scholarly journals Antimicrobial Resistance Profiles of Adherent Invasive Escherichia coli Show Increased Resistance to β-Lactams

Antibiotics ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 251 ◽  
Author(s):  
Margarita Martinez-Medina ◽  
Francesco Strozzi ◽  
Belén Ruiz Del Castillo ◽  
Natalia Serrano-Morillas ◽  
Nuria Ferrer Bustins ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Antimicrobial Therapy ◽  
De Novo ◽  
Genomic Analysis ◽  
The Other ◽  
Phenotypic Resistance ◽  
E Coli ◽  
Gut Mucosa

The adherent invasive Escherichia coli (AIEC) pathotype has been associated with the aetiology of Crohn’s disease (CD). Scarce reports have shown the antimicrobial resistance (AMR) profiles of AIEC. Despite antibiotics not being recommended to treat CD, antimicrobial therapy could be useful in stratified patients, such as AIEC carriers. We examined the antimicrobial resistance profiles of AIEC strains to identify which therapies could be effective or confer a risk for such patients. Phenotypic resistance to 30 antimicrobials was tested according to CLSI standards. AIEC (n = 22) and non-pathogenic E. coli (non-AIEC) strains (n = 37) isolated from the gut mucosa of 31 CD patients and 18 controls were studied. De novo genome sequencing was carried out for 39 of the 59 strains, and AMR genes were searched using the DeepARG database in these genomes and 33 additional AIEC publicly available genomes. The strains isolated from CD and controls showed similar phenotypic AMR profiles. The genomic analysis did not reveal an increased prevalence of AMR genes. However, AIEC strains were more frequently resistant to β-lactams than non-AIEC strains (11 AIEC (50%) and 5 non-AIEC (22%) strains were resistant to at least one β-lactam; p < 0.042). Two AIEC strains were resistant to expanded-spectrum cephalosporins. One strain carried a plasmid-mediated AmpC β-lactamase (CMY-69), and the other presented mutations in the promotor of the intrinsic chromosomal AmpC related to the hyperproduction of this enzyme. The rest of the strains were resistant to β-lactams not including expanded-spectrum cephalosporins. The majority carried TEM-related β-lactamases. Genomic analysis including external AIEC revealed that the gene sul1 encoding for sulphonamide resistance was more frequent in AIEC strains than non-AIEC strains (34.6% vs. 9.5%, p = 0.030). AMR in AIEC is a matter of concern regarding the putative implication of the pathotype in CD. The high proportion of AIEC resistant to β-lactams warrants caution about the risk there may be in the use of these antimicrobials in AIEC-colonized CD patients.

scholarly journals Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

2020 ◽  
Vol 6 (7) ◽  
Author(s):  
Bede Constantinides ◽  
Kevin K. Chau ◽  
T. Phuong Quan ◽  
Gillian Rodger ◽  
Monique I. Andersson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Type Species ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Antimicrobial Resistance Genes

Escherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonized with diverse populations of E. coli , Klebsiella pneumoniae and Klebsiella oxytoca , including both antimicrobial-resistant and susceptible strains. Using whole-genome sequencing of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies, which may vary as a result of different inputs and selection pressures. Whole-genome sequencing of 46 contemporaneous patient isolates identified one (2 %; 95 % CI 0.05–11 %) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10 % of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including bla CTX-M, bla SHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention. This article contains data hosted by Microreact.

scholarly journals The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

2008 ◽  
Vol 190 (20) ◽  
pp. 6881-6893 ◽  
Author(s):  
David A. Rasko ◽  
M. J. Rosovitz ◽  
Garry S. A. Myers ◽  
Emmanuel F. Mongodin ◽  
W. Florian Fricke ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequencing ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Whole Genome ◽  
E Coli ◽  
Important Group ◽  
Commensal Species

ABSTRACT Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.

scholarly journals Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Max Laurence Cummins ◽  
Piklu Roy Chowdhury ◽  
Marc Serge Marenda ◽  
Glenn Francis Browning ◽  
Steven Philip Djordjevic
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Genomic Island ◽  
Sequence Type ◽  
Genomic Islands ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACT Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry blaNDM-1, blaVEB-6, and blaCTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3′ end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli. The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023. IMPORTANCE SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the Enterobacteriaceae. SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3′ end of trmE. For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.

