria or bladder infection (cystitis). Within the E. coli population, distinct invasive UPEC lineages emerged through repeated horizontal acquisition of diverse papGII-containing pathogenicity islands. Our findings elucidate the molecular determinants of severe UTI and have implications for the early detection of this pathogen.
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Affiliation(s)
- Michael Biggel
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Basil B Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - James R Johnson
- Veterans Affairs Medical Center and University of Minnesota, Minneapolis, MN, USA
| | - Karen L Nielsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | | | - Veerle Matheeussen
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Laboratory of Clinical Microbiology, Antwerp University Hospital, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Laboratory of Clinical Microbiology, Antwerp University Hospital, Antwerp, Belgium
| | - Pieter Moons
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sandra Van Puyvelde
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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21
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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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22
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Martinson JNV, Walk ST. Escherichia coli Residency in the Gut of Healthy Human Adults. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0003-2020. [PMID: 32978935 PMCID: PMC7523338 DOI: 10.1128/ecosalplus.esp-0003-2020] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Indexed: 12/22/2022]
Abstract
Escherichia coli is one of the most well-studied bacterial species, but several significant knowledge gaps remain regarding its ecology and natural history. Specifically, the most important factors influencing its life as a member of the healthy human gut microbiome are either underevaluated or currently unknown. Distinct E. coli population dynamics have been observed over the past century from a handful of temporal studies conducted in healthy human adults. Early studies using serology up to the most recent studies using genotyping and DNA sequencing approaches have all identified long-lived E. coli residents and short-lived transients. This review summarizes these discoveries and other studies that focused on the underlying mechanisms that lead to establishment and maintenance of E. coli residency in healthy human adults. Many fundamental knowledge gaps remain and are highlighted with the hope of facilitating future studies in this exciting research area.
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Affiliation(s)
| | - Seth T Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717
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23
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Massip C, Oswald E. Siderophore-Microcins in Escherichia coli: Determinants of Digestive Colonization, the First Step Toward Virulence. Front Cell Infect Microbiol 2020; 10:381. [PMID: 32974212 PMCID: PMC7472721 DOI: 10.3389/fcimb.2020.00381] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Siderophore-microcins are antimicrobial peptides produced by enterobacteria, especially Escherichia coli and Klebsiella pneumoniae strains. The antibiotic peptide is post-translationally modified by the linkage of a siderophore moiety. Therefore, it can enter and kill phylogenetically related bacteria by a “Trojan Horse” stratagem, by mimicking the iron–siderophore complexes. Consequently, these antimicrobial peptides are key determinants of bacterial competition within the intestinal niche, which is the reservoir for pathogenic E. coli. The most frequent extraintestinal infections caused by E. coli are urinary tract infections. Uropathogenic E. coli (UPEC) can produce many virulence factors, including siderophore-microcins. Siderophore-microcins are chromosomally encoded by small genomic islands that exhibit conserved organization. In UPEC, the siderophore-microcin gene clusters and biosynthetic pathways differ from the “archetypal” models described in fecal strains. The gene cluster is shorter. Thus, active siderophore-microcin production requires proteins from two other genomic islands that also code for virulence factors. This functional and modular synergy confers a strong selective advantage for the domination of the colonic niche, which is the first step toward infection. This optimization of genetic resources might favor the selection of additional virulence factors, which are essential in the subsequent steps of pathogenesis in E. coli infection.
