scholarly journals Genetic characterisation of a large antibiotic resistant environmental ST131 E. coli plasmid using a long read hybrid assembly approach

2020 ◽  
Author(s):  
R.S. James ◽  
S. Rangama ◽  
V. Clark ◽  
E.M.H. Wellington
Keyword(s):  
Hybrid Assembly ◽  
Insertion Element ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Long Read ◽  
Pipe Line ◽  
Strain Type ◽  
Coli Plasmid ◽  
Genetic Context

AbstractEscherichia coli Strain Type 131 are a globally disseminated environmental E. coli that has been linked to the capture and spread of plasmid mediated blaCTX-M type extended spectrum beta-lactamase (ESBLs). Accurately identifying such resistance genes in their wider genetic context provides a greater understanding of the mechanisms of selection and persistence in the environment. In this study we use a novel DNA extraction and enrichment method in combination with a custom long-read scaffold hybrid-assembly and polishing pipe line to identify the genetic context of the plasmid borne blaCTX-M gene previously identified in an ST131 environmental E. coli isolate. This has allowed us to discern the complete structure of a ~100kb environmental plasmid and further resolve the blaCTX-M variant to the group 9 blaCTX-M-27 gene. The upstream IS26 insertion element associated with the global capture and dissemination of blaCTX-M-15 was also identified in proximity to blaCTX-M-27. Furthermore, the lack of conjugative machinery identified on this plasmid, in combination with a toxin-antitoxin and plasmid partitioning system, indicates a mechanism of vertical transmission to maintain persistence in a population.

scholarly journals Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

2021 ◽  
Vol 9 (8) ◽  
pp. 1613
Author(s):  
Julian A. Paganini ◽  
Nienke L. Plantinga ◽  
Sergio Arredondo-Alonso ◽  
Rob J. L. Willems ◽  
Anita C. Schürch
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Special Focus ◽  
Valuable Insight ◽  
Sequencing Data ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Long Read

The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.

scholarly journals Antibiotic-Resistant Escherichia coli and Salmonella from the Feces of Food Animals in the East Province of Rwanda

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1013
Author(s):  
Rosine Manishimwe ◽  
Paola M. Moncada ◽  
Vestine Musanayire ◽  
Anselme Shyaka ◽  
H. Morgan Scott ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Culture Media ◽  
Future Research ◽  
Third Generation ◽  
Antibiotic Resistant ◽  
Disk Diffusion Test ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Food Animals ◽  
Third Generation Cephalosporins

In Rwanda, information on antibiotic resistance in food animals is scarce. This study was conducted to detect and phenotypically characterize antibiotic-resistant Escherichia coli and Salmonella in feces of cattle, goats, pigs, and poultry in the East province of Rwanda. We isolated non-type-specific (NTS) E. coli and Salmonella using plain culture media. In addition, we used MacConkey agar media supplemented with cefotaxime at 1.0 μg/mL and ciprofloxacin at 0.5 μg/mL to increase the probability of detecting E. coli with low susceptibility to third-generation cephalosporins and quinolones, respectively. Antibiotic susceptibility testing was performed using the disk diffusion test. Among 540 NTS E. coli isolates, resistance to tetracycline was the most frequently observed (35.6%), followed by resistance to ampicillin (19.6%) and streptomycin (16.5%). Percentages of NTS E. coli resistant to all three antibiotics and percentages of multidrug-resistant strains were higher in isolates from poultry. All isolated Salmonella were susceptible to all antibiotics. The sample-level prevalence for resistance to third-generation cephalosporins was estimated at 35.6% with all third-generation cephalosporin-resistant E. coli, expressing an extended-spectrum beta-lactamase phenotype. The sample-level prevalence for quinolone resistance was estimated at 48.3%. These results provided a baseline for future research and the development of integrated surveillance initiatives.

scholarly journals Clinical and demographic features associated with infections with extended-spectrum beta-lactamase–producing Escherichia coli in a health system in Maine, 2017

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Eugene W. Liu ◽  
Sarah N. Buss ◽  
Jennifer L. Trumbo ◽  
Tina M. Temples
Keyword(s):  
Escherichia Coli ◽  
Case Control Study ◽  
Infection Risk ◽  
Infection Prevalence ◽  
Beta Lactamase ◽  
Hospital System ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Control Study