FOLIC ACID INHIBITION OF NON-PROLIFERATING BACTERIA

1964 ◽  
Vol 10 (3) ◽  
pp. 345-350 ◽  
Author(s):  
Robert F. Pittillo ◽  
Annie Jo Narkates
Keyword(s):  
Escherichia Coli ◽  
Folic Acid ◽  
De Novo ◽  
Acid Inhibition ◽  
The Other ◽  
Purine Biosynthesis ◽  
Nutrient Agar ◽  
E Coli ◽  
De Novo Purine Biosynthesis ◽  
Acid Toxicity

Certain non-proliferating bacteria, suspended in saline, are inhibited by folic acid as judged by the ability of the cells to form visible colonies on a nutrient agar subsequent to exposure to folic acid. On the other hand, some yeasts (three strains) are insensitive to folic acid. In Escherichia coli ATCC 9637, folic acid toxicity can be prevented by a variety of metabolites. Although a purine-requiring strain of E. coli is resistant to folic acid, and purines prevent folic acid toxicity in another strain of E. coli, experiments with C14-formate failed to demonstrate an unequivocal effect of folic acid on de novo purine biosynthesis.

scholarly journals Antimicrobial resistance prevalence of pathogenic and commensal Escherichia coli in food-producing animals in Belgium

2014 ◽  
Vol 83 (5) ◽  
pp. 225-233 ◽  
Author(s):  
I. Chantziaras ◽  
J. Dewulf ◽  
F. Boyen ◽  
B. Callens ◽  
P. Butaye
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Broiler Chickens ◽  
Broiler Chicken ◽  
Susceptibility Testing ◽  
Commensal Bacteria ◽  
The Other ◽  
E Coli ◽  
Veal Calves ◽  
Veal Calf

In this article, detailed studies on antimicrobial resistance to commensal E. coli (in pigs, meatproducing bovines, broiler chickens and veal calves) and pathogenic E. coli (in pigs and bovines) in Belgium are presented for 2011. Broiler chicken and veal calf isolates of commensal E. coli demonstrated higher antimicrobial resistance prevalence than isolates from pigs and bovines. Fifty percent of E. coli isolates from broiler chickens were resistant to at least five antimicrobials, whereas sixty-one percent of bovine E. coli isolates were susceptible to all antimicrobials tested. On the other hand, bovine pathogenic E. coli isolates showed an extended resistance profile with more than half of the isolates being resistant to ten or more antimicrobials. The results are not significantly different from the results from previously published studies on commensal bacteria in pigs in Belgium, although different methodologies of sampling and susceptibility testing were used.

scholarly journals Diverse commensal E. coli clones and plasmids disseminate antimicrobial resistance genes in domestic animals and children in a semi-rural community in Ecuador

2019 ◽  
Author(s):  
Liseth Salinas ◽  
Paúl Cárdenas ◽  
Timothy J. Johnson ◽  
Karla Vasco ◽  
Jay Graham ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Rural Community ◽  
Resistance Genes ◽  
Domestic Animals ◽  
Drug Resistant ◽  
Phenotypic Resistance ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Resistance Patterns

ABSTRACTThe increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts in human medicine. Many of the multi-drug resistant (MDR) Enterobacteriaceae found in humans are community-acquired and linked to food animals (i.e. livestock raised for meat and dairy products). In this study, we examined whether numerically dominant, commensal Escherichia coli strains from humans (n=63 isolates) and domestic animals (n=174 isolates) in the same community and with matching phenotypic AMR patterns, were clonally related or shared the same plasmids. We identified 25 multi-drug resistant isolates (i.e. resistant to 3 or more antimicrobial classes) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes and plasmids carrying the AMR genes using conjugation, replicon typing and whole genome sequencing. None of the MDR E. coli isolates (from children and domestic animals) analyzed were clonal. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. Our findings suggest that nonclonal resistance gene dissemination is common in this community and that diverse plasmids carrying AMR genes presents a significant challenge for understanding the movement of AMR in a community.IMPORTANCEEven though Escherichia coli strains may share nearly identical AMR profiles, AMR genes, and overlap in space and time, the diversity of clones and plasmids challenges to research that aims to identify sources of AMR. Horizontal gene transfer appears to play a much larger role than clonal expansion in the spread of AMR in the community.

