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Maldonado N, López-Hernández I, López-Cortés LE, Martínez Pérez-Crespo PM, Retamar-Gentil P, García-Montaner A, De la Rosa Riestra S, Sousa-Domínguez A, Goikoetxea J, Pulido-Navazo Á, Del Valle Ortíz M, Natera-Kindelán C, Jover-Sáenz A, Arco-Jiménez AD, Armiñanzas-Castillo C, Aller-García AI, Fernández-Suárez J, Marrodán-Ciordia T, Boix-Palop L, Smithson-Amat A, Reguera-Iglesias JM, Galán-Sánchez F, Bahamonde A, Sánchez-Calvo JM, Gea-Lázaro I, Pérez-Camacho I, Reyes-Bertos A, Becerril-Carral B, Pascual Á, Rodríguez-Baño J. Association of microbiological factors with mortality in Escherichia coli bacteraemia presenting with sepsis/septic shock: a prospective cohort study. Clin Microbiol Infect 2024; 30:1035-1041. [PMID: 38599464 DOI: 10.1016/j.cmi.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
OBJECTIVES This study aimed to determine the association of Escherichia coli microbiological factors with 30-day mortality in patients with bloodstream infection (BSI) presenting with a dysregulated response to infection (i.e. sepsis or septic shock). METHODS Whole-genome sequencing was performed on 224 E coli isolates of patients with sepsis/septic shock, from 22 Spanish hospitals. Phylogroup, sequence type, virulence, antibiotic resistance, and pathogenicity islands were assessed. A multivariable model for 30-day mortality including clinical and epidemiological variables was built, to which microbiological variables were hierarchically added. The predictive capacity of the models was estimated by the area under the receiver operating characteristic curve (AUROC) with 95% confidence intervals (CI). RESULTS Mortality at day 30 was 31% (69 patients). The clinical model for mortality included (adjusted OR; 95% CI) age (1.04; 1.02-1.07), Charlson index ≥3 (1.78; 0.95-3.32), urinary BSI source (0.30; 0.16-0.57), and active empirical treatment (0.36; 0.11-1.14) with an AUROC of 0.73 (95% CI, 0.67-0.80). Addition of microbiological factors selected clone ST95 (3.64; 0.94-14.04), eilA gene (2.62; 1.14-6.02), and astA gene (2.39; 0.87-6.59) as associated with mortality, with an AUROC of 0.76 (0.69-0.82). DISCUSSION Despite having a modest overall contribution, some microbiological factors were associated with increased odds of death and deserve to be studied as potential therapeutic or preventive targets.
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Affiliation(s)
- Natalia Maldonado
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamentos de Medicina y Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain
| | - Inmaculada López-Hernández
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamentos de Medicina y Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Eduardo López-Cortés
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamentos de Medicina y Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Pilar Retamar-Gentil
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamentos de Medicina y Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrea García-Montaner
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamentos de Medicina y Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain
| | - Sandra De la Rosa Riestra
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamentos de Medicina y Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain
| | - Adrián Sousa-Domínguez
- Unidad de Enfermedades Infecciosas, Departamento de Medicina Interna, Complejo Hospitalario Universitario de Vigo, Spain
| | - Josune Goikoetxea
- Unidad de Enfermedades Infecciosas, Hospital Universitario de Cruces, Baracaldo, Spain
| | | | | | - Clara Natera-Kindelán
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Unidad de Gestión Clínica de Enfermedades Infecciosas, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Alfredo Jover-Sáenz
- Unidad de Enfermedades Infecciosas, Hospital Universitario Arnau de Vilanova, Lleida, Spain
| | | | - Carlos Armiñanzas-Castillo
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Unidad de Enfermedades Infecciosas, Hospital Universitario de Marqués de Valdecilla-IDIVAL, Santander, Spain
| | - Ana Isabel Aller-García
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - Jonathan Fernández-Suárez
- Servicio de Microbiología, Hospital Universitario Central de Asturias. Oviedo, Spain. Área de Microbiología y Patología Infecciosa, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA). Oviedo, Spain
| | | | - Lucía Boix-Palop
- Departamento de Enfermedades Infecciosas, Hospital Universitario Mutua Terrassa, Terrassa, Spain
| | | | - José María Reguera-Iglesias
- Unidad de Gestión Clínica de Enfermedades Infecciosas, Hospital Regional Universitario de Málaga. Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | | | - Alberto Bahamonde
- Departamento de Medicina Interna, Hospital Universitario El Bierzo, Ponferrada, Spain
| | - Juan Manuel Sánchez-Calvo
- Unidad de Gestión Clínica de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario de Jerez. Departamento de Biomedicina, Biotecnología y Salud Pública, Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Jerez de la Frontera, Spain
| | - Isabel Gea-Lázaro
- Unidad de Enfermedades Infecciosas, Hospital Universitario de Jaén, Jaén, Spain
| | - Inés Pérez-Camacho
- Unidad de Medicina Tropical, Hospital Universitario Poniente-El Ejido, Almería, Spain
| | - Armando Reyes-Bertos
- Servicio de Microbiología, Unidad de Gestión Clínica de Laboratorio, Hospital Universitario Torrecárdenas, Almería, Spain
| | - Berta Becerril-Carral
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Punta de Europa, Algeciras, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamentos de Medicina y Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamentos de Medicina y Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla (IBiS)/CSIC, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
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da Silva TF, Glória RDA, de Sousa TJ, Americo MF, Freitas ADS, Viana MVC, de Jesus LCL, da Silva Prado LC, Daniel N, Ménard O, Cochet MF, Dupont D, Jardin J, Borges AD, Fernandes SOA, Cardoso VN, Brenig B, Ferreira E, Profeta R, Aburjaile FF, de Carvalho RDO, Langella P, Le Loir Y, Cherbuy C, Jan G, Azevedo V, Guédon É. Comprehensive probiogenomics analysis of the commensal Escherichia coli CEC15 as a potential probiotic strain. BMC Microbiol 2023; 23:364. [PMID: 38008714 PMCID: PMC10680302 DOI: 10.1186/s12866-023-03112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND Probiotics have gained attention for their potential maintaining gut and immune homeostasis. They have been found to confer protection against pathogen colonization, possess immunomodulatory effects, enhance gut barrier functionality, and mitigate inflammation. However, a thorough understanding of the unique mechanisms of effects triggered by individual strains is necessary to optimize their therapeutic efficacy. Probiogenomics, involving high-throughput techniques, can help identify uncharacterized strains and aid in the rational selection of new probiotics. This study evaluates the potential of the Escherichia coli CEC15 strain as a probiotic through in silico, in vitro, and in vivo analyses, comparing it to the well-known probiotic reference E. coli Nissle 1917. Genomic analysis was conducted to identify traits with potential beneficial activity and to assess the safety of each strain (genomic islands, bacteriocin production, antibiotic resistance, production of proteins involved in host homeostasis, and proteins with adhesive properties). In vitro studies assessed survival in gastrointestinal simulated conditions and adhesion to cultured human intestinal cells. Safety was evaluated in BALB/c mice, monitoring the impact of E. coli consumption on clinical signs, intestinal architecture, intestinal permeability, and fecal microbiota. Additionally, the protective effects of both strains were assessed in a murine model of 5-FU-induced mucositis. RESULTS CEC15 mitigates inflammation, reinforces intestinal barrier, and modulates intestinal microbiota. In silico analysis revealed fewer pathogenicity-related traits in CEC15, when compared to Nissle 1917, with fewer toxin-associated genes and no gene suggesting the production of colibactin (a genotoxic agent). Most predicted antibiotic-resistance genes were neither associated with actual resistance, nor with transposable elements. The genome of CEC15 strain encodes proteins related to stress tolerance and to adhesion, in line with its better survival during digestion and higher adhesion to intestinal cells, when compared to Nissle 1917. Moreover, CEC15 exhibited beneficial effects on mice and their intestinal microbiota, both in healthy animals and against 5FU-induced intestinal mucositis. CONCLUSIONS These findings suggest that the CEC15 strain holds promise as a probiotic, as it could modulate the intestinal microbiota, providing immunomodulatory and anti-inflammatory effects, and reinforcing the intestinal barrier. These findings may have implications for the treatment of gastrointestinal disorders, particularly some forms of diarrhea.
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Affiliation(s)
- Tales Fernando da Silva
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rafael de Assis Glória
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Thiago Jesus de Sousa
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Monique Ferrary Americo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andria Dos Santos Freitas
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Marcus Vinicius Canário Viana
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Luís Cláudio Lima de Jesus
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Nathalie Daniel
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Olivia Ménard
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Marie-Françoise Cochet
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Didier Dupont
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Julien Jardin
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Amanda Dias Borges
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Simone Odília Antunes Fernandes
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Valbert Nascimento Cardoso
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Department of Molecular Biology of Livestock, Institute of Veterinary Medicine, Georg-August Universität Göttingen, Göttingen, Germany
| | - Enio Ferreira
- Department of general pathology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Flavia Figueira Aburjaile
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Veterinary school, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Yves Le Loir
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Claire Cherbuy
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Gwénaël Jan
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Éric Guédon
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France.
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Roshani M, Taheri M, Goodarzi A, Yosefimashouf R, Shokoohizadeh L. Evaluation of antibiotic resistance, toxin-antitoxin systems, virulence factors, biofilm-forming strength and genetic linkage of Escherichia coli strains isolated from bloodstream infections of leukemia patients. BMC Microbiol 2023; 23:327. [PMID: 37925405 PMCID: PMC10625236 DOI: 10.1186/s12866-023-03081-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/22/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND One of the most common complications in patients with febrile neutropenia, lymphoma, leukemia, and multiple myeloma is a bloodstream infection (BSI). OBJECTIVE This study aimed to evaluate the antibiotic resistance patterns, virulence factors, biofilm-forming strength, and genetic linkage of Escherichia coli strains isolated from bloodstream infections (BSIs) of leukemia patients. METHODS The study conducted in Iran from June 2021 to December 2022, isolated 67 E. coli strains from leukemia patients' bloodstream infections in hospitals in two different areas. Several techniques including disk diffusion and broth microdilution were used to identify patterns of antibiotic resistance, microtiter plate assay to measure biofilm formation, and PCR to evaluate the prevalence of different genes such as virulence factors, toxin-antitoxin systems, resistance to β-lactams and fluoroquinolone antibiotics of E. coli strains. Additionally, the genetic linkage of the isolates was analyzed using the Enterobacterial Repeat Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) method. RESULTS The results showed that higher frequency of BSI caused by E. coli in man than female patients, and patients with acute leukemia had a higher frequency of BSI. Ampicillin and Amoxicillin-clavulanic acid showed the highest resistance, while Imipenem was identified as a suitable antibiotic for treating BSIs by E. coli. Multidrug-resistant (MDR) phenotypes were present in 22% of the isolates, while 53% of the isolates were ESBL-producing with the blaCTX-M gene as the most frequent β-lactamase gene. The fluoroquinolone resistance genes qnrB and qnrS were present in 50% and 28% of the isolates, respectively. More than 80% of the isolates showed the ability to form biofilms. The traT gene was more frequent than other virulence genes. The toxin-antitoxin system genes (mazF, ccdAB, and relB) showed a comparable frequency. The genetic diversity was detected in E. coli isolates. CONCLUSION Our results demonstrate that highly diverse, resistant and pathogenic E. coli clones are circulating among leukemia patients in Iranian hospitals. More attention should be paid to the treatment and management of E. coli bloodstream infections in patients with leukemia.
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Affiliation(s)
- Mahdaneh Roshani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Taheri
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Alireza Goodarzi
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rassoul Yosefimashouf
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Leili Shokoohizadeh
- Department of Medical Laboratory Sciences, School of Paramedicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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Mirzahosseini HK, Najmeddin F, Najafi A, Ahmadi A, Sharifnia H, Khaledi A, Mojtahedzadeh M. Correlation of biofilm formation, virulence factors, and phylogenetic groups among Escherichia coli strains causing urinary tract infection: A global systematic review and meta-analysis. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2023; 28:66. [PMID: 38024522 PMCID: PMC10668210 DOI: 10.4103/jrms.jrms_637_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/22/2023] [Accepted: 05/18/2023] [Indexed: 12/01/2023]
Abstract
Background Different virulence factors are involved in the pathogenesis of urinary tract infection (UTI) caused by Uropathogenic Escherichia coli (UPEC); hence, this study aimed to study the prevalence of biofilm formation, virulence factors, and phylogenetic groups and their correlation with biofilm formation among UPEC isolates through a systematic review and meta-analysis. Materials and Methods A literature search was conducted from 1, 2000, to the end of 2021 in different databases for studies that reported biofilm together with virulence genes or phylogenetic groups in UPEC isolates from patients with UTI according to PRISMA protocol. Data were analyzed by Comprehensive meta-analysis software. Results The pooled prevalence of biofilm formers was 74.7%. The combined prevalence of phylogenetic Groups A, B1, B2, and D (s) were reported at 19.6%, 11%, 50.7%, and 20.5%, respectively. The most common virulence genes reported worldwide were fimA, ecpA, and fimH, with a combined prevalence of 90.3%, 86.6%, and 64.9%, respectively. The pooled prevalence of biofilm formation in UPEC isolates with phylogenetic Groups A, B1, B2, D, C, and F were 12.4%, 8.7%, 33.7%, 12.4%, 2.6%, and 2.65%, respectively. Several studies showed a correlation between biofilm production and virulence genes, or phylogenetic groups. Conclusion Regarding data obtained, the high level of combined biofilm formation (74.7%) and the presence of a positive correlation between biofilm production and virulence genes, or phylogenetic groups as reported by the most studies included in the present review, indicates an important role of biofilm in the persistence of UPEC in the UTI.
