scholarly journals Genomic Characterization of Multidrug-Resistant Escherichia coli BH100 Sub-strains

2021 ◽  
Vol 11 ◽  
Author(s):  
Rodrigo Carvalho ◽  
Flavia Aburjaile ◽  
Marcus Canario ◽  
Andréa M. A. Nascimento ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
E Coli ◽  
Brazilian Woman ◽  
Genomic Characterization

The rapid emergence of multidrug-resistant (MDR) bacteria is a global health problem. Mobile genetic elements like conjugative plasmids, transposons, and integrons are the major players in spreading resistance genes in uropathogenic Escherichia coli (UPEC) pathotype. The E. coli BH100 strain was isolated from the urinary tract of a Brazilian woman in 1974. This strain presents two plasmids carrying MDR cassettes, pBH100, and pAp, with conjugative and mobilization properties, respectively. However, its transposable elements have not been characterized. In this study, we attempted to unravel the factors involved in the mobilization of virulence and drug-resistance genes by assessing genomic rearrangements in four BH100 sub-strains (BH100 MG2014, BH100 MG2017, BH100L MG2017, and BH100N MG2017). Therefore, the complete genomes of the BH100 sub-strains were achieved through Next Generation Sequencing and submitted to comparative genomic analyses. Our data shows recombination events between the two plasmids in the sub-strain BH100 MG2017 and between pBH100 and the chromosome in BH100L MG2017. In both cases, IS3 and IS21 elements were detected upstream of Tn21 family transposons associated with MDR genes at the recombined region. These results integrated with Genomic island analysis suggest pBH100 might be involved in the spreading of drug resistance through the formation of resistance islands. Regarding pathogenicity, our results reveal that BH100 strain is closely related to UPEC strains and contains many IS3 and IS21-transposase-enriched genomic islands associated with virulence. This study concludes that those IS elements are vital for the evolution and adaptation of BH100 strain.

scholarly journals An Epidemiological Study of Drug Resistance and Resistance Genes in Bovine Escherichia coli Isolates in Heilongjiang Province of China

2018 ◽  
Vol 46 (1) ◽  
pp. 9
Author(s):  
Jia-San Zheng ◽  
Ting-Ting Zhu ◽  
Yun Liu ◽  
Ting Liu ◽  
Yan-Qing Li ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Diffusion Method ◽  
Heilongjiang Province ◽  
Antibacterial Drugs ◽  
Resistance Phenotype ◽  
E Coli

Background: To explore the epidemiology of bovine multidrug-resistant Escherichia coli isolates and resistance genes in Heilongjiang province of China. This study examined the prevalence of genes in bovine E. coli isolates, which confer resistance to antibiotics that are commonly used in the clinic, in regions of Baiquan, Shangzhi, and Songbei of Harbin. The purpose of the study was to investigate the epidemiology of the main resistance genes of bovine E. coli isolates in clinical veterinary medicine, and to provide a theoretical basis for preventing the spread of drug-resistant bacteria, as well as for rational drug use.Materials, Methods & Results: The sensitivity of 105 isolates to 22 antibiotics was determined using the KirbyBauer disk diffusion method, and the distribution of 19 kinds of common drug resistance genes was investigated using Polymerase Chain Reaction. The results showed that the resistance rate to nine antibiotics was over 50%, including rifampin (84.76%), ampicillin (73.58%), tetracycline (69.52%), and sulfisoxazole (59.05%). In total, 105 strains of bovine E. coli presented 21 spectra of drug resistance, including eight strains (7.62%, 8/105) that were resistant to one antibiotic and four strains (3.81%, 4/105) that were resistant to 21 antibiotics. The resistance gene detection results showed that the streptomycin-resistance gene strA was found in 73 isolates, accounting for 69.52% of the isolates, followed by the sulfanilamide-resistance genes sul3/sul2 and the aminoglycoside-resistance gene aphA, which accounted for 57.14%, 51.43%, and 50.48%, respectively, of the isolates.Discussion: This study revealed serious drug resistance of bovine E. coli isolates in some areas of Heilongjiang province. Of 105 E. coli isolates, more than 50% were resistant to the following antibacterial drugs: rifampicin, ampicillin, tetracycline, sulfisoxazole, and cephalothin. The isolates were the most sensitive to amikacin, with a sensitivity of 84.76%, followed by sensitivity to ofloxacin, ciprofloxacin, norfloxacin, cefoxitin, and tobramycin. Drug sensitivity tests showed that the drug resistance spectra of the bovine E. coli isolates was different in different regions, indicating that there were multidrug-resistant bovine E. coli isolates in different regions of Heilongjiang province, and that drug resistance differed among different regions. This may be due to prolonged use or overuse of antibiotics in a particular locality. Additionally, because of different management modes of livestock farms, the application of antimicrobial drugs in some farms may have imposed selective pressure on the intestinal flora including E. coli, resulting in the horizontal transmission of drug resistance among the bacteria. The study found that some strains had a resistance phenotype, but no resistance gene, while some had a resistance gene without expressing a resistance phenotype, which is consistent with relevant reports in the literature. This may be related to the same genotype corresponding to different resistance phenotypes, or different levels of gene expression, or different drug metabolic rates. In our study, some strains with certain drug resistance genes were sensitive to the corresponding drug, which may be due to mutations of drug-resistance genes, the loss of a strains resistance phenotype, or the loss of gene function. These issues require further study. This study revealed serious drug resistance of bovine E. coli isolates in some areas of Heilongjiang province. Of 105 E. coli isolates, more than 50% were resistant to the following antibacterial drugs: rifampicin, ampicillin, tetracycline, sulfisoxazole, and cephalothin. The isolates were the most sensitive to amikacin, with a sensitivity of 84.76%, followed by sensitivity to ofloxacin, ciprofloxacin, norfloxacin, cefoxitin, and tobramycin.

