scholarly journals Genomic evolution of antimicrobial resistance in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Markus Hans Kristofer Johansson ◽  
Patrick Munk ◽  
Burkhard Malorny ◽  
Magdalena Skarżyńska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Mobile Genetic Elements ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
E Coli ◽  
Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

scholarly journals Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

mBio ◽  
2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Nicole Stoesser ◽  
Anna E. Sheppard ◽  
Louise Pankhurst ◽  
Nicola De Maio ◽  
Catrin E. Moore ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Evolutionary History ◽  
Mobile Genetic Elements ◽  
The United States ◽  
Sequence Type ◽  
E Coli ◽  
Genetic Elements ◽  
Extended Spectrum ◽  
History Of

ABSTRACT Escherichia coli sequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection ( n = 215) of sequenced ST131 E. coli isolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/ H 30R and C2/ H 30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/ H 30Rx clade driven by the acquisition of a bla CTX-M-15 -containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration of bla CTX-M within subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, the bla CTX-M-14/14-like group. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages of E. coli . These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages. IMPORTANCE Escherichia coli , perennially a major bacterial pathogen, is becoming increasingly difficult to manage due to emerging resistance to all preferred antimicrobials. Resistance is concentrated within specific E. coli lineages, such as sequence type 131 (ST131). Clarification of the genetic basis for clonally associated resistance is key to devising intervention strategies. We used high-resolution genomic analysis of a large global collection of ST131 isolates to define the evolutionary history of extended-spectrum beta-lactamase production in ST131. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance elements. Both global distribution and regional segregation were evident. The diversity of resistance element acquisition and propagation within ST131 indicates a need for control and surveillance strategies that target both bacterial strains and mobile genetic elements.

scholarly journals Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

2021 ◽  
Vol 22 (11) ◽  
pp. 5905
Author(s):  
Olivia M. Grünzweil ◽  
Lauren Palmer ◽  
Adriana Cabal ◽  
Michael P. Szostak ◽  
Werner Ruppitsch ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Marine Mammals ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Healthcare Sector ◽  
Whole Genome ◽  
E Coli ◽  
High Prevalence ◽  
Lactamase Gene ◽  
Sequence Types

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces†

2016 ◽  
Vol 79 (1) ◽  
pp. 66-74 ◽  
Author(s):  
P. B. SHRIDHAR ◽  
L. W. NOLL ◽  
X. SHI ◽  
B. AN ◽  
N. CERNICCHIARO ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Quantitative Pcr ◽  
Foodborne Pathogens ◽  
Virulence Genes ◽  
Target Genes ◽  
Culture Methods ◽  
Fecal Samples ◽  
E Coli ◽  
Cattle Feces ◽  
Before And After

ABSTRACT Shiga toxin–producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens. Cattle, a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx1, stx2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces. The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture–spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment). Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P < 0.01) as positive for one or more serogroups compared with cPCR and culture methods. This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.

scholarly journals Integron Expression in Multidrug-Resistant Escherichia coli Isolated from House Flies within the Hospital

2018 ◽  
Vol 16 (5) ◽  
pp. 319-327
Author(s):  
Atchariya YOSBOONRUANG ◽  
Anong KIDDEE ◽  
Chatsuda BOONDUANG ◽  
Phannarai PIBALPAKDEE
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Hospital Environment ◽  
Sequencing Analysis ◽  
Class 1 Integron ◽  
House Flies ◽  
E Coli ◽  
Class 1 Integrons ◽  
Class 1