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Affiliation(s)
- Clémence Massip
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,Service de Bactériologie-Hygiène, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,Service de Bactériologie-Hygiène, Hôpital Purpan, CHU de Toulouse, Toulouse, France
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24
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Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020; 12:71. [PMID: 32791981 PMCID: PMC7427293 DOI: 10.1186/s13073-020-00765-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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25
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Matsui Y, Hu Y, Rubin J, de Assis RS, Suh J, Riley LW. Multilocus sequence typing of Escherichia coli isolates from urinary tract infection patients and from fecal samples of healthy subjects in a college community. Microbiologyopen 2020; 9:1225-1233. [PMID: 32189451 PMCID: PMC7294302 DOI: 10.1002/mbo3.1032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
Community-acquired urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. Escherichia coli is the most common cause of community-acquired UTI. In general, UTI results from E. coli in the intestine that enters the bladder via the urethra. However, whether these E. coli strains that cause UTI represent members of the intestinal commensal E. coli or a distinct subgroup of pathogenic E. coli remains unestablished. Here, we analyzed E. coli isolates from fecal samples of healthy volunteers and urine samples of UTI patients obtained from a university-affiliated health center. The E. coli isolates were genotyped by multilocus sequence typing (MLST). From May to October 2018, we analyzed 89 E. coli isolates from 76 (75%) rectal swabs from 113 unique healthy volunteers. We also analyzed 106 (27%) E. coli isolates from 398 unique urine samples collected between August and October 2018. Fecal and urine E. coli isolates each contained 31 distinct sequence types (STs). Nine STs were shared by fecal and urine E. coli isolates, which accounted for approximately 50% of urine isolates typed by MLST. Among the shared genotypes, ST10 and ST131 were significantly more frequently found in fecal samples, whereas ST95 and ST127 were significantly more frequently recovered from UTI samples. ST73 was found only among urine samples. These E. coli genotypes clustered and fluctuated over time. These observations suggest that E. coli genotypes found to cause UTI transiently colonize the intestine and that their primary reservoir may reside outside of the human intestine.
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Affiliation(s)
- Yusuke Matsui
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Yuan Hu
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Julia Rubin
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Reginara Souza de Assis
- Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Joy Suh
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
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26
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Coussement J, Argudín MA, Heinrichs A, Racapé J, de Mendonça R, Nienhaus L, Le Moine A, Roisin S, Dodémont M, Jacobs F, Abramowicz D, Johnston BD, Johnson JR, Denis O. Host and microbial factors in kidney transplant recipients with Escherichia coli acute pyelonephritis or asymptomatic bacteriuria: a prospective study using whole-genome sequencing. Nephrol Dial Transplant 2020; 34:878-885. [PMID: 30304506 DOI: 10.1093/ndt/gfy292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Urinary tract infection is the most common infection among kidney transplant recipients (KTRs). Many transplant physicians fear that host compromise will allow low-virulence strains to cause pyelonephritis in KTRs, so they often treat asymptomatic bacteriuria with antibiotics. Identification of the host/microbe factors that determine the clinical presentation (i.e. pyelonephritis versus asymptomatic bacteriuria) once an Escherichia coli strain enters a KTRs bladder could inform management decisions. METHODS We prospectively collected all E. coli isolates causing either pyelonephritis or asymptomatic bacteriuria in KTRs at our institution (December 2012-June 2015). Whole-genome sequencing was used to assess bacterial characteristics (carriage of 48 virulence genes and phylogenetic and clonal background). Host parameters were also collected. RESULTS We analysed 72 bacteriuria episodes in 54 KTRs (53 pyelonephritis, 19 asymptomatic bacteriuria). The pyelonephritis and asymptomatic bacteriuria isolates exhibited a similar total virulence gene count per isolate [median 18 (range 5-33) and 18 (5-30), respectively; P = 0.57] and for individual virulence genes differed significantly only for the prevalence of the pap operon (pyelonephritis 39%,versus asymptomatic bacteriuria 0%; P = 0.002). No other significant between-group differences were apparent for 86 other bacterial and host variables. CONCLUSIONS Our findings suggest that bacterial adherence plays a role in the pathogenesis of pyelonephritis in KTRs despite significantly altered host urinary tract anatomy and weakened immunity. Whether KTRs might benefit from targeted therapies (e.g. vaccination or inhibitors of fimbrial adhesion) has yet to be studied.
