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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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Increased Levels of (p)ppGpp Correlate with Virulence and Biofilm Formation, but Not with Growth, in Strains of Uropathogenic Escherichia coli. Int J Mol Sci 2023; 24:ijms24043315. [PMID: 36834725 PMCID: PMC9962837 DOI: 10.3390/ijms24043315] [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: 12/21/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Urinary tract infections are one of the most frequent bacterial diseases worldwide. UPECs are the most prominent group of bacterial strains among pathogens responsible for prompting such infections. As a group, these extra-intestinal infection-causing bacteria have developed specific features that allow them to sustain and develop in their inhabited niche of the urinary tract. In this study, we examined 118 UPEC isolates to determine their genetic background and antibiotic resistance. Moreover, we investigated correlations of these characteristics with the ability to form biofilm and to induce a general stress response. We showed that this strain collection expressed unique UPEC attributes, with the highest representation of FimH, SitA, Aer, and Sfa factors (100%, 92.5%, 75%, and 70%, respectively). According to CRA (Congo red agar) analysis, the strains particularly predisposed to biofilm formation represented 32.5% of the isolates. Those biofilm forming strains presented a significant ability to accumulate multi-resistance traits. Most notably, these strains presented a puzzling metabolic phenotype-they showed elevated basal levels of (p)ppGpp in the planktonic phase and simultaneously exhibited a shorter generation time when compared to non-biofilm-forming strains. Moreover, our virulence analysis showed these phenotypes to be crucial for the development of severe infections in the Galleria mellonella model.
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Elias P, Barraud O, El Hamel C, Chainier D, Dallochio A, Grélaud C, Ploy MC, Guigonis V, Garnier F. Integron detection for prediction of trimethoprim/sulfamethoxazole susceptibility in children with Enterobacterales urinary tract infections. J Antimicrob Chemother 2022; 77:767-770. [DOI: 10.1093/jac/dkab431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
Abstract
Objectives
In some countries, third-generation cephalosporins (3GCs) serve as first-line therapy in children with urinary tract infections (UTIs). However, their use may contribute to the emergence of antibiotic resistance, notably among Gram-negative bacteria (GNB). Integrons are bacterial genetic elements involved in antibiotic resistance in GNB. Their absence is associated with >97% susceptibility to trimethoprim/sulfamethoxazole in adults infected with GNB. The objective of this study was to examine the value of integron detection directly from urine samples as a predictive marker of resistance to trimethoprim/sulfamethoxazole in children with GNB-related UTIs.
Methods
Children admitted to the Limoges University Hospital’s paediatric emergency department between February 2018 and March 2019 with a suspicion of UTI were eligible for the study. Only confirmed cases presenting a positive urine culture with unique GNB were retained for further study analyses. Integrons were detected directly from urines using real-time PCR.
Results
The data of 72 patients were analysed and integrons were detected in 15 urine samples. The negative predictive value of integron detection for resistance to trimethoprim/sulfamethoxazole was 100% as all of the GNB (all were Enterobacterales) isolated from patients with no integrons detected in their urine samples were susceptible to trimethoprim/sulfamethoxazole.
Conclusions
The detection of integrons in cases of paediatric patients with suspected UTI could help limit 3GC empirical use and empower an empirical first-line strategy better tailored to the needs of each patient.
