scholarly journals Genomic epidemiology of globalKlebsiella pneumoniaecarbapenemase (KPC)-producingEscherichia coli

2017 ◽  
Author(s):  
N Stoesser ◽  
AE Sheppard ◽  
G Peirano ◽  
LW Anson ◽  
L Pankhurst ◽  
...  
Keyword(s):  
Core Genome ◽  
Horizontal Transmission ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
E Coli ◽  
Genomic Epidemiology ◽  
Genetic Features ◽  
Human Infections ◽  
Sequence Types ◽  
Animal Reservoirs

ABSTRACTThe dissemination of carbapenem resistance inEscherichia colihas major implications for the management of common human infections.blaKPC,encoding a transmissible carbapenemase (KPC), has historically largely been associated withKlebsiella pneumoniae,a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401,~10kb). Here we characterize the genetic features of the emergence ofblaKPCin globalE. coli,2008-2013, using both long-and short-read whole genome sequencing.Amongst 43/45 successfully sequencedblaKPC-E. colistrains, we identified high strain (n=21 sequence types, 18% of annotated genes in the core genome); plasmid (≥9 replicon types); andblaKPC-associated, mobile genetic element (MGE) diversity (50% not within complete Tn4401elements). We also found evidence of interspecies, regional and international plasmid spread. In several casesblaKPCwas found on high copy number, small Col-like plasmids, previously associated with horizontal transmission of resistance genes in the absence of antimicrobial selection pressures.E. coliis a common human pathogen, but also a commensal in a multiple environmental and animal reservoirs, and easily transmissible. The association ofblaKPCwith a range of MGEs previously linked to the successful spread of widely endemic resistance mechanisms (e.g.blaTEM,blaCTX-M) suggests that it is likely to become similarly prevalent.

scholarly journals Human carriage of cefotaxime-resistant Escherichia coli in North-East India: an analysis of STs and associated resistance mechanisms

2019 ◽  
Author(s):  
Deepjyoti Paul ◽  
Dmitriy Babenko ◽  
Mark A Toleman
Keyword(s):  
Escherichia Coli ◽  
Core Genome ◽  
In Silico Analysis ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
E Coli ◽  
North East India ◽  
North East ◽  
The City ◽  
Silico Analysis

Abstract Objectives To determine the prevalence of Escherichia coli STs and associated resistance mechanisms carried by the community in North-East India. Methods E. coli (108) were isolated from sewage collected from 19 sites across the city of Silchar by plating on MacConkey agar with/without selection (50 mg/L cefotaxime). Species identification was confirmed by MALDI-TOF MS for 82 isolates. Common resistance mechanisms were determined by WGS of pooled E. coli isolates. PFGE combined with specific probes determined the presence of common resistance mechanisms in all isolates. Phylotypes, multilocus STs, core-genome multilocus STs, resistance genes and virulence genes were determined by in silico analysis of 38 genomes. Results and conclusions Analysis of isolates collected without selection (n = 33) indicated that cefotaxime resistance in E. coli was 42% (14/33) and estimated meropenem resistance at 9%. The remaining 58% (19/33) were additionally susceptible to ampicillin, trimethoprim, ciprofloxacin and aminoglycosides. The most common ST among the cefotaxime-resistant E. coli was ST167 (29%), followed by ST410 (17%) and ST648 (10%). E. coli ST131 was absent from the collection. Sixty-three isolates were resistant to cefotaxime and harboured blaCTX-M-15 [54% (34/63)] or blaCMY-42 [46% (29/63)], of which 10% (6/63) harboured both genes. Carbapenem resistance was due to blaNDM-5, found in 10/63 cefotaxime-resistant isolates, and/or blaOXA-181, found in 4/63 isolates. NDM-5 was encoded by IncX3 and/or IncFII plasmids and CMY-42 was mostly encoded by IncI plasmids. NDM-5 appears to have replaced NDM-1 in this region and CMY-42 appears to be in the process of replacing CTX-M-15.

scholarly journals An Application of Imipenem Discs or P. aeruginosa ATCC 27853 Reference Strain Increases Sensitivity of Carbapenem Inactivation Method for Non-Fermenting Gram-Negative Bacteria

Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 875
Author(s):  
Tomasz Bogiel ◽  
Mateusz Rzepka ◽  
Eugenia Gospodarek-Komkowska
Keyword(s):  
Human Population ◽  
Reference Strain ◽  
Resistance Mechanisms ◽  
Gram Negative Bacteria ◽  
Opportunistic Pathogens ◽  
Beta Lactams ◽  
Gram Negative ◽  
E Coli ◽  
Human Infections ◽  
Reliable Diagnostic Method

Non-fermenting Gram-negative rods are one of the most commonly isolated bacteria from human infections. These microorganisms are typically opportunistic pathogens that pose a serious threat to public health due to possibility of transmission in the human population. Resistance to beta-lactams, due to carbapenemases synthesis, is one of the most important antimicrobial resistance mechanisms amongst them. The aim of this study was to evaluate the usefulness of the Carbapenem Inactivation Method (CIM), and its modifications, for the detection of carbapenemase activity amongst non-fermenting Gram-negative rods. This research involved 81 strains of Gram-negative rods. Of the tested strains, 55 (67.9%) synthesized carbapenemases. For non-fermenting rods, 100% sensitivity and specificity was obtained in the version of the CIM test using imipenem discs and E. coli ATCC 25922 strain. The CIM test allows for differentiation of carbapenems resistance mechanisms resulting from carbapenemase synthesis from other resistance types. It is a reliable diagnostic method for the detection of carbapenemase activity amongst non-fermenting Gram-negative rods. Application of imipenem discs and P. aeruginosa ATCC 27853 reference strain increases CIM results sensitivity, while imipenem discs and E. coli ATCC 25922 strain use maintains full precision of the test for non-fermenting rods.

scholarly journals Population Structure and Antimicrobial Resistance of Canine UropathogenicEscherichia coli

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Tessa E. LeCuyer ◽  
Barbara A. Byrne ◽  
Joshua B. Daniels ◽  
Dubraska V. Diaz-Campos ◽  
G. Kenitra Hammac ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Companion Animals ◽  
Sequence Type ◽  
Content Type ◽  
E Coli ◽  
Extraintestinal Disease ◽  
Human Infections ◽  
Sequence Types

ABSTRACTEscherichia coliis the most common cause of human and canine urinary tract infection (UTI). Clonal groups, often with high levels of antimicrobial resistance, are a major component of theE. colipopulation that causes human UTI. While little is known about the population structure ofE. colithat causes UTI in dogs, there is evidence that dogs and humans can share fecal strains ofE. coliand that human-associated strains can cause disease in dogs. In order to better characterize theE. colistrains that cause canine UTI, we analyzed 295E. coliisolates obtained from canine urine samples from five veterinary diagnostic laboratories and analyzed their multilocus sequence types, phenotypic and genotypic antimicrobial resistance profiles, and virulence-associated gene repertoires. Sequence type 372 (ST372), an infrequent human pathogen, was the predominant sequence type in dogs at all locations. Extended-spectrum β-lactamase-producing isolates withblaCTX-Mgenes were uncommon in canine isolates but when present were often associated with sequence types that have been described in human infections. This provides support for occasional cross-host-species sharing of strains that cause extraintestinal disease and highlights the importance of understanding the role of companion animals in the overall transmission patterns of extraintestinal pathogenicE. coli.

scholarly journals 480. Molecular Characterization of Multidrug-Resistant Gram-Negative Pathogens in Three Tertiary Care Hospitals in Egypt

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S235-S235
Author(s):  
Amani Kholy ◽  
Samia A Girgis ◽  
Arwa R Elmanakhly ◽  
Mervat A F Shetta ◽  
Dalia El- Kholy ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Resistance Genes ◽  
Genetic Basis ◽  
Tertiary Care ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
Gram Negative ◽  
E Coli ◽  
Tertiary Care Hospitals

