Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Klebsiella pneumoniae and Escherichia coli Isolates

Objectives: Drug resistance among gram-negative bacteria is a worldwide challenge. Due to the importance of drug-resistant Klebsiella pneumoniae and Escherichia coli strains in hospital-acquired infections, we aimed to determine the phenotypic and genotypic characteristics of ESBL-, AmpC-, and carbapenemase-producing isolates obtained from hospitalized patients in Tehran and Ilam (Iran). Materials and Methods: In total, 90 K. pneumoniae isolates and 65 E. coli isolates were collected from various infections. Phenotypic identification of bacterial isolates was performed using standard methods. Phenotypic screening of ESBL, AmpC, and carbapenemase enzymes was carried out. Detection of ESBL, AmpC, and carbapenemase genes was also performed by the PCR method. Results: Phenotypic detection tests showed that 36 (40%) K. pneumoniae and 23 (35.4%) E. coli isolates were ESBL producers. Moreover, 18 (20%) and 6 (9.2%) K. pneumoniae and E. coli isolates were AmpC producers, respectively. Modified Hodge test results indicated that 39 (43.3%) K. pneumoniae and 18 (27.7%) E. coli isolates produced carbapenemase. Molecular tests showed that 40% of K. pneumoniae and 36.9% of E. coli isolates were ESBL positive. AmpC was detected in 24.4 and 13.8% of K. pneumoniae and E. coli isolates. Carbapenemase was detected in 34 (37.8%) K. pneumoniae and 13 (20%) E. coli isolates. Conclusion: In this study, 3 K. pneumoniae isolates simultaneously carried ESBL, AmpC, and carbapenemase genes. Up-to-date strategies such as combination therapy or utilization of new antimicrobial agents might help to combat such drug-resistant organisms.

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Research of Associated Resistance to Antimicrobial Agents of Extended Spectrum Beta-Lactamases Escherichia Coli and Klebsiella pneumoniae Strains Isolated in Senegal

Austin Journal of Microbiology ◽

10.26420/austinjmicrobiol.2021.1029 ◽

2021 ◽

Vol 6 (1) ◽

Author(s):

Ngom B ◽

◽

Wade SF ◽

Diop TA ◽

Diagne R ◽

...

Keyword(s):

Escherichia Coli ◽

Klebsiella Pneumoniae ◽

Antimicrobial Agents ◽

Diffusion Method ◽

Drug Resistant ◽

Beta Lactamases ◽

E Coli ◽

Sick People ◽

Extended Spectrum ◽

Extended Spectrum Beta Lactamases

Introduction: Some strains of Escherichia coli and Klebsiella pneumoniae produce Extended Spectrum Beta-Lactamases (ESBL) may be responsible for various infections such as urinary infections. These Sick people are treated in the very serious cases by association antibiotics to class to betalactamins, aminosids and quinolons. But proliferation of multi-drug resistant strains involves decreasing therapeutic success. That’s why epidemiological study must be done in all laboratories of bacteriology. Purpose: The aim of the study was to research the resistance phenotypes of our E. coli and K. pneumoniae ESBL strains compared to others families of antibiotics. Material and methods: Thirty two (32) Extended Spectrum betalactamases E. coli and K. pneumoniae strains isolated from either hospitalized patients or sick people who came for consultation were studied. Susceptibility to antimicrobial agents was determined using an antibiotic disk (Bio-Rad) diffusion method on Mueller-Hinton agar (Bio-Rad). The results were interpreted according to the Standards of the French Antibiogram Committee (CA-SFM). Results: The study showed that most of these strains were multi-drug resistant. They were resistant to many beta-lactamines antibiotics. E. coli strains were also resistant at 70,34% to aminosids, at 96,72% to quinolons, at 58,3% to cotrimoxazol, at 26,1% to chloramphénicol and at 21,4% to colistin ; about K. pneumoniae, they were resistant at 72,6% to aminosids, at 88,95% to quinolons, at 86,7% to cotrimoxazol, at 44,4% to chloramphénicol and at 25% to colistin. But all these strains were sensitive at 100% to l’imipenem.