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Affiliation(s)
- Peter Elias
- Service de Pédiatrie, Hôpital Mère Enfant, CHU Limoges, 8 Ave D Larrey, Limoges, France
| | - Olivier Barraud
- Université Limoges, INSERM, CHU Limoges, UMR 1092, 2 Ave M Luther King, Limoges, France
| | - Chahrazed El Hamel
- Service de Pédiatrie, Hôpital Mère Enfant, CHU Limoges, 8 Ave D Larrey, Limoges, France
- CB-HME, Hôpital Mère Enfant, CHU Limoges, 8 Ave D Larrey, Limoges, France
| | - Delphine Chainier
- Université Limoges, INSERM, CHU Limoges, UMR 1092, 2 Ave M Luther King, Limoges, France
| | - Aymeric Dallochio
- Service de Pédiatrie, Hôpital Mère Enfant, CHU Limoges, 8 Ave D Larrey, Limoges, France
| | - Carole Grélaud
- Université Limoges, INSERM, CHU Limoges, UMR 1092, 2 Ave M Luther King, Limoges, France
| | - Marie-Cécile Ploy
- Université Limoges, INSERM, CHU Limoges, UMR 1092, 2 Ave M Luther King, Limoges, France
| | - Vincent Guigonis
- Service de Pédiatrie, Hôpital Mère Enfant, CHU Limoges, 8 Ave D Larrey, Limoges, France
- CB-HME, Hôpital Mère Enfant, CHU Limoges, 8 Ave D Larrey, Limoges, France
| | - Fabien Garnier
- Université Limoges, INSERM, CHU Limoges, UMR 1092, 2 Ave M Luther King, Limoges, France
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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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5
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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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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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7
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Ranjbar R, Nazari S, Farahani O. Phylogenetic Analysis and Antimicrobial Resistance Profiles of Escherichia coli Strains Isolated from UTI-Suspected Patients. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:1743-1749. [PMID: 33643950 PMCID: PMC7898090 DOI: 10.18502/ijph.v49i9.4094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Background: Escherichia coli as one of the most predominant pathogens is the major cause of urinary tract infections (UTI) worldwide. E. coli strains could be classified into distinct phylo-groups based on PCR method. Additionally, studying the antimicrobial resistance profiles of these strains is essential for finding the effective selection of treatment and evaluating the differences among resistance patterns of particular phylogenetic groups. This study aimed to determine the phylogroups of E. coli isolated from patients with UTI in Tehran, Iran. Methods: The urine samples were collected from patients suspected to UTI from four hospitals in Tehran, Iran; Mofid, Vali-Asr, Bu-Ali and Tehran Heart Center (THC) Hospitals during 2014–2016. Assessing the antimicrobial resistance profile of the identified strains was accomplished using ampicillin, ceftriaxone, cefotaxime, and ceftazidime among β-lactam group; gentamicin, and streptomycin among aminoglycosides; nalidixic acid and norfloxacin from quinolones; and chloramphenicol disks. The phylogenetic characterization of 60 E. coli isolates obtained from patients with UTI was done by triplex PCR method. Results: E. coli strains showed high resistance toward streptomycin (93.33%), ampicillin (86.6%) and nalidixic acid (73.33%) while resistance against chloramphenicol showed the lowest (10%). The prevalent groups were B2 (n=50/60, 83%), followed by D (n=6/60, 10%), B1 (n=3/60, 5%), and A (n=1, 1.6%). Conclusion: The most predominant phylogenetic group was B2 with the major frequent detected with the major drug resistant (48%) compared to other Phylogenetic groups.
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Affiliation(s)
- Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sedigheh Nazari
- Department of Microbiology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | - Omid Farahani
- Department of Microbiology, Varamin-Pishva Branch, Islamic Azad University, Tehran, Iran
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8
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Characterization of antibiotic resistance integrons harbored by Romanian Escherichia coli uropathogenic strains. REV ROMANA MED LAB 2020. [DOI: 10.2478/rrlm-2020-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Because little is known about the integrons which constitute an important means of spreading resistance in bacteria circulating in Romania, this study aimed to detect antibiotic resistance gene cassettes embedded in integrons in a convenient collection of 60 ciprofloxacin-resistant Escherichia coli isolates of various phylogroups, associated with community-acquired urinary tract infections. Characterization of the integrons was accomplished by PCR, restriction fragment length polymorphism typing, and DNA sequencing of each identified type. More than half of the tested E. coli strains were positive for integrons of class 1 (31 strains) or 2 (1 strain). These strains derived more frequently from phylogenetic groups A (15 of 21 strains), B1 (10 of 14 strains), and F (3 of 4 strains), respectively. While 20 strains carried class 1 integrons which could be assigned to nine types, eleven strains carried integrons that lacked the 3’-end conserved segment. The attempts made to characterize the gene cassettes located within the variable region of the various integrons identified in this study revealed the presence of genes encoding resistance to trimethoprim, aminoglycosides, beta-lactams or chloramphenicol. The evidence of transferable resistance determinants already established in the autochthonous E. coli strains highlights the need for improved control of resistance-carrying bacteria.
