scholarly journals PlaScope: a targeted approach to assess the plasmidome of Escherichia coli strains

2018 ◽  
Author(s):  
G. Royer ◽  
J.W. Decousser ◽  
C. Branger ◽  
C. Médigue ◽  
E. Denamur ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sensitivity And Specificity ◽  
Virulence Genes ◽  
List Type ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum ◽  
Targeted Approach

AbstractPlasmid prediction may be of great interest when studying bacteria such as Enterobacteriaceae. Indeed many resistance and virulence genes are located on such replicons and can have major impact in terms of pathogenicity and spreading capacities. Beyond strains outbreak, plasmids outbreaks have been reported especially for some extended-spectrum beta-lactamase or carbapenemase producing Enterobacteriaceae. Several tools are now available to explore the “plasmidome” from whole-genome sequence data, with many interesting and various approaches. However recent benchmarks have highlighted that none of them succeed to combine high sensitivity and specificity. With this in mind we developed PlaScope, a targeted approach to recover plasmidic sequences in Escherichia coli. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, it performs a classification of contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, Plasflow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes containing plasmids. Finally we tested our method on a dataset of E. coli strains exhibiting an elevated rate of extended-spectrum beta-lactamase coding gene chromosomal integration, and we were able to identify 20/21 of these events. Moreover virulence genes and operons predicted locations were also in agreement with the literature. Similar approaches could also be developed for other well-characterized bacteria such as Klebsiella pneumoniae.Data summaryAll the genomes were downloaded from the National Center for Biotechnology Information Sequence Read Archive and Genome database (Supplementary table 1 and 2).The source code of PlaScope is available on Github (https://github.com/GuilhemRoyer/PlaScope).ImportancePlasmid exploration could be of great interest since these replicons are pivotal in the adaptation of bacteria to their environment. They are involved in the exchange of many genes within and between species, with a significant impact on antibiotic resistance and virulence in particular. However, plasmid characterization has been a laborious task for many years, requiring complex conjugation or electroporation manipulations for example. With the advent of whole genome sequencing techniques, access to these sequences is now potentially easier provided that appropriate tools are available. Many softwares have been developed to explore the plasmidome of a large variety of bacteria, but they rarely managed to combine sensitivity and specificity. Here, we focus on a single species, E. coli, and we use the many data available to overcome this problem. With our tool called PlaScope, we achieve high performance compared with two other classifiers, Plasflow and cBar, and we demonstrate the utility of such an approach to determine the location of virulence or resistance genes. We think that PlaScope could be very useful in the analysis of specific and well-known bacteria.

scholarly journals Whole-Genome Sequencing-Based Characteristics in Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Retail Meats in Korea

2020 ◽  
Vol 8 (4) ◽  
pp. 508
Author(s):  
Seokhwan Kim ◽  
Hansol Kim ◽  
Yonghoon Kim ◽  
Migyeong Kim ◽  
Hyosun Kwak ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum ◽  
Retail Meat ◽  
Meat Samples

The spread of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) has posed a critical health risk to both humans and animals, because resistance to beta-lactam antibiotics makes treatment for commonly infectious diseases more complicated. In this study, we report the prevalence and genetic characteristics of ESBL-ECs isolated from retail meat samples in Korea. A total of 1205 E. coli strains were isolated from 3234 raw meat samples, purchased from nationwide retail stores between 2015 and 2018. Antimicrobial susceptibility testing was performed for all isolates by a broth microdilution method, and the ESBL phenotype was determined according to the Clinical and Laboratory Standards Institute (CLSI) confirmatory method. All ESBL-EC isolates (n = 29) were subjected to whole-genome sequencing (WGS). The antimicrobial resistance genes, plasmid incompatibility types, E. coli phylogroups, and phylogenetic relations were investigated based on the WGS data. The prevalence of ESBL-ECs in chicken was significantly higher than that in other meat samples. The results in this study demonstrate that clonally diverse ESBL-ECs with a multidrug resistance phenotype were distributed nationwide, although their prevalence from retail meat was 0.9%. The dissemination of ESBL-ECs from retail meat poses a potential risk to consumers and food-handlers, suggesting that the continuous surveillance of ESBL-ECs in retail meat should be conducted at the national level.

