scholarly journals Phylogenetic Analysis and Antimicrobial Resistance Profiles of Escherichia coli Strains Isolated from UTI-Suspected Patients

2020 ◽  
Author(s):  
Reza RANJBAR ◽  
Sedigheh NAZARI ◽  
Omid FARAHANI
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Nalidixic Acid ◽  
Phylogenetic Groups ◽  
Phylogenetic Characterization ◽  
E Coli ◽  
Effective Selection ◽  
Resistance Patterns ◽  
Pcr Method ◽  
Tract Infections

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.

scholarly journals 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

2020 ◽  
Vol 44 (1) ◽  
pp. 27-33 ◽  
Author(s):  
Shiva Mirkalantari ◽  
Faramarz Masjedian ◽  
Gholamreza Irajian ◽  
Emmanuel Edwar Siddig ◽  
Azam Fattahi
Keyword(s):  
Escherichia Coli ◽  
Resistance Pattern ◽  
Phylogenetic Groups ◽  
Accurate Identification ◽  
E Coli ◽  
Resistance Patterns ◽  
Phylogenetic Grouping ◽  
Pcr Method ◽  
Tract Infections

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.

scholarly journals Antimicrobial Resistance Patterns and ESBL of Uropathogens Isolated from Adult Females in Najran Region of Saudi Arabia

2021 ◽  
Vol 11 (3) ◽  
pp. 650-658
Author(s):  
Mohammed Yahia Alasmary
Keyword(s):  
Escherichia Coli ◽  
Saudi Arabia ◽  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Urine Samples ◽  
Klebsiella Species ◽  
E Coli ◽  
Government Hospitals ◽  
Resistance Patterns ◽  
Tract Infections

Background: To explore the prevalence of urinary tract infections (UTIs) among female patients in the Najran region of Saudi Arabia and determine their antimicrobial resistance pattern. Methods: This study was conducted on 136 urine samples collected from outpatient departments (OPDs) of the different government hospitals in the Najran region of Saudi Arabia. Over one year, the results of susceptibility testing reports of outpatient midstream urine samples from three government hospitals were prospectively evaluated. Results: Of 136 urine samples, only 123 (90.45%) were found to show significant growth for UTIs, from which 23 different uropathogens were identified. Escherichia coli (58.5%) was the most commonly isolated organism, followed by Klebsiella pneumoniae (8.1%). The isolated microorganism showed increased resistance patterns from 3.3% to 62.6%, with an overall resistance of 27.19%. Meropenem was the most effective antimicrobial, followed by amikacin and ertapenem (0.47%, 0.91%, and 1.5% resistance, respectively). At the same time, ampicillin and cephazolin were the least (62.6% and 59.5% resistance, respectively) effective. Overall, eleven (8.94%) uropathogens isolates were ESBLs, among which there were eight (6.5%) Escherichia coli, one (0.81%) Klebsiella pneumoniae, one (0.81%) Klebsiella oxytoca, and one (0.81%) Citrobacter amalonaticus. Conclusions: E. coli remains the most commonly isolated causative uropathogens, followed by Klebsiella species. The prevalence of pathogenic E. coli and Klebsiella species underscores the importance of developing cost-effective, precise, and rapid identification systems to minimize public exposure to uropathogens. Antibiotic susceptibility data revealed that most of the isolates were resistant to the majority of the antibiotics. The patients with UTIs in the Najran region of Saudi Arabia are at a high risk of antibiotic resistance, leading to significant problems in outpatient department (OPD) treatment outcomes and raising the alarm for the physician to change their empiric treatment.

scholarly journals Phylogenetic groups and antimicrobial susceptibility patterns of uropathogenic Escherichia coli clinical isolates from patients at Mulago National Referral Hospital, Kampala, Uganda

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1828 ◽  
Author(s):  
Paul Katongole ◽  
Daniel Bulwadda Kisawuzi ◽  
Henry Kyobe Bbosa ◽  
David Patrick Kateete ◽  
Christine Florence Najjuka
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Susceptibility ◽  
Phylogenetic Group ◽  
Diffusion Method ◽  
Clinical Microbiology Laboratory ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Pcr Method ◽  
Tract Infections ◽  
Susceptibility Patterns

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.