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9
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Halaji M, Feizi A, Mirzaei A, Sedigh Ebrahim-Saraie H, Fayyazi A, Ashraf A, Havaei SA. The Global Prevalence of Class 1 Integron and Associated Antibiotic Resistance in Escherichia coli from Patients with Urinary Tract Infections, a Systematic Review and Meta-Analysis. Microb Drug Resist 2020; 26:1208-1218. [PMID: 32282274 DOI: 10.1089/mdr.2019.0467] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Objectives: The present systematic review and meta-analysis study aimed to investigate the prevalence of class 1 integrons and their associated antibiotic resistance in uropathogenic Escherichia coli. Materials and Methods: A systematic search was conducted to identify studies meeting our inclusion criteria in the Web of Science, PubMed, Embase, Scopus, and Google Scholar electronic databases to the end of July 2019. Finally, 35 articles were selected for data extraction, and meta-analysis was performed using the metaprop program in the STATA, version 11.0, software. Results: The pooled prevalence of class 1 integrons was 47% (95% confidence interval [CI]: 40-54), ranging from 6% to 90%. There was significant heterogeneity among the 35 studies (χ2 = 840.37; p < 0.001; I2 = 95.95%). The results of the subgroup analysis based on characterization of patients indicated that pooled prevalence of class 1 integrons was 52% (95% CI: 41-63; n = 14 studies) and 43% (95% CI: 34-54; n = 19 studies) in hospitalized and community patients, respectively. The lowest and highest prevalence of antibiotic resistance was observed for imipenem and ampicillin, respectively. According to the results of Begg's and Egger's tests, we did not find significant publication bias both in the included studies and in the subgroup analysis. Conclusions: The results show the high prevalence of class 1 integrons and high level of antibiotic resistance in association with those among uropathogenic E. coli. Moreover, the prevalence of class 1 integrons in Asian countries, as well as hospital-acquired urinary tract infection (UTI), was higher than in other countries and community-acquired UTI.
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Affiliation(s)
- Mehrdad Halaji
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Clinical Research Development Unit of Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran
| | - Awat Feizi
- Department of Biostatistics and Epidemiology, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Arezoo Mirzaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hadi Sedigh Ebrahim-Saraie
- Razi Clinical Research Development Center, Razi Hospital, Guilan University of Medical Sciences, Rasht, Iran
| | - Amirhossein Fayyazi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Ashraf
- Clinical Research Development Unit of Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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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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Ouchar Mahamat O, Tidjani A, Lounnas M, Hide M, Benavides J, Somasse C, Ouedraogo AS, Sanou S, Carrière C, Bañuls AL, Jean-Pierre H, Dumont Y, Godreuil S. Fecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae in hospital and community settings in Chad. Antimicrob Resist Infect Control 2019; 8:169. [PMID: 31695911 PMCID: PMC6824111 DOI: 10.1186/s13756-019-0626-z] [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: 07/22/2019] [Accepted: 10/15/2019] [Indexed: 11/29/2022] Open
Abstract
Background Fecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) remains poorly documented in Africa. The objective of this study was to determine the prevalence of ESBL-PE fecal carriage in Chad. Methods In total, 200 fresh stool samples were collected from 100 healthy community volunteers and 100 hospitalized patients from January to March 2017. After screening using ESBL-selective agar plates and species identification by MALDI-TOF mass spectrometry, antibiotic susceptibility was tested using the disk diffusion method, and ESBL production confirmed with the double-disc synergy test. The different ESBL genes in potential ESBL-producing isolates were detected by PCR and double stranded DNA sequencing. Escherichia coli phylogenetic groups were determined using a PCR-based method. Results ESBL-PE fecal carriage prevalence was 44.5% (51% among hospitalized patients vs 38% among healthy volunteers; p < 0.05). ESBL-producing isolates were mostly Escherichia coli (64/89) and Klebsiella pneumoniae (16/89). PCR and sequencing showed that 98.8% (87/89) of ESBL-PE harbored blaCTX-M genes: blaCTX-M-15 in 94.25% (82/87) and blaCTX-M-14 in 5.75% (5/87). Phylogroup determination by quadruplex PCR indicated that ESBL-producing E. coli isolates belonged to group A (n = 17; 27%), C (n = 17; 27%), B2 (n = 9; 14%), B1 (n = 8; 13%), D (n = 8; 13%), E (n = 1; 1.6%), and F (n = 1; 1.6%). The ST131 clone was identified in 100% (9/9) of E. coli B2 strains. Conclusions The high fecal carriage rate of ESBL-PE associated with CTX-M-15 in hospital and community settings of Chad highlights the risk for resistance transmission between non-pathogenic and pathogenic bacteria.
