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Timm MR, Russell SK, Hultgren SJ. Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01092-4. [PMID: 39251839 DOI: 10.1038/s41579-024-01092-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2024] [Indexed: 09/11/2024]
Abstract
Urinary tract infections (UTIs), which include any infection of the urethra, bladder or kidneys, account for an estimated 400 million infections and billions of dollars in health-care spending per year. The most common bacterium implicated in UTI is uropathogenic Escherichia coli, but diverse pathogens including Klebsiella, Enterococcus, Pseudomonas, Staphylococcus and even yeast such as Candida species can also cause UTIs. UTIs occur in both women and men and in both healthy and immunocompromised patients. However, certain patient factors predispose to disease: for example, female sex, history of prior UTI, or the presence of a urinary catheter or other urinary tract abnormality. The current clinical paradigm for the treatment of UTIs involves the use of antibiotics. Unfortunately, the efficacy of this approach is dwindling as the prevalence of antimicrobial resistance rises among UTI isolates, and the immense quantity of antibiotics prescribed annually for these infections contributes to the emergence of resistant pathogens. Therefore, there is an urgent need for new antibiotics and non-antibiotic treatment and prevention strategies. In this Review, we discuss how recent studies of bacterial pathogenesis, recurrence, persistence, host-pathogen interactions and host susceptibility factors have elucidated new and promising targets for the treatment and prevention of UTIs.
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Affiliation(s)
- Morgan R Timm
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Seongmi K Russell
- Department of Paediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA.
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Gavilanes-Parra S, Chavero-Guerra P, Hernández-Castro R, Villanueva-Recillas S, Manjarrez-Hernández A. Antimicrobial Resistance in Uropathogenic Escherichia coli Strains Isolated from Relapses from Recurrent Urinary Tract Infections. Microb Drug Resist 2024; 30:304-313. [PMID: 38949898 DOI: 10.1089/mdr.2023.0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024] Open
Abstract
Little is known about the characteristics of uropathogenic Escherichia coli (UPEC) associated with recurrent urinary tract infections (RUTIs). The present study aimed to analyze the phenotypic antimicrobial resistance of recurrent UPEC isolates attributable to either relapse or reinfection. A total of 140 E. coli strains were isolated from 70 outpatients with RUTIs. All isolates were analyzed by random amplified polymorphic DNA-polymerase chain reaction to evaluate genetic similarity between the first and second isolates. We found that 64.2% (45/70) of outpatients had a relapse with the primary infecting E. coli strain and 35.7% (25/70) had reinfection with a new E. coli strain. Compared with reinfecting strains, relapse UPEC isolates exhibited much higher antimicrobial resistance; 89% of these isolates were multidrug-resistant and 46.6% were extended-spectrum β-lactamase producers. Our study provides evidence that RUTIs are mainly driven by the persistence of the original strain in the host (relapses) despite appropriate antibiotic treatments, and only RUTIs attributed to relapses seem to favor multidrug resistance in UPEC isolates.
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Affiliation(s)
- Sandra Gavilanes-Parra
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- Departamento de Ecología de Agentes Patógenos, Hospital General Dr. Manuel Gea González, Ciudad de México, México
| | - Pedro Chavero-Guerra
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rigoberto Hernández-Castro
- Departamento de Ecología de Agentes Patógenos, Hospital General Dr. Manuel Gea González, Ciudad de México, México
| | | | - Angel Manjarrez-Hernández
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- Departamento de Ecología de Agentes Patógenos, Hospital General Dr. Manuel Gea González, Ciudad de México, México
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Flores-Oropeza MA, Ochoa SA, Cruz-Córdova A, Chavez-Tepecano R, Martínez-Peñafiel E, Rembao-Bojórquez D, Zavala-Vega S, Hernández-Castro R, Flores-Encarnacion M, Arellano-Galindo J, Vélez D, Xicohtencatl-Cortes J. Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection. Front Microbiol 2024; 14:1340427. [PMID: 38328583 PMCID: PMC10848155 DOI: 10.3389/fmicb.2023.1340427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction Recurrent urinary tract infections (RUTIs) caused by uropathogenic Escherichia coli are costly public health problems impacting patients' quality of life. Aim In this work, a comparative genomics analysis of three clinical RUTI strains isolated from bladder biopsy specimens was performed. Materials and methods One hundred seventy-two whole genomes of urinary tract E. coli strains were selected from the NCBI database. The search for virulence factors, fitness genes, regions of interest, and genetic elements associated with resistance was manually carried out. The phenotypic characterization of antibiotic resistance, haemolysis, motility, and biofilm formation was performed. Moreover, adherence and invasion assays with human bladder HTB-5 cells, and transmission electron microscopy (TEM) were performed. Results The UTI-1_774U and UTI-3_455U/ST1193 strains were associated with the extraintestinal pathotypes, and the UTI-2_245U/ST295 strain was associated with the intestinal pathotype, according to a phylogenetic analysis of 172 E. coli urinary strains. The three RUTI strains were of clinical, epidemiological, and zoonotic relevance. Several resistance genes were found within the plasmids of these strains, and a multidrug resistance phenotype was revealed. Other virulence genes associated with CFT073 were not identified in the three RUTI strains (genes for type 1 and P fimbriae, haemolysin hlyA, and sat toxin). Quantitative adherence analysis showed that UTI-1_774U was significantly (p < 0.0001) more adherent to human bladder HTB-5 cells. Quantitative invasion analysis showed that UTI-2_245U was significantly more invasive than the control strains. No haemolysis or biofilm activity was detected in the three RUTI strains. The TEM micrographs showed the presence of short and thin fimbriae only in the UTI-2_245U strain. Conclusion The high variability and genetic diversity of the RUTI strains indicate that are a mosaic of virulence, resistance, and fitness genes that could promote recurrence in susceptible patients.
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Affiliation(s)
- Marco A. Flores-Oropeza
- Posgrado en Ciencias Biomédicas, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Sara A. Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Eva Martínez-Peñafiel
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Daniel Rembao-Bojórquez
- Departamento de Patología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
| | - Sergio Zavala-Vega
- Departamento de Patología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
- Laboratorio Clínico y Banco de Sangre, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Mexico City, Mexico
| | - Rigoberto Hernández-Castro
- Departmento de Ecología de Agentes Patógenos, Hospital General “Dr. Manuel Gea González”, Mexico City, Mexico
| | - Marcos Flores-Encarnacion
- Laboratorio de Microbiología Molecular y Celular, Biomedicina, Facultad de Medicina, BUAP, Puebla, Mexico
| | - José Arellano-Galindo
- Laboratorio de Virología Clínica y Experimental, Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Daniel Vélez
- Hospital Militar de Especialidades de la Mujer y Neonatología, Mexico City, Mexico
- Unidad Médica de Alta Especialidad, Hospital de Ginecología y Obstetricia No. 3 IMSS, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Unidad de Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Urbaniec J, Getino M, McEwan TBD, Sanderson-Smith ML, McFadden J, Hai F, La Ragione R, Hassan MM, Hingley-Wilson S. Anti-persister efficacy of colistin and meropenem against uropathogenic Escherichia coli is dependent on environmental conditions. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37990974 DOI: 10.1099/mic.0.001403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Antibiotic persistence is a phenomenon observed when genetically susceptible cells survive long-term exposure to antibiotics. These 'persisters' are an intrinsic component of bacterial populations and stem from phenotypic heterogeneity. Persistence to antibiotics is a concern for public health globally, as it increases treatment duration and can contribute to treatment failure. Furthermore, there is a growing array of evidence that persistence is a 'stepping-stone' for the development of genetic antimicrobial resistance. Urinary tract infections (UTIs) are a major contributor to antibiotic consumption worldwide, and are known to be both persistent (i.e. affecting the host for a prolonged period) and recurring. Currently, in clinical settings, routine laboratory screening of pathogenic isolates does not determine the presence or the frequency of persister cells. Furthermore, the majority of research undertaken on antibiotic persistence has been done on lab-adapted bacterial strains. In the study presented here, we characterized antibiotic persisters in a panel of clinical uropathogenic Escherichia coli isolates collected from hospitals in the UK and Australia. We found that a urine-pH mimicking environment not only induces higher levels of antibiotic persistence to meropenem and colistin than standard laboratory growth conditions, but also results in rapid development of transient colistin resistance, regardless of the genetic resistance profile of the isolate. Furthermore, we provide evidence for the presence of multiple virulence factors involved in stress resistance and biofilm formation in the genomes of these isolates, whose activities have been previously shown to contribute to the formation of persister cells.
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Affiliation(s)
- Joanna Urbaniec
- Department of Microbial Sciences, University of Surrey, Guildford, UK
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Maria Getino
- School of Veterinary Medicine, University of Surrey, Guildford, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Tahnee B-D McEwan
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Martina L Sanderson-Smith
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Johnjoe McFadden
- Department of Microbial Sciences, University of Surrey, Guildford, UK
| | - Faisal Hai
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, Australia
| | - Roberto La Ragione
- Department of Microbial Sciences, University of Surrey, Guildford, UK
- School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Marwa M Hassan
- School of Veterinary Medicine, University of Surrey, Guildford, UK
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Le T, Nang SC, Zhao J, Yu HH, Li J, Gill JJ, Liu M, Aslam S. Therapeutic Potential of Intravenous Phage as Standalone Therapy for Recurrent Drug-Resistant Urinary Tract Infections. Antimicrob Agents Chemother 2023; 67:e0003723. [PMID: 36975787 PMCID: PMC10112157 DOI: 10.1128/aac.00037-23] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Recurrent urinary tract infections (rUTI) are common in kidney transplant recipients (KTR) and are associated with multidrug resistance and increased morbidity/mortality. Novel antibiotic alternatives to reduce UTI recurrence are critically needed. We describe a case of rUTI due to extended spectrum beta lactamase (ESBL) Klebsiella pneumoniae in a KTR that was treated successfully with 4 weeks of adjunctive intravenous bacteriophage therapy alone, without concomitant antibiotics, and with no recurrence in a year of follow-up.
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Affiliation(s)
- Tram Le
- Center for Phage Technology, Texas A&M AgriLife Research, Texas A&M University, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Sue C. Nang
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Jinxin Zhao
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Heidi H. Yu
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Jian Li
- Biomedicine Discovery Institute, Infection Program and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Jason J. Gill
- Center for Phage Technology, Texas A&M AgriLife Research, Texas A&M University, College Station, Texas, USA
- Department of Animal Science, Texas A&M University, College Station, Texas, USA
| | - Mei Liu
- Center for Phage Technology, Texas A&M AgriLife Research, Texas A&M University, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Saima Aslam
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, California, USA
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Kao CY, Zhang YZ, Yang DC, Chen PK, Teng CH, Lin WH, Wang MC. Characterization of host and escherichia coli strains causing recurrent urinary tract infections based on molecular typing. BMC Microbiol 2023; 23:90. [PMID: 36997841 PMCID: PMC10061793 DOI: 10.1186/s12866-023-02820-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/11/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Escherichia coli is the leading pathogen responsible for urinary tract infection (UTI) and recurrent UTI (RUTI). Few studies have dealt with the characterization of host and bacteria in RUTI caused by E. coli with genetically identical or different strains. This study aimed to investigate the host and bacterial characteristics of E. coli RUTI based on molecular typing. RESULTS Patients aged 20 years or above who presented with symptoms of UTI in emergency department or outpatient clinics between August 2009 and December 2010 were enrolled. RUTI was defined as patients had 2 or more infections in 6 months or 3 or more in 12 months during the study period. Host factors (including age, gender, anatomical/functional defect, and immune dysfunction) and bacterial factors (including phylogenicity, virulence genes, and antimicrobial resistance) were included for analysis. There were 41 patients (41%) with 91 episodes of E. coli RUTI with highly related PFGE (HRPFGE) pattern (pattern similarity > 85%) and 58 (59%) patients with 137 episodes of E. coli RUTI with different molecular typing (DMT) pattern, respectively. There was a higher prevalence of phylogenetic group B2 and neuA and usp genes in HRPFGE group if the first episode of RUTI caused by HRPFGE E. coli strains and all episodes of RUTI caused by DMT E. coli strains were included for comparison. The uropathogenic E. coli (UPEC) strains in RUTI were more virulent in female gender, age < 20 years, neither anatomical/ functional defect nor immune dysfunction, and phylogenetic group B2. There were correlations among prior antibiotic therapy within 3 months and subsequent antimicrobial resistance in HRPFGE E. coli RUTI. The use of fluoroquinolones was more likely associated with subsequent antimicrobial resistance in most types of antibiotics. CONCLUSIONS This study demonstrated that the uropathogens in RUTI were more virulent in genetically highly-related E. coli strains. Higher bacterial virulence in young age group (< 20 years) and patients with neither anatomical/functional defect nor immune dysfunction suggests that virulent UPEC strains are needed for the development of RUTI in healthy populations. Prior antibiotic therapy, especially the fluoroquinolones, within 3 months could induce subsequent antimicrobial resistance in genetically highly-related E. coli RUTI.