Abstract In this case–case control study, we identified receipt of β-lactam antibiotics and older age as independently associated with increased infection risk with ESBL-producing Escherichia coli among residents aged 20–88 years in a rural Maine hospital system where the infection prevalence of antibiotic-resistant E. coli is low.

scholarly journals Chromosome Mediated Fluoroquinolone and Extended Spectrum Beta-lactamase Resistant Genes in E. coli of Poultry Origin in Ekiti State

2021 ◽  
pp. 35-51
Author(s):  
A. O. Oluyege ◽  
K. O. Ojo
Keyword(s):  
Antibiotic Treatment ◽  
Waste Disposal ◽  
Beta Lactamase ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Resistant Genes ◽  
Band Size ◽  
Poultry Droppings ◽  
Relationship Of

Background: One health approach aimed at solving global health crisis links human, animal, and environmental health. This inclusive strategy has contributed to antibiotic classification in both human and animal medicine. Aims: The aims of this research work are to determine the phylogenetic relationship of E. coli isolated from poultry and waste sources. The presence of chromosome mediated fluoroquinolone and extended spectrum beta-lactamase resistant genes will also be detected in the isolates. Study Design: Experimental design. Methodology: Data on farming attitudes of poultry farmers were collected using a questionnaire. E. coli was isolated from fresh poultry droppings and waste disposal sites using eosine methylene blue agar. The antibiotic sensitivity profile of the isolates was determined using the modified Kirby Bauer disc diffusion method. Phenotypic expression of fluoroquinolone (qnrS) and beta-lactamase (blaCMY) resistant traits were further detected using Polymerase Chain Reaction. The 16S rRNA gene sequencing was carried out followed by sequence alignment of E. coli genes with those from GenBank sources to determine the molecular identity of the isolates. Spearman’s correlation coefficient (rs) was run to determine the relationship between antibiotic treatment and resistant profile of the isolates. The phylogenetic relationship of the isolates was determined using Bio edit and Mega 6 software. Results: Organic poultry farming was practiced by small-scaled, peasant farmers who raised free range birds while antibiotics were widely used on farms that adopted intensive mode of               farming. The percentage occurrence of E. coli from waste disposal sources was lesser than that from fresh poultry droppings. Highest percentage of antibiotic resistance to the fluoroquinolones was found while the carbapenemase recorded the lowest. Statistical analysis shows that antibiotic treatment in poultry and resistant profile of isolates to antibiotics are directly related. The percentage similarity of gene sequence with those from Gene Data Bank (≥99.29%) validates the identity of the isolates as E. coli. About, 60% of the sampled population had the qnrS gene with a band size of approximately 322 base pair. Besides, 40% of the sampled isolates possessed the blaCMY gene with a band size of approximately 460 base pair. Both genes co-existed in the chromosome of 15% of the sampled isolates sourced from poultry droppings and waste sources. Phylogenetic classification links the origin of isolates from waste disposal sources to poultry production sites. Besides, variant strains of multiple antibiotic resistant E. coli from poultry with antibiotic treatment were more diverse compared to those obtained from birds raised without antibiotics. Conclusion: The qnrS and blaCMY genes found in multiple antibiotic resistant E. coli mediated resistance to critically important antibiotics. The co-existence of these genes in variants strains of E. coli occupying different phylogenetic clusters suggests that antibiotics were widely used on the   birds. Antibiotic treatment regimen in poultry may be responsible for the expression of antibiotic resistant genes found in the chromosome of the variant strains of E. coli.

scholarly journals Antimicrobial Resistance and Molecular Detection of Extended Spectrum β-Lactamase Producing Escherichia coli Isolates from Raw Meat in Greater Accra Region, Ghana

2020 ◽  
Author(s):  
Esther Dsani ◽  
Edwin Andrews Afari ◽  
Anthony Danso-Appiah ◽  
Ernest Kenu ◽  
Basil Benduri Kaburi ◽  
...  
Keyword(s):  
Total Coliform ◽  
Multi Drug Resistance ◽  
Resistant Bacteria ◽  
Antibiotic Resistant ◽  
Raw Meat ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Acceptable Limit ◽  
Extended Spectrum ◽  
Meat Samples