Abstract Background High rates of AMR among Gram-negative bacilli (GNB) have been reported from Egypt for almost 2 decades. Surveillance and identifying the genetic basis of AMR provide important information to optimize patient care. As there is no adequate data on the genetic basis of AMR in Egypt, we aimed to identify the molecular characterization of multi-drug-resistant (MDR) Gram-negative pathogens (GNP). Methods Three major tertiary-care hospitals in Egypt participated in the “Study for Monitoring Antimicrobial Resistance Trends” (SMART) from 2014 to 2016. Consecutive GNPs were identified and their susceptibility to antimicrobials were tested. Molecular identification of ESBL, AmpC, and carbapenemase resistance genes was conducted on MDR isolates. Results We enrolled 1,070 consecutive Gram-negative isolates; only one isolate per patient according to the standard protocol of (SMART). During 2014–2015, 578 GNP were studied. Enterobacteriaceae comprised 66% of the total isolates. K. pneumoniae and E. coli were the most common (29.8% and 29.4%). K. pneumoniae and E. coli were the predominant organisms in IAI (30.5% and 30.1%, respectively) and UTI (and 38.9% and 48.6%, respectively), while Acinetobacter baumannii was the most prevalent in RTI (40.2%). ESBL producers were phenotypically detected in 53% of K. pneumoniae, and 68% of E. coli. During 2016, 495 GNP were studied. ESBL continued to be high. For E. coli and K. pneunomiea, the most active antimicrobials were amikacin (≥93%), imipenem/meropenem (≥87%) and colistin (97%). Genetic study of ertapenem-resistant isolates and 50% of isolates with ESBL phenotype revealed ESβL production in more than 90% of isolates; blaCTXM-15 was detected in 71.4% and 68.5% in K. pneumoniae and E. coli, respectively, blaTEM-OSBL in 48.5% and47.5% of K. pneumoniae and E. coli, respectively. Carbapenem resistance genes were detected in 45.4% of isolates. In K. pneumoniae, OXA-48 dominated (40.6%), followed by NDM1 (23.7%) and OXA-232 (4.5%). Conclusion Our study detected alarming rates of resistance and identified many resistance mechanisms in clinical isolates from Egyptian hospitals. These high rates highlight the importance of continuous monitoring of the resistance trend and discovering the novel resistant mechanisms of resistance, and the underscores a national antimicrobial stewardship plan in Egypt. Disclosures All authors: No reported disclosures.

scholarly journals Diversity of sequence types and impact of fitness cost among carbapenem-resistant Acinetobacter baumannii isolates from Tripoli, Libya

2021 ◽  
Author(s):  
Antoine G. Abou Fayad ◽  
Louis-Patrick Haraoui ◽  
Ahmad Sleiman ◽  
Mohamad Jaafar ◽  
Abdulaziz Zorgani ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Acinetobacter Baumannii ◽  
Doubling Time ◽  
Core Genome ◽  
Carbapenem Resistance ◽  
Relative Fitness ◽  
Fitness Advantage ◽  
Carbapenem Resistant ◽  
Sequence Types ◽  
Hospital Transmission

We investigated the molecular epidemiology of 21 carbapenem-resistant A. baumannii from Libya, and assessed their relative fitness. Core-genome MLST revealed five inter-hospital transmission clusters. Three clusters were associated with the international clones (IC) IC1, IC2, and IC7. Carbapenem-resistance was associated with bla OXA-23, bla GES-11 , or bla NDM-1 . Compared to A. baumannii DSM 30008, the doubling time was similar over 10 hours, but after 16 hours, half the isolates grew to higher densities, suggesting a fitness advantage.

scholarly journals Carbapenem Resistance: Mechanisms and Drivers of Global Menace

2020 ◽  
Author(s):  
Bilal Aslam ◽  
Maria Rasool ◽  
Saima Muzammil ◽  
Abu Baker Siddique ◽  
Zeeshan Nawaz ◽  
...  
Keyword(s):  
Global Health ◽  
Protein Modification ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
Health Concern ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Global Health Issue ◽  
Class I Integrons ◽  
Day By Day

The emergence of carbapenem-resistant bacterial pathogens is a significant and mounting health concern across the globe. At present, carbapenem resistance (CR) is considered as one of the most concerning resistance mechanisms and mainly found in gram-negative bacteria of the Enterobacteriaceae family. Although carbapenem resistance has been recognized in Enterobacteriaceae from last 20 years or so, recently it emerged as a global health issue as CR clonal dissemination of various Enterobacteriaceae members especially E. coli, and Klebsiella pneumoniae are reported from across the globe at an alarming rate. Phenotypically, carbapenems resistance is in due to the two key mechanisms, like structural mutation coupled with β-lactamase production and the ability of the pathogen to produce carbapenemases which ultimately hydrolyze the carbapenem. Additionally, penicillin-binding protein modification and efflux pumps are also responsible for the development of carbapenem resistance. Carbapenemases are classified into different classes which include Ambler classes A, B, and D. Several mobile genetic elements (MGEs) have their potential role in carbapenem resistance like Tn4401, Class I integrons, IncFIIK2, IncF1A, and IncI2. Taking together, resistance against carbapenems is continuously evolving and posing a significant health threat to the community. Variable mechanisms that are associated with carbapenem resistance, different MGEs, and supplementary mechanisms of antibiotic resistance in association with virulence factors are expanding day by day. Timely demonstration of this global health concern by using molecular tools, epidemiological investigations, and screening may permit the suitable measures to control this public health menace.