scholarly journals Molecular Epidemiology of Escherichia coli Sequence Type 131 and Its H30 and H30-Rx Subclones among Extended-Spectrum-β-Lactamase-Positive and -Negative E. coli Clinical Isolates from the Chicago Region, 2007 to 2010

2013 ◽  
Vol 57 (12) ◽  
pp. 6385-6388 ◽  
Author(s):  
Ritu Banerjee ◽  
Ari Robicsek ◽  
Michael A. Kuskowski ◽  
Stephen Porter ◽  
Brian D. Johnston ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Sequence Type ◽  
Beta Lactamase ◽  
Esbl Production ◽  
Content Type ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum

ABSTRACTWe assessedEscherichia coliST131 and its H30 and H30-Rx subclones for virulence genes, antimicrobial resistance, and extended-spectrum beta-lactamase (ESBL) type. Although both subclones were associated with ESBL production, H30-Rx isolates had higher resistance scores and were associated specifically with CTX-M-15. Three virulence genes (iha,sat, andiutA) were more prevalent among H30 than non-H30 ST131 isolates. Thus, the H30 and H30-Rx subclones are more antimicrobial resistant and have virulence profiles that are distinct from those of non-H30 ST131 isolates.

scholarly journals Multidrug-Resistant, Including Extended-Spectrum Beta Lactamase-Producing and Quinolone-Resistant, Escherichia coli Isolated from Poultry and Domestic Pigs in Dar es Salaam, Tanzania

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 406
Author(s):  
Zuhura I. Kimera ◽  
Fauster X. Mgaya ◽  
Gerald Misinzo ◽  
Stephen E. Mshana ◽  
Nyambura Moremi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistant ◽  
Antibiotics Resistance ◽  
Beta Lactamase ◽  
Domestic Pigs ◽  
Extended Spectrum Beta Lactamase ◽  
Phenotypic Profile ◽  
E Coli ◽  
Extended Spectrum ◽  
Esbl Producers

We determined the phenotypic profile of multidrug-resistant (MDR) Escherichia coli isolated from 698 samples (390 and 308 from poultry and domestic pigs, respectively). In total, 562 Enterobacteria were isolated. About 80.5% of the isolates were E. coli. Occurrence of E. coli was significantly higher among domestic pigs (73.1%) than in poultry (60.5%) (p = 0.000). In both poultry and domestic pigs, E. coli isolates were highly resistant to tetracycline (63.5%), nalidixic acid (53.7%), ampicillin (52.3%), and trimethoprim/sulfamethoxazole (50.9%). About 51.6%, 65.3%, and 53.7% of E. coli were MDR, extended-spectrum beta lactamase-producing enterobacteriaceae (ESBL-PE), and quinolone-resistant, respectively. A total of 68% of the extended-spectrum beta lactamase (ESBL) producers were also resistant to quinolones. For all tested antibiotics, resistance was significantly higher in ESBL-producing and quinolone-resistant isolates than the non-ESBL producers and non-quinolone-resistant E. coli. Eight isolates were resistant to eight classes of antimicrobials. We compared phenotypic with genotypic results of 20 MDR E. coli isolates, ESBL producers, and quinolone-resistant strains and found 80% harbored blaCTX-M, 15% aac(6)-lb-cr, 10% qnrB, and 5% qepA. None harbored TEM, SHV, qnrA, qnrS, qnrC, or qnrD. The observed pattern and level of resistance render this portfolio of antibiotics ineffective for their intended use.

scholarly journals Evaluation of extended spectrum beta lactamase enzymes prevalence in clinical isolates of Escherichia coli