Escherichia coli is a serious cause of a variety of hospital-acquired infections and commonly contributes to the environment by house flies. Integrons, particularly class 1 integrons, are the genetic elements that play an important role in the horizontal transfer of antimicrobial resistance mechanism. This mechanism is commonly found in Enterobacteriaceae, especially E. coli. In this study, we aim to investigate the occurrence and antimicrobial resistance patterns of E. coli isolated from the house flies in Phayao hospital and to determine the gene expression of class 1 integrons in those isolates of E. coli. Totally, 70 isolates of E. coli were isolated from 60 house flies collected from the hospital. Fifty-seven of the isolates (81.43 %) were multidrug resistance (MDR) and highly resistant to b-lactams, tetracyclines, and sulfonamides. Of 57 isolates of MDR-E. coli, 20 isolates (35 %) were found to carry class 1 integron genes. Fifteen patterns of antimicrobial resistance occurred in the isolates of integron-positive E. coli. Most integron-positive E. coli isolates were resistant to 7 antimicrobials. Two isolates of these bacteria (10 %) were able to resist 13 out of 14 tested antimicrobials. Using PCR and sequencing analysis, an investigation showed that dfrA17-aadA5, dfrA12-aadA2 gene cassette was the most prevalent cassette (n = 10; 50 %) among the integron-positive E. coli isolates. Our results indicated that the presences of multidrug resistance and class 1 integrons were common in E. coli isolated from the houseflies in hospital. Therefore, screening for integron-positive E. coli from the hospital environment might be necessary for prevention of nosocomial infections.

scholarly journals Molecular characterisation of antimicrobial resistance and virulence genes in Escherichia coli strains isolated from diarrhoeic and healthy rabbits in Tunisia

2020 ◽  
Vol 28 (2) ◽  
pp. 81
Author(s):  
Raouia Ben Rhouma ◽  
Ahlem Jouini ◽  
Amira Klibi ◽  
Safa Hamrouni ◽  
Aziza Boubaker ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Antimicrobial Agents ◽  
Antibiotic Resistance Genes ◽  
Virulence Gene ◽  
Diffusion Method ◽  
Class 1 Integron ◽  
E Coli ◽  
Class 1

The purpose of this study was to identify <em>Escherichia coli</em> isolates in diarrhoeic and healthy rabbits in Tunisia and characterise their virulence and antibiotic resistance genes. In the 2014-2015 period, 60 faecal samples from diarrhoeic and healthy rabbits were collected from different breeding farms in Tunisia. Susceptibility to 14 antimicrobial agents was tested by disc diffusion method and the mechanisms of gene resistance were evaluated using polymerase chain reaction and sequencing methods. Forty <em>E. coli</em> isolates were recovered in selective media. High frequency of resistance to tetracycline (95%) was detected, followed by different levels of resistance to sulphonamide (72.5%), streptomycin (62.5%), trimethoprim-sulfamethoxazole (60%), nalidixic acid (32.5%), ampicillin (37.5%) and ticarcillin (35%). <em>E. coli</em> strains were susceptible to cefotaxime, ceftazidime and imipenem. Different variants of bla<sub>TEM</sub>, <em>tet</em>, <em>sul</em> genes were detected in most of the strains resistant to ampicillin, tetracycline and sulphonamide, respectively. The presence of class 1 integron was studied in 29 sulphonamide-resistant <em>E. coli</em> strains from which 15 harboured class 1 integron with four different arrangements of gene cassettes, <em>dfrA17</em>+<em>aadA5</em> (n=9), <em>dfrA1</em> + <em>aadA1</em> (n=4), <em>dfrA12</em> + <em>addA2</em> (n=1), <em>dfrA12</em>+<em>orf</em>+<em>addA2</em> (n=1). The <em>qnrB</em> gene was detected in six strains out of 13 quinolone-resistant <em>E. coli</em> strains. Seventeen <em>E. coli</em> isolates from diarrhoeic rabbits harboured the enteropathogenic eae genes associated with different virulence genes tested (<em>fimA</em>, <em>cnf1</em>, <em>aer</em>), and affiliated to B2 (n=8) and D (n=9) phylogroups. Isolated <em>E. coli</em> strains from healthy rabbit were harbouring <em>fim A</em> and/or <em>cnf1</em> genes and affiliated to A and B1 phylogroups. This study showed that <em>E. coli</em> strains from the intestinal tract of rabbits are resistant to the widely prescribed antibiotics in medicine. Therefore, they constitute a reservoir of antimicrobial-resistant genes, which may play a significant role in the spread of antimicrobial resistance. In addition, the eae virulence gene seemed to be implicated in diarrhoea in breeder rabbits in Tunisia.

