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Halaji M, Shahidi S, Ataei B, Atapour A, Feizi A, Havaei SA. Molecular epidemiology of bla CTX-M gene-producing uropathogenic Escherichia coli among Iranian kidney transplant patients: clonal dissemination of CC131 and CC10. Ann Clin Microbiol Antimicrob 2021; 20:65. [PMID: 34496873 PMCID: PMC8424993 DOI: 10.1186/s12941-021-00470-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 08/31/2021] [Indexed: 11/25/2022] Open
Abstract
Background This study aimed to investigate the phylogenetic characterization and virulence traits of uropathogenic Escherichia coli (UPEC) isolated from kidney transplant patients (KTPs) as well as non-KTPs and analyze the clonal distribution of Extended spectrum β-lactamases (ESBLs)-producing UPEC containing blaCTX-M gene. Methods To this end, we determined virulence marker and the phylogenetic characterization of UPEC in non-KTPs (n = 65) and KTPs (n = 46). The non-KTPs were considered the control group of the study. Also, according to the Achtman scheme, we performed multilocus sequence typing to assess the relationship between twenty-nine of ESBL-producing isolates containing blaCTX-M gene. Results According to the results of PCR assay, the prevalence of virulence factor genes ranged from 0% (cnf and papG III) to 93.7% (fimH). Also, KTP isolates significantly differed from non-KTP isolates only in terms of the prevalence of pap GI elements. Moreover, the most frequent UPEC isolates were in phylogenetic group B2, followed by group D (18.9%), and group A (13.5%). Furthermore, except for phylogenetic group C, there was no significant correlation between phylogenetic distribution in KTPs and non-KTPs. Additionally, MLST analysis of blaCTX-M carrying isolates identified 18 unique sequence types (ST) the most common of which was ST131 (24.1%), followed by ST1193 (10.3%), while fourteen STs were detected only once. Conclusions The results further revealed significant differences between the UPEC isolates from KTPs and non-KTPs regarding the phylogroups C and PAI gene. Based on MLST analysis, we also observed a relatively high diversity in UPEC isolates obtained from KTPs and non-KTPs. Moreover, clonal complex (CC) 131 and ST131 were found to be the most prevalent clones and ST types, respectively. Besides, for the first time, ST8503 were reported in KTPs. These results suggested regular studies on characterization of UPEC isolates among KTPs. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-021-00470-7.
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Affiliation(s)
- Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Shahrzad Shahidi
- Isfahan Kidney Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behrooz Ataei
- Nosocomial Infection Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abdolamir Atapour
- Isfahan Kidney Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Biostatistics and Epidemiology, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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Coussement J, Argudín MA, Heinrichs A, Racapé J, de Mendonça R, Nienhaus L, Le Moine A, Roisin S, Dodémont M, Jacobs F, Abramowicz D, Johnston BD, Johnson JR, Denis O. Host and microbial factors in kidney transplant recipients with Escherichia coli acute pyelonephritis or asymptomatic bacteriuria: a prospective study using whole-genome sequencing. Nephrol Dial Transplant 2020; 34:878-885. [PMID: 30304506 DOI: 10.1093/ndt/gfy292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Urinary tract infection is the most common infection among kidney transplant recipients (KTRs). Many transplant physicians fear that host compromise will allow low-virulence strains to cause pyelonephritis in KTRs, so they often treat asymptomatic bacteriuria with antibiotics. Identification of the host/microbe factors that determine the clinical presentation (i.e. pyelonephritis versus asymptomatic bacteriuria) once an Escherichia coli strain enters a KTRs bladder could inform management decisions. METHODS We prospectively collected all E. coli isolates causing either pyelonephritis or asymptomatic bacteriuria in KTRs at our institution (December 2012-June 2015). Whole-genome sequencing was used to assess bacterial characteristics (carriage of 48 virulence genes and phylogenetic and clonal background). Host parameters were also collected. RESULTS We analysed 72 bacteriuria episodes in 54 KTRs (53 pyelonephritis, 19 asymptomatic bacteriuria). The pyelonephritis and asymptomatic bacteriuria isolates exhibited a similar total virulence gene count per isolate [median 18 (range 5-33) and 18 (5-30), respectively; P = 0.57] and for individual virulence genes differed significantly only for the prevalence of the pap operon (pyelonephritis 39%,versus asymptomatic bacteriuria 0%; P = 0.002). No other significant between-group differences were apparent for 86 other bacterial and host variables. CONCLUSIONS Our findings suggest that bacterial adherence plays a role in the pathogenesis of pyelonephritis in KTRs despite significantly altered host urinary tract anatomy and weakened immunity. Whether KTRs might benefit from targeted therapies (e.g. vaccination or inhibitors of fimbrial adhesion) has yet to be studied.