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Detection of Multiple-Antimicrobial Resistance and Characterization of the Implicated Genes in Escherichia coli Isolates from Foods of Animal Origin in Tunis

Journal of Food Protection ◽

10.4315/0362-028x-72.5.1082 ◽

2009 ◽

Vol 72 (5) ◽

pp. 1082-1088 ◽

Cited By ~ 20

Author(s):

AHLEM JOUINI ◽

KARIM BEN SLAMA ◽

YOLANDA SÁENZ ◽

NAOUEL KLIBI ◽

DANIELA COSTA ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

Food Samples ◽

Animal Origin ◽

E Coli ◽

Antimicrobial Resistance Genes ◽

Class 1 ◽

Agar Dilution

Phenotypic and genotypic characterization of antimicrobial resistance was conducted for 98 Escherichia coli isolates recovered from 40 food samples of animal origin (poultry, sheep, beef, fish, and others) obtained in supermarkets and local butcheries in Tunis during 2004 and 2005. Susceptibility to 15 antimicrobial agents was tested by disk diffusion and agar dilution methods, the mechanisms of resistance were evaluated using PCR and sequencing methods, and the clonal relationship among isolates was evaluated using pulsed-field gel electrophoresis. High resistance was detected to tetracycline, sulphonamides, nalidixic acid, ampicillin, streptomycin, and trimethoprim-sulfamethoxazole (29 to 43% of isolates), but all isolates were susceptible to cefotaxime, ceftazidime, cefoxitin, azthreonam, and amikacin. One-third of the isolates had multiresistant phenotypes (resistance to at least five different families of antimicrobial agents). Different variants of blaTEM, tet, sul, dfrA, aadA, and aac(3) genes were detected in most of the strains resistant to ampicillin, tetracycline, sulphonamide, trimethoprim, streptomycin, and gentamicin, respectively. The presence of class 1 and class 2 integrons was studied in 15 sulphonamide-resistant unrelated E. coli strains, and 14 of these strains harbored class 1 integrons with five different arrangements of gene cassettes, and a class 2 integron with the dfrA1 + sat + aadA1 arrangement was found in one strain. This study revealed the high diversity of antimicrobial resistance genes, some of them included in integrons, in E. coli isolates of food origin.

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Characterization of auto-agglutinating and non-typeable uropathogenic Escherichia coli strains

The Journal of Infection in Developing Countries ◽

10.3855/jidc.11098 ◽

2019 ◽

Vol 13 (06) ◽

pp. 465-472

Author(s):

Ulises Hernández-Chiñas ◽

Alejandro Pérez-Ramos ◽

Laura Belmont-Monroy ◽

María E Chávez-Berrocal ◽

Edgar González-Villalobos ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Antimicrobial Agents ◽

Multidrug Resistant ◽

Uropathogenic Escherichia Coli ◽

E Coli ◽

Resistant Strains ◽

Tract Infections ◽

Disk Method

Introduction: Uropathogenic Escherichia coli (UPEC) are the main etiological agent of urinary tract infections (UTIs). Association between different serotypes and UTIs is known, however, some strains are incapable to be serotyped. The aim of this work was to study bthe phenotypical and genotypical characteristics of 113 non-typeable (NT) and auto-agglutinating (AA) E. coli strains, isolated from UTIs in children and adults. Methodology: The 113 UPEC strains were analyzed by PCR assays using specific primers to determine their serogroups, fimH, papC, iutA, sat, hlyCA and cnf1, virulence associated genes, and chuA, yjaA and TSPE4.C2 for phylogroup determination. Additionally, the diffusion disk method was performed to evaluate the antimicrobial resistance to 18 antimicrobial agents. Results: Using the PCR assay, 63% (71) of the strains were genotyped showing O25 and O75 as the most common serogroups. The virulence genes fimH (86%) and iutA (74%) were the most prevalent, in relation to the phylogroups the commensal (A and B1) and virulent (B2 and D) showed similar frequencies (P > 0.05). The antimicrobial susceptibility test showed a high percentage (73%) of multidrug-resistant strains. Conclusions: The genotyping allowed identifying the serogroup in many of the strains that could not be typed by traditional serology. The strains carried virulence genes and were multidrug-resistant in both, commensal and virulent phylogroups. Our findings revealed that, in addition to the classical UPEC serogroups, there are pathogenic serogroups not reported yet.