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Affiliation(s)
- Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yen-Zheng Zhang
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Deng-Chi Yang
- Department of Geriatrics and Gerontology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pek Kee Chen
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Hung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan City, 701, Taiwan.
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Microbiota Ecosystem in Recurrent Cystitis and the Immunological Microenvironment of Urothelium. Healthcare (Basel) 2023; 11:healthcare11040525. [PMID: 36833059 PMCID: PMC9956625 DOI: 10.3390/healthcare11040525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Urinary tract infections (UTIs) represent one of the most frequent low genital tract diseases in the female population. When UTIs occur with a frequency of at least three times per year or two times in the last six month, we speak of recurrent UTI (rUTI) and up to 70% of women will have rUTI within 1 year. It was previously thought that antibiotic resistance was principally responsible for the recurrence of UTIs, but nowadays new diagnostic technologies have shown the role of microbiota in the pathophysiology of these diseases. Much research has been conducted on the role of gut microbiome in the development of rUTI, while little is known yet about vaginal and urinary microbiome and the possible immunological and microscopical mechanisms through which they trigger symptoms. New discoveries and clinical perspectives are arising, and they all agree that a personalized, multi-modal approach, treating vaginal and urinary dysbiosis, may reduce rUTIs more successfully.
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Thuy TTD, Lu HF, Kuo PY, Lin WH, Lin TP, Lee YT, Duong TTT, Wang MC, Lee YH, Wen LL, Chen YC, Kao CY. Whole-genome-sequence-based characterization of an NDM-5-producing uropathogenic Escherichia coli EC1390. BMC Microbiol 2022; 22:150. [PMID: 35668362 PMCID: PMC9172118 DOI: 10.1186/s12866-022-02562-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background Urinary tract infection (UTI) is one of the most common outpatient bacterial infections. In this study, we isolated and characterized an extensively-drug resistant (XDR) NDM-5-producing Escherichia coli EC1390 from a UTI patient by using whole-genome sequencing (WGS) in combination with phenotypic assays. Methods Antimicrobial susceptibility to 23 drugs was determined by disk diffusion method. The genome sequence of EC1390 was determined by Nanopore MinION MK1C platform. Conjugation assays were performed to test the transferability of EC1390 plasmids to E. coli recipient C600. Phenotypic assays, including growth curve, biofilm formation, iron acquisition ability, and cell adhesion, were performed to characterize the function of EC1390 plasmids. Results Our results showed that EC1390 was only susceptible to tigecycline and colistin, and thus was classified as XDR E. coli. A de novo genome assembly was generated using Nanopore 73,050 reads with an N50 value of 20,936 bp and an N90 value of 7,624 bp. WGS analysis showed that EC1390 belonged to the O101-H10 serotype and phylogenetic group A E. coli. Moreover, EC1390 contained 2 conjugative plasmids with a replicon IncFIA (pEC1390-1 with 156,286 bp) and IncFII (pEC1390-2 with 71,840 bp), respectively. No significant difference was observed in the bacterial growth rate in LB broth and iron acquisition ability between C600, C600 containing pEC1390-1, C600 containing pEC1390-2, and C600 containing pEC1390-1 and pEC1390-2. However, the bacterial growth rate in nutrition-limited M9 broth was increased in C600 containing pEC1390-2, and the cell adhesion ability was increased in C600 containing both pEC1390-1 and pEC1390-2. Moreover, these plasmids modulated the biofilm formation under different conditions. Conclusions In summary, we characterized the genome of XDR-E. coli EC1390 and identified two plasmids contributing to the antimicrobial resistance, growth of bacteria in a nutrition-limited medium, biofilm formation, and cell adhesion. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02562-6.
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Affiliation(s)
- Tran Thi Dieu Thuy
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan
| | - Hsu-Feng Lu
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung City, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan
| | - Wei-Hung Lin
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Tzu-Ping Lin
- Department of Urology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Tzu Lee
- Department of Emergency Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tran Thi Thuy Duong
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan
| | - Ming-Cheng Wang
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Hong Lee
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan
| | - Li-Li Wen
- Department of Clinical Laboratory, En Chu Kong Hospital, New Taipei City, Taiwan
| | - Yu-Chen Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan.
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Stepanova N. How Advanced Is Our Understanding of the Role of Intestinal Barrier Dysfunction in the Pathogenesis of Recurrent Urinary Tract Infections. Front Pharmacol 2022; 13:780122. [PMID: 35359839 PMCID: PMC8960443 DOI: 10.3389/fphar.2022.780122] [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: 09/20/2021] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
A comprehensive understanding of urinary tract infections (UTIs), one of the most common human infections, is required as they are complex and poorly understood diseases. Periurethral and vaginal colonization by rectal flora, with the constant presence of pathogens in the urethra, is the initial step of the recurrent UTIs pathway. Current scientific data describe the genetic, etiological, biological, and behavioral risk factors for recurring UTIs, but they do not include the effect of intestinal barrier function on the disease. Although gut microbiota has been proposed as the main source for UTIs, the cross-talk between intestinal barrier dysfunction and the recurrence of UTIs has not yet been supported by scientific data. In this opinion review, based on published data and the results of our clinical studies, I aimed to outline the possible contribution of intestinal barrier dysfunction to the pathogenesis of recurrent UTIs. I believe that the unanswered questions raised by this review can guide further experimental and controlled studies to clarify the mechanisms underlying the role of intestinal barrier dysfunction in the pathogenesis of recurrent UTIs.
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10
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Worby CJ, Olson BS, Dodson KW, Earl AM, Hultgren SJ. Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections. J Clin Invest 2022; 132:158497. [PMID: 35229729 PMCID: PMC8884912 DOI: 10.1172/jci158497] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Colin J Worby
- Broad Institute of MIT and Harvard, Infectious Disease and Microbiome Program, Cambridge, Massachusetts, USA
| | - Benjamin S Olson
- Department of Molecular Microbiology and.,Center for Women's Infectious Disease Research (cWIDR), Washington University School of Medicine, St. Louis, Missouri, USA
| | - Karen W Dodson
- Department of Molecular Microbiology and.,Center for Women's Infectious Disease Research (cWIDR), Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Infectious Disease and Microbiome Program, Cambridge, Massachusetts, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology and.,Center for Women's Infectious Disease Research (cWIDR), Washington University School of Medicine, St. Louis, Missouri, USA
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O’Brien VP, Lewis AL, Gilbert NM. Bladder Exposure to Gardnerella Activates Host Pathways Necessary for Escherichia coli Recurrent UTI. Front Cell Infect Microbiol 2021; 11:788229. [PMID: 34938672 PMCID: PMC8685330 DOI: 10.3389/fcimb.2021.788229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022] Open
Abstract
Recurrent urinary tract infections (rUTI) are a costly clinical problem affecting millions of women worldwide each year. The majority of rUTI cases are caused by uropathogenic Escherichia coli (UPEC). Data from humans and mouse models indicate that some instances of rUTI are caused by UPEC emerging from latent reservoirs in the bladder. Women with vaginal dysbiosis, typically characterized by high levels of Gardnerella and other anaerobes, are at increased risk of UTI. Multiple studies have detected Gardnerella in urine collected by transurethral catheterization (to limit vaginal contamination), suggesting that some women experience routine urinary tract exposures. We recently reported that inoculation of Gardnerella into the bladder triggers rUTI from UPEC bladder reservoirs in a mouse model. Here we performed whole bladder RNA-seq to identify host pathways involved in Gardnerella-induced rUTI. We identified a variety host pathways differentially expressed in whole bladders following Gardnerella exposure, such as pathways involved in inflammation/immunity and epithelial turnover. At the gene level, we identified upregulation of Immediate Early (IE) genes, which are induced in various cell types shortly following stimuli like infection and inflammation. One such upregulated IE gene was the orphan nuclear receptor Nur77 (aka Nr4a1). Pilot experiments in Nur77-/- mice suggest that Nur77 is necessary for Gardnerella exposure to trigger rUTI from UPEC reservoirs. These findings demonstrate that bladder gene expression can be impacted by short-lived exposures to urogenital bacteria and warrant future examination of responses in distinct cell types, such as with single cell transcriptomic technologies. The biological validation studies in Nur77-/- mice lay the groundwork for future studies investigating Nur77 and the Immediate Early response in rUTI.
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Affiliation(s)
- Valerie P. O’Brien
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Amanda L. Lewis
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, San Diego, CA, United States
| | - Nicole M. Gilbert
- Department of Pediatrics, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO, United States
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Javed S, Mirani ZA, Pirzada ZA. Phylogenetic Group B2 Expressed Significant Biofilm Formation among Drug Resistant Uropathogenic Escherichia coli. Libyan J Med 2021; 16:1845444. [PMID: 33170767 PMCID: PMC7671661 DOI: 10.1080/19932820.2020.1845444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/29/2020] [Indexed: 10/31/2022] Open
Abstract
Biofilm is an important virulent marker attributed to the development of urinary tract infections (UTIs) by uropathogenic E. coli (UPEC). Drug-resistant and biofilm-producing UPEC are highly problematic causing catheter-associated or recurrent UTIs with significant morbidity and mortality. The aim of the current study was to investigate the prevalence of biofilm formation and phylogenetic groups in drug-resistant UPEC to predict their ability to cause disease. This prospective study was conducted at the Department of Microbiology, University of Karachi from January to June 2019. A total of 50 highly drug-resistant UPEC were selected for this study. UPEC isolates were screened to form biofilm by Congo-red agar (CRA) and microtiter plate (MTP) technique. The representative biofilm-producing isolates were analysed by scanning electron microscopy (SEM) monitoring. Phylogenetic analysis was done by PCR method based on two preserved genes; chuA, yjaA and TspE4-C2 DNA fragment. On CRA 34 (68%) UPEC were slime producers, while on MTP 20 (40%) were strong biofilm producers, 19 (38%) moderate and 11 (22%) were low to negligible biofilm producers. Molecular typing confirmed that phylogenetic group B2 was prevalent in drug resistant UPEC strains. Pathogenic strains belonged to phylogenetic group B2 and D were found to have greater biofilm forming ability as compare to non-pathogenic commensal strains that belonged to phylogenetic group A. Our results indicate that biofilm formation vary in drug resistant UPEC belonged to different phylogenetic groups. This study indicates possible link between in vitro biofilm formation and phylogenetic groups of UPEC, therefore this knowledge might be helpful to predict the pathogenic potential of UPEC and help design strategies for controlling UTIs.