Abstract BackgroundTypically, raw meat can be contaminated with antibiotic resistant pathogens at unhygienic slaughter and sale points. Consumption of meat contaminated with antibiotic resistant E. coli is associated with grave health care consequences. The aim of this study was to determine the microbial quality of raw meat, the antimicrobial susceptibility and Extended Spectrum Beta Lactamase (ESBL) production in E. coli isolates from raw meat. ResultsTotal Plate Counts exceeded the acceptable limit of 5.0 log CFU/ cm2 in 60.5% (124/205) of raw meat samples. Total Coliform Counts in 70.7% (145/205) of samples were in excess of the acceptable limit of 2.5 log CFU/cm2. E. coli was detected in about half of raw meat samples (48%), ranging from 9.5% -79.0% among the slaughter sites. Isolates were susceptible to meropenem (100%), ceftriaxone (99%), cefotaxime (98%), chloramphenicol (97%), gentamycin (97%), ciprofloxacin (92%) and amikacin (92%), but resistant to ampicillin (57%), tetracycline (45%), sulfamethoxazole-trimethoprim (21%) and cefuroxime (17%). Multi-drug resistance (MDR) was identified in 22% of the isolates. The blaTEM gene was detected in 4% (4/98) of E. coli isolates in this study. ConclusionThe levels of microbial contamination of raw meat in this study were unacceptable. Meat handlers and consumers are at risk of foodborne infections from E. coli including ESBL producing E. coli that are resistant to most antibiotics in use. We recommend an enhanced surveillance for antibiotic resistance in food products for the early detection of emerging resistant bacteria species in the food chain.

scholarly journals Frequency of antibiotic resistant enteropathogenic Escherichia coli (EPEC) in bovine carcasses at a slaughterhouse in Brazil

2020 ◽  
Vol 9 (7) ◽  
pp. e475974339
Author(s):  
Ariel Eurides Stella ◽  
Gracielle Teles Pádua ◽  
Cecília Nunes Moreira ◽  
Paula Siqueira Martins ◽  
Maurício Costa Montes ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Microbiological Quality ◽  
Foodborne Diseases ◽  
Beta Lactamase ◽  
Drug Resistant ◽  
Enteropathogenic Escherichia Coli ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli

Escherichia coli (E. coli) comes in second place among microorganisms involved in outbreaks of foodborne diseases in Brazil and is among the 4 most prominent worldwide. Due to its importance, the purpose of this work is to verify microbiological quality by the presence of E. coli in bovine carcasses. A total of 365 E. coli were isolated by swabs of 154 carcasses of cattle, slaughtered in the municipality of Mineiros – GO, Brazil. The frequency of E. coli in the samples collected was 81% (125/154). Of these E. coli, 16 had the gene eae, and none presented the genes stx1 or stx2, so were therefore classified as EPEC. Thus, the frequency of EPEC in the carcasses was 9.7% (15/154). The strains were classified as part of the A or B1 groups. As for antimicrobial resistance, the antibiotics with the highest percentages of resistance were Cephalothin with 82% (41/50), followed by Gentamicin and Amikacin with 26% (13/50) each. None of the samples showed any production of the extended-spectrum beta-lactamase enzyme, but three EPECs were classified as multi-drug resistant. The results demonstrate the presence of multi-resistant EPEC in bovine carcasses slaughtered in Mineiros city, Brazil.

scholarly journals Antibiotic resistance profile of E. coli isolates in 17 municipal wastewater utilities across Oregon

2021 ◽  
Author(s):  
Marjan Khorshidi Zadeh ◽  
Sue Yee Yiu ◽  
Jacquelynn N Nguyen ◽  
Gabriela L Garza ◽  
Joy Waite-Cusic ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Antimicrobial Resistance ◽  
Multi Drug Resistance ◽  
Beta Lactamase ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Ciprofloxacin Resistance