2011 ◽  
Vol 2 (1) ◽  
pp. 8
Author(s):  
Ronak Bakhtiari ◽  
Jalil Fallah Mehrabadi ◽  
Hedroosha Molla Agamirzaei ◽  
Ailar Sabbaghi ◽  
Mohammad Mehdi Soltan Dallal
Keyword(s):  
Escherichia Coli ◽  
Disk Diffusion ◽  
Confirmatory Test ◽  
Diffusion Method ◽  
Multi Drug Resistance ◽  
Beta Lactamase ◽  
Disk Diffusion Method ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum

Resistance to b-lactam antibiotics by gramnegative bacteria, especially <em>Escherichia coli (E. coli)</em>, is a major public health issue worldwide. The predominant resistance mechanism in gram negative bacteria particularly <em>E. coli </em>is via the production of extended spectrum beta lactamase (ESBLs) enzymes. In recent years, the prevalence of b-lactamase producing organisms is increased and identification of these isolates by using disk diffusion method and no-one else is not satisfactory. So, this investigation focused on evaluating the prevalence of ESBL enzymes by disk diffusion method and confirmatory test (Combined Disk). Five hundred clinical samples were collected and 200 <em>E. coli </em>isolates were detected by standard biochemical tests. To performing initial screening of ESBLs was used from Disk diffusion method on <em>E. coli </em>isolates. A confirmation test (Combined Disk method) was performed on isolates of resistant to cephalosporin's indicators. Up to 70% isolates exhibited the Multi Drug Resistance phenotype. In Disk diffusion method, 128(64%) <em>E. coli </em>isolates which resistant to ceftazidime and cefotaxime while in Combined Disk, among 128 screened isolates, 115 (89.8%) isolates were detected as ESBLs producers. This survey indicate beta lactamase enzymes are playing a significant role in antibiotic resistance and correct detection of them in phenotypic test by using disk diffusion and combined Disk is essential for accurate recognition of ESBLs.

scholarly journals Extended Spectrum Beta-Lactamase Escherichia coli in River Waters Collected from Two Cities in Ghana, 2018–2020

2021 ◽  
Vol 6 (2) ◽  
pp. 105
Author(s):  
Regina Ama Banu ◽  
Jorge Matheu Alvarez ◽  
Anthony J. Reid ◽  
Wendemagegn Enbiale ◽  
Appiah-Korang Labi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
River Waters ◽  
E Coli ◽  
Extended Spectrum ◽  
Two Cities ◽  
Animal Wastewater ◽  
Sources Of Contamination

Infections by Extended-Spectrum Beta-Lactamase producing Escherichia coli (ESBL-Ec) are on the increase in Ghana, but the level of environmental contamination with this organism, which may contribute to growing Antimicrobial Resistance (AMR), is unknown. Using the WHO OneHealth Tricycle Protocol, we investigated the contamination of E. coli (Ec) and ESBL-Ec in two rivers in Ghana (Odaw in Accra and Okurudu in Kasoa) that receive effluents from human and animal wastewater hotspots over a 12-month period. Concentrations of Ec, ESBL-Ec and percent ESBL-Ec/Ec were determined per 100 mL sample. Of 96 samples, 94 (98%) were positive for ESBL-Ec. concentrations per 100 mL (MCs100) of ESBL-Ec and %ESBL-Ec from both rivers were 4.2 × 104 (IQR, 3.1 × 103–2.3 × 105) and 2.79 (IQR, 0.96–6.03), respectively. MCs100 were significantly lower in upstream waters: 1.8 × 104 (IQR, 9.0 × 103–3.9 × 104) as compared to downstream waters: 1.9 × 106 (IQR, 3.7 × 105–5.4 × 106). Both human and animal wastewater effluents contributed to the increased contamination downstream. This study revealed high levels of ESBL-Ec in rivers flowing through two cities in Ghana. There is a need to manage the sources of contamination as they may contribute to the acquisition and spread of ESBL-Ec in humans and animals, thereby contributing to AMR.