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Affiliation(s)
- Julien Coussement
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Division of Infectious Diseases, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Maria Angeles Argudín
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Amélie Heinrichs
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Judith Racapé
- Research Center "Biostatistiques, Epidémiologie et Recherche Clinique", École de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium.,Department of Nephrology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Ricardo de Mendonça
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Louise Nienhaus
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Alain Le Moine
- Department of Nephrology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Sandrine Roisin
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Magali Dodémont
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Frédérique Jacobs
- Division of Infectious Diseases, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Daniel Abramowicz
- Department of Nephrology-Hypertension, Universitair Ziekenhuis Antwerpen, Antwerp University, Antwerpen, Belgium
| | | | - James R Johnson
- Minneapolis Veterans Health Care System, Minneapolis, MN, USA
| | - Olivier Denis
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,École de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
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27
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Urinary tract infections: microbial pathogenesis, host-pathogen interactions and new treatment strategies. Nat Rev Microbiol 2020; 18:211-226. [PMID: 32071440 DOI: 10.1038/s41579-020-0324-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
Urinary tract infections (UTIs) are common, recurrent infections that can be mild to life-threatening. The continued emergence of antibiotic resistance, together with our increasing understanding of the detrimental effects conferred by broad-spectrum antibiotic use on the health of the beneficial microbiota of the host, has underscored the weaknesses in our current treatment paradigm for UTIs. In this Review, we discuss how recent microbiological, structural, genetic and immunological studies have expanded our understanding of host-pathogen interactions during UTI pathogenesis. These basic scientific findings have the potential to shift the strategy for UTI treatment away from broad-spectrum antibiotics targeting conserved aspects of bacterial replication towards pathogen-specific antibiotic-sparing therapeutics that target core determinants of bacterial virulence at the host-pathogen interface.
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28
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Risk factors for fecal carriage of drug-resistant Escherichia coli: a systematic review and meta-analysis. Antimicrob Resist Infect Control 2020; 9:31. [PMID: 32046786 PMCID: PMC7014593 DOI: 10.1186/s13756-020-0691-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/30/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Antimicrobial resistance is a serious public health problem. Fecal carriage of drug-resistant bacteria has been suggested as an important source of antimicrobial resistant genes (ARGs). We aimed to identify risk factors associated with fecal carriage of drug-resistant commensal Escherichia coli among healthy adult population. METHODS We conducted a systematic review and meta-analysis following the PRISMA guideline. We identified observational studies published from 2014 to 2019 through PubMed, Embase, and Web of Science. Studies were eligible if they investigated and reported risk factors and accompanying measure of associations for fecal carriage of drug-resistant E. coli for healthy population aged 18-65. Data on risk factors assessed in three or more studies were extracted. RESULTS Fifteen of 395 studies involving 11480 healthy individuals were included. The pooled prevalence of drug-resistant Enterobacteriaceae was 14% (95% confidence interval [CI] 8-23%). Antimicrobial use within the 12 months prior to stool culture (odds ratio [OR] 1.84 [95%CI 1.35-2.51]), diarrhea symptoms (OR 1.56 [95%CI 1.09-2.25]), travel to India (OR 4.15 [95%CI 2.54-6.78]), and vegetarian diet (OR 1.60 [95%CI 1.00(1.0043)-2.56(2.5587)]) were associated with increased risk of fecal carriage of drug-resistant E. coli. Among travellers, antimicrobial use (OR 2.81 [95%CI 1.47-5.36]), diarrhea symptoms (OR 1.65 [95%CI 1.02-2.68]), travel to India (OR 3.80 [95%CI 2.23-6.47]), and vegetarian diet (OR 1.92 [95%CI 1.13-3.26]) were associated with increased risk. Among general adult population, antimicrobial use (OR 1.51 [95%CI 1.17-1.94]), diarrhea symptoms (OR 1.53 [95%CI 1.27-1.84]), and travel to Southeast Asia (OR 1.67 [95%CI 1.02-2.73]) were associated with the increased risk of drug-resistant E. coli carriage. CONCLUSIONS The findings indicate that dietary habit as well as past antimicrobial use and travel to high-risk country are associated with the risk of fecal carriage of drug-resistant commensal E. coli.