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Affiliation(s)
| | - Farhad Najmeddin
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Atabak Najafi
- Department of Anesthesiology and Critical Care Medicine, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Arezoo Ahmadi
- Department of Anesthesiology and Critical Care Medicine, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Sharifnia
- Department of Anesthesiology and Critical Care, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Azad Khaledi
- Infectious Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
- Department of Microbiology and Immunology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Mojtaba Mojtahedzadeh
- Department of Clinical Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Pharmaceutical Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Djomgoue NG, Fonbah LJ, Mbulli AI, Ousenu K, Bonglavnyuy TC. Risk Factors and Associated Outcomes of Virulence Genes eae, entB, and pipD Carriage in Escherichia coli, Klebsiella pneumoniae, and Salmonella spp. From HIV-1 and HIV-Negative Gastroenteritis Patients in the Dschang Regional Hospital Annex. Cureus 2023; 15:e42329. [PMID: 37614275 PMCID: PMC10443731 DOI: 10.7759/cureus.42329] [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: 07/23/2023] [Indexed: 08/25/2023] Open
Abstract
Background Enterobacteriaceae is one of the main families of gram-negative bacilli responsible for serious infections in humans. The severity of infection by these bacteria is a product of many factors, including virulence properties and antimicrobial resistance. This severity may be further intensified if there is an association between these factors and a depressed immune system, such as in HIV patients. This study aimed to determine the distribution of representative virulence genes among key Enterobacteriaceae isolates from HIV-1 and non-HIV gastroenteritis patients and the relationship between carrying these virulence genes and antimicrobial susceptibility, seropositive status, and severity of symptoms associated with Enterobacteriaceae infections in Dschang Regional Hospital Annex. Methodology A total of 200 gastroenteritis patients (100 HIV-1 and 100 non-HIV patients) were selected and evaluated for symptoms associated with gastroenteritis. Stool samples were obtained and cultured, from which Escherichia coli, Klebsiella pneumoniae, and Salmonella spp. isolates were obtained. Antibiotic susceptibility tests were performed on the isolates by agar disc diffusion using commonly used antibiotics. These isolates were tested for the possession of virulence genes by polymerase chain reaction (PCR); eae for E. coli, entB for K. pneumoniae, and pipD for Salmonella spp. Correlation tests and risk assessments were performed between the presence of virulence genes, antibiotic resistance, and specific symptoms. Results The isolates obtained from HIV-positive and HIV-negative patients were, respectively, 61 against 62 for E. coli, 10 against 21 for K. pneumoniae, and 11 against 15 for Salmonella spp.These organisms showed the highest resistance to amoxicillin and clavulanic acid, while the least resistance was observed against ofloxacin, gentamicin, and amikacin in both groups of patients. The virulence genes showed a generally higher occurrence in isolates from HIV-negative patients than HIV-positive patients, with the eae gene 5/61 (8.20%) against 12/62 (19.35%), the entB gene 4/10 (40.00%) against 14/21 (66.66%), and the pipD gene 5/11 (45.45%) against 7/15 (46.46%) in HIV-positive and negative patients, respectively. There was a significant correlation between eae gene carriage and resistance against imipenem (p = 0.047), gentamycin (p = 0.047), and doxycycline (p = 0.029); entB gene carriage and resistance toward levofloxacin (p = 0.017) in K. pneumoniae; and pipD gene carriage and resistance against levofloxacin (p = 0.039), imipenem (p = 0.041), and doxycycline (p = 0.042). The carriage of the virulence genes was seen to be a stronger risk only for the resistance of K. pneumoniae to ceftriaxone (odds ratio (OR) = 2.286) and gentamycin (OR = 3.000), and Salmonella spp. against imipenem (OR = 2.750) and doxycycline (OR = 2.118). The development of severe symptoms correlated significantly with virulence gene carriage in isolates, mainly in HIV-positive patients with eae (p = 0.017) and pipD (p = 0.025), with a strong risk association with the pipD gene (OR = 2.665). Conclusions Antibiotic resistance was associated with virulence gene carriage, indicating that virulence and antibiotic resistance can associate their effects and contribute to poor outcomes in the treatment of bacterial diseases in HIV patients. The possession of virulence genes increased the severity of symptoms associated with gastroenteritis in HIV-positive patients.
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Affiliation(s)
- Ngangoum G Djomgoue
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, CMR
| | - Leinyuy J Fonbah
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, CMR
| | - Ali I Mbulli
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, CMR
| | - Karimo Ousenu
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, CMR
| | - Tume C Bonglavnyuy
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, CMR
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Aklilu E, Harun A, Singh KKB. Molecular characterization of bla NDM, bla OXA-48, mcr-1 and bla TEM-52 positive and concurrently carbapenem and colistin resistant and extended spectrum beta-lactamase producing Escherichia coli in chicken in Malaysia. BMC Vet Res 2022; 18:190. [PMID: 35590358 PMCID: PMC9118571 DOI: 10.1186/s12917-022-03292-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/05/2022] [Indexed: 11/25/2022] Open
Abstract
Background Antimicrobial resistance (AMR) is a global public health threat and the use of antibiotics growth promoters in food animals has been implicated as a potential contributing factor in the emergence and spread of AMR. This study was conducted to investigate colistin and carbapenem resistance and extended spectrum beta-lactamase producing E. coli from live broiler chicken and chicken meat in Kelantan, Malaysia. Results Among the E. coli isolates, 37.5% (27/72 were positive for at least one of the resistance genes and one isolate was positive for mcr-1, blaTEM-52, blaNDM and blaOXA-48 whereas 4.17% (3/72) and 2.78% (2/72) were positive for mcr-1, blaTEM-52 and blaOXA-48, and mcr-1, blaTEM-52 and blaIMP. Multilocus sequence typing (MLST) results revealed the presence of widespread E. coli strains belonging to the sequence types ST410 and ST155 and other extra-intestinal E. coli (ExPEC) strains. Phylogroup A made up the majority 51.85% (14/27) followed by phylogroup B1 22.22% (6/27). Conclusions The findings imply the potential threats of colistin, extended-spectrum beta-lactamase producing and carbapenem resistant E. coli in food animals to the public health and underscores the need for judicious use of antibiotics in animal production and good hygiene practices to curb the rising risks of AMR.
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Affiliation(s)
- Erkihun Aklilu
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Locked Box 36, Pengkalan Chepa, 16100, Kota Bharu, Kelantan, Malaysia. .,Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kota Bharu, Kelantan, Malaysia.
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kota Bharu, Kelantan, Malaysia.
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kota Bharu, Kelantan, Malaysia
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7
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Escherichia coli community-acquired meningitis in adults: a case series of 29 patients in France. Clin Microbiol Infect 2022; 28:1304-1305. [PMID: 35568305 DOI: 10.1016/j.cmi.2022.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/22/2022]
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8
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O'Donnell L, Hill EC, Anderson AS, Edgar HJH. A biological approach to adult sex differences in skeletal indicators of childhood stress. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 177:381-401. [PMID: 36787691 DOI: 10.1002/ajpa.24424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/01/2021] [Accepted: 09/24/2021] [Indexed: 05/05/2023]
Abstract
OBJECTIVES In previous work examining the etiology of cribra orbitalia (CO) and porotic hyperostosis (PH) in a contemporary juvenile mortality sample, we noted that males had higher odds of having CO lesions than females. Here, we examine potential reasons for this pattern in greater detail. Four non-mutually exclusive mechanisms could explain the observed sex differences: (1) sex-biased mortality; (2) sexual dimorphism in immune responses; (3) sexual dimorphism in bone turnover; or (4) sexual dimorphism in marrow conversion. SUBJECTS AND METHODS The sample consists of postmortem computed tomography scans and autopsy reports, field reports, and limited medical records of 488 individuals from New Mexico (203 females; 285 males) aged between 0.5 and 15 years. We used Kaplan-Meier survival analysis, predicted probabilities, and odds ratios to test each mechanism. RESULTS Males do not have lower survival probabilities than females, and we find no indications of sex differences in immune response. Overall, males have a higher probability of having CO or PH lesions than females. CONCLUSIONS All results indicate that lesion formation in juveniles is influenced by some combination of sex differences in the pace of red-yellow conversion of the bone marrow and bone turnover. The preponderance of males with CO and PH likely speaks to the potential for heightened osteoblastic activity in males. We find no support for the hypotheses that sex biases in mortality or immune responses impacted lesion frequency in this sample. Sex differences in biological processes experienced by children may affect lesion formation and lesion expression in later life.
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Affiliation(s)
- Lexi O'Donnell
- Department of Sociology and Anthropology, University of Mississippi, Oxford, Mississippi, USA
| | - Ethan C Hill
- Division of Physical Therapy, Department of Orthopaedics and Rehabilitation, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Amy S Anderson
- Department of Anthropology, University of California, Santa Barbara, California, USA
| | - Heather Joy Hecht Edgar
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, USA
- Office of the Medical Investigator, University of New Mexico, Albuquerque, New Mexico, USA
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9
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Kim B, Kim JH, Lee Y. Virulence Factors Associated With Escherichia coli Bacteremia and Urinary Tract Infection. Ann Lab Med 2022; 42:203-212. [PMID: 34635614 PMCID: PMC8548248 DOI: 10.3343/alm.2022.42.2.203] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/05/2021] [Accepted: 09/13/2021] [Indexed: 01/03/2023] Open
Abstract
Background Extraintestinal pathogenic Escherichia coli (ExPEC) causes various infections, including urinary tract infection (UTI), sepsis, and neonatal meningitis. ExPEC strains have virulence factors (VFs) that facilitate infection by allowing bacterial cells to migrate into and multiply within the host. We compared the microbiological characteristics of ExPEC isolates from blood and urine specimens from UTI patients. Methods We conducted a single-center, prospective study in an 855-bed tertiary-care hospital in Korea. We consecutively recruited 80 hospitalized UTI patients with E. coli isolates, which were isolated from blood and/or urine, and urine alone between March 2019 and May 2020. We evaluated the 80 E. coli isolates for the presence of bacterial genes encoding the sequence types (STs), antimicrobial resistance, and VFs using whole-genome sequencing (WGS). Results We found no significant differences in STs, antimicrobial resistance patterns, or VFs between isolates from blood and urine specimens. ST131, a pandemic multidrug-resistant clone present in both blood and urine, was the most frequent ST (N=19/80, 24%), and ST131 isolates carried more virulence genes, especially, tsh and espC, than non-ST131 isolates. The virulence scores of the ST131 group and the ST69, ST95, and ST1193 groups differed significantly (P<0.05). Conclusions We found no STs and VFs associated with bacteremia in WGS data of E. coli isolates from UTI patients. ST131 was the most frequent ST among UTI causing isolates and carried more VF genes than non-ST131 isolates.
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Affiliation(s)
- Bongyoung Kim
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Jin-Hong Kim
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Yangsoon Lee
- Department of Laboratory Medicine, Hanyang University College of Medicine, Seoul, Korea
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10
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Denamur E, Condamine B, Esposito-Farèse M, Royer G, Clermont O, Laouenan C, Lefort A, de Lastours V, Galardini M. Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome. PLoS Genet 2022; 18:e1010112. [PMID: 35324915 PMCID: PMC8946752 DOI: 10.1371/journal.pgen.1010112] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli is an important cause of bloodstream infections (BSI), which is of concern given its high mortality and increasing worldwide prevalence. Finding bacterial genetic variants that might contribute to patient death is of interest to better understand infection progression and implement diagnostic methods that specifically look for those factors. E. coli samples isolated from patients with BSI are an ideal dataset to systematically search for those variants, as long as the influence of host factors such as comorbidities are taken into account. Here we performed a genome-wide association study (GWAS) using data from 912 patients with E. coli BSI from hospitals in Paris, France. We looked for associations between bacterial genetic variants and three patient outcomes (death at 28 days, septic shock and admission to intensive care unit), as well as two portals of entry (urinary and digestive tract), using various clinical variables from each patient to account for host factors. We did not find any association between genetic variants and patient outcomes, potentially confirming the strong influence of host factors in influencing the course of BSI; we however found a strong association between the papGII operon and entrance of E. coli through the urinary tract, which demonstrates the power of bacterial GWAS when applied to actual clinical data. Despite the lack of associations between E. coli genetic variants and patient outcomes, we estimate that increasing the sample size by one order of magnitude could lead to the discovery of some putative causal variants. Given the wide adoption of bacterial genome sequencing of clinical isolates, such sample sizes may be soon available.