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Prevalence and characterization of multi-drug resistant Escherichia coli from urine samples

Dhaka University Journal of Biological Sciences ◽

10.3329/dujbs.v20i1.8834 ◽

1970 ◽

Vol 20 (1) ◽

pp. 23-30

Author(s):

Augustin Kakon Gomes ◽

Humaira Akhter ◽

Belal Mahmud ◽

Sirajul Islam Khan ◽

Anowara Begum

Keyword(s):

Escherichia Coli ◽

Urinary Tract Infection ◽

Profile Analysis ◽

Plasmid Profile ◽

Urine Samples ◽

Drug Resistant ◽

Methyl Red ◽

E Coli ◽

Identification And Characterization

Isolation, identification and characterization of Escherichia coli were carried out in terms of biochemical, serological, antibiogram, plasmid profile and culture condition of urine samples. Out of 50 urine samples, 36 were positive for E. coli that were confirmed by biochemical (e.g. oxidase, kligler’s iron agar, indole, methyl red-voges proskauer and citrate utilization) tests and 4-methyl-umbelliferyl-β-D-glucoronide (MUG) test. Twenty seven strains gave positive result with different antisera whereas nine strains were untypable (UT), respectively. Thirty six strains were also tested by antibiogram against ten different antibiotics. Most E. coli strains were resistant to bacitracin, ampicillin, novobiocin, kanamycin and streptomycin. Eighty three per cent strains were sensitive to ciprofloxacin and gentamycin while 11 and 12% showed resistance to ciprofloxacin and gentamycin, respectively. By plasmid profile analysis of the 36 strains seven different plasmid patterns were observed. Comparison of the plasmid profiles with the antibiogram results indicated the presence of resistant (R) plasmid. Thirty four isolates of E. coli contained a common 25 kb plasmid that may possibly be responsible for drug resistance in this study. The results suggested that the prevalence of multi-drug resistant and new serotype of E. coli may be increasing rapidly which is alarming for treatment of urinary tract infection in Bangladesh.Key words: Prevalence; Characterization; E. coli; Multi-drug resistant; Serotype; Clinical sampleDOI: http://dx.doi.org/10.3329/dujbs.v20i1.8834Dhaka Univ. J. Biol. Sci. 20(1): 23-30, 2011 (January)

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Detection and Molecular Characterization of Escherichia coli CTX-M-15 and Klebsiella pneumoniae SHV-12 β-Lactamases from Bovine Mastitis Isolates in the United Kingdom

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00752-13 ◽

2013 ◽

Vol 58 (2) ◽

pp. 789-794 ◽

Cited By ~ 53

Author(s):

Dorina Timofte ◽

Iuliana E. Maciuca ◽

Nicholas J. Evans ◽

Helen Williams ◽

Andrew Wattret ◽

...

Keyword(s):