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29
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Nielsen DW, Ricker N, Barbieri NL, Allen HK, Nolan LK, Logue CM. Outer membrane protein A (OmpA) of extraintestinal pathogenic Escherichia coli. BMC Res Notes 2020; 13:51. [PMID: 32005127 PMCID: PMC6995065 DOI: 10.1186/s13104-020-4917-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/22/2020] [Indexed: 02/05/2023] Open
Abstract
Objective Extraintestinal Pathogenic E. coli (ExPEC), are responsible for host diseases such as Neonatal Meningitis Escherichia coli (NMEC), the second-leading cause of neonatal bacterial meningitis, Avian Pathogenic E. coli (APEC), a cause of extraintestinal disease in poultry, and Uropathogenic E. coli (UPEC), the most common cause of urinary tract infections. Virulence factors associated with NMEC include outer membrane protein A (OmpA) and type I fimbriae (FimH), which also occur in APEC and UPEC. OmpA contributes to NMEC’s ability to cross the blood–brain barrier, persist in the bloodstream and has been identified as a potential vaccine target for ExPEC, however the protein has amino acid variants, which may influence virulence of strains or alter vaccine efficacy. Although OmpA is present in virtually all E. coli, differences in its amino acid residues have yet to be surveyed in ExPEC. Results Here the ompA gene (n = 399) from ExPEC collections were sequenced and translated in silico. Twenty-five different OmpA polymorphism patterns were identified. Seven polymorphism patterns were significantly associated with an ExPEC subpathotype, but chromosomal history most likely accounts for most differences found. The differences in OmpA protein sequences suggest that OmpA may influence variation in virulence and host specificity within ExPEC subpathotypes.
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Affiliation(s)
- Daniel W Nielsen
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1802 University Blvd, Ames, IA, 50011, USA.,Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, USA
| | - Nicole Ricker
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, USA.,Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Nicolle L Barbieri
- Department of Population Health, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA, 30602, USA
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, USA
| | - Lisa K Nolan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Catherine M Logue
- Department of Population Health, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Drive, Athens, GA, 30602, USA.
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30
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Stegger M, Leihof RF, Baig S, Sieber RN, Thingholm KR, Marvig RL, Frimodt-Møller N, Nielsen KL. A snapshot of diversity: Intraclonal variation of Escherichia coli clones as commensals and pathogens. Int J Med Microbiol 2020; 310:151401. [PMID: 32037036 DOI: 10.1016/j.ijmm.2020.151401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/17/2019] [Accepted: 01/12/2020] [Indexed: 12/31/2022] Open
Abstract
Whole-genome sequencing has enabled detailed studies on bacterial evolution during infection, but there is limited knowledge on intraclonal variation. In this study, we sought to provide a snapshot of the intraclonal diversity of Escherichia coli as both commensal in the faecal environment and pathogen during urinary tract infection, respectively. This was performed by whole-genome sequencing and analyses of single nucleotide polymorphisms (SNPs) and gene-content variation in ten isolates belonging to the same clone and isolated from rectal swabs or urine samples. We identified only one clone in eight of the nine urines sampled (89 %). In both the commensal and pathogenic state, the within-host diversity was limited with intraclonal SNP diversity of 0-2 non-synonymous SNPs for each clone. The genetic diversity showed variation in gene content in a range of 2-15 genes in total for all clones, including genes positioned on plasmids, and in the K- and O-antigen cluster. The observed SNP- and gene variation shows that sampling of one colony would be enough for surveillance, outbreak investigations and clonal evolution. However, for studies of adaptation during or between colonization and infection, this variation is relevant to consider.