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Affiliation(s)
- Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | | | - Marina Esposito-Farèse
- Département d’épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, Paris, France
| | - Guilhem Royer
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil, France
| | | | - Cédric Laouenan
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- Département d’épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, Paris, France
| | - Agnès Lefort
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- Service de Médecine Interne, Hôpital Beaujon, AP-HP, Clichy, France
| | - Victoire de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, Paris, France
- Service de Médecine Interne, Hôpital Beaujon, AP-HP, Clichy, France
| | - Marco Galardini
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
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11
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Genetic Characterization of Multidrug-Resistant E. coli Isolates from Bloodstream Infections in Lithuania. Microorganisms 2022; 10:microorganisms10020449. [PMID: 35208903 PMCID: PMC8880137 DOI: 10.3390/microorganisms10020449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) isolates are a main cause of bloodstream infections. The aim of this study was to characterize 256 β-lactam–resistant, bacteremia-causing E. coli isolates collected from 12 healthcare institutions in Lithuania in 2014 and 2018. All isolates were identified as E. coli via MALDI-TOF MS and VITEK ®2. In addition, the isolates were analyzed for the presence of 29 resistance genes and 13 virulence genes, divided into phylogenetic groups (A, B1, B2, C, D, E, and F), and characterized using rep-PCR genotyping methods (BOX-PCR and (GTG)5-PCR). Analyzing the results of this study showed tetA-strB-sul2-TEM-NDM-strA-fosA-AIM-sul3-aadA-CTX-M-9 to be the most common resistance gene combination (67.2% of all isolates). Additionally, the most common virulence genes established were fimH (98.4% of all isolates), fyuA (91.8%), and traT (81.3%) and the most common gene combination was fuyA-fimH-iroN (58.6% of all isolates). Next, the isolates were separated into four phylogenetic groups: A, B1, B2, and F, where group A isolates were detected at a significantly higher frequency (79.3% of all isolates). Finally, a total of 235 genotyping profiles were established using rep-PCR methods, and all profiles were separated into fourteen genotypic clusters, with each cluster containing profiles with a variety of virulence and resistance genes not restricted to any specific cluster. The results of this study elucidate E. coli antimicrobial resistance patterns by highlighting the variability and diversity of resistance and virulence genes and providing phylogenetic classification, genetic profiling, and clustering data. These results may improve clinical control of multidrug-resistant infections in healthcare institutions and contribute to the prevention of potential outbreaks.
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12
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Hyun M, Lee JY, Kim HA. Differences of virulence factors, and antimicrobial susceptibility according to phylogenetic group in uropathogenic Escherichia coli strains isolated from Korean patients. Ann Clin Microbiol Antimicrob 2021; 20:77. [PMID: 34758824 PMCID: PMC8579644 DOI: 10.1186/s12941-021-00481-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Background Escherichia coli is among the most common uropathogens. Increased antibiotic resistance in Gram negative bacilli is global concern. Alternative therapeutic options including vaccines against uropathogenic E. coli (UPEC) have been developed. In this study, we compared the genotypic characteristics and antimicrobial susceptibility of UPEC according to phylogenetic groups. Methods We retrospectively reviewed the medical records of pyelonephritis patients with UPEC between February 2015 and June 2018. The study was conducted at a medical center in Korea. We compared the clinical and genotypic characteristics of UPEC according to phylogenetic groups. The phylogenetic groups and 29 virulence factors were identified using multiplex polymerase chain reaction. Results Phylogenetic group analysis revealed that most uropathogenic E. coli belonged to groups B2 and D: B2 (276, 77.7%), D (62, 17.5%), B1 (12, 3.4%), and A (5, 1.4%). Among the virulence factors, fyuA, fimH, traT, iutA, papG allele II, and papC were the most frequently observed. Phylogenetic group B2 was more closely related to virulence factors, including fimH, sfa/focED, focG, hlyA, cnf1, fyuA, and PAI, than group D. Groups B2 and D showed similar clinical presentations and complications. Group B2 had mostly healthcare-associated infections and antimicrobial resistance. Group D mostly had community-acquired infections. The K1 serotype was prevalent in group B2, and K5 was the most prevalent in group D. Conclusions Phylogenetic group B2 had more proportions and types of virulence factors than group D. Group B2 showed a high presentation of virulence factors related to adhesions and toxins. An increased presentation of antimicrobial resistance and healthcare-associated infections was also noted. Considering the genetic characteristics of UPEC, alternative therapeutic options targeting frequent virulence factors might be considered in addition to antibiotics.
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Affiliation(s)
- Miri Hyun
- Department of Infectious Diseases, Keimyung University School of Medicine, 1095 Dalgubeol-daero, Dalseo-gu, Daegu, 42601, Republic of Korea.,Institute for Medical Science, Keimyung University, Daegu, Korea
| | - Ji Yeon Lee
- Department of Infectious Diseases, Keimyung University School of Medicine, 1095 Dalgubeol-daero, Dalseo-gu, Daegu, 42601, Republic of Korea.,Institute for Medical Science, Keimyung University, Daegu, Korea
| | - Hyun Ah Kim
- Department of Infectious Diseases, Keimyung University School of Medicine, 1095 Dalgubeol-daero, Dalseo-gu, Daegu, 42601, Republic of Korea. .,Institute for Medical Science, Keimyung University, Daegu, Korea.
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13
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Antimicrobial Susceptibility and Detection of Virulence-Associated Genes in Escherichia coli Strains Isolated from Commercial Broilers. Antibiotics (Basel) 2021; 10:antibiotics10111303. [PMID: 34827241 PMCID: PMC8614860 DOI: 10.3390/antibiotics10111303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to investigate the presence of iron-uptake and virulence genes, antibiotic resistance profiles, and phylogenetic relatedness in 115 Escherichia coli (E. coli) strains isolated from broilers in Slovakia and to determine their potential threat to human health. The most frequent phylogroups were B1 (37%) and A (21%), and 33.9% strains were included in pathogenic groups. The commonly observed iron-uptake genes were feoB (94%), sitA (83%), and iutA (58%). Protectins (iss, kpsMTII) were identified in 30% of samples. Four percent of B2-associated broilers carried the papC (P fimbria) gene connected with upper urinary tract infection. The dominant resistance was to tetracycline (49%), ampicillin (66%), ampicillin + sulbactam (27%), ciprofloxacin (61%), and trimethoprim + sulfonamide (34%); moreover, sporadically occurring resistance to cephalosporins, aminoglycosides, fluoroquinolones, and polypeptide colistin was observed. Genotypic analysis of resistance revealed the presence of blaCTX-M-1 and blaCTX-M-2 in two isolates from broilers. Commercial broilers can be reservoirs of virulent and resistant genes as well as E. coli causing (extra-)intestinal infections, which can be a potential threat to humans via direct contact and food.
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14
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de Lastours V, Laouénan C, Royer G, Carbonnelle E, Lepeule R, Esposito-Farèse M, Clermont O, Duval X, Fantin B, Mentré F, Decousser JW, Denamur E, Lefort A. Mortality in Escherichia coli bloodstream infections: antibiotic resistance still does not make it. J Antimicrob Chemother 2021; 75:2334-2343. [PMID: 32417924 DOI: 10.1093/jac/dkaa161] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/18/2020] [Accepted: 03/30/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Escherichia coli bloodstream infections (BSIs) account for high mortality rates (5%-30%). Determinants of death are unclear, especially since the emergence of ESBL producers. OBJECTIVES To determine the relative weight of host characteristics, bacterial virulence and antibiotic resistance in the outcome of patients suffering from E. coli BSI. METHODS All consecutive patients suffering from E. coli BSI in seven teaching hospitals around Paris were prospectively included for 10 months. E. coli isolates were sequenced using Illumina NextSeq technology to determine the phylogroup, ST/ST complex (STc), virulence and antimicrobial resistance gene content. Risk factors associated with death at discharge or Day 28 were determined. RESULTS Overall, 545 patients (mean ± SD age 68.5 ± 16.5 years; 52.5% male) were included. Mean Charlson comorbidity index (CCI) was 5.6 (± 3.1); 19.6% and 12.8% presented with sepsis and septic shock, respectively. Portals of entry were mainly urinary (51.9%), digestive (41.9%) and pulmonary (3.5%); 98/545 isolates (18%) were third-generation cephalosporin resistant (3GC-R), including 86 ESBL producers. In-hospital death (or at Day 28) was 52/545 (9.5%). Factors independently associated with death were a pulmonary portal of entry [adjusted OR (aOR) 6.54, 95% CI 2.23-19.2, P = 0.0006], the iha_17 virulence gene (aOR 4.41, 95% CI 1.23-15.74, P = 0.022), the STc88 (aOR 3.62, 95% CI 1.30-10.09, P = 0.014), healthcare-associated infections (aOR 1.98, 95% CI 1.04-3.76, P = 0.036) and high CCI (aOR 1.14, 95% CI 1.04-1.26, P = 0.006), but not ESBL/3GC-R. CONCLUSIONS Host factors, portal of entry and bacterial characteristics remain major determinants associated with mortality in E. coli BSIs. Despite a high prevalence of ESBL producers, antibiotic resistance did not impact mortality. (ClinicalTrials.gov identifier: NCT02890901.).
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Affiliation(s)
- V de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Service de Médecine Interne, Hôpital Beaujon, APHP, F-92100 Clichy, France
| | - C Laouénan
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018 Paris, France.,Unité de recherche clinique, HUPNVS, Hôpital Bichat, AP-HP F-75018 Paris, France
| | - G Royer
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000 Créteil, France
| | - E Carbonnelle
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Service de Microbiologie, Hôpital Avicenne, AP-HP, F-93000 Bobigny, France
| | - R Lepeule
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000 Créteil, France
| | - M Esposito-Farèse
- Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018 Paris, France.,Unité de recherche clinique, HUPNVS, Hôpital Bichat, AP-HP F-75018 Paris, France
| | - O Clermont
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France
| | - X Duval
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Centre Investigation Clinique INSERM CIC-1425, Bichat Hospital, F-75018 France
| | - B Fantin
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Service de Médecine Interne, Hôpital Beaujon, APHP, F-92100 Clichy, France
| | - F Mentré
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018 Paris, France.,Unité de recherche clinique, HUPNVS, Hôpital Bichat, AP-HP F-75018 Paris, France
| | - J W Decousser
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000 Créteil, France
| | - E Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, F-75018 Paris, France
| | - A Lefort
- Université de Paris, IAME, UMR 1137, INSERM, Paris F-75018, France.,Service de Médecine Interne, Hôpital Beaujon, APHP, F-92100 Clichy, France
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15
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Royer G, Darty MM, Clermont O, Condamine B, Laouenan C, Decousser JW, Vallenet D, Lefort A, de Lastours V, Denamur E. Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period. Genome Med 2021; 13:77. [PMID: 33952335 PMCID: PMC8097792 DOI: 10.1186/s13073-021-00892-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/22/2021] [Indexed: 11/12/2022] Open
Abstract
Background Escherichia coli is the leading cause of bloodstream infections, associated with a significant mortality. Recent genomic analyses revealed that few clonal lineages are involved in bloodstream infections and captured the emergence of some of them. However, data on within sequence type (ST) population genetic structure evolution are rare. Methods We compared whole genome sequences of 912 E. coli isolates responsible for bloodstream infections from two multicenter clinical trials that were conducted in the Paris area, France, 12 years apart, in teaching hospitals belonging to the same institution (“Assistance Publique-Hôpitaux de Paris”). We analyzed the strains at different levels of granularity, i.e., the phylogroup, the ST complex (STc), and the within STc clone taking into consideration the evolutionary history, the resistance, and virulence gene content as well as the antigenic diversity of the strains. Results We found a mix of stability and changes overtime, depending on the level of comparison. Overall, we observed an increase in antibiotic resistance associated to a restricted number of genetic determinants and in strain plasmidic content, whereas phylogroup distribution and virulence gene content remained constant. Focusing on STcs highlighted the pauci-clonality of the populations, with only 11 STcs responsible for more than 73% of the cases, dominated by five STcs (STc73, STc131, STc95, STc69, STc10). However, some STcs underwent dramatic variations, such as the global pandemic STc131, which replaced the previously predominant STc95. Moreover, within STc131, 95 and 69 genomic diversity analysis revealed a highly dynamic pattern, with reshuffling of the population linked to clonal replacement sometimes coupled with independent acquisitions of virulence factors such as the pap gene cluster bearing a papGII allele located on various pathogenicity islands. Additionally, STc10 exhibited huge antigenic diversity evidenced by numerous O:H serotype/fimH allele combinations, whichever the year of isolation. Conclusions Altogether, these data suggest that the bloodstream niche is occupied by a wide but specific phylogenetic diversity and that highly specialized extra-intestinal clones undergo frequent turnover at the within ST level. Additional worldwide epidemiological studies overtime are needed in different geographical and ecological contexts to assess how generalizable these data are. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00892-0.
