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

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.

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P1023 Clonality and presence of antibiotic resistance genes of E. coli isolated in recurrent urinary tract infections

International Journal of Antimicrobial Agents ◽

10.1016/s0924-8579(07)70864-6 ◽

2007 ◽

Vol 29 ◽

pp. S274

Author(s):

K. Truusalu ◽

E. Sepp ◽

J. Shchepetova ◽

S. Koljalg ◽

I. Vainumäe ◽

...

Keyword(s):

Antibiotic Resistance ◽

Urinary Tract ◽

Urinary Tract Infections ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

E Coli ◽

Recurrent Urinary Tract Infections ◽

Tract Infections

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

F1000Research ◽

10.12688/f1000research.20930.1 ◽

2019 ◽

Vol 8 ◽

pp. 1828 ◽

Cited By ~ 1

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.

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Uropathogenic Escherichia coli in the Urine Samples of Iranian Dogs: Antimicrobial Resistance Pattern and Distribution of Antibiotic Resistance Genes

BioMed Research International ◽

10.1155/2017/4180490 ◽

2017 ◽

Vol 2017 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Amirhossein Yousefi ◽

Saam Torkan

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Urine Samples ◽

Disk Diffusion ◽

Resistance Pattern ◽

E Coli ◽

Tract Infections

Resistant uropathogenic Escherichia coli is the most common cause of urinary tract infections in dogs. The present research was done to study the prevalence rate and antimicrobial resistance properties of UPEC strains isolated from healthy dogs and those which suffered from UTIs. Four-hundred and fifty urine samples were collected and cultured. E. coli-positive strains were subjected to disk diffusion and PCR methods. Two-hundred out of 450 urine samples (44.4%) were positive for E. coli. Prevalence of E. coli in healthy and infected dogs was 28% and 65%, respectively. Female had the higher prevalence of E. coli (P=0.039). Marked seasonality was also observed (P=0.024). UPEC strains had the highest levels of resistance against gentamicin (95%), ampicillin (85%), amikacin (70%), amoxicillin (65%), and sulfamethoxazole-trimethoprim (65%). We found that 21.50% of UPEC strains had simultaneously resistance against more than 10 antibiotics. Aac(3)-IV (77%), CITM (52.5%), tetA (46.5%), and sul1 (40%) were the most commonly detected antibiotic resistance genes. Findings showed considerable levels of antimicrobial resistance among UPEC strains of Iranian dogs. Rapid identification of infected dogs and their treatment based on the results of disk diffusion can control the risk of UPEC strains.

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Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis

Microbiology ◽

10.1099/mic.0.27499-0 ◽

2005 ◽

Vol 151 (6) ◽

pp. 2097-2110 ◽

Cited By ~ 227

Author(s):

Kylie E. Rodriguez-Siek ◽

Catherine W. Giddings ◽

Curt Doetkott ◽

Timothy J. Johnson ◽

Mohamed K. Fakhr ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract Infection ◽

Urinary Tract ◽

Virulence Genes ◽

Phylogenetic Group ◽

Human Beings ◽

Phylogenetic Groups ◽

E Coli ◽

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

Iranian Journal of Microbiology ◽

10.18502/ijm.v12i5.4598 ◽

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.

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Mechanisms of Resistance in Multiple-Antibiotic-Resistant Escherichia coli Strains of Human, Animal, and Food Origins

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.10.3996-4001.2004 ◽

2004 ◽

Vol 48 (10) ◽

pp. 3996-4001 ◽

Cited By ~ 269

Author(s):

Yolanda Sáenz ◽

Laura Briñas ◽

Elena Domínguez ◽

Joaquim Ruiz ◽

Myriam Zarazaga ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Amino Acid ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Mechanisms Of Resistance ◽

Antibiotic Resistant ◽

E Coli ◽

Class 1 ◽

Human Animal

ABSTRACT Seventeen multiple-antibiotic-resistant nonpathogenic Escherichia coli strains of human, animal, and food origins showed a wide variety of antibiotic resistance genes, many of them carried by class 1 and class 2 integrons. Amino acid changes in MarR and mutations in marO were identified for 15 and 14 E. coli strains, respectively.