Escherichia Coli ◽

United Kingdom ◽

Klebsiella Pneumoniae ◽

Bovine Mastitis ◽

Conjugative Plasmid ◽

Sensitivity Testing ◽

Content Type ◽

E Coli ◽

The United Kingdom

ABSTRACTRecent reports raised concerns about the role that farm stock may play in the dissemination of extended-spectrum β-lactamase (ESBL)-producing bacteria. This study characterized the ESBLs in twoEscherichia coliand threeKlebsiella pneumoniaesubsp.pneumoniaeisolates from cases of clinical bovine mastitis in the United Kingdom. Bacterial culture and sensitivity testing of bovine mastitic milk samples identified Gram-negative cefpodoxime-resistant isolates, which were assessed for their ESBL phenotypes. Conjugation experiments and PCR-based replicon typing (PBRT) were used for characterization of transferable plasmids.E. coliisolates belonged to sequence type 88 (ST88; determined by multilocus sequence typing) and carriedblaCTX-M-15andblaTEM-1, whileK. pneumoniaesubsp.pneumoniaeisolates carriedblaSHV-12andblaTEM-1. Conjugation experiments demonstrated thatblaCTX-M-15andblaTEM-1were carried on a conjugative plasmid inE. coli, and PBRT identified this to be an IncI1 plasmid. The resistance genes were nontransferable inK. pneumoniaesubsp.pneumoniaeisolates. Moreover, in theE. coliisolates, an association of ISEcp1 and IS26withblaCTX-M-15was found where the IS26element was inserted upstream of both ISEcp1and theblaCTX-Mpromoter, a genetic arrangement highly similar to that described in some United Kingdom human isolates. We report the first cases in Europe of bovine mastitis due toE. coliCTX-M-15 and also of bovine mastitis due toK. pneumoniaesubsp.pneumoniaeSHV-12 β-lactamases in the United Kingdom. We also describe the genetic environment ofblaCTX-M-15and highlight the role that IncI1 plasmids may play in the spread and dissemination of ESBL genes, which have been described in both human and cattle isolates.

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Characterization of multidrug-resistant Escherichia coli isolated from extraintestinal clinical infections in animals

Journal of Medical Microbiology ◽

10.1099/jmm.0.018002-0 ◽

2010 ◽

Vol 59 (5) ◽

pp. 592-598 ◽

Cited By ~ 19

Author(s):

Justine S. Gibson ◽

Rowland N. Cobbold ◽

Darren J. Trott

Keyword(s):

Escherichia Coli ◽

Antimicrobial Susceptibility ◽

Animal Species ◽

Antimicrobial Agents ◽

Multidrug Resistant ◽

Phylogenetic Group ◽

Phylogenetic Groups ◽

Diagnostic Laboratory ◽

E Coli

Multidrug-resistant (MDR) Escherichia coli causes extraintestinal infections in both humans and animals. This study aimed to determine whether MDR E. coli isolates cultured from extraintestinal infections in several animal species were clonal and crossed host-species boundaries, as suggested by initial characterization of a subset of canine and human isolates, or whether they represented a diverse group of host-specific strains. Isolates were obtained either from The University of Queensland Veterinary Diagnostic Laboratory or from an independent diagnostic laboratory between October 1999 and December 2007. Ninety-six MDR E. coli isolates cultured from extraintestinal clinical infections in 55 animals comprising dogs (n=45), cats (n=5), horses (n=4) and a koala (n=1) were analysed by phylogenetic grouping, antimicrobial susceptibility testing and PFGE. The isolates were cultured from the urinary tract (n=61), reproductive tract (n=11), wounds (n=11), surgical site infections (n=4) and other sites (n=9). Isolates from the same E. coli phylogenetic group with 100 % PFGE similarity and the same antimicrobial susceptibility pattern were considered to be repeat clones and excluded from further analysis. Three of the four E. coli phylogenetic groups (A, n=19; B1, n=8; and D, n=49) were represented. Analysis of PFGE similarity identified clusters of related phylogenetic group A isolates [clonal group (CG) 1] and group D isolates (CG2 and CG3), with the remainder of the isolates demonstrating diversity. The majority of CG2 isolates contained a plasmid-borne AmpC β-lactamase, imparting resistance to cefoxitin and third-generation cephalosporins, and were obtained between 2000 and 2003. CG3 isolates were sensitive to these antimicrobial agents and appeared to replace CG2 isolates as the dominant clones from 2003 to 2007. Apart from several canine and feline isolates that demonstrated clonality, PFGE profiles tended to be divergent across species. Whilst MDR E. coli isolates from extraintestinal infections in different animal species are diverse, some dominant CGs may persist over several years.