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Affiliation(s)
- Oumar Ouchar Mahamat
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France.,Service de laboratoire Hôpital de la Mère et de l'Enfant, N'Djaména, Chad
| | | | - Manon Lounnas
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Mallorie Hide
- 2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Julio Benavides
- 57 Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Calèbe Somasse
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Abdoul-Salam Ouedraogo
- Service de bactériologie-virologie, Département des laboratoires, Centre Hospitalier Universitaire Souro Sanou, Bobo Dioulasso, Burkina Faso
| | - Soufiane Sanou
- Service de bactériologie-virologie, Département des laboratoires, Centre Hospitalier Universitaire Souro Sanou, Bobo Dioulasso, Burkina Faso
| | - Christian Carrière
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Anne-Laure Bañuls
- 2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France.,7Laboraoire Mixte International, DRISA, IRD, Montpellier, France
| | - Hélène Jean-Pierre
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Yann Dumont
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Sylvain Godreuil
- 1Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, France.,2MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France.,7Laboraoire Mixte International, DRISA, IRD, Montpellier, France
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Singh T, Das S, Ramachandran VG, Dar SA, Snehaa K, Saha R, Shah D. Spectrum of diarrhoeagenic Escherichia coli in paediatric population suffering from diarrhoea and as commensals in healthy children. Indian J Med Microbiol 2018; 35:204-210. [PMID: 28681807 DOI: 10.4103/ijmm.ijmm_16_21] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Diarrhoeagenic Escherichia coli (DEC) is associated with early death of children in developing countries and are being identified now as an important evolving pathogen. The objective of this study was to perform multiplex polymerase chain reaction (PCR) for simultaneous detection of six categories of DEC in two sets of PCR reactions using 11 virulent genes. MATERIALS AND METHODS During 1-year study period, forty isolates each from outpatient, inpatient and healthy groups were collected from children. E. coli was identified using conventional biochemical methods. DNA extraction was done using kit, and the extracted DNA was used as a template for multiplex PCR. RESULTS Virulent genes of DEC were detected in 106 (88.33%) samples. Overall, elt and est were detected in 8.33% and 30.83% of specimens; typical, atypical enteropathogenic E. coli and bfp were detected in 13.33%, 29.16% and 19.16% specimens; eagg was detected in 39.16% and east in 13.33% specimens and stx and hyla were isolated in 1.66% specimens each. While diffusely adherent E. coli and enteroinvasive E. coli genes were not isolated. CONCLUSION Multiplex PCR is a rapid method for the simultaneous detection of 11 virulent genes of DEC at a time and it will provide a platform in understanding the diarrheal diseases in a more improved manner.