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Affiliation(s)
- Julien Coussement
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Division of Infectious Diseases, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Maria Angeles Argudín
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Amélie Heinrichs
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Judith Racapé
- Research Center "Biostatistiques, Epidémiologie et Recherche Clinique", École de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium.,Department of Nephrology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Ricardo de Mendonça
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Louise Nienhaus
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Alain Le Moine
- Department of Nephrology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Sandrine Roisin
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Magali Dodémont
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Frédérique Jacobs
- Division of Infectious Diseases, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Daniel Abramowicz
- Department of Nephrology-Hypertension, Universitair Ziekenhuis Antwerpen, Antwerp University, Antwerpen, Belgium
| | | | - James R Johnson
- Minneapolis Veterans Health Care System, Minneapolis, MN, USA
| | - Olivier Denis
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,École de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
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Abo Basha J, Kiel M, Görlich D, Schütte-Nütgen K, Witten A, Pavenstädt H, Kahl BC, Dobrindt U, Reuter S. Phenotypic and Genotypic Characterization of Escherichia coli Causing Urinary Tract Infections in Kidney-Transplanted Patients. J Clin Med 2019; 8:jcm8070988. [PMID: 31284699 PMCID: PMC6678207 DOI: 10.3390/jcm8070988] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/01/2019] [Accepted: 07/05/2019] [Indexed: 12/19/2022] Open
Abstract
Urinary tract infection (UTI), frequently caused by uropathogenic Escherichia coli (UPEC), is the most common infection after kidney transplantation (KTx). Untreated, it can lead to urosepsis and impairment of the graft function. We questioned whether the UPEC isolated from KTx patients differed from the UPEC of non-KTx patients. Therefore, we determined the genome sequences of 182 UPEC isolates from KTx and control patients in a large German university clinic and pheno- and genotypically compared these two isolated groups. Resistance to the β-lactams, trimethoprim or trimethoprim/sulfamethoxazole was significantly higher among UPEC from KTx than from control patients, whereas both the isolated groups were highly susceptible to fosfomycin. Accordingly, the gene content conferring resistance to β-lactams or trimethoprim, but also to aminoglycosides, was significantly higher in KTx than in control UPEC isolates. E. coli isolates from KTx patients more frequently presented with uncommon UPEC phylogroups expressing higher numbers of plasmid replicons, but interestingly, less UPEC virulence-associated genes than the control group. We conclude that there is no defining subset of virulence traits for UPEC from KTx patients. The clinical history and immunocompromised status of KTx patients enables E. coli strains with low uropathogenic potential, but with increased antibiotic resistance to cause UTIs.
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Affiliation(s)
- Jonas Abo Basha
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Matthias Kiel
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
| | - Dennis Görlich
- Institute of Biostatistics and Clinical Research, University of Münster, 48149 Münster, Germany
| | - Katharina Schütte-Nütgen
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Anika Witten
- Institute for Human Genetics, University of Münster, 48149 Münster, Germany
| | - Hermann Pavenstädt
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, 48149 Münster, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, 48149 Münster, Germany.
| | - Stefan Reuter
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, 48149 Münster, Germany.