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Affiliation(s)
- Guilhem Royer
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Mélanie Mercier Darty
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Olivier Clermont
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France
| | | | - Cédric Laouenan
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Jean-Winoc Decousser
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - David Vallenet
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France
| | - Agnès Lefort
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Victoire de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France. .,Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, F-75018, Paris, France.
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16
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Li D, Reid CJ, Kudinha T, Jarocki VM, Djordjevic SP. Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections. Microb Genom 2020; 6:mgen000475. [PMID: 33206038 PMCID: PMC8116683 DOI: 10.1099/mgen.0.000475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Urinary tract infections (UTIs) are the most common bacterial infections requiring medical attention and a leading justification for antibiotic prescription. Trimethoprim is prescribed empirically for uncomplicated cases. UTIs are primarily caused by extraintestinal pathogenic Escherichia coli (ExPEC) and ExPEC strains play a central role in disseminating antimicrobial-resistance genes worldwide. Here, we describe the whole-genome sequences of trimethoprim-resistant ExPEC and/or ExPEC from recurrent UTIs (67 in total) from patients attending a regional Australian hospital from 2006 to 2008. Twenty-three sequence types (STs) were observed, with ST131 predominating (28 %), then ST69 and ST73 (both 7 %). Co-occurrence of trimethoprim-resistance genes with genes conferring resistance to extended-spectrum β-lactams, heavy metals and quaternary ammonium ions was a feature of the ExPEC described here. Seven trimethoprim-resistance genes were identified, most commonly dfrA17 (38 %) and dfrA12 (18 %). An uncommon dfrB4 variant was also observed. Two blaCTX-M variants were identified - blaCTX-M-15 (16 %) and blaCTX-M-14 (10 %). The former was always associated with dfrA12, the latter with dfrA17, and all blaCTX-M genes co-occurred with chromate-resistance gene chrA. Eighteen class 1 integron structures were characterized, and chrA featured in eight structures; dfrA genes featured in seventeen. ST131 H30Rx isolates possessed distinct antimicrobial gene profiles comprising aac(3)-IIa, aac(6)-Ib-cr, aph(3')-Ia, aadA2, blaCTX-M-15, blaOXA-1 and dfrA12. The most common virulence-associated genes (VAGs) were fimH, fyuA, irp2 and sitA (all 91 %). Virulence profile clustering showed ST131 H30 isolates carried similar VAGs to ST73, ST405, ST550 and ST1193 isolates. The sole ST131 H27 isolate carried molecular predictors of enteroaggregative E. coli/ExPEC hybrid strains (aatA, aggR, fyuA). Seven isolates (10 %) carried VAGs suggesting ColV plasmid carriage. Finally, SNP analysis of serial UTI patients experiencing worsening sequelae demonstrated a high proportion of point mutations in virulence factors.
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Affiliation(s)
- Dmitriy Li
- Ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Cameron J. Reid
- Ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Timothy Kudinha
- NSW Health Pathology, Microbiology, Orange Hospital, Orange, NSW 2800, Australia
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW 2800, Australia
| | - Veronica M. Jarocki
- Ithree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia
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17
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dos Santos Ramos MA, dos Santos KC, da Silva PB, de Toledo LG, Marena GD, Rodero CF, de Camargo BAF, Fortunato GC, Bauab TM, Chorilli M. Nanotechnological strategies for systemic microbial infections treatment: A review. Int J Pharm 2020; 589:119780. [PMID: 32860856 PMCID: PMC7449125 DOI: 10.1016/j.ijpharm.2020.119780] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/27/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
Systemic infections is one of the major causes of mortality worldwide, and a shortage of drug approaches applied for the rapid and necessary treatment contribute to increase the levels of death in affected patients. Several drug delivery systems based in nanotechnology such as metallic nanoparticles, liposomes, nanoemulsion, microemulsion, polymeric nanoparticles, solid lipid nanoparticles, dendrimers, hydrogels and liquid crystals can contribute in the biological performance of active substances for the treatment of microbial diseases triggered by fungi, bacteria, virus and parasites. In the presentation of these statements, this review article present and demonstrate the effectiveness of these drug delivery systems for the treatment of systemic diseases caused by several microorganisms, through a review of studies on scientific literature worldwide that contributes to better information for the most diverse professionals from the areas of health sciences. The studies demonstrated that the drug delivery systems described can contribute to the therapeutic scenario of these diseases, being classified as safe, active platforms and with therapeutic versatility.
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Affiliation(s)
- Matheus Aparecido dos Santos Ramos
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil,Corresponding authors
| | - Karen Cristina dos Santos
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Patrícia Bento da Silva
- Department of Genetic and Morphology, Brasília University (UNB), Institute of Biological Sciences, Zip Code: 70735100, Brazil
| | - Luciani Gaspar de Toledo
- Department of Biological Sciences, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Gabriel Davi Marena
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Camila Fernanda Rodero
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Bruna Almeida Furquim de Camargo
- Department of Biological Sciences, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Giovanna Capaldi Fortunato
- Department of Biological Sciences, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Taís Maria Bauab
- Department of Biological Sciences, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil
| | - Marlus Chorilli
- Department of Drugs and Medicines, São Paulo State University (UNESP), School of Pharmaceutical Sciences, Campus Araraquara, São Paulo State Zip Code: 14.800-903, Brazil.
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18
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Phylogenetic Classification, Biofilm-Forming Capacity, Virulence Factors, and Antimicrobial Resistance in Uropathogenic Escherichia coli (UPEC). Curr Microbiol 2020; 77:3361-3370. [PMID: 32910213 DOI: 10.1007/s00284-020-02173-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/21/2020] [Indexed: 10/23/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) is the main cause of urinary tract infections; in recent years, its importance as a pathogen has increased due to the emergence of hypervirulent and multiresistant strains. In this study, 190 urinary isolates of E. coli were assigned into the seven phylogenetic groups A (11.1%), B1 (4.7%), B2 (46.8%), C (5.8%) D (25.3%) F (2.6%), and Clade I (2.1%), and various virulence genes were examined with polymerase chain reaction methods. All isolates had at least one virulence factor of the 9 analyzed fyuA (81.1%), fimH (96.8%), iutA (74.7%), ompT (66.8%), kpsMTII (66.8%), traT (58.9%), PAI (43.6%), PapAH (26.3%), and usp (3.2%). The results showed a direct relationship between the virulence factors and phylogenetic group A and B2. Further, virulence genetic profiles fimH, fyuA, ompT, traT, and kpsMTII correlated with the production of strong biofilm, multidrug resistance, and the production of moderate hemolysin. These results suggest that these strains may become reservoirs of genes that encode virulence factors, which could be transferred horizontally enhancing their genomic background and high possibility of acquiring new genetic information for possible dissemination. This study provides the first description of phylogroups in UPEC in the Colombian Caribbean and the association with virulence factor profile, antimicrobial susceptibility, and their possible role in the epidemiology in Colombia.
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19
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Mahmoud AT, Ibrahem RA, Salim MT, Gabr A, Halby HM. Prevalence of some virulence factors and genotyping of hospital-acquired uropathogenic Escherichia coli isolates recovered from cancer patients. J Glob Antimicrob Resist 2020; 23:211-216. [PMID: 32916331 DOI: 10.1016/j.jgar.2020.08.003] [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: 05/30/2020] [Revised: 07/03/2020] [Accepted: 08/03/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVES This study aimed to determine the prevalence of virulence factors among uropathogenic Escherichia coli (UPEC) isolates from cancer patients and to investigate their genetic diversity using ERIC-PCR. METHODS A total of 42 E. coli were recovered from urine samples from cancer patients admitted to Assiut University Hospital. PCR was used to detect the presence of three virulence genes (papC, iutA and cnf1). Genetic diversity of the isolates was determined using the ERIC-PCR fingerprinting method, and amplified products were separated by agarose gel electrophoresis. Gel electrophoresis banding patterns were used for dendrogram generation using NTSYSpc software. RESULTS Among the 42 UPEC isolates, papC was the most common virulence gene (55% of isolates), followed by iutA (38%) and cnf1 (2%). ERIC-PCR successfully produced multiple amplicons (range 2-11 bands) in each strain, with molecular weights ranging from 285 to 3000 bp. Some UPEC isolates had identical ERIC-PCR profiles (identical banding patterns), whilst 22 UPEC isolates had different ERIC-PCR profiles. The phylogenetic dendrogram of ERIC-PCR showed that the 42 isolates can be differentiated into three major clusters (I, II and III), with cluster I representing 76% of isolates, cluster II representing 19% and cluster III representing 5%. CONCLUSIONS The results of this study suggest that both papC and iutA genes may have an important role in the pathogenesis of overt urinary tract infection. Dendrogram analysis of the ERIC-PCR profiles revealed that all UPEC isolates were assigned into three main clusters, indicating the spread of distinct clonal groups that are responsible for hospital-acquired infections.
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Affiliation(s)
- Ahmed Talaat Mahmoud
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assuit 71524, Egypt
| | - Reham Ali Ibrahem
- Department of Microbiology and Immunology, Faculty of Pharmacy, El-Minia University, Minia 61111, Egypt
| | - Mohamed Taha Salim
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assuit 71524, Egypt
| | - Adel Gabr
- Department of Medical Oncology and Malignant Hematology, South Egypt Cancer Institute, Assuit University, Assuit 71515, Egypt
| | - Hamada Mohamed Halby
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assuit 71524, Egypt.
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Adefioye OJ, Weinreich J, Rödiger S, Schierack P, Olowe OA. Phylogenetic Characterization and Multilocus Sequence Typing of Extended-Spectrum Beta Lactamase-Producing Escherichia coli from Food-Producing Animals, Beef, and Humans in Southwest Nigeria. Microb Drug Resist 2020; 27:111-120. [PMID: 32522073 DOI: 10.1089/mdr.2019.0397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Multidrug-resistant extended-spectrum beta lactamase (ESBL)-producing Escherichia coli strains are emerging globally in both humans and animals. Antimicrobial susceptibility testing and ESBL screening were performed on pure cultures of 216 E. coli isolates from human and animal fecal samples as well as beef. Polymerase chain reaction was performed for the detection of resistance genes. Representative isolates of ESBL-producing E. coli were randomly selected for multilocus sequence typing and pulsed field gel electrophoresis (PFGE). Sixty of the isolates were identified as ESBL producers, and seven resistance genes were amplified in them: TEM (61.7%), blaCTX-M-15 (51.7%), AAC-6-LB (43.3%), blaCTX-M-1 (38.3%), blaCTX-M-9 (33.3%), blaCTX-M-2 (21.7%), and SHV (11.7%); they were classified into four phylogroups: A (25%), B1 (45%), B2 (20%), and D (10%). Thirty of these isolates were clustered into 10 sequence types with ST131 being mostly prevalent. Six PFGE types were discovered, each of which was shared by isolates from different subjects and had the same phylogroups and resistance gene profiles. There was a dissemination of PFGE types across various groups among humans, animals, and beef. This underlines the fact that the spread of ESBL E. coli could be from humans to animals, from animals to humans, as well as across animal species.
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Affiliation(s)
- Olusolabomi J Adefioye
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Ladoke Akintola University of Technology, Osogbo, Nigeria
| | - Jörg Weinreich
- Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Peter Schierack
- Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Olugbenga Adekunle Olowe
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Ladoke Akintola University of Technology, Osogbo, Nigeria
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21
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Abd El-Baky RM, Ibrahim RA, Mohamed DS, Ahmed EF, Hashem ZS. Prevalence of Virulence Genes and Their Association with Antimicrobial Resistance Among Pathogenic E. coli Isolated from Egyptian Patients with Different Clinical Infections. Infect Drug Resist 2020; 13:1221-1236. [PMID: 32425560 PMCID: PMC7196243 DOI: 10.2147/idr.s241073] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/04/2020] [Indexed: 12/20/2022] Open
Abstract
Introduction Escherichia (E.) coli can cause intestinal and extra-intestinal infections which ranged from mild to life-threatening infections. The severity of infection is a product of many factors including virulence properties and antimicrobial resistance. Objectives To determine the antibiotic resistance pattern, the distribution of virulence factors and their association with one another and with some selected resistance genes. Methods Virulence properties were analyzed phenotypically while antimicrobial susceptibility was tested by Kirby-Bauer agar disc diffusion method. In addition, 64 E. coli isolates were tested for 6 colicin genes, fimH, hlyA, traT, csgA, crl virulence genes and bla−CTX-M-15, bla−oxa-2, and bla−oxa-10 resistance genes by polymerase chain reaction (PCR). Results Extra-intestinal pathogenic E. coli isolated from urine and blood samples represented a battery of virulence factors and resistance genes with a great ability to produce biofilm. Also, a significant association (P<0.05) among most of the tested colicin, virulence and resistance genes was observed. The observed associations indicate the importance and contribution of the tested factors in the establishment and the progress of infection especially with Extra-intestinal E. coli (ExPEC) which is considered a great challenging health problem. Conclusion There is a need for studying how to control these factors to decrease the rate and the severity of infections. The relationship between virulence factors and resistance genes is complex and needs more studies that should be specific for each area.