scholarly journals Molecular Characterization of Uropathogenic Escherichia coli Reveals Emergence of Drug Resistant O15, O22 and O25 Serogroups

Medicina ◽  
2019 ◽  
Vol 55 (11) ◽  
pp. 733 ◽  
Author(s):  
Ruta Prakapaite ◽  
Frederic Saab ◽  
Rita Planciuniene ◽  
Vidmantas Petraitis ◽  
Thomas J. Walsh ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Asymptomatic Bacteriuria ◽  
Empirical Therapy ◽  
Uropathogenic Escherichia Coli ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Tract Infections ◽  
Resistance Rates

Background and Objectives: Uropathogenic Escherichia coli (UPEC) are common pathogens causing urinary tract infections (UTIs). We aimed to investigate the relationship among clinical manifestation, serogroups, phylogenetic groups, and antimicrobial resistance among UPEC. Materials and Methods: One-hundred Escherichia coli isolates recovered from urine and ureteral scrapings were used for the study. The prevalence of antimicrobial resistance was determined by using European Committee on Antimicrobial Susceptibility Testing (EUCAST) recommendations. E. coli serogroups associated with UTI, as well as phylogenetic diversity were analyzed using multiplex PCR reactions. Results: Eighty-seven strains (87%) were isolated from females, while 13 (13%) from males. A high frequency of resistance to cephalosporins (43%) and fluoroquinolones (31%) was observed. Among UTI-associated serogroups O15 (32.8%), O22 (23.4%), and O25 (15.6%) were dominant and demonstrated elevated resistance rates. The E. coli phylogenetic group B2 was most common. These observations extended to pregnant patients with asymptomatic bacteriuria. Conclusions: Due to high rates of resistance, strategies using empirical therapy of second-generation cephalosporins and fluoroquinolones should be reconsidered in this population.

scholarly journals Detection of Phylogenetic Groups and Drug Resistance Genes of Escherichia coli Causing Urinary Tract Infection in Southwest Iran

2021 ◽  
Vol 14 (2) ◽  
Author(s):  
Mostafa Boroumand Boroumand ◽  
Mohsen Naghmachi ◽  
Mohammad Amin Ghatee
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Phylogenetic Group ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Pcr Method ◽  
Tract Infections

Background: Many bacteria can cause urinary tract infections (UTIs), among which Escherichia coli is the most common causative agent. E. 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.

scholarly journals Molecular Characterisation of Uropathogenic Escherichia coli Reveals Emergence of Drug Resistant O15, O22, and O25 Serogroups

2019 ◽  
Author(s):  
Ruta Prakapaite ◽  
Frederic Saab ◽  
Rita Planciuniene ◽  
Vidmantas Petraitis ◽  
Thomas J. Walsh ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Asymptomatic Bacteriuria ◽  
Empirical Therapy ◽  
Uropathogenic Escherichia Coli ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Tract Infections ◽  
Resistance Rates ◽  
The Relationship

Abstract Background Uropathogenic Escherichia coli (UPEC) are common pathogens causing urinary tract infections (UTIs). We aimed to investigate the relationship among clinical manifestation, serogroups, phylogenetic groups, and antimicrobial resistance among UPEC. Methods One-hundred Escherichia coli isolates recovered from urine and ureteral scrapings were used for the study. The prevalence of antimicrobial resistance was determined by using EUCAST recommendations. E. coli serogroups associated with UTI, as well as phylogenetic diversity was analysed using multiplex PCR reactions. Results Eighty-seven strains (87%) were isolated from females, while 13 (13%) from males. A high frequency of resistance to cephalosporins (43%) and fluoroquinolones (31%) was observed. Among UTI-associated serogroups, O15 (32.8%), O22 (23.4%), and O25 (15.6%) were dominant and demonstrated elevated resistance rates. The E. coli phylogenetic group B2 was most common. These observations extended to pregnant patients with asymptomatic bacteriuria. Conclusions Due to high rates of resistance, strategies using empirical therapy of second-generation cephalosporins and fluoroquinolones for treatment of UPEC infections should be reconsidered.

scholarly journals Prevalence of Resistance to Quinolone and Fluoroquinolone Antibiotics and Screening of qnr Genes Among Escherichia coli Isolates From Urinary Tract Infection