scholarly journals Incidence and Antimicrobial Susceptibility of Escherichia coli and Klebsiella pneumoniae with Extended-Spectrum β-Lactamases in Community- and Hospital-Associated Intra-Abdominal Infections in Europe: Results of the 2008 Study for Monitoring Antimicrobial Resistance Trends (SMART)

2010 ◽  
Vol 54 (7) ◽  
pp. 3043-3046 ◽  
Author(s):  
Stephen P. Hawser ◽  
Samuel K. Bouchillon ◽  
Daryl J. Hoban ◽  
Robert E. Badal ◽  
Rafael Cantón ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Antimicrobial Susceptibility ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum ◽  
Abdominal Infections

ABSTRACT From 2002 to 2008, there was a significant increase in extended-spectrum beta-lactamase (ESBL)-positive Escherichia coli isolates in European intra-abdominal infections, from 4.3% in 2002 to 11.8% in 2008 (P < 0.001), but not for ESBL-positive Klebsiella pneumoniae isolates (16.4% to 17.9% [P > 0.05]). Hospital-associated isolates were more common than community-associated isolates, at 14.0% versus 6.5%, respectively, for E. coli (P < 0.001) and 20.9% versus 5.3%, respectively, for K. pneumoniae (P < 0.01). Carbapenems were consistently the most active drugs tested.

scholarly journals Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

2019 ◽  
Author(s):  
Denise van Hout ◽  
Tess D. Verschuuren ◽  
Patricia C.J. Bruijning-Verhagen ◽  
Thijs Bosch ◽  
Anita C. Schürch ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
The Netherlands ◽  
Resistance Gene ◽  
Acquired Resistance ◽  
Virulence Gene ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum ◽  
Clonal Distribution

ABSTRACTBackgroundKnowledge on the molecular epidemiology of Escherichia coli causing E. coli bacteremia (ECB) in the Netherlands is mostly based on extended-spectrum beta-lactamase-producing E. coli (ESBL-Ec). We determined differences in clonality and resistance and virulence gene (VG) content between non-ESBL-producing E. coli (non-ESBL-Ec) and ESBL-Ec blood isolates with different epidemiological characteristics.Materials/methodsA random selection of non-ESBL-Ec isolates as well as all available ESBL-Ec blood isolates was obtained from two Dutch hospitals between 2014 and 2016. Whole genome sequencing was performed to infer sequence types (STs), serotypes, acquired antibiotic resistance genes and VG scores, based on presence of 49 predefined putative pathogenic VG.ResultsST73 was most prevalent among the 212 non-ESBL-Ec (N=26, 12.3%) and ST131 among the 69 ESBL-Ec (N=30, 43.5%). Prevalence of ST131 among non-ESBL-Ec was 10.4% (N=22, P value < 0.001 compared to ESBL-Ec). O25:H4 was the most common serotype in both non-ESBL-Ec and ESBL-Ec. Median acquired resistance gene counts were 1 (IQR 1 – 6) and 7 (IQR 4 – 9) for non-ESBL-Ec and ESBL-Ec, respectively (P value < 0.001). Among non-ESBL-Ec, acquired resistance gene count was highest among blood isolates from a primary gastro-intestinal focus (median 4, IQR 1 – 8). Median VG scores were 13 (IQR 9 – 20) and 12 (IQR 8 – 14) for non-ESBL-Ec and ESBL-Ec, respectively (P value = 0.002). VG scores among non-ESBL-Ec from a primary urinary focus (median 15, IQR 11 – 21) were higher compared to non-ESBL-Ec from a primary gastro-intestinal (median 10, IQR 6 – 13) or hepatic-biliary focus (median 11, IQR 5 – 18) (P values = 0.007 and 0.036, respectively). VG content varied between different E. coli STs.ConclusionsNon-ESBL-Ec and ESBL-Ec blood isolates from two Dutch hospitals differed in clonal distribution, resistance gene and VG content. Also, resistance gene and VG content differed between non-ESBL-Ec from different primary foci of ECB.

scholarly journals Molecular detection and antibiotic resistance pattern of extended-spectrum beta-lactamase producing Escherichia coli in a Tertiary Hospital in Enugu, Nigeria