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Affiliation(s)
- Saima Javed
- Department of Microbiology, University of Karachi, Karachi, Pakistan
| | - Zulfiqar Ali Mirani
- Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi, Pakistan
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Distinct Characteristics of Escherichia coli Isolated from Patients with Urinary Tract Infections in a Medical Center at a Ten-Year Interval. Pathogens 2021; 10:pathogens10091156. [PMID: 34578189 PMCID: PMC8469484 DOI: 10.3390/pathogens10091156] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 01/13/2023] Open
Abstract
Escherichia coli causing urinary tract infections (UTIs) are one of the most common outpatient bacterial infections. This study aimed to compare the characteristics of E. coli isolated from UTI patients in a single medical center in 2009-2010 (n = 504) and 2020 (n = 340). The antimicrobial susceptibility of E. coli was determined by the disk diffusion method. PCRs were conducted to detect phylogenetic groups, ST131, K1 capsule antigen, and 15 virulence factors. Phylogenetic group B2 dominated in our 2009-2010 and 2020 isolates. Moreover, no phylogenetic group E strains were isolated in 2020. E. coli isolates in 2020 were more susceptible to amoxicillin, ampicillin/sulbactam, cefuroxime, cefmetazole, ceftazidime, cefoxitin, tetracycline, and sulfamethoxazole/trimethoprim, compared to the isolates in 2009-2010. Extensively drug-resistant (XDR)-E. coli in 2009-2010 were detected in groups B1 (5 isolates), B2 (12 isolates), F (8 isolates), and unknown (1 isolate). In 2020, XDR-E. coli were only detected in groups A (2 isolates), B2 (5 isolates), D (1 isolate), and F (4 isolates). The prevalence of virulence factor genes aer and fimH were higher in E. coli in 2009-2010 compared to those in 2020. In contrast, afa and sat showed higher frequencies in E. coli isolates in 2020 compared to E. coli in 2009-2010.
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Josephs-Spaulding J, Krogh TJ, Rettig HC, Lyng M, Chkonia M, Waschina S, Graspeuntner S, Rupp J, Møller-Jensen J, Kaleta C. Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs. Front Cell Infect Microbiol 2021; 11:562525. [PMID: 34368008 PMCID: PMC8340884 DOI: 10.3389/fcimb.2021.562525] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.
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Affiliation(s)
- Jonathan Josephs-Spaulding
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Mark Lyng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mariam Chkonia
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Silvio Waschina
- Research Group Nutriinformatics, Institute of Human Nutrition and Food Science, Christian-Albrechts-Universität, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
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Detection of Phylogenetic Groups and Drug Resistance Genes of Escherichia coli Causing Urinary Tract Infection in Southwest Iran. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.112547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Many bacteria can cause urinary tract infections (UTIs), among which Escherichia coli is the most common causative agent. Escherichia coli strains are divided into eight phylogenetic groups based on the new Quadroplex-PCR method, which are different in terms of patterns of resistance to antibiotics, virulence, and environmental characteristics. Objectives: This study aimed to determine the phylogenetic groups and the prevalence of drug resistance genes in E. coli strains causing UTIs. Methods: In this descriptive cross-sectional study, 129 E. coli isolates obtained from the culture of patients with UTIs were evaluated for phylogenetic groups using the new method of Clermont et al. The identification of phylogenetic groups and antibiotic resistance genes was performed using the multiplex polymerase chain reaction (PCR) method. Results: In this study, concerning the distribution of phylogenetic groups among E. coli isolates, the phylogenetic group B2 (36.4%) was the most common phylogenetic group, followed by phylogroups C (13.2%), clade I (10.1%), D (9.3%), and A (3.1%) while groups B1 and F were not observed in any of the isolates, and 20.2% had an unknown state. Also, out of 129 E. coli isolates, the total frequency of tetA, tetB, sul1, sul2, CITM, DfrA, and qnr resistance genes was 59.7%, 66.7, 69, 62, 30.2, 23.3, and 20.2%, respectively. In this study, there was a significant relationship between antibiotics (P = 0.026), cefotaxime (P = 0.003), and nalidixic acid (P = 0.044) and E. coli phylogenetic groups. No significant relationship was observed between E. coli phylogenetic groups and antibiotic resistance genes. Conclusions: The results of this study showed that strains belonging to group B2 had the highest prevalence among other phylogroups, and also, the frequency of antibiotic resistance genes and drug-resistant isolates had a higher prevalence in this phylogroup. These results show that phylogroup B2 has a more effective role in causing urinary tract infections compared to other phylogroups, and this phylogroup can be considered a genetic reservoir of antibiotic resistance.
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Lin WH, Wang MC, Liu PY, Chen PS, Wen LL, Teng CH, Kao CY. Escherichia coli urinary tract infections: Host age-related differences in bacterial virulence factors and antimicrobial susceptibility. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 55:249-256. [PMID: 33972179 DOI: 10.1016/j.jmii.2021.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are one of the most common outpatient bacterial infections. Although bacterial and host factors are reported to be associated with UTI pathogenesis, little is known about the host age-related differences in bacterial virulence factors and antimicrobial susceptibility. METHODS PCRs were carried out to detect K1 capsule antigen, 15 virulence factors, and phylogenetic groups in E. coli isolates. Antimicrobial susceptibility of selected agents was determined by the disk diffusion method. Isolates were divided into 6 groups based on their host age. RESULTS The results showed that virulence factors PapGII, PapGIII, Cnf1, Aer, Usp, Iha, OmpT, HlyA, and Sat, had highest frequencies in the host age group 0-3. Phylogenetic group B2 dominated in our isolates (59.6%) followed by group D (20.7%). In addition, 77.4% of strains isolated from 0 to 3 age group belonged to phylogenetic group B2. Antimicrobial susceptibility tests showed that E. coli strains isolated were significantly more resistant to antimicrobial agents as host age increased. Phylogenetic group B2 isolates were more susceptible to antimicrobial agents, compared to A, B1, and D isolates. CONCLUSION We found E. coli isolated from elders were more resistant to antimicrobial agents and had less virulence factors.
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Affiliation(s)
- Wei-Hung Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Cheng Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Yao Liu
- Institute of Microbiology and Immunology, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Po-Shun Chen
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089-0482, United States
| | - Li-Li Wen
- Department of Clinical Laboratory, En Chu Kong Hospital, New Taipei City, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Yen Kao
- Institute of Microbiology and Immunology, School of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Hashimoto M, Ma YF, Wang ST, Chen CS, Teng CH. Iron Acquisition of Urinary Tract Infection Escherichia coli Involves Pathogenicity in Caenorhabditis elegans. Microorganisms 2021; 9:microorganisms9020310. [PMID: 33540892 PMCID: PMC7913171 DOI: 10.3390/microorganisms9020310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/16/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is a major bacterial pathogen that causes urinary tract infections (UTIs). The mouse is an available UTI model for studying the pathogenicity; however, Caenorhabditis elegans represents as an alternative surrogate host with the capacity for high-throughput analysis. Then, we established a simple assay for a UPEC infection model with C. elegans for large-scale screening. A total of 133 clinically isolated E. coli strains, which included UTI-associated and fecal isolates, were applied to demonstrate the simple pathogenicity assay. From the screening, several virulence factors (VFs) involved with iron acquisition (chuA, fyuA, and irp2) were significantly associated with high pathogenicity. We then evaluated whether the VFs in UPEC were involved in the pathogenicity. Mutants of E. coli UTI89 with defective iron acquisition systems were applied to a solid killing assay with C. elegans. As a result, the survival rate of C. elegans fed with the mutants significantly increased compared to when fed with the parent strain. The results demonstrated, the simple assay with C. elegans was useful as a UPEC infectious model. To our knowledge, this is the first report of the involvement of iron acquisition in the pathogenicity of UPEC in a C. elegans model.
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Affiliation(s)
- Masayuki Hashimoto
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (S.-T.W.); (C.-S.C.)
- Correspondence: (M.H.); (C.-H.T.)
| | - Yi-Fen Ma
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
| | - Sin-Tian Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (S.-T.W.); (C.-S.C.)
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chang-Shi Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (S.-T.W.); (C.-S.C.)
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (S.-T.W.); (C.-S.C.)
- Center of Allergy and Clinical Immunology Research (ACIR), National Cheng Kung University, Tainan 70101, Taiwan
- Correspondence: (M.H.); (C.-H.T.)
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18
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Xu Y, Liu S, Zhang Y, Zhang W. DNA adenine methylation is involved in persister formation in E. coli. Microbiol Res 2021; 246:126709. [PMID: 33578264 DOI: 10.1016/j.micres.2021.126709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 10/22/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract infections (UTI). UPEC persister bacteria play crucial roles in clinical treatment failure and relapse. Although DNA methylation is known to regulate gene expression, its role in persister formation has not been investigated. Here, we show that Δdam (adenine methylase) mutant from UPEC strain UTI89 had significant defect in persister formation and complementation of the Δdam mutant restored this defect. Using PacBio sequencing of methylome and RNA sequencing of Δdam, we defined, for the first time, the role of Dam in persister formation. We found that Δdam mutation had an overwhelming effect on demethylation of the genome and the demethylation sites affected expression of genes involved in broad transcriptional and metabolic processes. Using comparative COG analysis of methylome and transcriptome, we demonstrate that Dam mediates persister formation through transcriptional control, cell motility, DNA repair and metabolite transport processes. These findings provide the first evidence and molecular basis for DNA methylation mediated persister formation and implicate Dam DNA methylation as a potential drug target for persister bacteria.
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Affiliation(s)
- Yuanyuan Xu
- Department of Infectious Diseases, Huashan Hospital of Fudan University, Shanghai, 200040, China
| | - Shuang Liu
- Department of Infectious Diseases, Huashan Hospital of Fudan University, Shanghai, 200040, China
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, 21205, USA.
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital of Fudan University, Shanghai, 200040, China.
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O'Brien VP, Joens MS, Lewis AL, Gilbert NM. Recurrent Escherichia coli Urinary Tract Infection Triggered by Gardnerella vaginalis Bladder Exposure in Mice. J Vis Exp 2020. [PMID: 33346201 DOI: 10.3791/61967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recurrent urinary tract infections (rUTI) caused by uropathogenic Escherichia coli (UPEC) are common and costly. Previous articles describing models of UTI in male and female mice have illustrated the procedures for bacterial inoculation and enumeration in urine and tissues. During an initial bladder infection in C57BL/6 mice, UPEC establish latent reservoirs inside bladder epithelial cells that persist following clearance of UPEC bacteriuria. This model builds on these studies to examine rUTI caused by the emergence of UPEC from within latent bladder reservoirs. The urogenital bacterium Gardnerella vaginalis is used as the trigger of rUTI in this model because it is frequently present in the urogenital tracts of women, especially in the context of vaginal dysbiosis that has been associated with UTI. In addition, a method for in situ bladder fixation followed by scanning electron microscopy (SEM) analysis of bladder tissue is also described, with potential application to other studies involving the bladder.