scholarly journals Antimicrobial resistance pattern of extended-spectrum β-lactamase-producing Escherichia coli isolated from fecal samples of piglets and pig farm workers of selected organized farms of India

2020 ◽  
Vol 13 (2) ◽  
pp. 360-363
Author(s):  
Shikha Tamta ◽  
Obli Rajendran Vinodh Kumar ◽  
Shiv Varan Singh ◽  
Bommenahalli Siddaramiah Pruthvishree ◽  
Ravichandran Karthikeyan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Susceptibility Testing ◽  
Farm Workers ◽  
Resistance Pattern ◽  
Antibiotic Susceptibility Testing ◽  
M Gene ◽  
Fecal Samples ◽  
E Coli ◽  
Pig Farm

Background and Aim: Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are gradually increasing worldwide and carry a serious public threat. This study aimed to determine the antimicrobial resistance pattern of ESBL-producing E. coli isolated from fecal samples of piglets and pig farm workers. Materials and Methods: Fecal samples from <3-month-old piglets (n=156) and farm workers (n=21) were processed for the isolation of ESBL-producing E. coli in MacConkey agar added with 1 μg/mL of cefotaxime. E. coli (piglets=124; farm workers=21) were tested for ESBL production by combined disk method and ESBL E-strip test. Each of the ESBL-positive isolate was subjected to antibiotic susceptibility testing. The ESBL-producing E. coli were further processed for genotypic confirmation to CTX-M gene. Results: A total of 55 (44.4%, 55/124) and nine (42.9%, 9/21) ESBL-producing E. coli were isolated from piglets and farm workers, respectively. Antibiotic susceptibility testing of the ESBL-positive E. coli isolates from piglets and farm workers showed 100% resistance to ceftazidime, cefotaxime, cefotaxime/clavulanic acid, ceftazidime/clavulanic acid, and cefpodoxime. A proportion of 100% (55/55) and 88.9% (8/9) ESBL-positive E. coli were multidrug resistance (MDR) in piglets and farm workers, respectively. On genotypic screening of the ESBL E. coli isolated from piglets (n=55), 15 were positive for the blaCTX-M gene and of the nine ESBL E. coli from farm workers, none were positive for the blaCTX-M gene. Conclusion: Although there was no significant difference in isolation of ESBL-producing E. coli between piglets and farm workers, the ESBL-positive E. coli from piglets showed relatively higher MDR than farm workers.

scholarly journals Effect of Antimicrobial Dosage Regimen on Salmonella and Escherichia coli Isolates from Feeder Swine

2008 ◽  
Vol 74 (6) ◽  
pp. 1731-1739 ◽  
Author(s):  
Bruce A. Wagner ◽  
Barbara E. Straw ◽  
Paula J. Fedorka-Cray ◽  
David A. Dargatz
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Commensal Bacteria ◽  
Antimicrobial Use ◽  
Control Analysis ◽  
Fecal Samples ◽  
E Coli ◽  
The Impact ◽  
Susceptibility And Resistance ◽  
Continuous Pulse