Wastewater treatment utilities are considered one of the main sources and reservoirs of antimicrobial resistance. The objective of this study was to determine the diversity and prevalence of antibiotic-resistant Escherichia coli in wastewater treatment systems across the state of Oregon. Influent, secondary effluent, final effluent, and biosolids were collected from 17 wastewater treatment utilities across Oregon during the winter and summer seasons of 2019 and 2020 (n = 246). E. coli strains were recovered from samples by culturing on mTEC, followed by confirmation with MacConkey with MUG agar plates. Antibiotic susceptibility of 1143 E. coli isolates against 8 antibiotics were determined, and resistance profiles and indices were analyzed between utilities, seasons, and flows. Antibiotic resistance phenotypes were detected in 31.6% of the collected E. coli isolates. Among those antibiotic-resistant E. coli isolates, multi-drug resistance (i.e., resistance to three or more classes of antibiotics) was harbored by 27.7% with some strains showing resistance to up to six classes of antibiotics. The most prevalent resistance was to ampicillin (n = 207) and the most common combinations of multi-drug resistance included simultaneous resistances to ampicillin, streptomycin, and tetracycline (n = 49), followed by ampicillin, streptomycin, and sulfamethoxazole/trimethoprim (n = 46). Significant correlations were observed between resistance to sulfamethoxazole/trimethoprim and resistances to ampicillin, ciprofloxacin, and tetracycline (p < 0.001). A small percentage (1.1%) of the E. coli isolates displayed extended-spectrum beta lactamase (ESBL) activity and a single isolate carried resistance to imipenem. Compared to wastewater influent, ciprofloxacin resistance was significantly more prevalent in biosolids (p <0.05) and tetracycline resistance was significantly lower in effluent (p <0.05). Seasonal impact on antibiotic-resistant E. coli in wastewater influent was observed through significantly higher multiple antibiotic resistance (MAR) index, ampicillin resistance prevalence, and ciprofloxacin resistance prevalence in summer compared to winter (p < 0.05). This state-wide study confirms the widespread distribution of antibiotic-resistant, multi-drug resistant, and extended-spectrum beta lactamase-producing E. coli in wastewater systems across different flows and seasonal variations, making them the recipients, reservoirs, and sources of antimicrobial resistance.

scholarly journals Survey of US wastewater for carbapenem-resistant Enterobacteriaceae

2019 ◽  
Vol 17 (2) ◽  
pp. 219-226 ◽  
Author(s):  
Jill Hoelle ◽  
James R. Johnson ◽  
Brian D. Johnston ◽  
Brian Kinkle ◽  
Laura Boczek ◽  
...  
Keyword(s):  
Wastewater Treatment Plants ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Geographically Dispersed ◽  
Carbapenem Resistant ◽  
Carbapenemase Gene ◽  
Clinically Significant ◽  
Sequence Types ◽  
Carbapenem Resistant Enterobacteriaceae

Abstract A survey for antibiotic-resistant (AR) Escherichia coli in wastewater was undertaken by collecting samples from primary clarifiers and secondary effluents from seven geographically dispersed US wastewater treatment plants (WWTPs). Samples were collected at each WWTP in cool and summer months and cultured using selective media. The resulting isolates were characterized for resistance to imipenem, ciprofloxacin, cefotaxime, and ceftazidime, presence of carbapenemase and extended-spectrum beta-lactamase (ESBL) genes, and phylogroups and sequence types (STs). In total, 322 AR E. coli isolates were identified, of which 65 were imipenem-resistant. Of the 65 carbapenem-resistant E. coli (CREC) isolates, 62% were positive for more than one and 31% were positive for two or more of carbapenemase and ESBL genes targeted. The most commonly detected carbapenemase gene was blaVIM (n = 36), followed by blaKPC (n = 2). A widespread dispersal of carbapenem-resistant STs and other clinically significant AR STs observed in the present study suggested the plausible release of these strains into the environment. The occurrence of CREC in wastewater is a potential concern because this matrix may serve as a reservoir for gene exchange and thereby increase the risk of AR bacteria (including CR) being disseminated into the environment and thence back to humans.

scholarly journals Antibiotic-Resistant Escherichia coli Bacteria, Including Strains with Genes Encoding the Extended-Spectrum Beta-Lactamase and QnrS, in Waterbirds on the Baltic Sea Coast of Poland

2010 ◽  
Vol 76 (24) ◽  
pp. 8126-8134 ◽  
Author(s):  
Ivan Literak ◽  
Monika Dolejska ◽  
Dagmar Janoszowska ◽  
Jolana Hrusakova ◽  
Wlodzimierz Meissner ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Baltic Sea ◽  
Wild Birds ◽  
Beta Lactamase ◽  
The Baltic Sea ◽  
Antibiotic Resistant ◽  
Extended Spectrum Beta Lactamase ◽  
E Coli ◽  
Extended Spectrum ◽  
The Baltic

