scholarly journals Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones

2019 ◽  
Author(s):  
Catherine Ludden ◽  
Arun Gonzales Decano ◽  
Dorota Jamrozy ◽  
Derek Pickard ◽  
Dearbhaile Morris ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Antibiotic Resistance Gene ◽  
Gene Variants ◽  
Term Care ◽  
E Coli ◽  
Esbl Gene ◽  
Combining Data ◽  
Clade C

AbstractEscherichia coli sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of E. coli ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (n=69) with other Irish (n=35) and global (n=690) ST131 genomes to reconstruct the evolutionary history and understand changes in population structure and genome architecture over time. This required a combination of short and long-read genome sequencing, de novo assembly, read mapping, ESBL gene screening, plasmid alignment and temporal phylogenetics. We found that clade C was the most prevalent (686 out of 794 isolates, 86%) of the three major ST131 clades circulating worldwide (A, B, C), and was associated with the presence of different ESBL alleles, diverse plasmids and transposable elements. Clade C was estimated to have emerged in ∼1985 and subsequently acquired different ESBL gene variants (blaCTX-M-14 vs blaCTX-M-15). An ISEcp1- mediated transposition of the blaCTX-M-15 gene further increased the diversity within Clade C. We discovered a local clonal expansion of a rare C2 lineage (C2_8) with a chromosomal insertion of blaCTX-M-15 at the mppA gene. This was acquired from an IncFIA plasmid. The C2_8 lineage clonally expanded in the Irish LTCF from 2006, displacing the existing C1 strain (C1_10) and highlighting the potential for novel ESBL-producing ST131 with a distinct genetic profile to cause outbreaks strongly associated with specific healthcare environments.ImportanceExtraintestinal pathogenic E. coli (ExPEC) ST131 is adapting in the context of antibiotic exposure, resulting in a pandemic with distinct genetic subtypes. Here, we track the evolution of antibiotic-resistance gene variants originally discovered in an ExPEC ST131 outbreak that was identified in a LTCF in Ireland. Analysis of 794 global ST131 genomes show that subclade C1 was associated with the initial infection outbreak, but that a new lineage from subclade C2 successfully displaced C1. This genetically distinct C2 subclade with a chromosomal insertion of a key antibiotic-resistance gene had clonally expanded within the LTCF. We provide new insights into the timing of genetic events driving the diversification of C2 subclades to show that that outbreak C2 strain likely evolved elsewhere before spreading to the LTCF. This study highlights the scope of antibiotic-resistance gene rearrangement within ST131, reinforcing the need to integrate genomic, epidemiological and microbiological approaches to understand ST131 transmission.

The influence of antibiotic resistance gene carriage on biofilm formation by two Escherichia coli strains associated with urinary tract infections

2014 ◽  
Vol 60 (2) ◽  
pp. 105-111 ◽  
Author(s):  
Amy Huei Teen Teh ◽  
Yi Wang ◽  
Gary A. Dykes
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Resistance Gene ◽  
Biofilm Formation ◽  
Antibiotic Resistance Gene ◽  
Kanamycin Resistance ◽  
Marker Genes ◽  
E Coli ◽  
Tract Infections

Urinary tract infections (UTI) caused by uropathogenic Escherichia coli are one of the most common forms of human disease. In this study, the effect of the presence of newly acquired antibiotic resistance genes on biofilm formation of UTI-associated E. coli strains was examined. Two clinical UTI-associated E. coli strains (SMC18 and SMC20) carrying different combinations of virulence genes were transformed with pGEM-T, pGEM-T::KmΔAmp, or pGEM-T::Km to construct ampicillin-resistant (KmSAmpR), kanamycin-resistant (KmRAmpS), or ampicillin- and kanamycin-resistant (KmRAmpR) strains. Transformed and wild-type strains were characterized for biofilm formation, bacterial surface hydrophobicity, auto-aggregation, morphology, and attachment to abiotic surfaces. Transformation with a plasmid carrying an ampicillin resistance gene alone decreased (p < 0.05) biofilm formation by SMC18 (8 virulence marker genes) but increased (p < 0.05) biofilm formation by SMC20 (5 virulence marker genes). On the other hand, transformation with a plasmid carrying a kanamycin resistance gene alone or both ampicillin and kanamycin resistance genes resulted in a decrease (p < 0.05) in biofilm formation by SMC18 but did not affect (p > 0.05) the biofilm formation by SMC20. Our results suggest that transformation of UTI-associated E. coli with plasmids carrying different antibiotic resistance gene(s) had a significant impact on biofilm formation and that these effects were both strain dependent and varied between different antibiotics.