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Antibiotic-resistant Escherichia coli and Salmonella spp. associated with dairy cattle and farm environment having public health significance

Veterinary World ◽

10.14202/vetworld.2019.984-993 ◽

2019 ◽

Vol 12 (7) ◽

pp. 984-993 ◽

Cited By ~ 14

Author(s):

Md. Abdus Sobur ◽

Abdullah Al Momen Sabuj ◽

Ripon Sarker ◽

A. M. M. Taufiqur Rahman ◽

S. M. Lutful Kabir ◽

...

Keyword(s):

Public Health ◽

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

One Health ◽

Dairy Farm ◽

Antibiotic Resistance Genes ◽

Salmonella Spp ◽

Antibiotic Resistant ◽

E Coli

Aim: The present study was carried out to determine load of total bacteria, Escherichia coli and Salmonella spp. in dairy farm and its environmental components. In addition, the antibiogram profile of the isolated bacteria having public health impact was also determined along with identification of virulence and resistance genes by polymerase chain reaction (PCR) under a one-health approach. Materials and Methods: A total of 240 samples of six types (cow dung - 15, milk - 10, milkers' hand wash - 10, soil - 10 water - 5, and vegetables - 10) were collected from four dairy farms. For enumeration, the samples were cultured onto plate count agar, eosin methylene blue, and xylose-lysine deoxycholate agar and the isolation and identification of the E. coli and Salmonella spp. were performed based on morphology, cultural, staining, and biochemical properties followed by PCR. The pathogenic strains of E. coli stx1, stx2, and rfbO157 were also identified through PCR. The isolates were subjected to antimicrobial susceptibility test against 12 commonly used antibiotics by disk diffusion method. Detection of antibiotic resistance genes ereA, tetA, tetB, and SHV were performed by PCR. Results: The mean total bacterial count, E. coli and Salmonella spp. count in the samples ranged from 4.54±0.05 to 8.65±0.06, 3.62±0.07 to 7.04±0.48, and 2.52±0.08 to 5.87±0.05 log colony-forming unit/g or ml, respectively. Out of 240 samples, 180 (75%) isolates of E. coli and 136 (56.67%) isolates of Salmonella spp. were recovered through cultural and molecular tests. Among the 180 E. coli isolates, 47 (26.11%) were found positive for the presence of all the three virulent genes, of which stx1 was the most prevalent (13.33%). Only three isolates were identified as enterohemorrhagic E. coli. Antibiotic sensitivity test revealed that both E. coli and Salmonella spp. were found highly resistant to azithromycin, tetracycline, erythromycin, oxytetracycline, and ertapenem and susceptible to gentamycin, ciprofloxacin, and imipenem. Among the four antibiotic resistance genes, the most observable was tetA (80.51-84.74%) in E. coli and Salmonella spp. and SHV genes were the lowest one (22.06-25%). Conclusion: Dairy farm and their environmental components carry antibiotic-resistant pathogenic E. coli and Salmonella spp. that are potential threat for human health which requires a one-health approach to combat the threat.

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Evaluation of Immunocompetent Urinary Tract Infected Balb/C Mouse Model For the Study of Antibiotic Resistance Development Using Escherichia Coli CFT073 Infection

Antibiotics ◽

10.3390/antibiotics8040170 ◽

2019 ◽

Vol 8 (4) ◽

pp. 170 ◽

Cited By ~ 1

Author(s):

Ashok Chockalingam ◽

Sharron Stewart ◽

Lin Xu ◽

Adarsh Gandhi ◽

Murali K. Matta ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Urinary Tract ◽