scholarly journals Phenotypic and genotypic characterization of mcr-1-positive multidrug-resistant Escherichia coli ST93, ST117, ST156, ST10, and ST744 isolated from poultry in Poland

2021 ◽  
Author(s):  
Katarzyna Ćwiek ◽  
Anna Woźniak-Biel ◽  
Magdalena Karwańska ◽  
Magdalena Siedlecka ◽  
Christine Lammens ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Bacterial Resistance ◽  
Antimicrobial Agents ◽  
Genetic Relatedness ◽  
Multidrug Resistant ◽  
E Coli ◽  
Antimicrobial Resistance Genes

Abstract Background A plasmid-mediated mechanism of bacterial resistance to polymyxin is a serious threat to public health worldwide. The present study aimed to determine the occurrence of plasmid-mediated colistin resistance genes and to conduct the molecular characterization of mcr-positive Escherichia coli strains isolated from Polish poultry. Methods In this study, 318 E. coli strains were characterized by the prevalence of mcr1–mcr5 genes, antimicrobial susceptibility testing by minimal inhibitory concentration method, the presence of antimicrobial resistance genes was screened by PCR, and the biofilm formation ability was tested using the crystal violet staining method. Genetic relatedness of mcr-1-positive E. coli strains was evaluated by multilocus sequence typing method. Results Among the 318 E. coli isolates, 17 (5.35%) harbored the mcr-1 gene. High antimicrobial resistance rates were observed for ampicillin (100%), tetracycline (88.24%), and chloramphenicol (82.35%). All mcr-1-positive E. coli strains were multidrug-resistant, and as many as 88.24% of the isolates contained the blaTEM gene, tetracycline (tetA and tetB), and sulfonamide (sul1, sul2, and sul3) resistance genes. Additionally, 41.18% of multidrug-resistant, mcr-1-positive E. coli isolates were moderate biofilm producers, while the rest of the strains showed weak biofilm production. Nine different sequence types were identified, and the dominant ST was ST93 (29.41%), followed by ST117 (17.65%), ST156 (11.76%), ST 8979 (11.76%), ST744 (5.88%), and ST10 (5.88%). Moreover, the new ST was identified in this study. Conclusions Our results showed a low occurrence of mcr-1-positive E. coli strains isolated from Polish poultry; however, all the isolated strains were resistant to multiple antimicrobial agents and were able to form biofilms at low or medium level.

scholarly journals Molecular survey of mcr1 and mcr2 plasmid mediated colistin resistance genes in Escherichia coli isolates of animal origin in Iran

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Kayhan Ilbeigi ◽  
Mahdi Askari Badouei ◽  
Hossein Vaezi ◽  
Hassan Zaheri ◽  
Sina Aghasharif ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Companion Animals ◽  
Multidrug Resistant ◽  
Animal Origin ◽  
Colistin Resistance ◽  
E Coli ◽  
High Level ◽  
Farming Industry