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Affiliation(s)
- Valerie P O'Brien
- Department of Molecular Microbiology, Washington University School of Medicine in Saint Louis; Center for Women's Infectious Disease Research, Washington University School of Medicine in Saint Louis; Fred Hutchinson Cancer Research Center
| | - Matthew S Joens
- Center for Cellular Imaging, Washington University School of Medicine in Saint Louis; TESCAN USA, Inc
| | - Amanda L Lewis
- Department of Molecular Microbiology, Washington University School of Medicine in Saint Louis; Center for Women's Infectious Disease Research, Washington University School of Medicine in Saint Louis; Department of Obstetrics and Gynecology, Washington University School of Medicine in Saint Louis; University of California San Diego
| | - Nicole M Gilbert
- Center for Women's Infectious Disease Research, Washington University School of Medicine in Saint Louis; Department of Pediatrics, Washington University School of Medicine in Saint Louis;
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Gozalan A, Unaldı O, Guldemir D, Aydogan S, Kuzucu C, Cakirlar FK, Açıkgoz ZC, Durmaz R. Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii Blood Culture Isolates from Three Hospitals in Turkey. Jpn J Infect Dis 2020; 74:200-208. [PMID: 33250488 DOI: 10.7883/yoken.jjid.2020.478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We aimed to investigate the clonal relationships, common sequence types, and carbapenemase genes in 177 non-repetitive blood culture isolates of Acinetobacter baumannii collected from patients at three university hospitals in Turkey in 2016. Molecular epidemiological characteristics of the isolates were examined using pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) (Pasteur scheme-cpn60, fusA, gltA, pyrG, recA, rplB, and rpoB). Multiplex PCR was used to investigate the carbapenemase genes, including blaOXA-23-like, blaOXA-24-like, blaOXA-48-like, blaOXA-58-like, blaIMP, blaVIM, and blaNDM. PFGE genotyping yielded 92 pulsotypes with a clustering ratio of 69.7%. As per a ≥85% similarity coefficient, 159 (90.9%) isolates were found to be clonally related. The blaOXA-23-like and blaOXA-58-like genes were identified in 100% and 28.2% of the isolates, respectively. The blaNDM gene was identified in two isolates. The MLST analysis included 54 isolates with different pulsotypes, and 29 sequence types (STs). Most of the isolates (n = 36) belonged to the clonal complex (CC)2, one isolate belonged to CC1, and one isolate belonged to CC164. Sixteen new STs (ST1235-ST1250) were identified. Identifying both global ST2 and a large number of new STs, revealed high genetic diversity in A. baumannii isolates in the study population.
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Affiliation(s)
- Aysegul Gozalan
- Department of Medical Microbiology, Faculty of Medicine, Alanya Alaaddin Keykubat University, Turkey
| | - Ozlem Unaldı
- National Molecular Microbiology Reference Laboratory, Public Health General Directorate, Ministry of Health, Sıhhiye, Turkey
| | - Dilek Guldemir
- National Molecular Microbiology Reference Laboratory, Public Health General Directorate, Ministry of Health, Sıhhiye, Turkey
| | - Sibel Aydogan
- Department of Medical Microbiology, Ankara City Hospital, Ministry of Health, Turkey
| | - Cigdem Kuzucu
- Department of Medical Microbiology, Faculty of Medicine, Tinaztepe İzmir University, Turkey
| | - Fatma Koksal Cakirlar
- Department of Medical Microbiology, Cerrahpaşa Faculty of Medicine, Istanbul University-Cerrahpaşa, Turkey
| | - Ziya Cibali Açıkgoz
- Department of Medical Microbiology, Faculty of Medicine, Yildirim Beyazit University, Turkey
| | - Riza Durmaz
- Department of Medical Microbiology, Faculty of Medicine, Yildirim Beyazit University, Turkey
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21
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Farahat EM, Hassuna NA, Hammad AM, Fattah MA, Khairalla AS. Distribution of integrons and phylogenetic groups among Escherichia coli causing community-acquired urinary tract infection in Upper Egypt. Can J Microbiol 2020; 67:451-463. [PMID: 33119995 DOI: 10.1139/cjm-2020-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Escherichia coli is a major cause of community-acquired urinary tract infections (CA-UTIs). In this study, we investigated the antimicrobial resistance patterns, the distribution of phylogenetic groups, and the prevalence and characteristics of integron-bearing E. coli isolates from outpatients with CA-UTIs in El-Minia governorate, in Upper Egypt. Out of the 583 urine samples collected, 134 were positive for E. coli, from which the most resistant isolates (n = 80) were selected for further analysis. The majority of these isolates (62.5%, 50/80) showed multidrug resistance profiles. Group B2 was the most predominant phylogenetic group (52.5%), followed by group F (21.25%), Clades I or II (12.5%), and finally isolates of unknown phylogroup (13.75%). Of the 80 isolates, 7 (8.75%) carried class 1 integrons, which contained 3 different types of integrated gene cassettes, including those conferring resistance to streptomycin/spectinomycin, trimethoprim, and some open reading frames of unknown function (gcuF). In conclusion, the types and combinations of the gene cassettes in our study may reflect the specific selective pressures to which the isolates were subjected within the study region, therefore, providing valuable data for future intervention strategies that are precisely tailored to prevent the dissemination of the uropathogenic E. coli strains circulating within Upper Egypt.
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Affiliation(s)
- Eman M Farahat
- Microbiology and Botany Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Noha A Hassuna
- Medical Microbiology and Immunology Department, Faculty of Medicine, Minia University, Minia, Egypt
| | - Adel M Hammad
- Microbiology Department, Faculty of Agriculture, Minia University, Minia, Egypt
| | - Medhat Abdel Fattah
- Microbiology and Botany Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Ahmed S Khairalla
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,Department of Biology, University of Regina, Saskatchewan, Canada; Department of Biology, Coast Mountain College, British Columbia, Canada
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Garretto A, Miller-Ensminger T, Ene A, Merchant Z, Shah A, Gerodias A, Biancofiori A, Canchola S, Canchola S, Castillo E, Chowdhury T, Gandhi N, Hamilton S, Hatton K, Hyder S, Krull K, Lagios D, Lam T, Mitchell K, Mortensen C, Murphy A, Richburg J, Rokas M, Ryclik S, Sulit P, Szwajnos T, Widuch M, Willis J, Woloszyn M, Brassil B, Johnson G, Mormando R, Maskeri L, Batrich M, Stark N, Shapiro JW, Montelongo Hernandez C, Banerjee S, Wolfe AJ, Putonti C. Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms. Front Microbiol 2020; 11:2094. [PMID: 33013764 PMCID: PMC7500147 DOI: 10.3389/fmicb.2020.02094] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/10/2020] [Indexed: 01/19/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant's symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition.
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Affiliation(s)
- Andrea Garretto
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | | | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Zubia Merchant
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Aashaka Shah
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Athina Gerodias
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Anthony Biancofiori
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Stacey Canchola
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Stephanie Canchola
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Emanuel Castillo
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Tasnim Chowdhury
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Nikita Gandhi
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Sarah Hamilton
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Kyla Hatton
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Syed Hyder
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Koty Krull
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Demetrios Lagios
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Thinh Lam
- Neuroscience Program, Loyola University Chicago, Chicago, IL, United States
| | - Kennedy Mitchell
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Christine Mortensen
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Amber Murphy
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Joseph Richburg
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Meghan Rokas
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Suzanne Ryclik
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Pauline Sulit
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Thomas Szwajnos
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Manuel Widuch
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Jessica Willis
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Mary Woloszyn
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Bridget Brassil
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Genevieve Johnson
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Rita Mormando
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Laura Maskeri
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Mary Batrich
- Niehoff School of Nursing, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Nicole Stark
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Jason W. Shapiro
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Swarnali Banerjee
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
- Department of Computer Science, Loyola University Chicago, Chicago, IL, United States
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Zhuge X, Zhou Z, Jiang M, Wang Z, Sun Y, Tang F, Xue F, Ren J, Dai J. Chicken-source Escherichia coli within phylogroup F shares virulence genotypes and is closely related to extraintestinal pathogenic E. coli causing human infections. Transbound Emerg Dis 2020; 68:880-895. [PMID: 32722875 DOI: 10.1111/tbed.13755] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
ExPEC is an important pathogen that causes diverse infection in the human extraintestinal sites. Although avian-source phylogroup F Escherichia coli isolates hold a high level of virulence traits, few studies have systematically assessed the pathogenicity and zoonotic potential of E. coli isolates within phylogroup F. A total of 1,332 E. coli strains were recovered from chicken colibacillosis in China from 2012 to 2017. About 21.7% of chicken-source E. coli isolates were presented in phylogroup F. We characterized phylogroup F E. coli isolates both genotypically and phenotypically. There was a widespread prevalence of ExPEC virulence-related genes among chicken-source E. coli isolates within phylogroup F. ColV/BM plasmid-related genes (i.e. hlyF, mig-14p, ompTp, iutA and tsh) occurred in the nearly 65% of phylogroup F E. coli isolates. Population structure of chicken-source E. coli isolates within phylogroup F was revealed and contained several dominant STs (such as ST59, ST354, ST362, ST405, ST457 and ST648). Most chicken-source phylogroup F E. coli held the property to produce biofilm and exhibited strongly swimming and swarming motilities. Our result showed that the complement resistance of phylogroup F E. coli isolates was closely associated with its virulence genotype. Our research further demonstrated the zoonotic potential of chicken-source phylogroup F E. coli isolates. The phylogroup F E. coli isolates were able to cause multiple diseases in animal models of avian colibacillosis and human infections (sepsis, meningitis and UTI). The chicken-source phylogroup F isolates, especially dominant ST types, might be recognized as a high-risk food-borne pathogen. This was the first study to identify that chicken-source E. coli isolates within phylogroup F were associated with human ExPEC pathotypes and exhibited zoonotic potential.
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Affiliation(s)
- Xiangkai Zhuge
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, P.R. China
| | - Zhou Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Min Jiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhongxing Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yu Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jianluan Ren
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,China Pharmaceutical University, Nanjing, China
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24
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Brannon JR, Dunigan TL, Beebout CJ, Ross T, Wiebe MA, Reynolds WS, Hadjifrangiskou M. Invasion of vaginal epithelial cells by uropathogenic Escherichia coli. Nat Commun 2020; 11:2803. [PMID: 32499566 PMCID: PMC7272400 DOI: 10.1038/s41467-020-16627-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 05/13/2020] [Indexed: 11/09/2022] Open
Abstract
Host-associated reservoirs account for the majority of recurrent and oftentimes recalcitrant infections. Previous studies established that uropathogenic E. coli - the primary cause of urinary tract infections (UTIs) - can adhere to vaginal epithelial cells preceding UTI. Here, we demonstrate that diverse urinary E. coli isolates not only adhere to, but also invade vaginal cells. Intracellular colonization of the vaginal epithelium is detected in acute and chronic murine UTI models indicating the ability of E. coli to reside in the vagina following UTI. Conversely, in a vaginal colonization model, E. coli are detected inside vaginal cells and the urinary tract, indicating that vaginal colonization can seed the bladder. More critically, bacteria are identified inside vaginal cells from clinical samples from women with a history of recurrent UTI. These findings suggest that E. coli can establish a vaginal intracellular reservoir, where it may reside safely from extracellular stressors prior to causing an ascending infection.
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Affiliation(s)
- John R Brannon
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Nashville, TN, USA.
| | - Taryn L Dunigan
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Nashville, TN, USA
| | - Connor J Beebout
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Nashville, TN, USA
| | - Tamia Ross
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Nashville, TN, USA
| | - Michelle A Wiebe
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Nashville, TN, USA
| | | | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology and Immunology, Division of Molecular Pathogenesis, Nashville, TN, USA.
- Department of Urology, Nashville, TN, USA.