Bladder Tissue ◽

Resistance Development ◽

Once Daily ◽

E Coli ◽

Low Levels ◽

Tract Infections

Urinary tract infections (UTI) are common worldwide and are becoming increasingly difficult to treat because of the development of antibiotic resistance. Immunocompetent murine models of human UTI have been used to study pathogenesis and treatment but not for investigating resistance development after treatment with antibiotics. In this study, intravesical inoculation of uropathogenic Escherichia coli CFT073 in immunocompetent Balb/c mice was used as a model of human UTI. The value of the model in investigating antibiotic exposure on in vivo emergence of antibiotic resistance was examined. Experimentally infected mice were treated with 20 or 200 mg/kg ampicillin, 5 or 50 mg/kg ciprofloxacin, or 100 or 1000 mg/kg of fosfomycin. Ampicillin and ciprofloxacin were given twice daily at 8 h intervals, and fosfomycin was given once daily. Antibiotic treatment began 24 h after bacterial inoculation and ended after 72 h following the initial treatment. Although minimum inhibitory concentrations (MIC) for the experimental strain of E. coli were exceeded at peak concentrations in tissues and consistently in urine, low levels of bacteria persisted in tissues in all experiments. E. coli from bladder tissue, kidney, and urine grew on plates containing 1× MIC of antibiotic, but none grew at 3× MIC. This model is not suitable for studying emergent resistance but might serve to examine bacterial persistence.

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F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli

mSphere ◽

10.1128/msphere.00709-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Craig Stephens ◽

Tyler Arismendi ◽

Megan Wright ◽

Austin Hartman ◽

Andres Gonzalez ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Transposable Elements ◽

Dna Sequencing ◽

Resistance Genes ◽

Bacterial Pathogens ◽

Acquired Resistance ◽

Antibiotic Resistance Genes ◽

Content Type ◽

E Coli

ABSTRACT The evolution and propagation of antibiotic resistance by bacterial pathogens are significant threats to global public health. Contemporary DNA sequencing tools were applied here to gain insight into carriage of antibiotic resistance genes in Escherichia coli, a ubiquitous commensal bacterium in the gut microbiome in humans and many animals, and a common pathogen. Draft genome sequences generated for a collection of 101 E. coli strains isolated from healthy undergraduate students showed that horizontally acquired antibiotic resistance genes accounted for most resistance phenotypes, the primary exception being resistance to quinolones due to chromosomal mutations. A subset of 29 diverse isolates carrying acquired resistance genes and 21 control isolates lacking such genes were further subjected to long-read DNA sequencing to enable complete or nearly complete genome assembly. Acquired resistance genes primarily resided on F plasmids (101/153 [67%]), with smaller numbers on chromosomes (30/153 [20%]), IncI complex plasmids (15/153 [10%]), and small mobilizable plasmids (5/153 [3%]). Nearly all resistance genes were found in the context of known transposable elements. Very few structurally conserved plasmids with antibiotic resistance genes were identified, with the exception of an ∼90-kb F plasmid in sequence type 1193 (ST1193) isolates that appears to serve as a platform for resistance genes and may have virulence-related functions as well. Carriage of antibiotic resistance genes on transposable elements and mobile plasmids in commensal E. coli renders the resistome highly dynamic. IMPORTANCE Rising antibiotic resistance in human-associated bacterial pathogens is a serious threat to our ability to treat many infectious diseases. It is critical to understand how acquired resistance genes move in and through bacteria associated with humans, particularly for species such as Escherichia coli that are very common in the human gut but can also be dangerous pathogens. This work combined two distinct DNA sequencing approaches to allow us to explore the genomes of E. coli from college students to show that the antibiotic resistance genes these bacteria have acquired are usually carried on a specific type of plasmid that is naturally transferrable to other E. coli, and likely to other related bacteria.

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Characterization of Antibiotic Resistance E. Coli and Antibiotic Resistance Genes in Aquatic Environment of Taihu Lake, China

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.295-298.630 ◽

2013 ◽

Vol 295-298 ◽

pp. 630-634 ◽

Cited By ~ 1

Author(s):

Ni Ni Han ◽

Song He Zhang ◽

Pei Fang Wang ◽

Chao Wang

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Surface Water ◽

Resistance Genes ◽

Taihu Lake ◽

Antibiotic Resistance Genes ◽

Antibiotic Resistant ◽

E Coli ◽

Realtime Pcr

The aims of this study are to evaluate multiple antibiotic resistant Escherichia coli isolated from surface water and to investigate the presence and distribution antibiotic resistance genes (ARGs) in sediments of Taihu Lake. The results show that the presentence of four ARGs concentrations in the sediments of the lake was in sequence: strB>qnrB>strA>qnrS, as determined by realtime-PCR technique. The southwest and east areas of Taihu Lake were polluted seriously than other areas from all kinds of antibiotics. The screening Escherichia coli had a higher resistance to streptomycin, tetracycline and ampicillin than other four antibiotics, and had a lowest resistance to levofloxacin.

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