2017 ◽  
Vol 5 (4) ◽  
pp. 100-105 ◽  
Author(s):  
Mohadese Amiri ◽  
Maziar Jajarmi ◽  
Reza Ghanbarpour
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Nalidixic Acid ◽  
Diffusion Method ◽  
Biochemical Tests ◽  
Phylogenetic Groups ◽  
Disk Diffusion Method ◽  
E Coli ◽  
Fluoroquinolone Antibiotics ◽  
Tract Infections

Background: Antibiotic resistance (AR) is an important challenge in prevention, treatment and control of infectious diseases and is a public health threat for human. Escherichia coli strains are the major causes of urinary tract infections (UTIs). Objective: This research aimed to determine prevalence of resistance to quinolone and fluoroquinolone antibiotics and screen qnr genes among E. coli isolates from UTIs. Materials and Methods: A total of 105 E. coli isolates were obtained from UTI cases in Bojnord city (northeast of Iran) and confirmed by biochemical tests. All strains were studied to determine their resistance to 3 antibiotics including ciprofloxacin, nalidixic acid, and levofloxacin via disk diffusion method. Moreover, the frequency of qnrA, qnrB and qnrS genes and phylogroups was studied by conventional Polymerase chain reaction (PCR). Results: In this study, prevalence of phenotypic AR to ciprofloxacin, nalidixic acid and levofloxacin was 47.6%, 44.8% and 38.1%, respectively. Three isolates were positive for qnrS and 1 isolate was positive for qnrA. Seven phylogenetic groups were also identified as follows: 18% A0, 6.7% A1, 7.6% B1, 1.9% B22, 23.8% B23, 15.3% D1 and 26.7% D2. Conclusion: Prevalence of qnr genes was very low; thus, other types of qnr and plasmid-mediated quinolone resistance genes were probably responsible for the resistance. Phenotypic AR to the 3 antibiotics was found in approximately half of E. coli strains. It is strongly recommended that antibiogram tests should be done before prescribing the ciprofloxacin, nalidixic acid and levofloxacin for UTIs.

scholarly journals Antibiotic resistance pattern and phylogenetic groups of the uropathogenic Escherichia coli isolates from urinary tract infections in Hamedan, west of Iran

2020 ◽  
Author(s):  
Somayeh Bakhtiari ◽  
Hassan Mahmoudi ◽  
Sara Khosravi Seftjani ◽  
Mohammad Ali Amirzargar ◽  
Sima Ghiasvand ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Nalidixic Acid ◽  
Urinary Tract Infections ◽  
Diffusion Method ◽  
Phylogenetic Groups ◽  
E Coli ◽  
Group A ◽  
Tract Infections

Background and Objectives: Escherichia coli is the most common causative agent of urinary tract infections (UTIs) in 90-80% of patients in all age groups. Phylogenetic groups of these bacteria are variable and the most known groups are A, B1, B2 and D. The present study aimed to evaluate the phylogenetic groups of E. coli samples obtained from UTIs and their relation with antibiotic resistance patterns of isolates. Materials and Methods: In this study 113 E. coli isolates were isolated from distinct patients with UTIs referred to Hamadan hospitals. After biochemical and molecular identification of the isolates, typing and phylogenetic grouping of E. coli strains were performed using multiplex PCR targeting chu, yjaA and TSPE4.C2 genes. The anti-microbial susceptibility of the isolates to amikacin, ampicillin, trimethoprim-sulfamethoxazole, amoxicillin/clavulanic acid, ciprofloxacin, cefotaxime, imipenem, aztreonam, gentamicin, meropenem, nitrofurantoin, nalidixic acid and cefazolin was determined using disk diffusion method. Results: Of 113 isolates, 50 (44.2%), 35 (31%), 23 (20.4%) and 5 (4.4%) of samples belonged to group B2, group D, group A and group B1 phylogenetic groups respectively. All isolates were susceptible to meropenem, imipenem (100%), followed by amikacin (99.1%). The highest resistance rates were observed against ampicillin (74.3%) and nalidixic acid (70.8%). Correlation between phylogenetic groups and antibiotic susceptibilities was significant only with co-amoxiclav (P = 0.006), which had the highest resistance in phylogenetic group A. Conclusion: Prevalence of different phylogroup and resistance associated with them in E. coli samples could be variable in each region. Therefore, investigating of these items in E. coli infections, could be more helpful in selecting the appropriate antibiotic treatment and epidemiological studies.