ABSTRACT Individual cloacal swabs of mallards (Anas platyrhynchos) and of herring gulls (Larus argentatus), as well as samples of waterbird feces obtained in 2008 and 2009, were cultivated for Escherichia coli. Isolates of E. coli were tested for susceptibilities to 12 antimicrobial agents by the disk diffusion method. Moreover, the samples were subcultivated on MacConkey agar (MCA) containing cefotaxime (2 mg liter−1) to detect E. coli with extended-spectrum beta-lactamase (ESBL) and subsequently on MCA supplemented with ciprofloxacin (0.05 mg liter−1) and MCA with nalidixic acid (20 mg liter−1) to isolate fluoroquinolone-resistant E. coli. PCR was used to detect specific antibiotic resistance genes. We found 9 E. coli isolates producing ESBL with bla genes: bla CTX-M-1 (6 isolates), bla CTX-M-9 plus bla TEM-1b (1 isolate), bla CTX-M-15 plus bla OXA-1 (1 isolate), and bla SHV-12 (1 isolate). In the isolate with bla CTX-M-15, the gene aac(6)-Ib-cr was also detected. The bla genes were harbored by transferable plasmids of the IncN and IncI1 groups. Nine quinolone-resistant E. coli isolates with qnrS genes were found and characterized. The gene qnrS was associated with a Tn3-like transposon on the IncX1 plasmid together with bla TEM-1 in two isolates. The gene qnrS was also harbored by conjugative plasmids of the IncN and IncX2 groups. Even if populations of wild birds are not directly influenced by antibiotic practice, we have demonstrated that antibiotic-resistant E. coli strains, including strains with various ESBL and qnrS genes, are found in the feces of wild birds on the coast of the Baltic Sea in Poland.

scholarly journals Characterisation of Early Positive mcr-1 Resistance Gene and Plasmidome in Escherichia coli Pathogenic Strains Associated with Variable Phylogroups under Colistin Selection

Antibiotics ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1041
Author(s):  
Guerrino Macori ◽  
Scott V. Nguyen ◽  
Ankita Naithani ◽  
Daniel Hurley ◽  
Li Bai ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Single Molecule ◽  
Bovine Mastitis ◽  
Antibiotic Resistance Genes ◽  
Genomic Context ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Faecal Samples ◽  
Long Read

An antibiotic susceptibility monitoring programme was conducted from 2004 to 2010, resulting in a collection of 143 Escherichia coli cultured from bovine faecal samples (diarrhoea) and milk-aliquots (mastitis). The isolates were subjected to whole-genome sequencing and were distributed in phylogroups A, B1, B2, C, D, E, and G with no correlation for particular genotypes with pathotypes. In fact, the population structure showed that the strains belonging to the different phylogroups matched broadly to ST complexes; however, the isolates are randomly associated with the diseases, highlighting the necessity to investigate the virulence factors more accurately in order to identify the mechanisms by which they cause disease. The antimicrobial resistance was assessed phenotypically, confirming the genomic prediction on three isolates that were resistant to colistin, although one isolate was positive for the presence of the gene mcr-1 but susceptible to colistin. To further characterise the genomic context, the four strains were sequenced by using a single-molecule long read approach. Genetic analyses indicated that these four isolates harboured complex and diverse plasmids encoding not only antibiotic resistant genes (including mcr-1 and bla) but also virulence genes (siderophore, ColV, T4SS). A detailed description of the plasmids of these four E. coli strains, which are linked to bovine mastitis and diarrhoea, is presented for the first time along with the characterisation of the predicted antibiotic resistance genes. The study highlighted the diversity of incompatibility types encoding complex antibiotic resistance elements such as Tn6330, ISEcp1, Tn6029, and IS5075. The mcr-1 resistance determinant was identified in IncHI2 plasmids pCFS3273-1 and pCFS3292-1, thus providing some of the earliest examples of mcr-1 reported in Europe, and these sequences may be a representative of the early mcr-1 plasmidome characterisation in the EU/EEA.

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