scholarly journals Arising Prevalence of OXA-48 producer Escherichia coli and OXA-48 with NDM co-producer Klebsiella pneumoniae Strains

2019 ◽  
Vol 27 (3) ◽  
pp. 319-326 ◽  
Author(s):  
Aylin Uskudar-Guclu ◽  
Mustafa Guney ◽  
Ali Korhan Sig ◽  
Selcuk Kilic ◽  
Mehmet Baysallar
Keyword(s):  
Antimicrobial Agents ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
Resistant Isolate ◽  
Diffusion Method ◽  
Clinical Samples ◽  
Disc Diffusion ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Resistance Rates

Abstract Background/aim: This prospective study aimed to determine the presence of the most common carbapenemase genes, blaOXA-48, blaKPC, blaIMP, blaVIM and blaNDM on carbapenem resistant clinical K.pneumoniae and E.coli isolates. Materials and methods: Isolates were selected according to EUCAST guideline; gradient test and disc diffusion with both meropenem and ertapenem discs. Resistance rates of these isolates to other antimicrobial agents were also examined by disc diffusion method. Carbapenem resistance gene were investigated by using Real-Time PCR. Results: A total of 3845 E. coli and 1689 K.pneumoniae isolates from clinical samples between January 2015 and April 2017 were evaluated. The 419 isolates were found as carbapenem resistant but only the first resistant isolate (n=155; 126 K.pneumoniae and 29 E.coli) of each patient were included. Carbapenem resistant isolates were most frequently isolated from intensive care units (48.8%). Colistin was the most effective antibiotic (91.0%). The 121 (78.1%) of the tested isolates were positive for OXA-48 (103 K.pneumoniae and 18 E.coli) and 9 K. pneumoniae carrying blaNDM were also positive for blaOXA-48. VIM, IMP and KPC type carbapenemases were not detected in any isolates. Conclusion: Carbapenem-resistant pathogens have been shown to be able to develop resistance mechanisms with more than one carbapenemase encoding gene.

scholarly journals Molecular Epidemiology of Fosfomycin Resistant E. coli from a Pigeon Farm in China

Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 777
Author(s):  
Lu Han ◽  
Xiao-Qing Lu ◽  
Xu-Wei Liu ◽  
Mei-Na Liao ◽  
Ruan-Yang Sun ◽  
...  
Keyword(s):  
Molecular Characteristics ◽  
Genomic Context ◽  
E Coli ◽  
High Prevalence ◽  
Potential Reservoir ◽  
Genomic Environment ◽  
High Level ◽  
Human Infections ◽  
Sequence Types ◽  
Level Resistance

We determined the prevalence and molecular characteristics of fosfomycin-resistant Escherichia coli from a domestic pigeon farm. A total of 79 samples collected from pigeons and their surrounding environments were screened for the presence of fosfomycin resistant isolates and these included 49 E. coli isolates that displayed high-level resistance (MIC ≥ 256 mg L−1) and carried the fosA3 gene on plasmids with sizes ranging from 80 to 370 kb. MLST analysis of these fosA3-positive E. coli isolates indicated the presence of nine sequence types (ST6856, ST8804, ST457, ST746, ST533, ST165, ST2614, ST362 and ST8805) of which ST6856 was the most prevalent (24.5%, 12/49). PFGE combined with genomic context comparative analyses indicated that the fosA3 gene was spread by horizontal transfer as well as via clonal transmission between E. coli in the pigeon farm, and IS26 played an important role in fosA3 transmission. The high prevalence of fosA3 in the pigeon farm and the high similarity of the fosA3 genomic environment between E. coli isolates from humans and pigeons indicated that the pigeon farm served as a potential reservoir for human infections. The pigeon farm was found to be an important reservoir for the fosA3 gene and this should be further monitored.