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Affiliation(s)
- Marc Stegger
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Rikke Fleron Leihof
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sharmin Baig
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Karen Rønø Thingholm
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark; Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | | | - Karen Leth Nielsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.
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Massip C, Chagneau CV, Boury M, Oswald E. The synergistic triad between microcin, colibactin, and salmochelin gene clusters in uropathogenic Escherichia coli. Microbes Infect 2020; 22:144-147. [PMID: 31954842 DOI: 10.1016/j.micinf.2020.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 01/12/2023]
Abstract
A functional synergy was previously demonstrated between microcin, salmochelin and colibactin islands in Escherichia coli strains from B2 phylogroup. We aimed to determine this association prevalence in uropathogenic E. coli, and whether it was predictive of the infection severity in a collection of 225 E. coli strains from urinary samples. The high prevalence of this triad, even if it wasn't correlated with infection severity, suggested that it might not be a virulence factor per se within the urinary tract, but would promote its colonization. This triad would enable the strain to dominate the rectal reservoir with a minimal genetic cost.
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Affiliation(s)
- Clémence Massip
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France; CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | | | - Michèle Boury
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France; CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France.
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Thingholm KR, Hertz FB, Løbner-Olesen A, Frimodt-Møller N, Nielsen KL. Escherichia coli belonging to ST131 rarely transfers bla ctx-m-15 to fecal Escherichia coli. Infect Drug Resist 2019; 12:2429-2435. [PMID: 31496755 PMCID: PMC6689528 DOI: 10.2147/idr.s208536] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/23/2019] [Indexed: 01/22/2023] Open
Abstract
Background Extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) causing urinary tract infections often belong to sequence type 131 (ST131), serotype O25, carrying bla CTX-M-15. Aim The main aim of this study was to examine the conjugational frequencies of E. coli with plasmids carrying bla CTX-M-15 to E. coli isolates from the fecal flora of healthy humans to determine whether ST131 is more likely to uptake or donate ESBL resistance compared to other E. coli clones. Methods Donors and recipients were all clinical isolates and did not harbor plasmids with identical incompatibility groups (Inc-groups) based on in silico analyses of Inc-groups and restriction/modification systems (R/M-systems). The in vitro conjugation experiments were performed as filter conjugation with verification of transconjugants by random amplified polymorphic DNA (RAPD) PCR and bla CTX-M-15 PCR. Results The frequencies of conjugation with bla CTX-M-15-carrying plasmids were found to be very rare with detectable conjugation frequencies in the range of 4x10-9-7x10-7 transconjugants/recipient. Recipients of O25/ST131 type yielded significantly lower conjugation frequencies compared to recipients of other O-types (P=0.004). The applied ST131/O25 donors did not yield detectable levels of transconjugants regardless of the applied recipient. Presence of sub-MIC levels of ampicillin increased plasmid transfer frequencies x100 fold (P=0.07). Conclusion The results indicate that bla CTX-M-15 is rarely transferred by conjugation to E. coli isolates of the intestinal flora, even when the gene is plasmid-borne.
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Affiliation(s)
| | - Frederik Boëtius Hertz
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen 2100, Denmark.,Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev 2730, Denmark
| | - Anders Løbner-Olesen
- Department of Biology, Section for Functional Genomics and Center for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | | | - Karen Leth Nielsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen 2100, Denmark
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.