- Vanderbilt Institute for Infection, Immunology & Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
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25
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Prattley S, Geraghty R, Moore M, Somani BK. Role of Vaccines for Recurrent Urinary Tract Infections: A Systematic Review. Eur Urol Focus 2020; 6:593-604. [DOI: 10.1016/j.euf.2019.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/05/2019] [Accepted: 11/03/2019] [Indexed: 10/25/2022]
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26
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Karami N, Lindblom A, Yazdanshenas S, Lindén V, Åhrén C. Recurrence of urinary tract infections with extended-spectrum β-lactamase-producing Escherichia coli caused by homologous strains among which clone ST131-O25b is dominant. J Glob Antimicrob Resist 2020; 22:126-132. [PMID: 32061816 DOI: 10.1016/j.jgar.2020.01.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Bacterial features associated with recurrent urinary tract infections (RUTIs) due to extended-spectrum β-lactamase-producingEscherichia coli (ESBL-E. coli) are not well understood. In this study, phylogenetic groups and ST131 subclones were investigated to assess strain homology of ESBL-E. coli isolates in patients with RUTIs in inpatient and outpatient settings in western Sweden. METHODS Almost all isolates (319/356) from 123 patients with 2-7 episodes (median 2 episodes) of ESBL-E. coli UTI within 1 year were examined for seven E. coli phylogroups, the ST131-O25b clone and its subclone fimH30-Rx. Antimicrobial resistance and ESBL genes were determined for the index isolates. A subset of isolates was typed using pulsed-field gel electrophoresis (PFGE). RESULTS The same phylogroup and ST131 subclones were seen for all recurrences in 119/123 patients, and PFGE confirmed strain homology in recurrences for 43/44 patients tested. Phylogroup B2 dominated (56%), followed by D (19%) and F (10%). ST131-O25b andfimH30-Rx isolates were detected in 44% and 30%, respectively. CTX-M group 1 (71%) predominated. Elderly patients were in the majority. There were no associations between patient demographics or time to recurrence and bacterial characteristics. The fimH30-Rx subclone was associated with a higher number of recurrences (P = 0.015) compared with the remaining B2 isolates. CONCLUSION In ESBL-E. coli RUTI, most recurrences were caused by the initial infecting strain. The high frequency of the multidrug-resistant fimH30-Rx subclone and its association with multiple recurrences warrants further attention and early detection of this subclone in patients at risk of developing RUTI with ESBL-E. coli.
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Affiliation(s)
- Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.
| | - Anna Lindblom
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Shora Yazdanshenas
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Viktoria Lindén
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Christina Åhrén
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy and Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Swedish Strategic Program against Antimicrobial Resistance (Strama), Region Västra Götaland, Gothenburg, Sweden
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27
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Norouzian H, Katouli M, Shahrokhi N, Sabeti S, Pooya M, Bouzari S. The relationship between phylogenetic groups and antibiotic susceptibility patterns of Escherichia coli strains isolated from feces and urine of patients with acute or recurrent urinary tract infection. IRANIAN JOURNAL OF MICROBIOLOGY 2019; 11:478-487. [PMID: 32148679 PMCID: PMC7048958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
BACKGROUND AND OBJECTIVES B2 and D have been mentioned as the most common phylogenetic groups among uropathogenic Escherichia coli. However, there is still controversy about the importance of these phylo-groups. This study was conducted to investigate the probable relation between these groups and antibiotic resistance patterns of E. coli isolates derived from urine and feces of the patients with acute or recurrent UTI. MATERIALS AND METHODS 10 isolates were recovered from urine and feces samples of patients with different phases of UTI in whom E. coli was causative pathogen. Biochemical fingerprinting was performed to classify the isolates and select their appropriate representatives. Phylogenetic grouping was performed using multiplex PCR, and antibiotic resistance was determined by disk diffusion method. RESULTS Five-hundred-sixty E. coli isolates were derived from 56 UTI patients (27 acute, 29 recurrent). Among them, 261 isolates were selected using biochemical fingerprinting. All the isolates were sensitive to imipenem and nitrofurantoin. Compared to other phylo-groups, the isolates in group D showed considerably different frequencies in acute vs. recurrent phase of UTI, in urine vs. stool samples, in males vs. females, and in- vs. out-patients. They were more resistant to the antibiotics (except norfloxacin), and in contrast to others, this was seen more in acute UTI, especially in urine samples. Multi-drug resistance pattern was also meaningfully higher in group D. CONCLUSION Although phylo-groups B2 and D of E. coli bacteria are more responsible for UTI, group D isolates seem to be more resistant and probably more virulent, even than the ones from group B2.
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Affiliation(s)
- Hossein Norouzian
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Katouli
- Genecology Research Centre, School of Health and Sport Sciences, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Nader Shahrokhi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
| | - Sharam Sabeti
- Deapartment of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Pooya
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran,Corresponding author: Mohammad Pooya, MD, PhD, Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran., Tel: +982164112220, Fax: +982164112803,
| | - Saeid Bouzari
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran,Corresponding author: Saeid Bouzari, PhD, Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran., Tel: +982164112220, Fax: +982164112803,
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28
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Mirkalantari S, Masjedian F, Irajian G, Siddig EE, Fattahi A. Determination of the frequency of β-lactamase genes (bla SHV, bla TEM, bla CTX-M) and phylogenetic groups among ESBL-producing uropathogenic Escherichia coli isolated from outpatients. J LAB MED 2019. [DOI: 10.1515/labmed-2018-0136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Escherichia coli accounts for 70–95% of community-acquired urinary tract infections (UTIs). Recently, there has been an increase in the prevalence of extended-spectrum β-lactamase (ESBL) in the community which required an accurate identification for better management. Therefore, the current study was performed to determine the antimicrobial resistance pattern, investigate ESBL phenotypes and genotypes (blaCTX-M, bla TEM and bla SHV genes) and determine the phylogenetic groups among ESBL-positive isolates from outpatients.
Methods
One hundred and eighty-three positive urine samples were collected from 4450 outpatient clinic attendees. Antibiotic susceptibility was determined and ESBL phenotype screening was carried out using disk diffusion agar and combination disk techniques, respectively. The assessment of the presence of the blaCTX-M, bla TEM and blaSHV genes and phylogenetic grouping were performed using the polymerase chain reaction (PCR) method.
Results
Out of 183 E. coli isolates, 59 (32.2%) showed a positive ESBL phenotype. The prevalence of ESBL-producing E. coli was higher in males (57.4%). Fifty-seven of the ESBL-producing strains carried at least one of the β-lactamase genes (bla CTX-M, bla TEM, bla SHV). Phylotyping of multi-drug resistant isolates indicated that the isolates belonged to B2, A and D phylogroups. Analysis of resistance patterns among these phylogroups revealed that 74.4%, 55.3% and 29.7% of the isolates in the B2 group were resistant to trimethoprim-sulfamethoxazole, ciprofloxacin and gentamicin, respectively. Most of the strains in the phylogroup B2 carried the bla CTX-M gene.
Conclusions
All the ESBL-producing isolates were placed in one of the four phylogenetic groups. The presence of CTX-M and resistance to quinolones were more frequent in B2 strains than in non-B2 strains.
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Affiliation(s)
- Shiva Mirkalantari
- Microbiology Department, Faculty of Medicine , Iran University of Medical Sciences , Tehran , Iran
| | - Faramarz Masjedian
- Microbiology Department, Faculty of Medicine , Iran University of Medical Sciences , Tehran , Iran
| | - Gholamreza Irajian
- Microbiology Department, Faculty of Medicine , Iran University of Medical Sciences , Tehran , Iran
| | | | - Azam Fattahi
- Department of Medical Parasitology and Mycology, School of Public Health , Tehran University of Medical Sciences , Tehran , Iran
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29
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Zhuge X, Jiang M, Tang F, Sun Y, Ji Y, Xue F, Ren J, Zhu W, Dai J. Avian-source mcr-1-positive Escherichia coli is phylogenetically diverse and shares virulence characteristics with E. coli causing human extra-intestinal infections. Vet Microbiol 2019; 239:108483. [PMID: 31699469 DOI: 10.1016/j.vetmic.2019.108483] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 12/30/2022]
Abstract
Colisepticemia caused by bloodstream infection of the extraintestinal pathogenic Escherichia coli (ExPEC) has become a serious public health problem. The recent emergence of the colistin-resistant Enterobacteriaceae, especially mcr-1-positive E. coli (MCRPEC) exerts great concern around the world. The molecular epidemiology and zoonosis risk of avian-origin MCRPEC are reported to be substantially lower. Here, we presented a system-wide analysis of emerging trends and zoonotic risk of MCRPEC recovered from avian colibacillosis in China. Our results showed the majority of avian-source MCRPEC isolates were classified as ExPECs. We also found that not only MCRPEC in phylogroups B2 and D, but also several E. coli populations in groups B1 and F possessed high virulence in the two models of avian colibacillosis and three rodent models for ExPEC-associated human infections. The high-virulent MCRPEC clones belong to ST131, as well as ST-types (such as ST48, ST117, ST162, ST501, ST648, and ST2085). Our data suggested the zoonotic risk of MCRPEC appeared to be a close association with ColV/ColBM type virulence plasmids. A comprehensive genomic analysis showed the overlapped of ColV/ColBM plasmids contents between MCRPEC isolates from humans and poultry. Identification of ColV/ColBM plasmids among human MCRPEC isolates revealed the potential transmission of avian-source mcr-1-positive ExPECs to humans. Moreover, the presence of ColV/ColBM plasmid-encoded virulence determinants, could be used as a predictive label for pathogenic MCRPEC. These findings highlighted avian-origin MCRPEC isolates could be recognized as a foodborne pathogen.
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Affiliation(s)
- Xiangkai Zhuge
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; Center for Post-doctoral Studies of Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Center for Post-doctoral Studies of Animal Husbandry, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Jiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China
| | - Yu Sun
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiming Ji
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China
| | - Jianluan Ren
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China
| | - Weiyun Zhu
- Center for Post-doctoral Studies of Animal Husbandry, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; China Pharmaceutical University, Nanjing 211198, China; Center for Post-doctoral Studies of Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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30
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Katongole P, Bulwadda Kisawuzi D, Kyobe Bbosa H, Patrick Kateete D, Florence Najjuka C. Phylogenetic groups and antimicrobial susceptibility patterns of uropathogenic Escherichia coli clinical isolates from patients at Mulago National Referral Hospital, Kampala, Uganda. F1000Res 2019. [DOI: 10.12688/f1000research.20930.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction: Uropathogenic Escherichia coli (UPEC) remains the most common cause of urinary tract infections (UTIs). They account for over 80-90% of all community-acquired and 30-50% of all hospital-acquired UTIs. E. coli strains have been found to belong to evolutionary origins known as phylogenetic groups. In 2013, Clermont classified E. coli strains into eight phylogenetic groups using the quadruplex PCR method. The aim of this study was to identify the phylogenetic groups of UPEC strains in Uganda using Clermont’s quadruplex PCR method and to assess their antibiotic susceptibility patterns in Uganda. Methods: In this cross-sectional study, 140 stored uropathogenic E. coli isolates from the Clinical Microbiology Laboratory, Department of Medical Microbiology, College of Health Sciences Makerere University were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was performed by disk diffusion method according to Clinical & Laboratory Standards Institute (CLSI) guidelines. Phenotypic detection of extended-spectrum beta-lactamase, AmpC and carbapenemases was done according to CLSI guidelines and Laboratory SOPs. Results: Phylogenetic group B2 (40%) was the most predominant, followed by A (6.23%), clade I and II (5%), D and E (each 2.14%), B1 (1.43%) and F and C (each 0.71%). The most common resistant antibiotic was trimethoprim-sulphamethoxazole (90.71%) and the least was imipenem (1.43%). In total, 73.57% of isolates were multi-drug resistant (MDR). Antibiotic resistance was mainly detected in phylogenetic group B2 (54%). Conclusions: Our findings showed the high prevalence of MDR E. coli isolates, with the dominance of phylogenetic group B2. About 9% of E. coli isolates belonged to the newly described phylogroups C, E, F, and clade I and II.