scholarly journals Antimicrobial resistance and plasmid profiles of urinary Escherichia coli isolates from Jordanian patients

2004 ◽  
Vol 10 (3) ◽  
pp. 322-328
Author(s):  
A. A. Shehabi ◽  
A. M. Mahafzah ◽  
K. Z. Al Khalili
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Nalidixic Acid ◽  
Uropathogenic Escherichia Coli ◽  
University Hospital ◽  
Multiple Antibiotic Resistance ◽  
E Coli ◽  
Plasmid Profiles ◽  
Resistance Patterns

Weinvestigated antimicrobial resistance patterns and plasmid profiles of uropathogenic Escherichia coli isolates from inpatients and outpatients at Jordan University Hospital in 2000 and 2001. E. coli accounted for 32.4% and 37.4% of all isolates respectively. The lowest susceptibility was for ampicillin [11%], cotrimoxazole [23%] and tetracycline [26%]. The relative incidence of resistant isolates of E. coli to nalidixic acid, gentamicin, norfloxacin, cefuroxime and nitrofurantoin was significantly greater for inpatients than for outpatients [P< 0.05]. A large, transferable R-plasmid of 28 kb was found in most E. coli isolates [67%] that were resistant to at least ampicillin, cotrimoxazole and tetracycline. This R-plasmid reservoir may contribute to the spread of multiple antibiotic resistance in our Region

scholarly journals Antimicrobial Resistance of Uropathogenic Escherichia coli from Elderly Patients at a General Hospital, Argentina

2018 ◽  
Vol 10 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Gastón Delpech ◽  
Natalia García Allende ◽  
Sabina Lissarrague ◽  
Mónica Sparo
Keyword(s):  
Risk Factors ◽  
Escherichia Coli ◽  
Urinary Tract ◽  
Antimicrobial Resistance ◽  
Elderly Patients ◽  
Nalidixic Acid ◽  
Urinary Tract Infections ◽  
E Coli ◽  
Amoxicillin Clavulanate ◽  
Tract Infections

Background:Urinary Tract Infection (UTI) is a common cause of morbidity and mortality in older adults.Objective:To investigate antimicrobial resistance of uropathogenicEscherichia colifrom elderly patients in a General Hospital, Argentina.Method:During the period July 2011-July 2015, patients over 70 years old with urinary tract infections, without urinary catheters and with no antimicrobial therapy the previous week before sampling, were included. Phenotypic characterization was carried out.In vitroqualitative and quantitative antimicrobial resistances were investigated. Antimicrobials assayed: ampicillin, amoxicillin-clavulanate, cefazolin, cefuroxime, cefoxitin, cefotaxime, ceftazidime, cefepime, imipenem, ertapenem, gentamicin, nalidixic acid, ciprofloxacin, trimethoprim-sulfamethoxazole (TMS) and nitrofurantoin. Patients’ medical records were produced, and risk factors were analyzed by multivariate analysis.Results:768 bacterial isolates were identified asE. coli. Resistances to ampicillin (80.5%), nalidixic acid (61.7%), ciprofloxacin (42.8%), TMS (37.6%), amoxicillin-clavulanate (28.6%), cefazolin (21.6%), cefuroxime (20.7%), gentamicin (13.8%), cefotaxime (9.7%), ceftazidime (9.7%), cefepime (8.4%), cefoxitin (3.1%) and nitrofurantoin (2.3%) were observed. Resistance to carbapenems was not expressed. Production of extended spectrum β-lactamases was detected (7.6%) in community acquired (96%) and healthcare associated (4%) isolates. The independent risk factors for urinary infections produced by multi-resistantE. coliwere: diabetes mellitus, recurrent infections, hospitalization during the last year and exposure to β-lactams in the last 3 months.Conclusion:A high prevalence of resistance to β-lactams and to other antimicrobials was observed. Detection of antimicrobial multi-resistant isolates highlights the need of antimicrobial resistance surveillance in elderly patients with urinary tract infections.

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