Abstract Objectives The emergence of colistin-resistant Enterobacteriaceae from human and animal sources is one of the major public health concerns as colistin is the last-resort antibiotic for treating infections caused by multidrug-resistant Gram-negative bacteria. We aimed to determine the prevalence of the prototype widespread colistin resistance genes (mcr-1 and mcr-2) among commensal and pathogenic Escherichia coli strains isolated from food-producing and companion animals in Iran. Results A total of 607 E. coli isolates which were previously collected from different animal sources between 2008 and 2016 used to uncover the possible presence of plasmid-mediated colistin resistance genes (mcr-1 and mcr-2) by PCR. Overall, our results could not confirm the presence of any mcr-1 or mcr-2 positive E. coli among the studied isolates. It is concluded that despite the important role of food-producing animals in transferring the antibiotic resistance, they were not the main source for carriage of mcr-1 and mcr-2 in Iran until 2016. This study suggests that the other mcr variants (mcr-3 to mcr-9) might be responsible for conferring colistin resistance in animal isolates in Iran. The possible linkage between pig farming industry and high level of mcr carriage in some countries needs to be clarified in future prospective studies.

scholarly journals Molecular Characterization of Plasmid-Mediated Non-O157 Verotoxigenic Escherichia coli Isolated from Infants and Children with Diarrhea

2020 ◽  
Vol 17 (3) ◽  
pp. 0710
Author(s):  
Md Fazlul Karim Khan ◽  
Shah Samiur Rashid
Keyword(s):  
Escherichia Coli ◽  
Virulence Gene ◽  
Multidrug Resistant ◽  
Plasmid Curing ◽  
Health Issues ◽  
E Coli ◽  
Disk Diffusion Assay ◽  
Microbiological Techniques ◽  
Polymerase Chain

A significant increase in the incidence of non-O157 verotoxigenic Escherichia coli (VTEC) infections have become a serious health issues, and this situation is worsening due to the dissemination of plasmid mediated multidrug-resistant microorganisms worldwide. This study aims to investigate the presence of plasmid-mediated verotoxin gene in non-O157 E. coli. Standard microbiological techniques identified a total of 137 E. coli isolates. The plasmid was detected by Perfectprep Plasmid Mini preparation kit. These isolates were subjected to disk diffusion assay, and plasmid curing with ethidium bromide treatment. The plasmid containing isolates were subjected to a polymerase chain reaction (PCR) for investigating the presence of plasmid mediated verotoxin gene (VT1 and VT2) in non-O157 E. coli. Among the 137 E. coli isolates, 49 isolates were non-O157 E. coli while 29 (59.1%) isolates were verotoxin producing non-O157 serotypes and 26 non-O157 VTEC isolates possessed plasmids. Certain isolates harboured single sized plasmid while others had multiple plasmids with different size varied from 1.8kb to 7.6kb. A plasmid containing all (100%) the isolates was multidrug-resistant. Eight isolates changed their susceptibility patterns while three isolates were found to lose plasmid after post plasmid curing treatment and the rest of the isolates (15) remained constant. Different PCR sets characterized 3 plasmid-mediated verotoxins producing non-O157 E. coli. This current study demonstrated the occurrence of plasmid mediated verotoxin gene in non-O157 E. coli. To the best of our knowledge, this is the first report in the global literature on plasmid-mediated verotoxin gene in non-O157 E. coli. Timely diagnosis and surveillance of VTEC infections should prioritize to stop or slow down the virulence gene for dissemination by plasmid-mediated gene transfer amongst the same bacteria or other species.

scholarly journals Genomic Characterization of A Multidrug-resistant Citrobacter freundii Strain ZT01-0079 Co-Producing blaNDM-1 and blaSHV-12 using MiSeq and MinION

2020 ◽  
Author(s):  
Tingyan Zhang ◽  
Yanfeng Lin ◽  
Zhonghong Li ◽  
Xiong Liu ◽  
Jinhui Li ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Southern Blotting ◽  
Multiple Drug Resistance ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Multiple Drug ◽  
Citrobacter Freundii ◽  
Rapid Spread ◽  
Genomic Characterization

Abstract Background: The emergence of multi-drug resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the blaNDM-1 and blaSHV-12 genes.Methods: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of blaNDM-1 was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the blaNDM-1- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain.Results: Strain ZT01-0079 was identified as C. freundii, and the coexistence of blaNDM-1 and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that blaNDM-1 was located on a ~53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68×10−3. Both blaNDM-1 and blaSHV-12 were located on the self-transferable IncX3 plasmid.Conclusion: The rapid spread of the IncX3 plasmid highlights the importance of continuous monitoring of the prevalence of NDM-1-encoding Enterobacteriaceae. Mutations of existing carbapenem resistance genes will bring formidable challenges to clinical treatment.