scholarly journals Associations between Antimicrobial Resistance Phenotypes, Antimicrobial Resistance Genes, and Virulence Genes of Fecal Escherichia coli Isolates from Healthy Grow-Finish Pigs

2009 ◽  
Vol 75 (5) ◽  
pp. 1373-1380 ◽  
Author(s):  
Leigh B. Rosengren ◽  
Cheryl L. Waldner ◽  
Richard J. Reid-Smith
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Large Scale ◽  
Virulence Genes ◽  
Antimicrobial Use ◽  
Phenotypic Resistance ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

ABSTRACT Escherichia coli often carries linked antimicrobial resistance genes on transmissible genetic elements. Through coselection, antimicrobial use may select for unrelated but linked resistance or virulence genes. This study used unconditional statistical associations to investigate the relationships between antimicrobial resistance phenotypes and antimicrobial resistance genes in 151 E. coli isolates from healthy pigs. Phenotypic resistance to each drug was significantly associated with phenotypic resistance to at least one other drug, and every association found that the probability of observing the outcome resistance was increased by the presence of the predictor resistance. With one exception, each statistical association that was identified between a pair of resistance genes had a corresponding significant association identified between the phenotypes mediated by those genes. This suggests that associations between resistance phenotypes might predict coselection. If this hypothesis is confirmed, evaluation of the associations between resistance phenotypes could improve our knowledge of coselection dynamics and provide a cost-effective way to evaluate existing data until large-scale genotypic data collection becomes feasible. This could enable policy makers and users of antimicrobials to consider coselection in antimicrobial use decisions. This study also considered the unconditional relationships between resistance and virulence genes in E. coli from healthy pigs (aidA-1, eae, elt, estA, estB, fedA1, stx1, and stx2). Positive statistical associations would suggest that antimicrobial use may select for virulence in bacteria that may contaminate food or cause diarrhea in pigs. Fortunately, the odds of detecting a virulence gene were rarely increased by the presence of an antimicrobial resistance gene. This suggests that on-farm antimicrobial use did not select for the examined virulence factors in E. coli carried by this population of healthy pigs.

scholarly journals Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France

2021 ◽  
Author(s):  
Afaf Hamame ◽  
Bernard DAVOUST ◽  
Jean Marc Rolain ◽  
Seydina M. Diene
Keyword(s):  
Escherichia Coli ◽  
Genome Sequencing ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Coli Strain ◽  
Circular Chromosome ◽  
Resistance Phenotype ◽  
E Coli ◽  
Pig Farm ◽  
Stool Samples

The current study is about genomic characterisation of an atypical multidrug-resistant Escherichia coli harbouring two mobilised colistin resistance (mcr) genes isolated from pigs in France. Stool samples taken from a pig farm in Avignon in the department of the Vaucluse were subjected to a molecular screening for the detection of mcr gene variants. These samples were cultured on selective LBJMR medium. Growing bacteria were identified using MALDI-TOF, followed by antibiotic susceptibility testing (AST). Whole genome sequencing (WGS) and bioinformatic genome analysis was performed. The selective culture of stools revealed the presence of an E. coli strain named Q4552 which was simultaneously positive for the mcr-1.1 and mcr-3.5 genes. This strain exhibited resistance phenotype to fourteen antibiotics, including colistin. Genome sequencing revealed a circular chromosome and eight plasmids. Genomic analysis revealed a chromosomic integration of a mobile genetic element (MGE) harbouring the mcr-1.1 gene, while the mcr-3.5 gene was plasmidic (i.e., an IncFII plasmid). Its resistome exhibited twenty-two resistance genes, explaining its multidrug resistance phenotype. The Q4552 strain is an ST-843 clone belonging to the clonal complex Cplx-568 and is the only ST type of this cplx-568 which has been isolated from animals, humans, and the environment. Here, we report the first co-occurrence of the mcr-1 and mcr-3 genes in France from a pathogenic E. coli strain isolated from a pig farm. Since this clone (ST-843) has been reported in zoonotic transmissions, programs to monitor such colistin resistant bacterium are urgently required to avoid its spread and zoonotic transmission to humans.