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Affiliation(s)
- Rehab Mahmoud Abd El-Baky
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia 61519, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia 11566, Egypt
| | - Reham Ali Ibrahim
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Doaa Safwat Mohamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia 11566, Egypt
| | - Eman Farouk Ahmed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia 11566, Egypt
| | - Zeinab Shawky Hashem
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
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22
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Tao X, Wang H, Min C, Yu T, Luo Y, Li J, Hu Y, Yan Q, Liu WE, Zou M. A retrospective study on Escherichia coli bacteremia in immunocompromised patients: Microbiological features, clinical characteristics, and risk factors for shock and death. J Clin Lab Anal 2020; 34:e23319. [PMID: 32267010 PMCID: PMC7439330 DOI: 10.1002/jcla.23319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
Background To evaluate clinical features, bacterial characteristics, and risk factors for shock and mortality of immunocompromised patients with Escherichia coli bacteremia. Methods A nearly 6‐year retrospective study of E coli bacteremia in 188 immunocompromised patients at Xiangya Hospital was conducted. Demographic, clinical, and laboratory data were documented. Phylogenetic background and virulence factors of E coli isolates were detected by polymerase chain reaction. Risk factors for shock and mortality were also investigated. Results Of all 188 E coli isolates, most prevalent virulence factors were fimH (91.0%), followed by traT (68.6%) and iutA (67.0%), while papG allele I, gafD, and cdtB were not detected. Phylogenetic group D was dominant (42.0%) among all isolates, and group B2 accounted for 17.6%, while group A and B1 accounted for 28.2% and 12.2%, respectively. In univariate analysis, ibeA and cnf1 were associated with mortality, which were not found in multivariate regression analysis. 22.3% of patients suffered shock, and 30‐day mortality rate was 21.3%. MDR (HR 2.956; 95% CI, 1.091‐8.012) was the only risk factor for shock, while adult (HR 0.239; 95% CI, 0.108‐0.527) was a protective factor. Multivariate analysis revealed that shock (HR 4.268; 95% CI, 2.208‐8.248; P < .001) and Charlson index > 2 (HR 2.073; 95% CI, 1.087‐3.952; P = .027) were associated with fatal outcome. Conclusions Escherichia coli bacteremia was highly lethal in immunocompromised patients, and host‐related factors played major roles in poor prognosis, while bacterial determinants had little effect on outcome. This study also provided additional information about the virulence and phylogenetic group characteristics of E coli bacteremia.
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Affiliation(s)
- Xiaoyan Tao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Haichen Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Changhang Min
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Ting Yu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Luo
- Faculty of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Jun Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Yongmei Hu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Wen' En Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Mingxiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
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Daga AP, Koga VL, Soncini JGM, de Matos CM, Perugini MRE, Pelisson M, Kobayashi RKT, Vespero EC. Escherichia coli Bloodstream Infections in Patients at a University Hospital: Virulence Factors and Clinical Characteristics. Front Cell Infect Microbiol 2019; 9:191. [PMID: 31245301 PMCID: PMC6563721 DOI: 10.3389/fcimb.2019.00191] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/20/2019] [Indexed: 01/24/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) isolates are responsible for many bloodstream infections. The aim of this study was to characterize E. coli isolated from the bloodstreams of patients (n = 48) at the University Hospital in Brazil. Epidemiological data were obtained through the analysis of medical records and laboratory tests. By PCR analysis, we investigated the presence of virulence factors (VFs), pathogenicity islands (PAIs), extended-spectrum β-lactamase (ESBL), phylogenetic classifications (A, B1, B2, C, D, E, and F) and molecular genotype by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). The mortality analysis showed that 33.3% of the deaths were associated with bacteraemia due to E. coli infections; in addition, an age between 60 and 75 years (p < 0.001; OR = 6.3[2.1–18.9]) and bacteraemia with an abdominal origin (p = 0.02; OR = 5[1.2–20.5]) were risk factors for the severity of the infection. Additionally, the presence of the afa gene was associated with mortality due to E. coli bacteraemia (p = 0.027; OR = 11.4[1.5–85.7]). Immunosuppression (27.1%), intestinal diseases (25.0%) and diabetes (18.8%), were prevalent among patients, and most of the bacteraemia cases were secondary to urinary tract infections (50.0%). The serum resistance gene traT was present in 77.1% of isolates, group capsular 2 (kpsMT II) was present in 45.8% and the K5 capsule was present in 20.8% of isolates. The isolates also showed a high prevalence for the siderophore yersiniabactina (fyuA) (70.8%) and PAI IV536 (77.1%). Phylogenetic analysis showed that group B2 (45.8%) was the most prevalent, and was the phylogroup that had a higher prevalence of VFs and PAIs. However, in this study, a considerable number of isolated bacteria were classified as group B1 (18.8%) and as group E (14.6%). Eight (16.7%) isolates were resistant to third and fourth generation cephalosporin and group CTX-M-1 (CTX-M-15) was the most prevalent ESBL type. The molecular genotyping showed two clonal lineages and several isolates that were not related to each other. This study provides additional information on the epidemiological and molecular characteristics of E. coli bloodstream infections in Brazil.
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Affiliation(s)
- Ana Paula Daga
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Vanessa Lumi Koga
- Laboratory of Microbiology, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - João Gabriel Material Soncini
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Caroline Martins de Matos
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Marcia Regina Eches Perugini
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Marsileni Pelisson
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | | | - Eliana Carolina Vespero
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
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24
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Lange A, Cajander S, Magnuson A, Sundén-Cullberg J, Strålin K, Hultgren O. Plasma concentrations of secretory leukocyte protease inhibitor (SLPI) differ depending on etiology and severity in community-onset bloodstream infection. Eur J Clin Microbiol Infect Dis 2019; 38:1425-1434. [PMID: 31089838 PMCID: PMC6647850 DOI: 10.1007/s10096-019-03567-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 11/24/2022]
Abstract
The severity of bloodstream infections (BSI) depends on pathogen, source, and host factors. Secretory leukocyte protease inhibitor (SLPI) counteracts tissue damage, balances inflammation, and is increased in pneumonia and sepsis. We aimed to evaluate whether SLPI production differs depending on etiology, disease severity, and sex in BSI and to correlate SLPI with markers of inflammation and immunosuppression. Of the adult patients with BSI, 109 were included and sampled repeatedly, from hospital admission through day 28. Controls (blood donors) were sampled twice. SLPI in plasma was measured with enzyme-linked immunosorbent assay (ELISA) technique. Streptococcus pneumoniae and Staphylococcus aureus etiology were associated with higher SLPI than Escherichia coli on days 1–2 and 3. On day 1–2, subjects with sepsis had higher SLPI concentrations than those with non-septic BSI. Pneumonia was associated with higher SLPI than a non-pulmonary source of infection. SLPI co-varied with inflammatory markers. SLPI concentrations did not differ with regard to sex in the full cohort, but men with pneumonia had higher SLPI than women on day 1–2. S. pneumoniae and S. aureus BSI were associated with higher SLPI, when compared to E. coli. Severity and pneumonia, as well as male sex in the pneumonia sub-cohort, were factors independently associated with higher SLPI.
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Affiliation(s)
- Anna Lange
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, SE-70182, Örebro, Sweden.
| | - Sara Cajander
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, SE-70182, Örebro, Sweden
| | - Anders Magnuson
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, SE-70182, Örebro, Sweden
| | - Jonas Sundén-Cullberg
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Olof Hultgren
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Faculty of Medicine and Health, Örebro University, SE-70182, Örebro, Sweden
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25
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Hung WT, Cheng MF, Tseng FC, Chen YS, Shin-Jung Lee S, Chang TH, Lin HH, Hung CH, Wang JL. Bloodstream infection with extended-spectrum beta-lactamase-producing Escherichia coli: The role of virulence genes. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 52:947-955. [PMID: 31076319 DOI: 10.1016/j.jmii.2019.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/05/2019] [Accepted: 03/20/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Extraintestinal pathogenic Escherichia coli (ExPEC) strains hold the responsibility for the majority of E. coli infections. Numerous extraintestinal virulence factors (VFs) were possessed by ExPEC which are involved in the pathogenesis of infection. However, the effect of comorbidities or infection syndrome in the association of VFs and mortality remains inconclusive. METHOD This study addressed whether specific sequence type (ST) and VFs of extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) are associated with different outcomes in patients with bloodstream infection. 121 adults from southern Taiwan with ESBL-EC bloodstream infections were enrolled during a 6-year period. Demographic data, including infection syndromes, underlying disease and outcomes, were collected. The virulence factors in isolates were analyzed by PCR and multilocus sequence typing analyses were also performed. RESULT Positivity for the virulence genes iha, hlyD, sat, iutA, fyuA, malX, ompT, and traT was associated with ST131 positivity (P < 0.05). Some ESBL-EC virulence genes associated with urinary tract infection (UTI) were revealed. Positivity for ST405 and the virulence genes iroN and iss were significantly associated with increased 30-day mortality (death within 30 days) on univariate analysis (P < 0.05). Independent risk factors of 30-day mortality in bacteremic patients with UTI included underlying chronic liver disease and malignancy. ST131 was borderline associated with 30-day mortality. Independent risk factors associated with 30-day mortality among bacteremic patients without UTI included comorbidities and iroN positivity. CONCLUSION In bacteremic patients with UTI, and the ST131 clone was borderline associated with mortality. Positivity for the virulence gene iroN may be linked to mortality in bacteremic patients without UTI.
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Affiliation(s)
- Wan-Ting Hung
- Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan.
| | - Ming-Fang Cheng
- Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan; School of Medicine, National Yang-Ming University, Taiwan; School of Nursing, Fooyin University, Kaohsiung, Taiwan.
| | - Fan-Chen Tseng
- Department of Nursing, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan; National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan.
| | - Yao-Shen Chen
- Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; School of Medicine, National Yang-Ming University, Taiwan.
| | - Susan Shin-Jung Lee
- Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; School of Medicine, National Yang-Ming University, Taiwan.
| | | | - Hsi-Hsun Lin
- E-Da Hospital, College of Medicine, I-Shou University, Kaohsiung, Taiwan.
| | - Chih-Hsin Hung
- Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan.
| | - Jiun-Ling Wang
- Department of Internal Medicine, National Cheng Kung University Hospital and College of Medicine, National Cheng Kung University Tainan, Taiwan.
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Kim DH, Subhadra B, Kang HY, Woo K, Kim J, Son YJ, Sohn KM, Kim HJ, Han K, Oh MH, Choi CH. Virulence properties of uropathogenic Escherichia coli isolated from children with urinary tract infection in Korea. Genes Genomics 2018; 40:625-634. [PMID: 29892947 DOI: 10.1007/s13258-018-0664-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/25/2018] [Indexed: 01/15/2023]
Abstract
Urinary tract infections (UTIs) are one of the most common types of bacterial infection in humans in various parts of the world and are caused mainly by uropathogenic Escherichia coli (UPEC). A total of 58 UPEC isolates from urine were characterized by serotyping and pulsed-field gel electrophoresis (PFGE). The majority of the UPEC strains belonged to serogroups O2 and O6. The UPEC strains were grouped under different pulsotypes and majority of them belonged to serogroups O2 and O6. Among the 14 virulence factors considered, 13 were present in various serogroups. The virulence genes fimH and sfa were present in all the isolates while none of the isolates carried lt-1. The strains exhibited 36 different virulence patterns, of which 11, referred to as UP (UPEC pattern) 1 to UP 11 were most common. Antibiotic resistance profiling of the UPEC isolates revealed that the serogroups O2 and O6 contain the highest number of resistant strains. The data from the current study depicting the distribution of UPEC strains among various serogroups and pulsotypes, and the occurrence of virulence genes and antibiotics resistance offer useful information on the epidemiological features of UPEC in Korea for the enhanced surveillance of potential emergence of UPEC.