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Abstract
Similarly to the general population, genitourinary tract infections are common conditions in theimmunocompromised host. They can be furthermore divided into infections of the urinary tract and genital tract infections. Transplant recipients are more likely to have infections of the urinary tract infections while persons with human immunodeficiency virus (HIV) are at higher risk for the second group of infections, especially sexually transmitted infections (STIs). Manifestations of these diseases can be associated with more complications and can be more severe. We provide an overview of manifestations, diagnosis, and management of these disorders.
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Abstract
The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinal Escherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. An E. coli chromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenic E. coli strains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival of E. coli as a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.
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Rahdar M, Rashki A, Miri HR, Rashki Ghalehnoo M. Detection of pap, sfa, afa, foc, and fim Adhesin-Encoding Operons in Uropathogenic Escherichia coli Isolates Collected From Patients With Urinary Tract Infection. Jundishapur J Microbiol 2015; 8:e22647. [PMID: 26464770 PMCID: PMC4600570 DOI: 10.5812/jjm.22647] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 11/19/2014] [Accepted: 01/05/2015] [Indexed: 02/07/2023] Open
Abstract
Background: Uropathogenic Escherichia coli (UPEC) with its virulence factors is the most prevalent cause of urinary tract infection (UTI). Objectives; This study aimed to determine the occurrence of fim, pap, sfa, and afa genes among 100 UPEC isolates collected from patients diagnosed with UTI. Materials and Methods A total of 100 UPEC isolates were obtained from urine samples of patients with UTI. The prevalence of 5 virulence genes encoding type 1 fimbriae (fimH), pili associated with pyelonephritis (pap), S and F1C fimbriae (sfa and foc) and afimbrial adhesins (afa) were determined through PCR method. We also investigated the phylogenetic background of all isolates. In addition, the distribution of adhesin-encoding operons between the phylogroups was assessed. Results: The prevalence of genes encoding for fimbrial adhesive systems was 95% for fim, 57% for pap, 16% for foc, and 81% for sfa. The operons encoding for afa afimbrial adhesins were identified in 12% of isolates. The various combinations of detected genes were designated as virulence patterns. The fim gene, which occurred in strains from all phylogenetic groups (A, B1, B2, and D) was evaluated and no significant differences were found among these groups. Conversely, significant differences were observed in relation to pap, afa, foc, and sfa operons. Conclusions: These results indicate that the PCR method is a powerful genotypic assay for the detection of adhesin-encoding operons. Thus, this assay can be recommended for clinical use to detect virulent urinary E. coli strains, as well as epidemiological studies.
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Affiliation(s)
- Masoud Rahdar
- Department of Biology, Faculty of Basic Sciences, University of Zabol, Zabol, IR Iran
| | - Ahmad Rashki
- Department of Physiopathology, Faculty of Vet-Medicine, University of Zabol, Zabol, IR Iran
- Corresponding author: Ahmad Rashki, Department of Physiopathology, Faculty of Vet-Medicine, University of Zabol, Zabol, IR Iran. Tel: +98-9151970877, Fax: +98-5424822251, E-mail:
| | - Hamid Reza Miri
- Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, IR Iran
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Fernández-Romero N, Quiles I, Jiménez C, Oliva MOL, Rivas B, Mingorance J, Romero-Gómez MP. Use of multiplex PCR in diagnosis of bloodstream infections in kidney patients. Diagn Microbiol Infect Dis 2014; 80:93-6. [PMID: 25107361 DOI: 10.1016/j.diagmicrobio.2014.07.001] [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: 01/26/2014] [Revised: 06/05/2014] [Accepted: 07/02/2014] [Indexed: 10/25/2022]
Abstract
The LightCycler® SeptiFast Test (Roche Diagnostics GmbH, Mannheim, Germany) was prospectively compared with the standard blood culture technique in a series of 86 kidney patients. The sensitivity of the PCR compared with the culture was 71%, and the specificity was 88%. All the species identified by culture in these patients were in the SeptiFast panel. The median time to results was 1 day for the PCR, 3 days for positive cultures, and 5 days for negative cultures.
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Affiliation(s)
- Natalia Fernández-Romero
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Inmaculada Quiles
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Carlos Jiménez
- Servicio de Nefrología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - María Ovidea Lopez Oliva
- Servicio de Nefrología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Begoña Rivas
- Servicio de Nefrología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - María Pilar Romero-Gómez
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de la Castellana, 261, 28046, Madrid, Spain.