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Microbial evolutionary medicine: from theory to clinical practice. THE LANCET. INFECTIOUS DISEASES 2019; 19:e273-e283. [PMID: 31053492 DOI: 10.1016/s1473-3099(19)30045-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 11/21/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022]
Abstract
Medicine and clinical microbiology have traditionally attempted to identify and eliminate the agents that cause disease. However, this traditional approach is becoming inadequate for dealing with a changing disease landscape. Major challenges to human health are non-communicable chronic diseases, often driven by altered immunity and inflammation, and communicable infections from agents which harbour antibiotic resistance. This Review focuses on the so-called evolutionary medicine framework, to study how microbial communities influence human health. The evolutionary medicine framework aims to predict and manipulate microbial effects on human health by integrating ecology, evolutionary biology, microbiology, bioinformatics, and clinical expertise. We focus on the potential of evolutionary medicine to address three key challenges: detecting microbial transmission, predicting antimicrobial resistance, and understanding microbe-microbe and human-microbe interactions in health and disease, in the context of the microbiome.
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Mintzer V, Moran-Gilad J, Simon-Tuval T. Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review. Clin Microbiol Infect 2019; 25:1086-1095. [PMID: 31039443 DOI: 10.1016/j.cmi.2019.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microbial whole genome sequencing (WGS) has many advantages over standard microbiological methods. However, it is not yet widely implemented in routine hospital diagnostics due to notable challenges. OBJECTIVES The aim was to extract managerial, financial and clinical criteria supporting the decision to implement WGS in routine diagnostic microbiology, across different operational models of implementation in the hospital setting. METHODS This was a systematic review of literature identified through PubMed and Web of Science. English literature studies discussing the applications of microbial WGS without limitation on publication date were eligible. A narrative approach for categorization and synthesis of the sources identified was adopted. RESULTS A total of 98 sources were included. Four main alternative operational models for incorporating WGS in clinical microbiology laboratories were identified: full in-house sequencing and analysis, full outsourcing of sequencing and analysis and two hybrid models combining in-house/outsourcing of the sequencing and analysis components. Six main criteria (and multiple related sub-criteria) for WGS implementation emerged from our review and included cost (e.g. the availability of resources for capital and operational investment); manpower (e.g. the ability to provide training programmes or recruit trained personnel), laboratory infrastructure (e.g. the availability of supplies and consumables or sequencing platforms), bioinformatics requirements (e.g. the availability of valid analysis tools); computational infrastructure (e.g. the availability of storage space or data safety arrangements); and quality control (e.g. the existence of standardized procedures). CONCLUSIONS The decision to incorporate WGS in routine diagnostics involves multiple, sometimes competing, criteria and sub-criteria. Mapping these criteria systematically is an essential stage in developing policies for adoption of this technology, e.g. using a multicriteria decision tool. Future research that will prioritize criteria and sub-criteria that were identified in our review in the context of operational models will inform decision-making at clinical and managerial levels with respect to effective implementation of WGS for routine use. Beyond WGS, similar decision-making challenges are expected with respect to future integration of clinical metagenomics.
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Affiliation(s)
- V Mintzer
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; Leumit Health Services, Israel
| | - J Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - T Simon-Tuval
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel.
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Bahadori M, Motamedifar M, Derakhshandeh A, Firouzi R, Motamedi Boroojeni A, Alinejad M, Naziri Z. Genetic relatedness of the Escherichia coli fecal population and strains causing urinary tract infection in the same host. Microbiologyopen 2018; 8:e00759. [PMID: 30358940 PMCID: PMC6562127 DOI: 10.1002/mbo3.759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 02/06/2023] Open
Abstract
It is common knowledge that fecal microbiota is a primary source of Escherichia coli causing urinary tract infections (UTIs) via the fecal-perineal-urethral route. But, it is still unknown whether E. coli UTI is mainly caused by dominant fecal E. coli isolates (prevalence hypothesis) or the isolates that possess more virulence factors (special pathogenicity hypothesis). In the present study, the urine E. coli isolates of 30 women with UTI were compared with the fecal E. coli isolates of the same patients and healthy control individuals according to the phylogenetic group, virulence genotype, and antibiotic susceptibility pattern. The genetic relatedness of the isolates was specified and compared by pulsed-field gel electrophoresis (PFGE). PFGE analysis showed that most patients (73.3%) had distinct urine isolates which were not similar to any of their fecal isolates. Based on the phylogenetic analysis, most of the urine and fecal isolates of healthy women were assigned to phylogenetic group B2, followed by D. The distribution of phylogenetic groups was significantly different between the urine and the fecal isolates of patients (p < 0.05). The prevalence of fimH and ompT among urine isolates was significantly more than that among fecal isolates. The level of multidrug resistance was higher among urine isolates. Although more in-depth researches are required, the present study could be supported by pathogenicity hypothesis. Furthermore, concerning the antibiotic resistance pattern among uropathogenic E. coli should be highly considered.