scholarly journals Genomic Epidemiology of Complex, Multispecies, Plasmid-Borne blaKPC Carbapenemase in Enterobacterales in the United Kingdom from 2009 to 2014

2020 ◽  
Vol 64 (5) ◽  
Author(s):  
Nicole Stoesser ◽  
Hang T. T. Phan ◽  
Anna C. Seale ◽  
Zoie Aiken ◽  
Stephanie Thomas ◽  
...  
Keyword(s):  
United Kingdom ◽  
Large Scale ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
Content Type ◽  
North West ◽  
Genomic Epidemiology ◽  
The United Kingdom ◽  
Long Read ◽  
Genetic Mechanisms

ABSTRACT Carbapenem resistance in Enterobacterales is a public health threat. Klebsiella pneumoniae carbapenemase (encoded by alleles of the blaKPC family) is one of the most common transmissible carbapenem resistance mechanisms worldwide. The dissemination of blaKPC historically has been associated with distinct K. pneumoniae lineages (clonal group 258 [CG258]), a particular plasmid family (pKpQIL), and a composite transposon (Tn4401). In the United Kingdom, blaKPC has represented a large-scale, persistent management challenge for some hospitals, particularly in North West England. The dissemination of blaKPC has evolved to be polyclonal and polyspecies, but the genetic mechanisms underpinning this evolution have not been elucidated in detail; this study used short-read whole-genome sequencing of 604 blaKPC-positive isolates (Illumina) and long-read assembly (PacBio)/polishing (Illumina) of 21 isolates for characterization. We observed the dissemination of blaKPC (predominantly blaKPC-2; 573/604 [95%] isolates) across eight species and more than 100 known sequence types. Although there was some variation at the transposon level (mostly Tn4401a, 584/604 [97%] isolates; predominantly with ATTGA-ATTGA target site duplications, 465/604 [77%] isolates), blaKPC spread appears to have been supported by highly fluid, modular exchange of larger genetic segments among plasmid populations dominated by IncFIB (580/604 isolates), IncFII (545/604 isolates), and IncR (252/604 isolates) replicons. The subset of reconstructed plasmid sequences (21 isolates, 77 plasmids) also highlighted modular exchange among non-blaKPC and blaKPC plasmids and the common presence of multiple replicons within blaKPC plasmid structures (>60%). The substantial genomic plasticity observed has important implications for our understanding of the epidemiology of transmissible carbapenem resistance in Enterobacterales for the implementation of adequate surveillance approaches and for control.

scholarly journals Carriage of Carbapenem-Resistant Enterobacterales in Adult Patients Admitted to a University Hospital in Italy

Antibiotics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 61
Author(s):  
Pamela Barbadoro ◽  
Daniela Bencardino ◽  
Elisa Carloni ◽  
Enrica Omiccioli ◽  
Elisa Ponzio ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Resistance Rate ◽  
Coli Strain ◽  
Adult Patients ◽  
University Hospital ◽  
E Coli ◽  
Genetic Features ◽  
Phenotypic Tests

The emerging spread of carbapenemase-producing Enterobacterales (CPE) strains, in particular, Klebsiella pneumoniae and Escherichia coli, has become a significant threat to hospitalized patients. Carbapenemase genes are frequently located on plasmids than can be exchanged among clonal strains, increasing the antibiotic resistance rate. The aim of this study was to determine the prevalence of CPE in patients upon their admission and to analyze selected associated factors. An investigation of the antibiotic resistance and genetic features of circulating CPE was carried out. Phenotypic tests and molecular typing were performed on 48 carbapenemase-producing strains of K. pneumoniae and E. coli collected from rectal swabs of adult patients. Carbapenem-resistance was confirmed by PCR detection of resistance genes. All strains were analyzed by PCR-based replicon typing (PBRT) and multilocus sequence typing (MLST) was performed on a representative isolate of each PBRT profile. More than 50% of the strains were found to be multidrug-resistant, and the blaKPC gene was detected in all the isolates with the exception of an E. coli strain. A multireplicon status was observed, and the most prevalent profile was FIIK, FIB KQ (33%). MLST analysis revealed the prevalence of sequence type 512 (ST512). This study highlights the importance of screening patients upon their admission to limit the spread of CRE in hospitals.

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