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Affiliation(s)
- Dong Ho Kim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, Republic of Korea
| | - Bindu Subhadra
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, Republic of Korea
| | - Hee Young Kang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeonsangbuk-do, Republic of Korea
| | - Kyungho Woo
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, Republic of Korea
| | - Jaeseok Kim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, Republic of Korea
| | - Yeo-Jin Son
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, Republic of Korea
| | - Kyung Mok Sohn
- Division of Infectious Diseases, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Hwa-Jung Kim
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan, 31116, Republic of Korea.,BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea
| | - Man Hwan Oh
- Department of Nanobiomedical Science, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan, 31116, Republic of Korea.
| | - Chul Hee Choi
- Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, Republic of Korea.
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Owrangi B, Masters N, Kuballa A, O'Dea C, Vollmerhausen TL, Katouli M. Invasion and translocation of uropathogenic Escherichia coli isolated from urosepsis and patients with community-acquired urinary tract infection. Eur J Clin Microbiol Infect Dis 2018; 37:833-839. [PMID: 29340897 DOI: 10.1007/s10096-017-3176-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023]
Abstract
Uropathogenic Escherichia coli (UPEC) strains are found in high numbers in the gut of patients with urinary tract infections (UTIs). We hypothesised that in hospitalised patients, UPEC strains might translocate from the gut to the blood stream and that this could be due to the presence of virulence genes (VGs) that are not commonly found in UPEC strains that cause UTI only. To test this, E. coli strains representing 75 dominant clonal groups of UPEC isolated from the blood of hospitalised patients with UTI (urosepsis) (n = 22), hospital-acquired (HA) UTI without blood infection (n = 24) and strains isolated from patients with community-acquired (CA)-UTIs (n = 29) were tested for their adhesion to, invasion and translocation through Caco-2 cells, in addition to the presence of 34 VGs associated with UPEC. Although there were no differences in the rate and degree of translocation among the groups, urosepsis and HA-UTI strains showed significantly higher abilities to adhere (P = 0.0095 and P < 0.0001 respectively) and invade Caco-2 cells than CA-UTI isolates (P = 0.0044, P = 0.0048 respectively). Urosepsis strains also carried significantly more VGs than strains isolated from patients with only UTI and/or CA-UTI isolates. In contrast, the antigen 43 allele RS218 was found more commonly among CA-UTI strains than in the other two groups. These data indicate that UPEC strains, irrespective of their source, are capable of translocating through gut epithelium. However, urosepsis and HA-UTI strains have a much better ability to interact with gut epithelia and have a greater virulence potential than CA-UPEC, which allows them to cause blood infection.
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Affiliation(s)
- B Owrangi
- Inflammation and Healing Cluster, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - N Masters
- Inflammation and Healing Cluster, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - A Kuballa
- Inflammation and Healing Cluster, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - C O'Dea
- Inflammation and Healing Cluster, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - T L Vollmerhausen
- Inflammation and Healing Cluster, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - M Katouli
- Inflammation and Healing Cluster, School of Health and Sport Sciences, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
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Abstract
Sepsis describes a broad-based syndrome covering many infectious agents, affecting various sites in patients of differing age, gender, and comorbidity and resulting in varying degrees and combinations of organ dysfunction. Protocolized care with rigid goals may suit populations, assuming the evidence-lite recommendations are beneficial, but not necessarily individual patients. A personalized approach to management is rational and preferable. Other than clinical heterogeneity, a range of biological signatures exist in sepsis, and these fluctuate over the disease course. Subsets of septic patients can display distinct biological signatures that may potentially be used to identify suitability for different treatments and titration to optimal effect.
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Messika J, Clermont O, Landraud L, Schmidt M, Aubry A, Sougakoff W, Fernandes R, Combes A, Denamur E, Ricard JD. Extra-corporeal membrane oxygenation-associated infections: implication of extra-intestinal pathogenic Escherichia coli clones. J Med Microbiol 2017; 66:1189-1195. [DOI: 10.1099/jmm.0.000554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Jonathan Messika
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700, Colombes, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Luce Landraud
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- AP-HP, Hôpital Louis Mourier, Service de Microbiologie, F-92700, Colombes, France
| | - Matthieu Schmidt
- Medical Intensive Care Unit, iCAN, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié–Salpêtrière, Assistance Publique–Hôpitaux de Paris, Université Pierre-et-Marie-Curie, Paris 6, 75651 Paris Cedex 13, France
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
| | - Alexandra Aubry
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyrMA), Bactériologie-Hygiène, Paris, France
| | - Wladimir Sougakoff
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyrMA), Bactériologie-Hygiène, Paris, France
| | - Romain Fernandes
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Alain Combes
- Medical Intensive Care Unit, iCAN, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié–Salpêtrière, Assistance Publique–Hôpitaux de Paris, Université Pierre-et-Marie-Curie, Paris 6, 75651 Paris Cedex 13, France
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, F-75018, Paris, France
| | - Jean-Damien Ricard
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700, Colombes, France
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
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30
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Tashk P, Lecronier M, Clermont O, Renvoisé A, Aubry A, Barrou B, Hertig A, Lescat M, Tenaillon O, Denamur E, Tourret J. [Molecular epidemiology and kinetics of early Escherichia coli urinary tract infections in kidney transplant recipients]. Nephrol Ther 2017; 13:236-244. [PMID: 28576434 DOI: 10.1016/j.nephro.2016.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/12/2016] [Accepted: 10/12/2016] [Indexed: 10/19/2022]
Abstract
BACKGROUND Escherichia coli strains causing Urinary Tract Infections (UTI) have a fecal origin. METHODS A fecal sample was collected before Kidney Transplantation (KT) and concomitantly with urine at each of the 15 E. coli UTIs which occurred in 11 KT recipients. Unique E. coli strains were identified among 25 isolates per feces and 5 isolates per urinary sample by random amplification of polymorphic DNA. Phylogenetic group (which is correlated to virulence in the E. coli species) was determined for each E. coli strain by a PCR based method. RESULTS Forty-three unique fecal strains and 14 unique urinary strains were identified among 650 fecal isolates and 75 urinary isolates. Urinary strains frequently (55% of the cases) belonged to a phylogroup usually not linked to virulence. They were detected in the feces collected concomitantly in 60% of the cases. Urinary strains belonging to a phylogroup usually linked to virulence were more frequently dominant in the feces (100%) than urinary strains belonging to a non-pathogenic phylogroup (42%; P<0.05). Vesical catheter was a facilitating factor only for urinary strains belonging to non-pathogenic phylogroups. Thirty-three percent of the fecal strains were persisting in two consecutive fecal samples and 62% were detected for the first time at the UTI. Numerous pathway lead to UTIs: from a unique, virulent and persisting strain to a non-virulent recently acquired strain facilitated by a vesical catheter. CONCLUSION Our work shows the diversity of host-microbial interactions which precede extra-intestinal virulence.
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Affiliation(s)
- Parvine Tashk
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Marie Lecronier
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Olivier Clermont
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Aurélie Renvoisé
- Service de bactériologie et d'hygiène, groupe hospitalier Pitié-Salpêtrière-Charles-Foix, AP-HP, 83, boulevard de l'Hôpital, 75013 Paris, France
| | - Alexandra Aubry
- Service de bactériologie et d'hygiène, groupe hospitalier Pitié-Salpêtrière-Charles-Foix, AP-HP, 83, boulevard de l'Hôpital, 75013 Paris, France; Université Pierre-et-Marie-Curie, Sorbonne universités, 91, boulevard de l'Hôpital, 75013 Paris, France
| | - Benoît Barrou
- Université Pierre-et-Marie-Curie, Sorbonne universités, 91, boulevard de l'Hôpital, 75013 Paris, France; Département d'urologie, néphrologie et transplantation, groupe hospitalier Pitié-Salpêtrière-Charles-Foix, AP-HP, 83, boulevard de l'Hôpital, 75013 Paris, France
| | - Alexandre Hertig
- Université Pierre-et-Marie-Curie, Sorbonne universités, 91, boulevard de l'Hôpital, 75013 Paris, France; Urgences néphrologiques et transplantation rénale, hôpital Tenon, AP-HP, 4, rue de la Chine, 75020 Paris, France
| | - Mathilde Lescat
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France; Laboratoire de microbiologie, hôpital Jean-Verdier, AP-HP, avenue, du 14-Juillet, 93140 Bondy, France
| | - Olivier Tenaillon
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Erick Denamur
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France
| | - Jérôme Tourret
- Inserm, IAME, UMR 1137, université Paris-Diderot, Sorbonne Paris Cité, Site Bichat-Claude-Bernard, 18, rue Henri-Huchard, 75018 Paris, France; Université Pierre-et-Marie-Curie, Sorbonne universités, 91, boulevard de l'Hôpital, 75013 Paris, France; Département d'urologie, néphrologie et transplantation, groupe hospitalier Pitié-Salpêtrière-Charles-Foix, AP-HP, 83, boulevard de l'Hôpital, 75013 Paris, France.
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Owrangi B, Masters N, Vollmerhausen T, O'Dea C, Kuballa A, Katouli M. Comparison between virulence characteristics of dominant and non-dominant Escherichia coli strains of the gut and their interaction with Caco-2 cells. Microb Pathog 2017; 105:171-176. [DOI: 10.1016/j.micpath.2017.02.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 01/14/2023]
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Melzer M, Welch C. Does the presence of a urinary catheter predict severe sepsis in a bacteraemic cohort? J Hosp Infect 2017; 95:376-382. [PMID: 28202189 DOI: 10.1016/j.jhin.2017.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Sepsis is a major cause of mortality with an estimated 37,000 deaths in the UK each year. This study aimed to determine host factors that can predict severe sepsis in a bacteraemic cohort. METHODS From December 2012 to November 2013, demographic, clinical and microbiological data were collected on consecutive patients with bacteraemia at a London teaching hospital. These data were used to categorize patients as having severe or non-severe sepsis. Multi-variate logistic regression was used to determine the association between host factors and severe sepsis. FINDINGS Five hundred and ninety-four bacteraemic episodes occurred in 500 patients. The majority of cases were in patients aged >50 years (382/594, 64.3%) and in males (346/594, 58.2%). The most common isolates were Escherichia coli (207/594, 34.8%) and meticillin-susceptible Staphylococcus aureus (57/594, 9.6%). In logistic regression multi-variable analysis, site of infection was significantly associated with severe sepsis. For catheter-associated urinary tract infections, the association was significant after adjustment for age, sex, Charlson comorbidity index and where infection was acquired (odds ratio 3.94, 95% confidence interval 1.70-9.11). CONCLUSIONS Urinary catheters increase the risk of severe sepsis. They should only be used if clinically indicated. If inserted, a care bundle approach should be used and the anticipated removal date should be recorded unless a long-term catheter is required. In the context of sepsis, the presence of a urinary catheter should prompt immediate implementation of 'Sepsis Six' and consideration of transfer to a critical care unit.
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Affiliation(s)
- M Melzer
- Royal London Hospital, Barts Health NHS Trust, London, UK.
| | - C Welch
- Department of Epidemiology and Public Health, University College London, London, UK
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33
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Abstract
The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinal Escherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. An E. coli chromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenic E. coli strains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival of E. coli as a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.
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Vading M, Kabir MH, Kalin M, Iversen A, Wiklund S, Nauclér P, Giske CG. Frequent acquisition of low-virulence strains of ESBL-producing Escherichia coli in travellers. J Antimicrob Chemother 2016; 71:3548-3555. [PMID: 27566312 DOI: 10.1093/jac/dkw335] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/08/2016] [Accepted: 07/19/2016] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES International travel is a risk factor for intestinal colonization with ESBL-producing Enterobacteriaceae (EPE). This prospective cohort study focuses on molecular features of and risk factors for travel-acquired EPE. METHODS Rectal swabs and survey data were collected from 188 Swedes travelling to four regions of high EPE prevalence. Samples were plated onto selective agars. ESBL producers were determined using phenotypic methods. Molecular characterization regarding virulence factors and phylogenetic grouping of ESBL-producing Escherichia coli was done using PCR. Isolates were also screened for the plasmid-mediated colistin resistance gene mcr-1. RESULTS Among 175 pre-travel EPE-negative participants, 32% were positive upon return. No carbapenemase-producing Enterobacteriaceae were found, but one CTX-M-producing E. coli harboured mcr-1 (travel to Thailand). Most E. coli strains (43.1%) belonged to phylogroup A and were rarely associated with extraintestinal infections and a few (9.2%) expressed uropathogenicity pap genes. During 10-26 months of follow-up, no clinical infections were observed. Colonization rates varied by visited region: the Indian subcontinent, 49.2%; northern Africa, 44.0%; South-East Asia, 19.1%; and Turkey, 9.5%. Travellers' diarrhoea (OR 2.5, P = 0.04) or antimicrobial treatment during the trip (OR 5.9, P = 0.02) were both independent risk factors for EPE colonization. CONCLUSIONS EPE acquired during travel have seemingly low pathogenicity, possibly indicating a low risk of clinical infection. Pre-travel advice should emphasize avoiding unnecessary antibiotic treatment during travel.