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Affiliation(s)
- Maryam Bahadori
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Mohammad Motamedifar
- Department of Bacteriology and Virology, Shiraz Medical School, Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdollah Derakhshandeh
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Roya Firouzi
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | | | - Mohsen Alinejad
- Faculty of medicine, Kerman University of medical sciences, Kerman, Iran
| | - Zahra Naziri
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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Stork C, Kovács B, Rózsai B, Putze J, Kiel M, Dorn Á, Kovács J, Melegh S, Leimbach A, Kovács T, Schneider G, Kerényi M, Emödy L, Dobrindt U. Characterization of Asymptomatic Bacteriuria Escherichia coli Isolates in Search of Alternative Strains for Efficient Bacterial Interference against Uropathogens. Front Microbiol 2018; 9:214. [PMID: 29491858 PMCID: PMC5817090 DOI: 10.3389/fmicb.2018.00214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 01/30/2018] [Indexed: 12/16/2022] Open
Abstract
Asymptomatic bacterial colonization of the urinary bladder (asymptomatic bacteriuria, ABU) can prevent bladder colonization by uropathogens and thus symptomatic urinary tract infection (UTI). Deliberate bladder colonization with Escherichia coli ABU isolate 83972 has been shown to outcompete uropathogens and prevent symptomatic UTI by bacterial interference. Many ABU isolates evolved from uropathogenic ancestors and, although attenuated, may still be able to express virulence-associated factors. Our aim was to screen for efficient and safe candidate strains that could be used as alternatives to E. coli 83972 for preventive and therapeutic bladder colonization. To identify ABU E. coli strains with minimal virulence potential but maximal interference efficiency, we compared nine ABU isolates from diabetic patients regarding their virulence- and fitness-associated phenotypes in vitro, their virulence in a murine model of sepsis and their genome content. We identified strains in competitive growth experiments, which successfully interfere with colonization of ABU isolate 83972 or uropathogenic E. coli strain 536. Six isolates were able to outcompete E. coli 83972 and two of them also outcompeted UPEC 536 during growth in urine. Superior competitiveness was not simply a result of better growth abilities in urine, but seems also to involve expression of antagonistic factors. Competitiveness in urine did not correlate with the prevalence of determinants coding for adhesins, iron uptake, toxins, and antagonistic factors. Three ABU strains (isolates 61, 106, and 123) with superior competitiveness relative to ABU model strain 83972 display low in vivo virulence in a murine sepsis model, and susceptibility to antibiotics. They belong to different phylogroups and differ in the presence of ExPEC virulence- and fitness-associated genes. Importantly, they all lack marked cytotoxic activity and exhibit a high LD50 value in the sepsis model. These strains represent promising candidates for a more detailed assessment of relevant fitness traits in urine and their suitability for therapeutic bladder colonization.
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Affiliation(s)
- Christoph Stork
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Beáta Kovács
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary.,First Department of Internal Medicine, University of Pécs, Pécs, Hungary
| | - Barnabás Rózsai
- Department of Paediatrics, University of Pécs, Pécs, Hungary
| | - Johannes Putze
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Matthias Kiel
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Ágnes Dorn
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Judit Kovács
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Szilvia Melegh
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | | | | | - György Schneider
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Monika Kerényi
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Levente Emödy
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
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