scholarly journals Genomic characterization of asymptomatic Escherichia coli isolated from the neobladder

Microbiology ◽  
2011 ◽  
Vol 157 (4) ◽  
pp. 1088-1102 ◽  
Author(s):  
Jason W. Sahl ◽  
Amanda L. Lloyd ◽  
Julia C. Redman ◽  
Thomas A. Cebula ◽  
David P. Wood ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Severe Disease ◽  
Comparative Genomic ◽  
Trauma Studies ◽  
Ileal Neobladder ◽  
E Coli ◽  
Genomic Characterization ◽  
Tract Infections ◽  
Ileal Tissue

The replacement of the bladder with a neobladder made from ileal tissue is the prescribed treatment in some cases of bladder cancer or trauma. Studies have demonstrated that individuals with an ileal neobladder have recurrent colonization by Escherichia coli and other species that are commonly associated with urinary tract infections; however, pyelonephritis and complicated symptomatic infections with ileal neobladders are relatively rare. This study examines the genomic content of two E. coli isolates from individuals with neobladders using comparative genomic hybridization (CGH) with a pan-E. coli/Shigella microarray. Comparisons of the neobladder genome hybridization patterns with reference genomes demonstrate that the neobladder isolates are more similar to the commensal, laboratory-adapted E. coli and a subset of enteroaggregative E. coli than they are to uropathogenic E. coli isolates. Genes identified by CGH as exclusively present in the neobladder isolates among the 30 examined isolates were primarily from large enteric isolate plasmids. Isolations identified a large plasmid in each isolate, and sequencing confirmed similarity to previously identified plasmids of enteric species. Screening, via PCR, of more than 100 isolates of E. coli from environmental, diarrhoeagenic and urinary tract sources did not identify neobladder-specific genes that were widely distributed in these populations. These results taken together demonstrate that the neobladder isolates, while distinct, are genomically more similar to gastrointestinal or commensal E. coli, suggesting why they can colonize the transplanted intestinal tissue but rarely progress to acute pyelonephritis or more severe disease.

scholarly journals Characterization of Multidrug-Resistant Escherichia coli Isolates from Animals Presenting at a University Veterinary Hospital

2011 ◽  
Vol 77 (20) ◽  
pp. 7104-7112 ◽  
Author(s):  
Maria Karczmarczyk ◽  
Yvonne Abbott ◽  
Ciara Walsh ◽  
Nola Leonard ◽  
Séamus Fanning
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Gene Array ◽  
Multidrug Resistant ◽  
Genetic Determinants ◽  
Gene Encoding ◽  
Content Type ◽  
E Coli ◽  
Class 1

ABSTRACTIn this study, we examined molecular mechanisms associated with multidrug resistance (MDR) in a collection ofEscherichia coliisolates recovered from hospitalized animals in Ireland. PCR and DNA sequencing were used to identify genes associated with resistance. Class 1 integrons were prevalent (94.6%) and contained gene cassettes recognized previously and implicated mainly in resistance to aminoglycosides, β-lactams, and trimethoprim (aadA1,dfrA1-aadA1,dfrA17-aadA5,dfrA12-orfF-aadA2,blaOXA-30-aadA1,aacC1-orf1-orf2-aadA1,dfr7). Class 2 integrons (13.5%) contained thedfrA1-sat1-aadA1gene array. The most frequently occurring phenotypes included resistance to ampicillin (97.3%), chloramphenicol (75.4%), florfenicol (40.5%), gentamicin (54%), neomycin (43.2%), streptomycin (97.3%), sulfonamide (98.6%), and tetracycline (100%). The associated resistance determinants detected includedblaTEM,cat,floR,aadB,aphA1,strA-strB,sul2, andtet(B), respectively. TheblaCTX-M-2gene, encoding an extended-spectrum β-lactamase (ESβL), andblaCMY-2, encoding an AmpC-like enzyme, were identified in 8 and 18 isolates, respectively. The mobility of the resistance genes was demonstrated using conjugation assays with a representative selection of isolates. High-molecular-weight plasmids were found to be responsible for resistance to multiple antimicrobial compounds. The study demonstrated that animal-associated commensalE. coliisolates possess a diverse repertoire of transferable genetic determinants. Emergence of ESβLs and AmpC-like enzymes is particularly significant. To our knowledge, theblaCTX-M-2gene has not previously been reported in Ireland.

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