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Genomic Characterization of MDR Escherichia coli Harboring blaOXA-48 on the IncL/M-type Plasmid Isolated from Blood Stream Infection

BioMed Research International ◽

10.1155/2018/3036143 ◽

2018 ◽

Vol 2018 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

S. Alousi ◽

T. Salloum ◽

H. Arabaghian ◽

G. M. Matar ◽

G. F. Araj ◽

...

Keyword(s):

Escherichia Coli ◽

Blood Stream Infection ◽

Genomic Analysis ◽

Blood Stream ◽

Population Movements ◽

E Coli ◽

Resistance Determinants ◽

Genomic Characterization ◽

Hospital Acquired

Escherichia coli is responsible for a wide variety of community and hospital acquired extraintestinal infections, and the emergence of ESBL resistant isolates is a major clinical concern. In this study, we characterized the genomic attributes of an OXA-48 and CTX-M-3 producing E. coli EC-IMP153. Whole-genome initial assembly produced 146 contigs with a combined 5,504,170 bp in size and a G+C content of 50.5%. wgSNPs-based phylogenetic comparison with 36 publically available genomes was also performed. Comprehensive genomic analysis showed that EC-IMP153 belonged to sequence type ST-405 and harbored several resistance determinants including the β-lactam resistance genes blaOXA-48, blaCTX-M-3, blaTEM-1B, blaOXA-1, and blaCMY-70, aminoglycoside fyuA and aac(3)IId, tetracycline tet(A) and tet(R), and fluoroquinolone gyrA, parC, and mfd resistance determinants. Plasmids with the following incompatibility groups were detected in silico and confirmed using PBRT: IncI1-α, IncL, IncW, Col (BS512), and IncF. To our knowledge this is the first in-depth genomic analysis of an OXA-48 producing E. coli ST-405 isolated from a patient in Lebanon and linked to a blood stream infection. Continuous monitoring is necessary to better understand the continued diffusion of such pathogens, especially in view of the population movements triggered by unrest in the Middle East.

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Characterization of Environmentally Persistent Escherichia coli Isolates Leached from an Irish Soil

Applied and Environmental Microbiology ◽

10.1128/aem.01944-09 ◽

2010 ◽

Vol 76 (7) ◽

pp. 2175-2180 ◽

Cited By ~ 38

Author(s):

Fiona P. Brennan ◽

Florence Abram ◽

Fabio A. Chinalia ◽

Karl G. Richards ◽

Vincent O'Flaherty

Keyword(s):

Escherichia Coli ◽

Genetic Diversity ◽

Soil Conditions ◽

E Coli ◽

Metabolic Capability ◽

Genotypic Analysis ◽

Pcr Method ◽

Favorable Conditions ◽

Environmental Fitness

ABSTRACT Soils are typically considered to be suboptimal environments for enteric organisms, but there is increasing evidence that Escherichia coli populations can become resident in soil under favorable conditions. Previous work reported the growth of autochthonous E. coli in a maritime temperate Luvic Stagnosol soil, and this study aimed to characterize, by molecular and physiological means, the genetic diversity and physiology of environmentally persistent E. coli isolates leached from the soil. Molecular analysis (16S rRNA sequencing, enterobacterial repetitive intergenic consensus PCR, pulsed-field gel electrophoresis, and a multiplex PCR method) established the genetic diversity of the isolates (n = 7), while physiological methods determined the metabolic capability and environmental fitness of the isolates, relative to those of laboratory strains, under the conditions tested. Genotypic analysis indicated that the leached isolates do not form a single genetic grouping but that multiple genotypic groups are capable of surviving and proliferating in this environment. In physiological studies, environmental isolates grew well across a broad range of temperatures and media, in comparison with the growth of laboratory strains. These findings suggest that certain E. coli strains may have the ability to colonize and adapt to soil conditions. The resulting lack of fecal specificity has implications for the use of E. coli as an indicator of fecal pollution in the environment.