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Affiliation(s)
- M Vading
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden .,Department of Infectious Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - M H Kabir
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - M Kalin
- Department of Medicine Solna, Infectious Diseases Unit, Karolinska Institutet, Stockholm, Sweden
| | - A Iversen
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - S Wiklund
- Department of Medicine Solna, Infectious Diseases Unit, Karolinska Institutet, Stockholm, Sweden.,Department of Infection Control and Hospital Hygiene, Stockholm County Council, Stockholm, Sweden
| | - P Nauclér
- Department of Infectious Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.,Department of Medicine Solna, Infectious Diseases Unit, Karolinska Institutet, Stockholm, Sweden
| | - C G Giske
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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35
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Characterization of Ciprofloxacin-Resistant and Ciprofloxacin-Susceptible Uropathogenic Escherichia coli Obtained from Patients with Gynecological Cancer. Curr Microbiol 2016; 73:624-632. [DOI: 10.1007/s00284-016-1104-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/18/2016] [Indexed: 11/26/2022]
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36
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Miajlovic H, Mac Aogáin M, Collins CJ, Rogers TR, Smith SGJ. Characterization of Escherichia coli bloodstream isolates associated with mortality. J Med Microbiol 2016; 65:71-79. [PMID: 26518234 DOI: 10.1099/jmm.0.000200] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) are the predominant cause of Gramnegative bloodstream infections. In this study, 20 E. coli isolates that were the causative agents of bacteraemia and subsequent mortality were characterized. Whole-genome sequencing was used to define the predominant sequence types (ST) among the isolates and to identify virulence factors associated with pathogenicity of ExPEC. The ability of the isolates to resist killing by both serum and polymorphonuclear leukocytes (PMNLs) was also assessed. In line with global trends, ST131 occurred most frequently among the bloodstream isolates and all isolates of this sequence type were multidrug resistant. Other common STs included ST73 and ST69. All isolates encoded multiple virulence factors across a range of categories, including factors involved in adhesion, immune evasion, iron acquisition and synthesis of toxins. None of these factors could be associated with serum and neutrophil resistance. The majority of isolates were resistant to the bactericidal action of serum and PMNLs, and most of those that were sensitive were isolated from patients with compromised immunity.
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Affiliation(s)
- Helen Miajlovic
- Department of Clinical Microbiology, Sir Patrick Dun Research Laboratory, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Micheál Mac Aogáin
- Department of Clinical Microbiology, Sir Patrick Dun Research Laboratory, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Cathal J Collins
- Department of Clinical Microbiology, Sir Patrick Dun Research Laboratory, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Thomas R Rogers
- Department of Clinical Microbiology, Sir Patrick Dun Research Laboratory, School of Medicine, Trinity College, Dublin 8, Ireland.,Microbiology Department, St James's Hospital, Dublin 8, Ireland
| | - Stephen G J Smith
- Department of Clinical Microbiology, Sir Patrick Dun Research Laboratory, School of Medicine, Trinity College, Dublin 8, Ireland
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Chakraborty A, Adhikari P, Shenoy S, Rao S, Dhanashree B, Saralaya V. Molecular characterization and clinical significance of extraintestinal pathogenic Escherichia coli recovered from a south Indian tertiary care hospital. Microb Pathog 2016; 95:43-48. [DOI: 10.1016/j.micpath.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/07/2016] [Accepted: 03/07/2016] [Indexed: 11/30/2022]
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Mora-Rillo M, Fernández-Romero N, Navarro-San Francisco C, Díez-Sebastián J, Romero-Gómez MP, Fernández FA, López JRA, Mingorance J. Impact of virulence genes on sepsis severity and survival in Escherichia coli bacteremia. Virulence 2016; 6:93-100. [PMID: 25654604 DOI: 10.4161/21505594.2014.991234] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) are a frequent cause of bacteremia and sepsis, but the role of ExPEC genetic virulence factors (VFs) in sepsis development and outcome is ill-defined. Prospective study including 120 adult patients with E. coli bacteremia to investigate the impact of bacterial and host factors on sepsis severity and mortality. Patients' clinical and demographic data were registered. Phylogenetic background of E. coli isolates was analyzed by SNP pyrosequencing and VFs by PCR. The E. coli isolates presented an epidemic population structure with 6 dominant clones making up to half of the isolates. VF gene profiles were highly diverse. Multivariate analysis for sepsis severity showed that the presence of cnf and blaTEM genes increased the risk of severe illness by 6.75 (95% confidence interval [CI] 1.79-24.71) and 2.59 (95% CI 1.04-6.43) times respectively, while each point in the Pitt score increased the risk by 1.34 (95% CI 1.02-1.76) times. Multivariate analysis for mortality showed that active chemotherapy (OR 17.87, 95% CI 3.35-95.45), McCabe-Jackson Index (OR for rapidly fatal category 120.15, 95% CI 4.19-3446.23), Pitt index (OR 1.78, 95% CI 1.25-2.56) and presence of fyuA gene (OR 8.05, 95% CI 1.37-47.12) were associated to increased mortality while the presence of P fimbriae genes had a protective role (OR 0.094, 95%IC 0.018-0.494). Bacteremic E. coli had a high diversity of genetic backgrounds and VF gene profiles. Bacterial VFs and host determinants had an impact on disease evolution and mortality.
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Affiliation(s)
- Marta Mora-Rillo
- a Unidad de Enfermedades Infecciosas y Microbiología Clínica; Servicio de Medicina Interna ; Hospital Universitario La Paz-IDIPAZ ; Madrid , Spain
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Lee JH, Subhadra B, Son YJ, Kim DH, Park HS, Kim JM, Koo SH, Oh MH, Kim HJ, Choi CH. Phylogenetic group distributions, virulence factors and antimicrobial resistance properties of uropathogenic Escherichia coli strains isolated from patients with urinary tract infections in South Korea. Lett Appl Microbiol 2015; 62:84-90. [PMID: 26518617 DOI: 10.1111/lam.12517] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/07/2015] [Accepted: 10/25/2015] [Indexed: 12/21/2022]
Abstract
UNLABELLED Urinary tract infections (UTIs) are one of the most common diseases by which humans seek medical help and are caused mainly by uropathogenic Escherichia coli (UPEC). Studying the virulence and antibiotic resistance of UPEC with respect to various phylogenetic groups is of utmost importance in developing new therapeutic agents. Thus, in this study, we analysed the virulence factors, antibiotic resistance and phylogenetic groups among various UPEC isolates from children with UTIs. The phylogenetic analysis revealed that majority of the strains responsible for UTIs belonged to the phylogenetic groups B2 and D. Of the 58 E. coli isolates, 79·31% belonged to group B2, 15·51% to group D, 3·44% to group A and 1·72% to B1. Simultaneously, the number of virulence factors and antibiotic resistance exhibited were also significantly high in groups B2 and D compared to other groups. Among the isolates, 44·8% were multidrug resistant and of that 73% belonged to the phylogenetic group B2, indicating the compatibility of antibiotic resistance and certain strains carrying virulence factor genes. The antibiotic resistance profiling of UPEC strains elucidates that the antimicrobial agents such as chloramphenicol, cefoxitin, cefepime, ceftazidime might still be used in the therapy for treating UTIs. SIGNIFICANCE AND IMPACT OF THE STUDY As the antibiotic resistance pattern of uropathogenic Escherichia coli varies depending on different geographical regions, the antibiotic resistance pattern from this study will help the physicians to effectively administer antibiotic therapy for urinary tract infections. In addition, the frequency of virulence factors and antibiotic resistance genes among various phylogenic groups could be effectively used to draw new targets for uropathogenic Escherichia coli antibiotic-independent therapies. The study emphasizes need of public awareness on multidrug resistance and for more prudent use of antimicrobials.
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Affiliation(s)
- J H Lee
- Department of Pediatrics, Chungnam National University Hospital, Daejeon, Korea
| | - B Subhadra
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Y-J Son
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, Korea
| | - D H Kim
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, Korea
| | - H S Park
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, Korea
| | - J M Kim
- Department of Pediatrics, Chungnam National University Hospital, Daejeon, Korea
| | - S H Koo
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - M H Oh
- Department of Nanobiomedical Science, Dankook University, Cheonan, Korea
| | - H-J Kim
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, Korea
| | - C H Choi
- Department of Microbiology, College of Medicine, Chungnam National University, Daejeon, Korea
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Multilocus Sequence Typing and Virulence Profiles in Uropathogenic Escherichia coli Isolated from Cats in the United States. PLoS One 2015; 10:e0143335. [PMID: 26587840 PMCID: PMC4654559 DOI: 10.1371/journal.pone.0143335] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/03/2015] [Indexed: 11/19/2022] Open
Abstract
The population structure, virulence, and antimicrobial resistance of uropathogenic E. coli (UPEC) from cats are rarely characterized. The aim of this study was to compare and characterize the UPEC isolated from cats in four geographic regions of USA in terms of their multilocus sequence typing (MLST), virulence profiles, clinical signs, antimicrobial resistance and phylogenetic grouping. The results showed that a total of 74 E. coli isolates were typed to 40 sequence types with 10 being novel. The most frequent phylogenetic group was B2 (n = 57). The most frequent sequence types were ST73 (n = 12) and ST83 (n = 6), ST73 was represented by four multidrug resistant (MDR) and eight non-multidrug resistant (SDR) isolates, and ST83 were significantly more likely to exhibit no drug resistant (NDR) isolates carrying the highest number of virulence genes. Additionally, MDR isolates were more diverse, and followed by SDR and NDR isolates in regards to the distribution of the STs. afa/draBC was the most prevalent among the 29 virulence-associated genes. Linking virulence profile and antimicrobial resistance, the majority of virulence-associated genes tested were more prevalent in NDR isolates, and followed by SDR and MDR isolates. Twenty (50%) MLST types in this study have previously been associated with human isolates, suggesting that these STs are potentially zoonotic. Our data enhanced the understanding of E. coli population structure and virulence association from cats. The diverse and various combinations of virulence-associated genes implied that the infection control may be challenging.
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Parker KS, Wilson JD, Marschall J, Mucha PJ, Henderson JP. Network Analysis Reveals Sex- and Antibiotic Resistance-Associated Antivirulence Targets in Clinical Uropathogens. ACS Infect Dis 2015; 1:523-532. [PMID: 26985454 PMCID: PMC4788272 DOI: 10.1021/acsinfecdis.5b00022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Indexed: 01/29/2023]
Abstract
Increasing antibiotic resistance among uropathogenic Escherichia coli (UPEC) is driving interest in therapeutic targeting of nonconserved virulence factor (VF) genes. The ability to formulate efficacious combinations of antivirulence agents requires an improved understanding of how UPEC deploy these genes. To identify clinically relevant VF combinations, we applied contemporary network analysis and biclustering algorithms to VF profiles from a large, previously characterized inpatient clinical cohort. These mathematical approaches identified four stereotypical VF combinations with distinctive relationships to antibiotic resistance and patient sex that are independent of traditional phylogenetic grouping. Targeting resistance- or sex-associated VFs based upon these contemporary mathematical approaches may facilitate individualized anti-infective therapies and identify synergistic VF combinations in bacterial pathogens.
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Affiliation(s)
| | | | - Jonas Marschall
- Department
of Infectious Diseases, Bern University Hospital and University of Bern, 3010 Bern, Switzerland
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Chakraborty A, Saralaya V, Adhikari P, Shenoy S, Baliga S, Hegde A. Characterization of Escherichia coli Phylogenetic Groups Associated with Extraintestinal Infections in South Indian Population. Ann Med Health Sci Res 2015; 5:241-6. [PMID: 26229711 PMCID: PMC4512115 DOI: 10.4103/2141-9248.160192] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background: Escherichia coli strains mainly fall into four phylogenetic groups (A, B1, B2, and D) and that virulent extra-intestinal strains mainly belong to groups B2 and D. Aim: The aim was to determine the association between phylogenetic groups of E. coli causing extraintestinal infections (ExPEC) regarding the site of infection, expression of virulence factors, antimicrobial resistance patterns, and clinical outcome. This descriptive study was carried out in a multi-specialty Tertiary Care Hospital. Materials and Methods: A total of 300 E. coli causing ExPEC were studied. Triplex polymerase chain reaction was used to classify the phylogenetic groups; hemolysin production was assessed on sheep blood agar and biofilm production in a microtiter plate assay. Production of extended spectrum of beta-lactamase (ESBLs) was detected by combination disk method; AmpC was detected by AmpC disk test, Carbapenemase production was detected by modified Hodge test and metallo-β-lactamase by metallo-beta-lactamases (MBL) E-test. Results: Of 300 isolates, 61/300 (20%) belonged to phylogroup A, 27/300 (9%) to phylogroup B1, 104/300 (35%) were B2 and 108/300 (36%) belonged to group D, respectively. Phylogroups B2 and D were the most predominant groups in urinary tract infection and sepsis. Prognoses were better in infections with group A and B1 isolates, and relapses and death were common in infections with B2 and D. Expression of biofilm was greatest in B1 and hemolysin in group B2. Group A and B1 showed higher resistance to ciprofloxacin and were most frequent β-lactamase (ESBL, AmpC, Carbapenemase and MBL) producers. Conclusions: Phylogenetic group B2 and D were predominant in ExPEC and exhibited least antimicrobial resistance among the groups. Resistance to multiple antibiotics was most prevalent in group A and B1. Regular monitoring of antimicrobial susceptibility in commensal strains is essential as they might transfer the property of antimicrobial resistance to pathogenic strains.