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31
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Rapid Growth and Metabolism of Uropathogenic Escherichia coli in Relation to Urine Composition. Clin Microbiol Rev 2019; 33:33/1/e00101-19. [PMID: 31619395 DOI: 10.1128/cmr.00101-19] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) strains cause a majority of urinary tract infections (UTIs). Since UPEC strains can become antibiotic resistant, adjunct or alternate therapies are urgently needed. UPEC strains grow extremely rapidly in patients with UTIs. Thus, this review focuses on the relation between urine composition and UPEC growth and metabolism. Compilation of urinary components from two major data sources suggests the presence of sufficient amino acids and carbohydrates as energy sources and abundant phosphorus, sulfur, and nitrogen sources. In a mouse UTI model, mutants lacking enzymes of the tricarboxylic acid cycle, gluconeogenesis, and the nonoxidative branch of the pentose cycle are less competitive than the corresponding parental strains, which is consistent with amino acids as major energy sources. Other evidence suggests that carbohydrates are required energy sources. UPEC strains in urine ex vivo and in vivo express transporters for peptides, amino acids, carbohydrates, and iron and genes associated with nitrogen limitation, amino acid synthesis, nucleotide synthesis, and nucleotide salvage. Mouse models confirm the requirement for many, but not all, of these genes. Laboratory evolution studies suggest that rapid nutrient uptake without metabolic rewiring is sufficient to account for rapid growth. Proteins and pathways required for rapid growth should be considered potential targets for alternate or adjunct therapies.
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Ramos JN, Souza C, Faria YV, da Silva EC, Veras JFC, Baio PVP, Seabra SH, de Oliveira Moreira L, Hirata Júnior R, Mattos-Guaraldi AL, Vieira VV. Bloodstream and catheter-related infections due to different clones of multidrug-resistant and biofilm producer Corynebacterium striatum. BMC Infect Dis 2019; 19:672. [PMID: 31357945 PMCID: PMC6664767 DOI: 10.1186/s12879-019-4294-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Corynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen associated with immunocompromised and chronically ill patients, as well as nosocomial outbreaks. In this study, we characterized 23 MDR C. striatum isolated of bloodstream and catheter-related infections from a hospital of Rio de Janeiro. METHODS C. striatum isolates were identified by 16S rRNA and rpoB genes sequencing. The dissemination of these isolates was accomplished by pulsed-field gel electrophoresis (PFGE). All isolates were submitted to antimicrobial susceptibility testing by disk diffusion and by minimum inhibitory concentration using E-test strips methods. Antimicrobial resistance genes were detected by polymerase chain reaction. Quantitative tests were performed on four different abiotic surfaces and the ability to produce biofilm on the surface of polyurethane and silicone catheter was also demonstrated by scanning electron microscopy. RESULTS Eleven PFGE profiles were found. The PFGE profile I was the most frequently observed among isolates. Five different MDR profiles were found and all PFGE profile I isolates presented susceptibility only to tetracycline, vancomycin, linezolid and daptomycin. Only the multidrug-susceptible isolate did not show mutations in the quinolone-resistance determinant region (QRDR) of the gyrA gene and was negative in the search of genes encoding antibiotic resistance. The other 22 isolates were positive to resistance genes to aminoglycoside, macrolides/lincosamides and chloramphenicol and showed mutations in the QRDR of the gyrA gene. Scanning electron microscopy illustrated the ability of MDR blood isolate partaker of the epidemic clone (PFGE profile I) to produce mature biofilm on the surface of polyurethane and silicone catheter. CONCLUSIONS Genotyping analysis by PFGE revealed the permanence of the MDR PFGE profile I in the nosocomial environment. Other new PFGE profiles emerged as etiologic agents of invasive infections. However, the MDR PFGE profile I was also found predominant among patients with hematogenic infections. The high level of multidrug resistance associated with biofilm formation capacity observed in MDR C. striatum is a case of concern.
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Affiliation(s)
- Juliana Nunes Ramos
- Laboratório de Difteria e Corinebactérias de Importância Clínica, Faculdade de Ciências Médicas, Centro Colaborador e Referência para pesquisa de Difteria/Ministério da Saúde, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
- Instituto Nacional de Controle de Qualidade em Saúde, Fundação Oswaldo Cruz, INCQS/FIOCRUZ, Rio de Janeiro, Brazil
- Laboratório Interdisciplinar de Pesquisas Médicas (LIPMED), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Pavilhão Cardoso Fontes, 10 andar, sala 17, Manguinhos, Rio de Janeiro, 21040-900 Brazil
| | - Cassius Souza
- Laboratório de Difteria e Corinebactérias de Importância Clínica, Faculdade de Ciências Médicas, Centro Colaborador e Referência para pesquisa de Difteria/Ministério da Saúde, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Yuri Vieira Faria
- Laboratório de Difteria e Corinebactérias de Importância Clínica, Faculdade de Ciências Médicas, Centro Colaborador e Referência para pesquisa de Difteria/Ministério da Saúde, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
- Laboratório de Tecnologia em Bioquímica e Microscopia, Centro Universitário Estadual da Zona Oeste, Rio de Janeiro, Brazil
| | - Eliane Cristine da Silva
- Laboratório de Difteria e Corinebactérias de Importância Clínica, Faculdade de Ciências Médicas, Centro Colaborador e Referência para pesquisa de Difteria/Ministério da Saúde, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - João Flávio Carneiro Veras
- Instituto Nacional de Controle de Qualidade em Saúde, Fundação Oswaldo Cruz, INCQS/FIOCRUZ, Rio de Janeiro, Brazil
| | - Paulo Victor Pereira Baio
- Laboratório de Difteria e Corinebactérias de Importância Clínica, Faculdade de Ciências Médicas, Centro Colaborador e Referência para pesquisa de Difteria/Ministério da Saúde, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
- Laboratório Interdisciplinar de Pesquisas Médicas (LIPMED), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Pavilhão Cardoso Fontes, 10 andar, sala 17, Manguinhos, Rio de Janeiro, 21040-900 Brazil
| | - Sérgio Henrique Seabra
- Laboratório de Tecnologia em Bioquímica e Microscopia, Centro Universitário Estadual da Zona Oeste, Rio de Janeiro, Brazil
| | - Lilian de Oliveira Moreira
- Laboratório de Bacteriologia e Imunologia Clínica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raphael Hirata Júnior
- Laboratório de Difteria e Corinebactérias de Importância Clínica, Faculdade de Ciências Médicas, Centro Colaborador e Referência para pesquisa de Difteria/Ministério da Saúde, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Ana Luíza Mattos-Guaraldi
- Laboratório de Difteria e Corinebactérias de Importância Clínica, Faculdade de Ciências Médicas, Centro Colaborador e Referência para pesquisa de Difteria/Ministério da Saúde, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Verônica Viana Vieira
- Laboratório Interdisciplinar de Pesquisas Médicas (LIPMED), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Pavilhão Cardoso Fontes, 10 andar, sala 17, Manguinhos, Rio de Janeiro, 21040-900 Brazil
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Bacterial Microcompartment-Mediated Ethanolamine Metabolism in Escherichia coli Urinary Tract Infection. Infect Immun 2019; 87:IAI.00211-19. [PMID: 31138611 PMCID: PMC6652756 DOI: 10.1128/iai.00211-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/23/2022] Open
Abstract
Urinary tract infections (UTIs) are common and in general are caused by intestinal uropathogenic Escherichia coli (UPEC) ascending via the urethra. Microcompartment-mediated catabolism of ethanolamine, a host cell breakdown product, fuels the competitive overgrowth of intestinal E. coli, both pathogenic enterohemorrhagic E. coli and commensal strains. During a UTI, urease-negative E. coli bacteria thrive, despite the comparative nutrient limitation in urine. Urinary tract infections (UTIs) are common and in general are caused by intestinal uropathogenic Escherichia coli (UPEC) ascending via the urethra. Microcompartment-mediated catabolism of ethanolamine, a host cell breakdown product, fuels the competitive overgrowth of intestinal E. coli, both pathogenic enterohemorrhagic E. coli and commensal strains. During a UTI, urease-negative E. coli bacteria thrive, despite the comparative nutrient limitation in urine. The role of ethanolamine as a potential nutrient source during UTIs is understudied. We evaluated the role of the metabolism of ethanolamine as a potential nitrogen and carbon source for UPEC in the urinary tract. We analyzed infected urine samples by culture, high-performance liquid chromatography, reverse transcription-quantitative PCR, and genomic sequencing. The ethanolamine concentration in urine was comparable to the concentration of the most abundant reported urinary amino acid, d-serine. Transcription of the eut operon was detected in the majority of urine samples containing E. coli screened. All sequenced UPEC strains had conserved eut operons, while metabolic genotypes previously associated with UTI (dsdCXA, metE) were mainly limited to phylogroup B2. In vitro ethanolamine was found to be utilized as a sole source of nitrogen by UPEC strains. The metabolism of ethanolamine in artificial urine medium (AUM) induced metabolosome formation and provided a growth advantage at the physiological levels found in urine. Interestingly, eutE (which encodes acetaldehyde dehydrogenase) was required for UPEC strains to utilize ethanolamine to gain a growth advantage in AUM, suggesting that ethanolamine is also utilized as a carbon source. These data suggest that urinary ethanolamine is a significant additional carbon and nitrogen source for infecting E. coli strains.
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Gajdács M, Ábrók M, Lázár A, Burián K. Comparative Epidemiology and Resistance Trends of Common Urinary Pathogens in a Tertiary-Care Hospital: A 10-Year Surveillance Study. MEDICINA (KAUNAS, LITHUANIA) 2019; 55:E356. [PMID: 31324035 PMCID: PMC6681214 DOI: 10.3390/medicina55070356] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]
Abstract
Background and Objective: Urinary tract infections (UTIs) are common in human medicine, affecting large patient populations worldwide. The principal cause of UTIs is uropathogenic Escherichia coli (UPEC) and Klebsiella, both in community and nosocomial settings. The assessment of local data on prevalence and resistance is essential to evaluate trends over time and to reflect on the national situation, compared to international data, using the methods of analytical epidemiology. Materials and Methods: The aim of this study was to assess resistance trends and epidemiology of UTIs caused by E. coli and Klebsiella species in inpatients and outpatients at a tertiary-care hospital in Hungary, using microbiological data. To evaluate resistance trends, several antibiotics were chosen as indicator drugs, based on local utilization data. Results: E. coli was the most prevalent isolate, representing 56.75 ± 4.86% for outpatients and 42.29 ± 2.94% for inpatients. For E. coli, the ratio of resistant strains for several antibiotics was significantly higher in the inpatient group, while in Klebsiella, similar trends were only observed for gentamicin. Extended-spectrum β-lactamase (ESBL)-producing isolates were detected in 4.33-9.15% and 23.22-34.22% from outpatient, 8.85-38.97% and 10.89-36.06% from inpatient samples for E. coli and Klebsiella, respectively. Conclusions: Resistance developments in common UTI pathogens (especially to fosfomycin, sulfamethoxazole-trimethoprim, fluoroquinolones, and 3rd generation cephalosporins), seriously curb therapeutic options, especially in outpatient settings.
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Affiliation(s)
- Márió Gajdács
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös utca 6., 6720 Szeged, Hungary.
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary.
| | - Marianna Ábrók
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary
| | - Andrea Lázár
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary
| | - Katalin Burián
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Semmelweis utca 6., 6725 Szeged, Hungary
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Dóm tér 10., 6720 Szeged, Hungary
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Lin WH, Tseng CC, Wu AB, Chang YT, Kuo TH, Chao JY, Wang MC, Wu JJ. Clinical and microbiological characteristics of peritoneal dialysis-related peritonitis caused by Escherichia coli in southern Taiwan. Eur J Clin Microbiol Infect Dis 2018; 37:1699-1707. [PMID: 29931659 DOI: 10.1007/s10096-018-3302-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/11/2018] [Indexed: 12/11/2022]
Abstract
Peritonitis is a serious complication and major cause of treatment failure in patients undergoing peritoneal dialysis (PD). Escherichia coli is the major pathogen in extraintestinal Gram-negative infections, including PD-related peritonitis. The outcomes of E. coli peritonitis in PD varied from relatively favorable outcomes to a higher incidence of treatment failure. The aim of this study was to investigate the impact of bacterial virulence and host characteristics on the outcomes of PD-related peritonitis caused by E. coli. From January 2000 to June 2016, a total of 47 episodes of monomicrobial and 10 episodes of polymicrobial E. coli PD-related peritonitis, as well as 89 episodes of monomicrobial Gram-positive (56 Staphylococcus spp. and 33 Streptococcus spp.) PD-related peritonitis cases, were retrospectively enrolled. Clinical features, E. coli bacterial virulence, and outcomes were analyzed. Compared to Streptococcus spp. peritonitis, E. coli peritonitis had a higher peritoneal catheter removal rate (38 versus 12%; P = 0.0115). Compared to the monomicrobial group, patients in polymicrobial group were older and had higher peritoneal catheter removal rate (80 versus 38%; P = 0.0324). Treatment failure of E. coli peritonitis was associated with more polymicrobial peritonitis and immunocompromised comorbidity, longer duration of PD therapy, and more antimicrobial resistance. E. coli isolates with more iron-related genes had higher prevalence of phylogenetic group B2 and papG II, iha, ompT, and usp genes. This study demonstrates the important roles of clinical and bacterial characteristics in the outcomes of monomicrobial and polymicrobial E. coli PD-related peritonitis.