ABSTRACT A body of evidence exists that suggests that antimicrobial use in food animals leads to resistance in both pathogenic and commensal bacteria. This study focused on the impact of three different antimicrobial regimes (low-level continuous, pulse, and no antimicrobial) for two antimicrobials (chlortetracycline and tylosin) on the presence of Salmonella spp. and on the prevalence of antimicrobial resistance of both Salmonella spp. and nonspecific Escherichia coli in fecal samples from feeder swine. The prevalence of fecal samples positive for Salmonella spp. significantly decreased between the samples taken at feeder placement compared to samples taken when the animals were close to market weight. Differences in resistance of Salmonella spp. did not appear to be influenced by dosing treatment including the control. Analysis of antimicrobial resistance examining both susceptibility and resistance, as well as MIC outcomes, demonstrated that only resistance to cephalothin increased in E. coli under the pulse chlortetracycline treatment. These results suggest that the dosing regimes examined in this study did not lead to an increase in either the prevalence of Salmonella spp. or the prevalence of antimicrobial resistance in isolates of Salmonella spp. or E. coli.

scholarly journals Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244358
Author(s):  
Rafika Indah Paramita ◽  
Erni Juwita Nelwan ◽  
Fadilah Fadilah ◽  
Editha Renesteen ◽  
Nelly Puspandari ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Bloodstream Infection ◽  
Genome Sequencing ◽  
Virulence Genes ◽  
Sequence Type ◽  
Whole Genome ◽  
National Hospital ◽  
Sequence Types

Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.

scholarly journals Plasmid-Borne and Chromosomal ESBL/AmpC Genes in Escherichia coli and Klebsiella pneumoniae in Global Food Products

2021 ◽  
Vol 12 ◽  
Author(s):  
Paula Kurittu ◽  
Banafsheh Khakipoor ◽  
Maria Aarnio ◽  
Suvi Nykäsenoja ◽  
Michael Brouwer ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Virulence Genes ◽  
Food Products ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Broiler Meat ◽  
E Coli ◽  
Meat Samples ◽  
Global Food

Plasmid-mediated extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase producing Enterobacteriaceae, in particular Escherichia coli and Klebsiella pneumoniae, with potential zoonotic transmission routes, are one of the greatest threats to global health. The aim of this study was to investigate global food products as potential vehicles for ESBL/AmpC-producing bacteria and identify plasmids harboring resistance genes. We sampled 200 food products purchased from Finland capital region during fall 2018. Products originated from 35 countries from six continents and represented four food categories: vegetables (n = 60), fruits and berries (n = 50), meat (n = 60), and seafood (n = 30). Additionally, subsamples (n = 40) were taken from broiler meat. Samples were screened for ESBL/AmpC-producing Enterobacteriaceae and whole genome sequenced to identify resistance and virulence genes and sequence types (STs). To accurately identify plasmids harboring resistance and virulence genes, a hybrid sequence analysis combining long- and short-read sequencing was employed. Sequences were compared to previously published plasmids to identify potential epidemic plasmid types. Altogether, 14 out of 200 samples were positive for ESBL/AmpC-producing E. coli and/or K. pneumoniae. Positive samples were recovered from meat (18%; 11/60) and vegetables (5%; 3/60) but were not found from seafood or fruit. ESBL/AmpC-producing E. coli and/or K. pneumoniae was found in 90% (36/40) of broiler meat subsamples. Whole genome sequencing of selected isolates (n = 21) revealed a wide collection of STs, plasmid replicons, and genes conferring multidrug resistance. blaCTX–M–15-producing K. pneumoniae ST307 was identified in vegetable (n = 1) and meat (n = 1) samples. Successful IncFII plasmid type was recovered from vegetable and both IncFII and IncI1-Iγ types from meat samples. Hybrid sequence analysis also revealed chromosomally located beta-lactamase genes in two of the isolates and indicated similarity of food-derived plasmids to other livestock-associated sources and also to plasmids obtained from human clinical samples from various countries, such as IncI type plasmid harboring blaTEM–52C from a human urine sample obtained in the Netherlands which was highly similar to a plasmid obtained from broiler meat in this study. Results indicate certain foods contain bacteria with multidrug resistance and pose a possible risk to public health, emphasizing the importance of surveillance and the need for further studies on epidemiology of epidemic plasmids.

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