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Affiliation(s)
- A Chakraborty
- Department of Microbiology Moti Lal Nehru Medical College, Allahabad, Uttar Pradesh, India
| | - V Saralaya
- Department of Microbiology, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | - P Adhikari
- Department of Medicine, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | - S Shenoy
- Department of Microbiology, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | - S Baliga
- Department of Microbiology, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
| | - A Hegde
- Department of Microbiology, Kasturba Medical College, Manipal University, Mangalore, Karnataka, India
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Yahiaoui M, Robin F, Bakour R, Hamidi M, Bonnet R, Messai Y. Antibiotic Resistance, Virulence, and Genetic Background of Community-Acquired Uropathogenic Escherichia coli from Algeria. Microb Drug Resist 2015; 21:516-26. [PMID: 26430940 DOI: 10.1089/mdr.2015.0045] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of the study was to investigate antibiotic resistance mechanisms, virulence traits, and genetic background of 150 nonrepetitive community-acquired uropathogenic Escherichia coli (CA-UPEC) from Algeria. A rate of 46.7% of isolates was multidrug resistant. bla genes detected were blaTEM (96.8% of amoxicillin-resistant isolates), blaCTX-M-15 (4%), overexpressed blaAmpC (4%), blaSHV-2a, blaTEM-4, blaTEM-31, and blaTEM-35 (0.7%). All tetracycline-resistant isolates (51.3%) had tetA and/or tetB genes. Sulfonamides and trimethoprim resistance genes were sul2 (60.8%), sul1 (45.9%), sul3 (6.7%), dfrA14 (25.4%), dfrA1 (18.2%), dfrA12 (16.3%), and dfrA25 (5.4%). High-level fluoroquinolone resistance (22.7%) was mediated by mutations in gyrA (S83L-D87N) and parC (S80I-E84G/V or S80I) genes. qnrB5, qnrS1, and aac(6')-Ib-cr were rare (5.3%). Class 1 and/or class 2 integrons were detected (40.7%). Isolates belonged to phylogroups B2+D (50%), A+B1 (36%), and F+C+Clade I (13%). Most of D (72.2%) and 38.6% of B2 isolates were multidrug resistant; they belong to 14 different sequence types, including international successful ST131, ST73, and ST69, reported for the first time in the community in Algeria and new ST4494 and ST4529 described in this study. Besides multidrug resistance, B2 and D isolates possessed virulence factors of colonization, invasion, and long-term persistence. The study highlighted multidrug-resistant CA-UPEC with high virulence traits and an epidemic genetic background.
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Affiliation(s)
- Merzouk Yahiaoui
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
| | - Frédéric Robin
- 2 CHU Clermont-Ferrand, Laboratoire de Bactériologie , Clermont-Ferrand, France .,3 Clermont Université, Université d'Auvergne , Evolution des Bactéries Pathogènes et Susceptibilité de l'Hôte, Clermont-Ferrand, France
| | - Rabah Bakour
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
| | | | - Richard Bonnet
- 2 CHU Clermont-Ferrand, Laboratoire de Bactériologie , Clermont-Ferrand, France .,3 Clermont Université, Université d'Auvergne , Evolution des Bactéries Pathogènes et Susceptibilité de l'Hôte, Clermont-Ferrand, France
| | - Yamina Messai
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
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A comparative study of antimicrobial resistance rates and phylogenetic groups of community-acquired versus hospital-acquired invasive Escherichia coli. Med Mal Infect 2015; 45:133-8. [DOI: 10.1016/j.medmal.2015.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 11/19/2014] [Accepted: 01/27/2015] [Indexed: 11/23/2022]
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45
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Shaw E, Benito N, Rodríguez-Baño J, Padilla B, Pintado V, Calbo E, Pallarés MA, Gozalo M, Ruiz-Garbajosa P, Horcajada JP. Risk factors for severe sepsis in community-onset bacteraemic urinary tract infection: impact of antimicrobial resistance in a large hospitalised cohort. J Infect 2015; 70:247-54. [PMID: 25305497 DOI: 10.1016/j.jinf.2014.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/12/2014] [Accepted: 09/15/2014] [Indexed: 02/08/2023]
Abstract
OBJECTIVE To determine risks factors associated with severe sepsis or septic shock (SS) at admission in patients with community-onset bacteraemic urinary tract infection (CO-BUTI) including the impact of multidrug-resistant (MDR) bacteria. METHODS We analysed a prospective cohort of all consecutive episodes of CO-BUTI requiring hospitalisation in 8 tertiary hospitals of Spain between October 2010 and June 2011. RESULTS Of an overall of 525 CO-BUTI episodes, 175 (33%) presented with SS at admission. MDR bacteria were isolated in 29% (51/175) of episodes with SS and in 33% (117/350) of those without SS (p = 0.32). The main MDR microorganism was Escherichia coli in both groups (25% and 28% respectively). Independent risk factors associated with SS at admission were: having fatal underlying conditions, McCabe score II/III (OR 1.90; 95%CI 1.23-2.92; p = 0.004), presence of an indwelling urethral catheter (OR 3.01; 95%CI 1.50-6.03; p = 0.002) and a history of urinary tract obstruction (OR 1.56; 95%CI 1.03-2.34; p = 0.03). After considering interactions, indwelling urethral catheters were a risk factor only for patients without fatal underlying conditions. CONCLUSIONS SS at hospital admission occurred in a third of CO-BUTI. Mainly host factors, and not the causative microorganisms or antimicrobial resistance patterns had an impact on the presence of SS.
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Affiliation(s)
- Evelyn Shaw
- Servicio de Enfermedades Infecciosas, Hospital Universitari de Bellvitge - IDIBELL, Barcelona, Spain.
| | - Natividad Benito
- Servicio de Enfermedades Infecciosas, Hospital de Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Barcelona, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Departamento de Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Belén Padilla
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital Gregorio Marañón, Madrid, Spain
| | - Vicente Pintado
- Servicio de Enfermedades Infecciosas, Hospital Ramón y Cajal, Madrid, Spain
| | - Esther Calbo
- Servicio de Medicina Interna, Hospital Mútua de Terrassa, Barcelona, Spain
| | | | - Mónica Gozalo
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - Juan Pablo Horcajada
- Servicio de Enfermedades Infecciosas, Hospital Universitari del Mar and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
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Morgand M, Vimont S, Bleibtreu A, Boyd A, Thien HV, Zahar JR, Denamur E, Arlet G. Extended-spectrum beta-lactamase-producing Escherichia coli infections in children: are community-acquired strains different from nosocomial strains? Int J Med Microbiol 2014; 304:970-6. [PMID: 25023074 DOI: 10.1016/j.ijmm.2014.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/04/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022] Open
Abstract
Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are an important cause of morbidity and mortality, especially in children. We compared 58 epidemiologically unrelated ESBL-producing E. coli strains that caused infections. They were isolated between 2008 and 2012 in two Parisian pediatric hospitals and grouped according to their origin into either community-acquired (CA) (n=37) or nosocomially acquired (NA) (n=21) strains. Molecular characteristics of the ESBLs, phylogenetic traits of the strains including their belonging to clone O25b-ST131, prevalence of associated virulence genes, growth capacities in different media, metabolic phenotype and biofilm formation abilities were studied. ESBL type, associated resistance and distribution of phylogenetic groups were similar in the CA and NA groups. More than 60% of the B2 phylogroup strains in both groups belonged to the ST131 clone. Interestingly, CA strains possessed more genes encoding virulence factors and the distribution of these genes differed significantly between the two groups: fyuA, hlyC, papC and papGII were more frequent in the CA group, whereas iroN was more frequent in the NA group. CA strains also showed enhanced growth capacities in Luria Bertani rich medium. They tended to produce more biofilm but the difference was not significant. This study confirms the wide spread of clone ST131 among infected children, regardless of whether their infections were community- or nosocomially acquired. It highlights genotypic and phenotypic differences according to the origin of the strains that could indicate adaptability of these multi-resistant bacteria to specific environmental and host factors.
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Affiliation(s)
- Marjolaine Morgand
- Université Pierre et Marie Curie, Faculté de Médecine, Département de Bactériologie, F-75012 Paris, France
| | - Sophie Vimont
- Université Pierre et Marie Curie, Faculté de Médecine, Département de Bactériologie, F-75012 Paris, France; Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaire de l'Est Parisien, Département de Bactériologie, F-75012 Paris, France
| | - Alexandre Bleibtreu
- IAME, UMR 1137, INSERM, F-75018 Paris, France; IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France
| | | | - Hoang Vu Thien
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaire de l'Est Parisien, Département de Bactériologie, F-75012 Paris, France
| | - Jean-Ralph Zahar
- Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Unité d'hygiène et de lutte contre les infections nosocomiales, F-75015 Paris, France
| | - Erick Denamur
- IAME, UMR 1137, INSERM, F-75018 Paris, France; IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France
| | - Guillaume Arlet
- Université Pierre et Marie Curie, Faculté de Médecine, Département de Bactériologie, F-75012 Paris, France; Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaire de l'Est Parisien, Département de Bactériologie, F-75012 Paris, France.
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Escherichia coli bacteraemia in adults: age-related differences in clinical and bacteriological characteristics, and outcome. Epidemiol Infect 2014; 142:2672-83. [PMID: 24559489 DOI: 10.1017/s0950268814000211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To explore the specificities of Escherichia coli bacteraemia in the elderly, the demographic, clinical and bacteriological characteristics and in-hospital mortality rate of 'young' (18-64 years, n = 395), 'old' (65-79 years, n = 372) and 'very old' (⩾80 years, n = 284) adult patients of the multicentre COLIBAFI cohort study were compared. Clinical and bacteriological risk factors for death were jointly identified by logistic regression and multivariate analysis within each group. 'Young' and 'old' patients had more comorbidities than 'very old' patients (comorbidity score: 1·5 ± 1·3 and 1·6 ± 1·2 vs. 1·2 ± 1·2, respectively; P < 0·001), and were more frequently nosocomially infected (22·3% and 23·8% vs. 8·8%, respectively; P < 0·001). 'Old' patients had the poorest prognosis (death rate: 16·4% vs.10·4% for 'young' and 12·0% for 'very old' patients, respectively; P = 0·039). Risk factors for death were age group-specific, suggesting a host-pathogen relationship evolving with age.
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48
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High rate of fecal carriage of extended-spectrum-β-lactamase-producing Escherichia coli in healthy children in Gipuzkoa, northern Spain. Antimicrob Agents Chemother 2014; 58:1822-4. [PMID: 24395224 DOI: 10.1128/aac.01503-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The prevalence of extended-spectrum-β-lactamase-producing Enterobacteriaceae (ESBLPE) was studied in stool samples from 125 8- to 16-month-old healthy children. Twenty-four percent of them and 10.7% of the 318 fecal samples studied yielded extended-spectrum-β-lactamase-producing Escherichia coli, with the types being SHV-12, CTX-M-1, CTX-M-14, and TEM-52, the most common types of β-lactamases. This high prevalence of ESBLPE in healthy people, which is to our knowledge the highest currently reported in Europe, may represent a risk for increased infections by these organisms in the future.
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Rodríguez-Baño J, Mingorance J, Fernández-Romero N, Serrano L, López-Cerero L, Pascual A. Outcome of bacteraemia due to extended-spectrum β-lactamase-producing Escherichia coli: Impact of microbiological determinants. J Infect 2013; 67:27-34. [DOI: 10.1016/j.jinf.2013.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 03/01/2013] [Accepted: 04/08/2013] [Indexed: 11/25/2022]
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Landraud L, Jauréguy F, Frapy E, Guigon G, Gouriou S, Carbonnelle E, Clermont O, Denamur E, Picard B, Lemichez E, Brisse S, Nassif X. Severity of Escherichia coli bacteraemia is independent of the intrinsic virulence of the strains assessed in a mouse model. Clin Microbiol Infect 2013; 19:85-90. [DOI: 10.1111/j.1469-0691.2011.03750.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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