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Momtaz H, Karimian A, Madani M, Safarpoor Dehkordi F, Ranjbar R, Sarshar M, Souod N. Uropathogenic Escherichia coli in Iran: serogroup distributions, virulence factors and antimicrobial resistance properties. Ann Clin Microbiol Antimicrob 2013; 12:8. [PMID: 23627669 PMCID: PMC3651382 DOI: 10.1186/1476-0711-12-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 04/21/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Urinary tract infections (UTIs) are one of the most common bacterial infections with global expansion. These infections are predominantly caused by uropathogenic Escherichia coli (UPEC). METHODS Totally, 123 strains of Escherichia coli isolated from UTIs patients, using bacterial culture method were subjected to polymerase chain reactions for detection of various O- serogroups, some urovirulence factors, antibiotic resistance genes and resistance to 13 different antibiotics. RESULTS According to data, the distribution of O1, O2, O6, O7 and O16 serogroups were 2.43%, besides O22, O75 and O83 serogroups were 1.62%. Furthermore, the distribution of O4, O8, O15, O21 and O25 serogroups were 5.69%, 3.25%, 21.13%, 4.06% and 26.01%, respectively. Overall, the fim virulence gene had the highest (86.17%) while the usp virulence gene had the lowest distributions of virulence genes in UPEC strains isolated from UTIs patients. The vat and sen virulence genes were not detected in any UPEC strains. Totally, aadA1 (52.84%), and qnr (46.34%) were the most prevalent antibiotic resistance genes while the distribution of cat1 (15.44%), cmlA (15.44%) and dfrA1 (21.95%) were the least. Resistance to penicillin (100%) and tetracycline (73.98%) had the highest while resistance to nitrofurantoin (5.69%) and trimethoprim (16.26%) had the lowest frequencies. CONCLUSIONS This study indicated that the UPEC strains which harbored the high numbers of virulence and antibiotic resistance genes had the high ability to cause diseases that are resistant to most antibiotics. In the current situation, it seems that the administration of penicillin and tetracycline for the treatment of UTIs is vain.
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Affiliation(s)
- Hassan Momtaz
- Department of Microbiology, ShahreKord Branch, Islamic Azad University, P.O. Box: 166, ShahreKord, Iran.
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Giessing M. Urinary tract infection in renal transplantation. Arab J Urol 2012; 10:162-8. [PMID: 26558020 PMCID: PMC4442899 DOI: 10.1016/j.aju.2012.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/05/2012] [Accepted: 01/07/2012] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION Urinary tract infection (UTI), especially recurrent UTI, is a common problem, occurring in >75% of kidney transplant (KTX) recipients. UTI degrades the health-related quality of life and can impair graft function, potentially reducing graft and patient survival. As urologists are often involved in treating UTI after KTX, previous reports were searched to elucidate underlying causes, risk factors and treatment options, as well as recommendations for prophylaxis of UTI after KTX. METHODS Pubmed/Medline was searched and international guidelines and recommendations for prevention and treatment of UTI after KTX were also assessed. RESULTS Most studies on UTI after KTX have a small sample, and are descriptive and retrospective. Many transplant- and recipient-related risk factors have been identified. While asymptomatic bacteriuria is often treated, even though some studies advise against it, symptomatic UTI should be treated empirically after collecting urine for microbiological analysis, to avoid the development of transplant pyelonephritis with a high chance of urosepsis. The duration of treatment has not been determined in studies and recommendations refer to the treatment of complicated UTI in the non-transplant population. Prophylaxis has not been the focus of studies either. CONCLUSION UTI after KTX is still largely an under-represented field of study, despite many recipients developing UTI after KTX. Prospective studies on this topic are urgently needed.
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Affiliation(s)
- Markus Giessing
- Department of Urology, Heinrich Heine University Hospital Duesseldorf, Moorenstr. 5, D-40225 Düsseldorf, Germany
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