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Affiliation(s)
- Wei-Hung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chin-Chung Tseng
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 138, Sheng-Li Road, Tainan, 70428, Taiwan
| | - An-Bang Wu
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 138, Sheng-Li Road, Tainan, 70428, Taiwan
| | - Yu-Tzu Chang
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 138, Sheng-Li Road, Tainan, 70428, Taiwan
| | - Te-Hui Kuo
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 138, Sheng-Li Road, Tainan, 70428, Taiwan
| | - Jo-Yen Chao
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 138, Sheng-Li Road, Tainan, 70428, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No. 138, Sheng-Li Road, Tainan, 70428, Taiwan. .,Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Jiunn-Jong Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, No. 155, Section 2, Li-Nong Street, Taipei, 11221, Taiwan.
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Purification of Intracellular Bacterial Communities during Experimental Urinary Tract Infection Reveals an Abundant and Viable Bacterial Reservoir. Infect Immun 2018; 86:IAI.00740-17. [PMID: 29378794 DOI: 10.1128/iai.00740-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/22/2018] [Indexed: 12/17/2022] Open
Abstract
Urinary tract infections (UTIs) are a major infection of humans, particularly affecting women. Recurrent UTIs can cause significant discomfort and expose patients to high levels of antibiotic use, which in turn contributes to the development of higher antibiotic resistance rates. Most UTIs are caused by uropathogenic Escherichia coli, which is able to form intracellular collections (termed intracellular bacterial communities [IBCs]) within the epithelial cells lining the bladder lumen. IBCs are seen in both infected mice and humans and are a potential cause of recurrent UTI. Genetic and molecular studies of IBCs have been hampered both by the low number of bacteria in IBCs relative to the number extracellular bacteria and by population bottlenecks that occur during IBC formation. We now report the development of a simple and rapid technique for isolating pure IBCs from experimentally infected mice. We verified the specificity and purity of the isolated IBCs via microscopy, gene expression, and culture-based methods. Our results further demonstrated that our isolation technique practically enables specific molecular studies of IBCs. In the first such direct measurement, we determined that a single epithelial cell containing an early IBC typically contains 103 viable bacteria. Our isolation technique complements recent progress in low-input, single-cell genomics to enable future genomic studies of the formation of IBCs and their activation pathways during recurrent UTI, which may lead to novel strategies to eliminate them from the bladder.
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Schreiber HL, Conover MS, Chou WC, Hibbing ME, Manson AL, Dodson KW, Hannan TJ, Roberts PL, Stapleton AE, Hooton TM, Livny J, Earl AM, Hultgren SJ. Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections. Sci Transl Med 2017; 9:9/382/eaaf1283. [PMID: 28330863 DOI: 10.1126/scitranslmed.aaf1283] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 05/12/2016] [Accepted: 12/12/2016] [Indexed: 01/01/2023]
Abstract
Urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC) strains. In contrast to many enteric E. coli pathogroups, no genetic signature has been identified for UPEC strains. We conducted a high-resolution comparative genomic study using E. coli isolates collected from the urine of women suffering from frequent recurrent UTIs. These isolates were genetically diverse and varied in their urovirulence, that is, their ability to infect the bladder in a mouse model of cystitis. We found no set of genes, including previously defined putative urovirulence factors (PUFs), that were predictive of urovirulence. In addition, in some patients, the E. coli strain causing a recurrent UTI had fewer PUFs than the supplanted strain. In competitive experimental infections in mice, the supplanting strain was more efficient at colonizing the mouse bladder than the supplanted strain. Despite the lack of a clear genomic signature for urovirulence, comparative transcriptomic and phenotypic analyses revealed that the expression of key conserved functions during culture, such as motility and metabolism, could be used to predict subsequent colonization of the mouse bladder. Together, our findings suggest that UTI risk and outcome may be determined by complex interactions between host susceptibility and the urovirulence potential of diverse bacterial strains.
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Affiliation(s)
- Henry L Schreiber
- Department of Molecular Microbiology, Washington University, St. Louis, MO 63110, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Matt S Conover
- Department of Molecular Microbiology, Washington University, St. Louis, MO 63110, USA
| | - Wen-Chi Chou
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael E Hibbing
- Department of Molecular Microbiology, Washington University, St. Louis, MO 63110, USA
| | - Abigail L Manson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University, St. Louis, MO 63110, USA
| | - Thomas J Hannan
- Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA
| | - Pacita L Roberts
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Ann E Stapleton
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Thomas M Hooton
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jonathan Livny
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Ashlee M Earl
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University, St. Louis, MO 63110, USA. .,Center for Women's Infectious Disease Research, Washington University, St. Louis, MO 63110, USA
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Plakunov VK, Mart’yanov SV, Teteneva NA, Zhurina MV. Controlling of microbial biofilms formation: Anti- and probiofilm agents. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717040129] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Molecular epidemiology of Escherichia coli sequence type 131 and its H30/H30-Rx subclones recovered from extra-intestinal infections: first report of OXA-48 producing ST131 clone from Iran. Eur J Clin Microbiol Infect Dis 2017; 36:1859-1866. [DOI: 10.1007/s10096-017-3021-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
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Stephenson S, Brown PD. Distribution of virulence determinants among antimicrobial-resistant and antimicrobial-susceptible Escherichia coli implicated in urinary tract infections. Indian J Med Microbiol 2017; 34:448-456. [PMID: 27934822 DOI: 10.4103/0255-0857.195354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Uropathogenic Escherichia coli (UPEC) rely on the correlation of virulence expression with antimicrobial resistance to persist and cause severe urinary tract infections (UTIs). OBJECTIVES We assessed the virulence pattern and prevalence among UPEC strains susceptible and resistant to multiple antimicrobial classes. METHODS A total of 174 non-duplicate UPEC strains from patients with clinically significant UTIs were analysed for susceptibility to aminoglycoside, antifolate, cephalosporin, nitrofuran and quinolone antibiotics for the production of extended-spectrum β-lactamases and for the presence of six virulence determinants encoding adhesins (afimbrial, Type 1 fimbriae, P and S-fimbriae) and toxins (cytotoxic necrotising factor and haemolysin). RESULTS Relatively high resistance rates to nalidixic acid, ciprofloxacin, cephalothin and trimethoprim-sulfamethoxazole (82%, 78%, 62% and 59%, respectively) were observed. Fourteen distinct patterns were identified for the virulence determinants such as afaBC, cnfI, fimH, hylA, papEF and sfaDE. The toxin gene, cnfI (75.3%), was the second most prevalent marker to the adhesin, fimH (97.1%). The significant association of sfaDE/hylA (P < 0.01) among antimicrobial resistant and susceptible strains was also observed notwithstanding an overall greater occurrence of virulence factors among the latter. CONCLUSIONS This study provides a snapshot of UPEC complexity in Jamaica and highlights the significant clonal heterogeneity among strains. Such outcomes emphasise the need for evidence-based strategies in the effective management and control of UTIs.
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Affiliation(s)
- Sam Stephenson
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
| | - P D Brown
- Department of Basic Medical Sciences, Faculty of Medical Sciences, University of the West Indies, Kingston, Jamaica
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Schreiber HL, Spaulding CN, Dodson KW, Livny J, Hultgren SJ. One size doesn't fit all: unraveling the diversity of factors and interactions that drive E. coli urovirulence. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:28. [PMID: 28217693 PMCID: PMC5300855 DOI: 10.21037/atm.2016.12.73] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/08/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Henry L. Schreiber
- Department of Molecular Microbiology, Washington University, St. Louis, MO, USA
- Center for Women’s Infectious Disease Research, Washington University, St. Louis, MO, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caitlin N. Spaulding
- Department of Molecular Microbiology, Washington University, St. Louis, MO, USA
- Center for Women’s Infectious Disease Research, Washington University, St. Louis, MO, USA
| | - Karen W. Dodson
- Department of Molecular Microbiology, Washington University, St. Louis, MO, USA
- Center for Women’s Infectious Disease Research, Washington University, St. Louis, MO, USA
| | - Jonathan Livny
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Scott J. Hultgren
- Department of Molecular Microbiology, Washington University, St. Louis, MO, USA
- Center for Women’s Infectious Disease Research, Washington University, St. Louis, MO, USA
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Jhang JF, Kuo HC. Recent advances in recurrent urinary tract infection from pathogenesis and biomarkers to prevention. Tzu Chi Med J 2017; 29:131-137. [PMID: 28974905 PMCID: PMC5615991 DOI: 10.4103/tcmj.tcmj_53_17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recurrent urinary tract infection (UTI) might be one of the most common problems in urological clinics. Recent research has revealed novel evidence about recurrent UTI and it should be considered a different disease from the first infection. The pathogenesis of recurrent UTI might include two mechanisms, bacterial factors and deficiencies in host defense. Bacterial survival in the urinary bladder after antibiotic treatment and progression to form intracellular bacterial communities might be the most important bacterial factors. In host defense deficiency, a defect in pathogen recognition and urothelial barrier function impairment play the most important roles. Immunodeficiency and urogenital tract anatomical abnormalities have been considered the essential risk factors for recurrent UTI. In healthy women, voiding dysfunction and behavioral factors also increase the risk of recurrent UTI. Sexual intercourse and estrogen deficiency in postmenopausal women might have the strongest association with recurrent UTI. Traditional lifestyle factors such as fluid intake and diet are not considered independent risk factors now. Serum and urine biomarkers to predict recurrent UTI from the first infection have also attracted a wide attention recently. Current clinical evidence suggests that serum macrophage colony-stimulating factor and urinary nerve growth factor have potential predictive value for recurrent UTI. Clinical trials have proven the efficacy of the oral immunoactive agent OM-89 for the prevention of UTI. Vaccines for recurrent UTI are recommended by the latest guidelines and are available on the market.