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Molecular and phenotypic typing of enteropathogenic Escherichia coli isolated in childhood acute diarrhea in Abuja, Nigeria

The Journal of Infection in Developing Countries ◽

10.3855/jidc.9338 ◽

2017 ◽

Vol 11 (07) ◽

pp. 527-535 ◽

Cited By ~ 1

Author(s):

Casmir Ifeanyichukwu Cajetan Ifeanyi ◽

Nkiruka Florence Ikeneche ◽

Bassey Enya Bassey ◽

Stefano Morabito ◽

Caterina Graziani ◽

...

Keyword(s):

Escherichia Coli ◽

Acute Diarrhea ◽

Antimicrobial Agents ◽

Virulence Gene ◽

Enteropathogenic Escherichia Coli ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Typical Epec ◽

Marked Resistance

Introduction: Enteropathogenic Escherichia coli (EPEC) causes infectious diarrhea among children in developing countries. However, in Nigeria, due to limited laboratory resources, the genetic diversity of its virulence factors, which include intimin subtypes, remains undefined. Methodology: EPEC isolates from diarrheic children 60 months of age and younger in Abuja, Nigeria, were analyzed. Polymerase chain reaction (PCR) for EPEC virulence gene, Hep-2 cell adherence, and serotyping were performed. EPEC strains were further subtyped by PCR for the identification of intimin subtype genes α (alpha), β (beta), γ1 (gamma-1), and έ (epsilon). Antibiotic resistance and extended-spectrum beta-lactamase (ESBL) production was determined by Clinical and Laboratory Standards Institute guidelines. Results: Overall, 18 (4.5%) out of 400 children with acute diarrhea had EPEC infection. Typical EPEC (tEPEC) strains were detected in 14 (3.5%), whereas 4 (1.1%) were atypical EPEC (aEPEC). A total of 15 (83.3%) of the EPEC isolated belonged to β intimin subtype gene, while the remaining 3 EPEC isolates possessed the intimin έ subtype. No α and γ intimin subtypes were detected. Traditional EPEC serotypes O114:H14 were detected only in tEPEC strains. Marked resistance to β-lactam agents were observed but no ESBL-producing tEPEC or aEPEC was detected. Conclusions: This is the first report of intimin subtype genes in Abuja, Nigeria. EPEC isolates of diverse serotypes resistant to β-lactam antimicrobial agents were observed. These data will be useful in facilitating the characterization of intimin variants of EPEC and some Shiga toxin-producing E. coli (STEC) in humans and other animal species.

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Antibacterial activities of aqueous and methanol extracts of Nigella sativa on some multiple drug resistant diarrheic bacterial agents

Journal of Medicinal Botany ◽

10.25081/jmb.2020.v4.6245 ◽

2020 ◽

pp. 14-19

Author(s):

Adedayo Emmanuel Ogunware ◽

Hassan Zainab Adewunmi

Keyword(s):

Escherichia Coli ◽

Antimicrobial Agents ◽

Nigella Sativa ◽

University Teaching ◽

Multiple Drug ◽

Significant Activity ◽

Drug Resistant ◽

E Coli ◽

Methanolic Extracts ◽

Multiple Drug Resistant

Combinations of various antimicrobial agents have been introduced as an extra successful strategy to combat multiple drug resistant infections. This study was undertaken to evaluate the effects of Nigella sativa seeds on several multi-drug resistant diarrheic bacterial agents. 30 Stool samples were collected from Lagos State University Teaching Hospital (LASUTH), in Nigeria and standard biochemical tests were performed to confirm the diarrheic isolates. Then, antimicrobial susceptibility testing was done on the organisms, followed by screening the effectiveness of Nigella sativa seed extracts on the bacterial agents obtained from the samples. 16 samples tested positive for diarrheic agents Escherichia coli, Escherichia coli 0157H:7 and Klebsiella pneumoniae. The methanolic extracts of Nigella sativa showed the highest zone of inhibition of 12mm for K. pneumoniae at a concentration of 300mg/dl ,10mm for E. coli 0157H:7 at a concentration of 200mg/dl, and 10mm for E. coli at a concentration of 200mg/dl, respectively. The methanolic extracts showed much stronger activity than the aqueous extracts of Nigella sativa which did not show significant activity towards the diarrheic agents isolated.

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