scholarly journals Bloodstream Infection due to Piperacillin/Tazobactam Non-Susceptible, Cephalosporin-Susceptible Escherichia coli: A Missed Opportunity for De-Escalation of Therapy

Antibiotics ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 104
Author(s):  
Leah Carlisle ◽  
Julie Justo ◽  
Majdi Al-Hasan
Keyword(s):  
Escherichia Coli ◽  
Bloodstream Infection ◽  
Antimicrobial Therapy ◽  
Metastatic Breast ◽  
Resistance Pattern ◽  
Rapid Diagnostics ◽  
Phenotypic Resistance ◽  
Microbial Identification ◽  
E Coli

An increasing number of reports describing Escherichia coli isolates with piperacillin/tazobactam resistance, despite retained cephalosporin susceptibility, suggest further emergence of this phenotypic resistance pattern. In this report, a patient with metastatic breast cancer presented to medical care after two days of chills, nausea, vomiting, reduced oral intake, and generalized weakness. Blood and urine cultures grew E. coli as identified by rapid diagnostics multiplex PCR and MALDI-TOF, respectively. The patient continued to manifest signs of sepsis with hypotension and tachypnea during the first three days of hospitalization despite empirical antimicrobial therapy with intravenous piperacillin/tazobactam. After in vitro antimicrobial susceptibility testing demonstrated a piperacillin/tazobactam minimal inhibitory concentration (MIC) of 64 and a ceftriaxone MIC of ≤1 mcg/mL, antimicrobial therapy was switched from intravenous piperacillin/tazobactam to ceftriaxone. All symptoms and signs of infection resolved within 48 h of starting ceftriaxone therapy. This report describes the clinical failure of piperacillin/tazobactam in the treatment of a bloodstream infection due to E. coli harboring a phenotypic resistance pattern of isolated piperacillin/tazobactam non-susceptibility. The case demonstrates the role of cephalosporins as potential treatment options and highlights the value of early de-escalation of antimicrobial therapy based on rapid diagnostic testing for microbial identification.

scholarly journals Diverse Commensal Escherichia coli Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Liseth Salinas ◽  
Paúl Cárdenas ◽  
Timothy J. Johnson ◽  
Karla Vasco ◽  
Jay Graham ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Domestic Animals ◽  
Whole Genome ◽  
Content Type ◽  
Phenotypic Resistance ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACT The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts on human medicine. Many of the multidrug-resistant (multiresistant) Enterobacteriaceae found in humans are community acquired, and some of them are possibly linked to food animals (i.e., livestock raised for meat and dairy products). In this study, we examined whether numerically dominant commensal Escherichia coli strains from humans (n = 63 isolates) and domestic animals (n = 174 isolates) in the same community and with matching phenotypic AMR patterns were clonally related or shared the same plasmids. We identified 25 multiresistant isolates (i.e., isolates resistant to more than one antimicrobial) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes, and plasmids carrying the AMR genes using conjugation, replicon typing, and whole-genome sequencing. All of the multiresistant E. coli isolates (from children and domestic animals) analyzed had at least 90 or more whole-genome SNP differences between one another, suggesting that none of the strains was recently transferred. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. We did not find evidence of the clonal spread of AMR in this community: instead, AMR genes were carried on diverse clones and plasmids. This presents a significant challenge for understanding the movement of AMR in a community. IMPORTANCE Even though Escherichia coli strains may share nearly identical phenotypic AMR profiles and AMR genes and overlap in space and time, the diversity of clones and plasmids challenges research that aims to identify sources of AMR. Horizontal gene transfer appears to play a more significant role than clonal expansion in the spread of AMR in this community.

Sign in / Sign up

Export Citation Format

Share Document