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Affiliation(s)
- Jia-Fong Jhang
- Department of Urology, Buddhist Tzu Chi General Hospital and Tzu Chi University, Hualien, Taiwan
| | - Hann-Chorng Kuo
- Department of Urology, Buddhist Tzu Chi General Hospital and Tzu Chi University, Hualien, Taiwan
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Ochoa SA, Cruz-Córdova A, Luna-Pineda VM, Reyes-Grajeda JP, Cázares-Domínguez V, Escalona G, Sepúlveda-González ME, López-Montiel F, Arellano-Galindo J, López-Martínez B, Parra-Ortega I, Giono-Cerezo S, Hernández-Castro R, de la Rosa-Zamboni D, Xicohtencatl-Cortes J. Multidrug- and Extensively Drug-Resistant Uropathogenic Escherichia coli Clinical Strains: Phylogenetic Groups Widely Associated with Integrons Maintain High Genetic Diversity. Front Microbiol 2016; 7:2042. [PMID: 28066364 PMCID: PMC5174082 DOI: 10.3389/fmicb.2016.02042] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022] Open
Abstract
In recent years, an increase of uropathogenic Escherichia coli (UPEC) strains with Multidrug-resistant (MDR) and Extensively Drug-resistant (XDR) profiles that complicate therapy for urinary tract infections (UTIs) has been observed and has directly impacted costs and extended hospital stays. The aim of this study was to determine MDR- and XDR-UPEC clinical strains, their virulence genes, their phylogenetic groups and to ascertain their relationship with integrons and genetic diversity. From a collection of 500 UPEC strains, 103 were selected with MDR and XDR characteristics. MDR-UPEC strains were mainly associated with phylogenetic groups D (54.87%) and B2 (39.02%) with a high percentage (≥70%) of several fimbrial genes (ecpA, fimH, csgA, and papGII), an iron uptake gene (chuA), and a toxin gene (hlyA). In addition, a moderate frequency (40–70%) of other genes (iutD, tosA, and bcsA) was observed. XDR-UPEC strains were predominantly associated with phylogenetic groups B2 (47.61%) and D (42.85%), which grouped with ≥80 virulence genes, including ecpA, fimH, csgA, papGII, iutD, and chuA. A moderate frequency (40–70%) of the tosA and hlyA genes was observed. The class 1 and 2 integrons that were identified in the MDR- and XDR-UPEC strains were associated with phylogenetic groups D, B2, and A, while the XDR-UPEC strains that were associated with phylogenetic groups B2, D, and A showed an extended-spectrum beta-lactamase (ESBL) phenotype. The modifying enzymes (aadA1, aadB, aacC, ant1, dfrA1, dfrA17, and aadA4) that were identified in the variable region of class 1 and 2 integrons from the MDR strains showed resistance to gentamycin (56.25 and 66.66%, respectively) and trimethoprim-sulfamethoxazole (84.61 and 66.66%, respectively). The MDR- and XDR-UPEC strains were distributed into seven clusters and were closely related to phylogenic groups B2 and D. The diversity analysis by PFGE showed 42.68% of clones of MDR-UPEC and no clonal association in the XDR-UPEC strains. In conclusion, phylogenetic groups including virulence genes are widely associated with two integron classes (1 and 2) in MDR- and XDR-UPEC strains.
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Affiliation(s)
- Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico GómezMexico City, Mexico; Posgrado en Ciencias Químico-Biológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico; Laboratorio de Bacteriología Médica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico NacionalMexico City, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - Victor M Luna-Pineda
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - Juan P Reyes-Grajeda
- Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica Mexico City, Mexico
| | - Vicenta Cázares-Domínguez
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - Gerardo Escalona
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - Ma Eugenia Sepúlveda-González
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - Fernanda López-Montiel
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - José Arellano-Galindo
- Área de Virología, Laboratorio de Infectología, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - Briceida López-Martínez
- Subdirección de Servicios Auxiliares de Diagnóstico, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - Israel Parra-Ortega
- Laboratorio Clínico, Hospital Infantil de México Federico Gómez Mexico City, Mexico
| | - Silvia Giono-Cerezo
- Laboratorio de Bacteriología Médica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico City, Mexico
| | - Rigoberto Hernández-Castro
- Departamento de Ecología de Agentes Patógenos, Hospital General "Dr. Manuel Gea González," Mexico City, Mexico
| | | | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez Mexico City, Mexico
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45
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Clustered, regularly interspaced short palindromic repeat (CRISPR) diversity and virulence factor distribution in avian Escherichia coli. Res Microbiol 2016; 168:147-156. [PMID: 27789334 DOI: 10.1016/j.resmic.2016.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/13/2016] [Accepted: 10/17/2016] [Indexed: 11/21/2022]
Abstract
In order to investigate the diverse characteristics of clustered, regularly interspaced short palindromic repeat (CRISPR) arrays and the distribution of virulence factor genes in avian Escherichia coli, 80 E. coli isolates obtained from chickens with avian pathogenic E. coli (APEC) or avian fecal commensal E. coli (AFEC) were identified. Using the multiplex polymerase chain reaction (PCR), five genes were subjected to phylogenetic typing and examined for CRISPR arrays to study genetic relatedness among the strains. The strains were further analyzed for CRISPR loci and virulence factor genes to determine a possible association between their CRISPR elements and their potential virulence. The strains were divided into five phylogenetic groups: A, B1, B2, D and E. It was confirmed that two types of CRISPR arrays, CRISPR1 and CRISPR2, which contain up to 246 distinct spacers, were amplified in most of the strains. Further classification of the isolates was achieved by sorting them into nine CRISPR clusters based on their spacer profiles, which indicates a candidate typing method for E. coli. Several significant differences in invasion-associated gene distribution were found between the APEC isolates and the AFEC isolates. Our results identified the distribution of 11 virulence genes and CRISPR diversity in 80 strains. It was demonstrated that, with the exception of iucD and aslA, there was no sharp demarcation in the gene distribution between the pathogenic (APEC) and commensal (AFEC) strains, while the total number of indicated CRISPR spacers may have a positive correlation with the potential pathogenicity of the E. coli isolates.
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46
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Kell DB, Pretorius E. On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death. Integr Biol (Camb) 2016; 7:1339-77. [PMID: 26345428 DOI: 10.1039/c5ib00158g] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have recently highlighted (and added to) the considerable evidence that blood can contain dormant bacteria. By definition, such bacteria may be resuscitated (and thus proliferate). This may occur under conditions that lead to or exacerbate chronic, inflammatory diseases that are normally considered to lack a microbial component. Bacterial cell wall components, such as the endotoxin lipopolysaccharide (LPS) of Gram-negative strains, are well known as potent inflammatory agents, but should normally be cleared. Thus, their continuing production and replenishment from dormant bacterial reservoirs provides an easy explanation for the continuing, low-grade inflammation (and inflammatory cytokine production) that is characteristic of many such diseases. Although experimental conditions and determinants have varied considerably between investigators, we summarise the evidence that in a great many circumstances LPS can play a central role in all of these processes, including in particular cell death processes that permit translocation between the gut, blood and other tissues. Such localised cell death processes might also contribute strongly to the specific diseases of interest. The bacterial requirement for free iron explains the strong co-existence in these diseases of iron dysregulation, LPS production, and inflammation. Overall this analysis provides an integrative picture, with significant predictive power, that is able to link these processes via the centrality of a dormant blood microbiome that can resuscitate and shed cell wall components.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester M1 7DN, Lancs, UK.
| | - Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia 0007, South Africa.
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Wu Y(R, Rego LL, Christie AL, Lavelle RS, Alhalabi F, Zimmern PE. Recurrent Urinary Tract Infections Due to Bacterial Persistence or Reinfection in Women—Does This Factor Impact Upper Tract Imaging Findings? J Urol 2016; 196:422-8. [DOI: 10.1016/j.juro.2016.01.111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2016] [Indexed: 10/22/2022]
Affiliation(s)
| | - Lauren L. Rego
- University of Texas Southwestern Medical Center, Dallas, Texas
| | - Alana L. Christie
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Rebecca S. Lavelle
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Feras Alhalabi
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Philippe E. Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas
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Kell DB, Kenny LC. A Dormant Microbial Component in the Development of Preeclampsia. Front Med (Lausanne) 2016; 3:60. [PMID: 27965958 PMCID: PMC5126693 DOI: 10.3389/fmed.2016.00060] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/04/2016] [Indexed: 12/12/2022] Open
Abstract
Preeclampsia (PE) is a complex, multisystem disorder that remains a leading cause of morbidity and mortality in pregnancy. Four main classes of dysregulation accompany PE and are widely considered to contribute to its severity. These are abnormal trophoblast invasion of the placenta, anti-angiogenic responses, oxidative stress, and inflammation. What is lacking, however, is an explanation of how these themselves are caused. We here develop the unifying idea, and the considerable evidence for it, that the originating cause of PE (and of the four classes of dysregulation) is, in fact, microbial infection, that most such microbes are dormant and hence resist detection by conventional (replication-dependent) microbiology, and that by occasional resuscitation and growth it is they that are responsible for all the observable sequelae, including the continuing, chronic inflammation. In particular, bacterial products such as lipopolysaccharide (LPS), also known as endotoxin, are well known as highly inflammagenic and stimulate an innate (and possibly trained) immune response that exacerbates the inflammation further. The known need of microbes for free iron can explain the iron dysregulation that accompanies PE. We describe the main routes of infection (gut, oral, and urinary tract infection) and the regularly observed presence of microbes in placental and other tissues in PE. Every known proteomic biomarker of "preeclampsia" that we assessed has, in fact, also been shown to be raised in response to infection. An infectious component to PE fulfills the Bradford Hill criteria for ascribing a disease to an environmental cause and suggests a number of treatments, some of which have, in fact, been shown to be successful. PE was classically referred to as endotoxemia or toxemia of pregnancy, and it is ironic that it seems that LPS and other microbial endotoxins really are involved. Overall, the recognition of an infectious component in the etiology of PE mirrors that for ulcers and other diseases that were previously considered to lack one.
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Affiliation(s)
- Douglas B. Kell
- School of Chemistry, The University of Manchester, Manchester, UK
- The Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of Manchester, Manchester, UK
- *Correspondence: Douglas B. Kell,
| | - Louise C. Kenny
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), University College Cork, Cork, Ireland
- Department of Obstetrics and Gynecology, University College Cork, Cork, Ireland
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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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Harwalkar A, Gupta S, Rao A, Srinivasa H. Prevalence of virulence factors and phylogenetic characterization of uropathogenic Escherichia coli causing urinary tract infection in patients with and without diabetes mellitus. Trans R Soc Trop Med Hyg 2015; 109:769-74. [PMID: 26567223 DOI: 10.1093/trstmh/trv086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/21/2015] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND We aimed to determine the virulence factor profile and phylogenetic grouping of uropathogenic Escherichia coli (UPEC) causing urinary tract infection (UTI) in patients with and without diabetes mellitus (DM). METHODS A total of 280 UPEC were collected from the urine samples of patients with DM (n=126) and patients suffering from non-DM UTIs (n=154). All isolates were subjected to phenotypic and genotypic virulence factor profile and phylogenetic grouping. RESULTS There was no significant difference in phenotypic virulence factors of UPEC causing UTI from patients with and without DM; alpha-haemolysin (DM=52, 41.2%; non-DM=69, 44.8%), mannose resistant haemagglutination (DM=6, 36.2%; non-DM=64, 41.5%), biofilm production (DM=33.3%; non-DM=25.9%), serum resistance (DM=27, 21.4%; non-DM=46, 29.8%), cell surface hydrophobicity (DM=22, 17.1%; non-DM=18, 11.6%) and mannose sensitive hemagglutnation (DM=18, 14.2%; non-DM=29, 18.8%). Among the genotypic virulence markers, papC gene was most prevalent in both patients with DM (n=65, 51.6%) and without DM (n=88, 57.1%), followed by hlyD gene (DM=36, 28.6%; non-DM=52, 33.8%). Only cnf-1 gene was observed to be significantly associated (p<0.05) with the non-DM status (n=35, 22.7%) than DM (n=15, 11.9%). Irrespective of the diabetic status, majority of the UPEC isolates (approximately 50%) belonged to phylogenetic group B2 predominantly harboring the virulence genes papC, hlyD and cnf-1. CONCLUSIONS This study demonstrates that there may not be a differential selection of virulence properties of UPEC causing UTI in patients with DM and in the general population.
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Affiliation(s)
| | - Soham Gupta
- Department of Microbiology, St. John's Medical College, Bangalore, Karnataka, India
| | - Achyut Rao
- Department of Microbiology, Navodaya Medical College, Raichur, Karnataka, India
| | - Hiresave Srinivasa
- Department of Microbiology, St. John's Medical College, Bangalore, Karnataka, India
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