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Affiliation(s)
- Taru Singh
- Department of Microbiology, UCMS, Guru Teg Bahadur Hospital, New Delhi, India
| | - Shukla Das
- Department of Microbiology, UCMS, Guru Teg Bahadur Hospital, New Delhi, India
| | - V G Ramachandran
- Department of Microbiology, UCMS, Guru Teg Bahadur Hospital, New Delhi, India
| | - Sajad Ahmad Dar
- Department of Microbiology, UCMS, Guru Teg Bahadur Hospital, New Delhi, India
| | - K Snehaa
- Department of Microbiology, UCMS, Guru Teg Bahadur Hospital, New Delhi, India
| | - Rumpa Saha
- Department of Microbiology, UCMS, Guru Teg Bahadur Hospital, New Delhi, India
| | - Dheeraj Shah
- Department of Paediatrics, UCMS, Guru Teg Bahadur Hospital, New Delhi, India
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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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Iranpour D, Hassanpour M, Ansari H, Tajbakhsh S, Khamisipour G, Najafi A. Phylogenetic groups of Escherichia coli strains from patients with urinary tract infection in Iran based on the new Clermont phylotyping method. BIOMED RESEARCH INTERNATIONAL 2015; 2015:846219. [PMID: 25692147 PMCID: PMC4322292 DOI: 10.1155/2015/846219] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 12/17/2014] [Accepted: 12/22/2014] [Indexed: 01/30/2023]
Abstract
OBJECTIVES In 2013, Clermont classified E. coli strains into eight phylogenetic groups using a new quadruplex PCR method. The aims of this study were to identify the phylogenetic groups of E. coli based on this method and to assess their antibiotic resistance patterns in Bushehr, Iran. METHODS In this cross-sectional study, 140 E. coli isolates were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was performed by disk diffusion method. RESULTS Phylogenetic group B2 was most predominant (39.3%), followed by unknown (27.1%), E (9.3%), C and clade I (each 6.4%), B1 (5%), F and D (each 2.9%), and A (0.7%). The most common antibiotic resistance was related to amoxicillin (82.1%) and the least to meropenem (0.7%). 82.14% of isolates were multiple drug resistant (MDR). Antibiotic resistance was mainly detected in group B2 (50%). CONCLUSIONS Our findings showed the high prevalence of MDR E. coli isolates with dominance of group B2. About 25% of E. coli isolates belong to the newly described phylogroups C, E, F, and clade I. Such studies need to be done also in other regions to provide greater understanding of the antibiotic resistance pattern and the prevalences of different phylogenetic groups.
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Affiliation(s)
- Darioush Iranpour
- Department of Internal Medicine, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Mojtaba Hassanpour
- Department of Genetics, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Hossein Ansari
- Department of Genetics, Islamic Azad University, Marvdasht Branch, Marvdasht, Iran
| | - Saeed Tajbakhsh
- Department of Microbiology and Parasitology, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Gholamreza Khamisipour
- Department of Hematology, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
| | - Akram Najafi
- Department of Marine Microbiology, The Persian Gulf Marine Biotechnology Medicine Research Center, Bushehr University of Medical Sciences, Bushehr 7514633196, Iran
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Integrons in uropathogenic Escherichia coli and their relationship with phylogeny and virulence. Microb Pathog 2014; 77:73-7. [DOI: 10.1016/j.micpath.2014.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/21/2014] [Accepted: 11/03/2014] [Indexed: 11/20/2022]
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Differences in extended-spectrum beta-lactamase producing Escherichia coli virulence factor genes in the Baltic Sea region. BIOMED RESEARCH INTERNATIONAL 2014; 2014:427254. [PMID: 25250320 PMCID: PMC4164513 DOI: 10.1155/2014/427254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/19/2014] [Indexed: 11/26/2022]
Abstract
The aim of this study was to compare the prevalence of different virulence factor (VF) genes in extended-spectrum beta-lactamase (ESBL) producing Escherichia coli strains isolated from the Baltic Sea region. A total of 432 strains of phenotypically ESBL positive E. coli were collected from 20 institutions located in Estonia, Latvia, Lithuania, and the region of St. Petersburg in Russia from January to May 2012 and analyzed for phylogenetic group and prevalence of 23 VF genes. The strains were collected from clinical material (urine, blood, wound, and respiratory tract). Bacterial isolates were compared according to phylogenetic group, clinical material, and geographical origin. Most of the VF genes were concentrated within phylogenetic group B2 and/or D. When comparing strains isolated from different countries, it was found that strains originating from Estonia and Latvia belonged mainly to group B2 and strains from Lithuania and Russia mainly to groups B2 and D. The P-fimbrial adhesin gene papEF was more prevalent in Russian strains, colicin gene cvaC in Lithuanian strains, and capsular gene kpsMTII in Latvian strains; serum resistant gene traT was less prevalent in Estonian strains. The regional differences of VF genes remained statistically significant after taking into account the phylogenetic distribution in the countries.
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