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Ifeyinwa N. Nwafia ◽  
Martin E. Ohanu ◽  
Samuel O. Ebede ◽  
Uchenna C. Ozumba
Keyword(s):  
Risk Factors ◽  
Escherichia Coli ◽  
Intensive Care Unit ◽  
Intensive Care ◽  
Intensive Care Unit Admission ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum ◽  
Associated Risk Factors

Abstract Background The use of antibiotic agents in the treatment of infectious diseases has greatly contributed to the decrease in morbidity and mortality, but these great advances in treatment are being undermined by the rapidly increasing antimicrobial resistant organisms. Extended-spectrum beta-lactamases are enzymes hydrolyzing the beta lactam antibiotics, including third generation cephalosporins and monobactams but not cephamycins and carbapenems. They pose a serious global health threat and have become a challenge for health care providers. The aim of this research was to assess the prevalence of extended-spectrum beta-lactamase producing Escherichia coli in University of Nigeria Teaching Hospital Ituku-Ozalla Enugu and to detect the risk factors for acquisition of the resistant organism. To proffer advice on antibiotic stewardship in clinical practice and public health interventions, to curb the spread of the resistant organisms in the hospital. Results Out of the 200 E. coli isolates, 70 (35.00%) were confirmed positive for extended-spectrum beta-lactamase production. Fifty-three (75.7%) were from hospital acquired infections. All the isolates were resistant to ampicillin, tetracycline and chloramphenicol while 68 (97.14%) of the 70 isolates were susceptible to imipenem. BlaTEM, blaSHV and blaTEM were detected in 66 (94%) of the 70 isolates. The ESBL bla genes detected were blaCTX-M (n = 26; 37.14%), blaTEM (n = 7; 10.00%), blaSHV (n = 2; 2.86%), blaCTX-M/TEM (n = 7; 10.0%), blaCTX-M/SHV (n = 14; 20.0%) and blaCTX-M/TEM/SHV (n = 10; 14.29%). The three bla genes were not detected in 4 (5.71%) of the isolates. Recent surgery, previous antibiotic and intensive care unit admission were the associated risk factors to infections caused by extended-spectrum beta-lactamase producing E. coli. Conclusion There is a high rate of infections caused by extended-spectrum beta-lactamase producing E. coli. Recent surgery, previous antibiotic and intensive care unit admission were associated risk factors.

scholarly journals Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli Isolated from Flies in the Urban Center of Berlin, Germany

2019 ◽  
Vol 16 (9) ◽  
pp. 1530 ◽  
Author(s):  
Wibke Wetzker ◽  
Yvonne Pfeifer ◽  
Solvy Wolke ◽  
Andrea Haselbeck ◽  
Rasmus Leistner ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Continuous Monitoring ◽  
Companion Animals ◽  
Multidrug Resistant ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum ◽  
Ciprofloxacin Resistance ◽  
Multiple Pathogens

Background: The monitoring of antimicrobial resistance (AMR) in microorganisms that circulate in the environment is an important topic of scientific research and contributes to the development of action plans to combat the spread of multidrug-resistant (MDR) bacteria. As a synanthropic vector for multiple pathogens and a reservoir for AMR, flies can be used for surveillance. Methods: We collected 163 flies in the inner city of Berlin and examined them for extended-spectrum β-lactamase (ESBL)-producing Escherichia coli genotypically and phenotypically. Results: The prevalence of ESBL-producing E. coli in flies was 12.9%. Almost half (47.6%) of the ESBL-positive samples showed a co-resistance to ciprofloxacin. Resistance to carbapenems or colistin was not detected. The predominant ESBL-type was CTX-M-1, which is associated with wildlife, livestock, and companion animals as a potential major source of transmission of MDR E. coli to flies. Conclusions: This field study confirms the permanent presence of ESBL-producing E. coli in an urban fly population. For continuous monitoring of environmental contamination with multidrug-resistant (MDR) bacteria, flies can be used as indicators without much effort.

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