scholarly journals Plasmid with Colistin Resistance Genemcr-1in Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains Isolated from Pig Slurry in Estonia

2016 ◽  
Vol 60 (11) ◽  
pp. 6933-6936 ◽  
Author(s):  
Age Brauer ◽  
Kaidi Telling ◽  
Mailis Laht ◽  
Piret Kalmus ◽  
Irja Lutsar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Antibiotic Resistance Gene ◽  
Dna Transfer ◽  
The Other ◽  
Pig Slurry ◽  
Colistin Resistance ◽  
Content Type ◽  
Slurry Sample

ABSTRACTA plasmid carrying the colistin resistance genemcr-1was isolated from a pig slurry sample in Estonia. The gene was present on a 33,311-bp plasmid of the IncX4 group.mcr-1is the only antibiotic resistance gene on the plasmid, with the other genes mainly coding for proteins involved in conjugative DNA transfer (taxA,taxB,taxC,trbM, and thepilXoperon). The plasmid pESTMCR was present in three phylogenetically very differentEscherichia colistrains, suggesting that it has high potential for horizontal transfer.

Antibiotic resistance gene cassettes derived from the π interposon for use in E. coli and Streptomyces

Gene ◽  
1997 ◽  
Vol 190 (2) ◽  
pp. 315-317 ◽  
Author(s):  
Marie-Hélène Blondelet-Rouault ◽  
Jaroslav Weiser ◽  
Ahmed Lebrihi ◽  
Pavel Branny ◽  
Jean-Luc Pernodet
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Antibiotic Resistance Gene ◽  
Gene Cassettes ◽  
E Coli

scholarly journals Is exposure to mercury a driving force for the carriage of antibiotic resistance genes?

2010 ◽  
Vol 59 (7) ◽  
pp. 804-807 ◽  
Author(s):  
David Skurnik ◽  
Raymond Ruimy ◽  
Derren Ready ◽  
Etienne Ruppe ◽  
Claire Bernède-Bauduin ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Driving Force ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Mercury Exposure ◽  
Mercury Resistance ◽  
High Exposure ◽  
E Coli

The mercury resistance gene merA has often been found together with antibiotic resistance genes in human commensal Escherichia coli. To study this further, we analysed mercury resistance in collections of strains from various populations with different levels of mercury exposure and various levels of antibiotic resistance. The first population lived in France and had no known mercury exposure. The second lived in French Guyana and included a group of Wayampi Amerindians with a known high exposure to mercury. Carriage rates of mercury resistance were assessed by measuring the MIC and by detecting the merA gene. Mercury-resistant E. coli was found significantly more frequently in the populations that had the highest carriage rates of antibiotic-resistant E. coli and in parallel antibiotic resistance was higher in the population living in an environment with a high exposure to mercury, suggesting a possible co-selection. Exposure to mercury might be a specific driving force for the acquisition and maintenance of mobile antibiotic resistance gene carriage in the absence of antibiotic selective pressure.

scholarly journals Multiple NDM-5-Expressing Escherichia Coli Isolates From an Immunocompromised Pediatric Host

2020 ◽  
Vol 7 (2) ◽  
Author(s):  
Tim Flerlage ◽  
Jessica N Brazelton de Cardenas ◽  
Cherilyn D Garner ◽  
Nur A Hasan ◽  
Hiren Karathia ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antibiotic Resistance Gene ◽  
The United States ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Invasive Infection ◽  
Anticancer Chemotherapy ◽  
E Coli ◽  
Sequence Types

Abstract Background Genes conferring carbapenem resistance have disseminated worldwide among Gram-negative bacteria. Here we present longitudinal changes in clinically obtained Escherichia coli isolates from 1 immunocompromised pediatric patient. This report demonstrates potential for antibiotic resistance genes and plasmids to emerge over time in clinical isolates from patients receiving intensive anticancer chemotherapy and broad-spectrum antibiotics. Methods Thirty-three isolates obtained over 7 months from 1 patient were included. Clinical data were abstracted from the medical record. For each isolate, studies included phenotypic antibacterial resistance patterns, sequence typing, bacterial isolate sequencing, plasmid identification, and antibiotic resistance gene identification. Results Sites of isolation included blood, wound culture, and culture for surveillance purposes from the perianal area. Isolates were of 5 sequence types (STs). All were resistant to multiple classes of antibiotics; 23 (69.6%) were phenotypically resistant to all carbapenems. The blaNDM-5 gene was identified in 22 (67%) isolates, all of ST-167 and ST-940, and appeared to coincide with the presence of the IncFII and IncX3 plasmid. Conclusions We present unique microbiologic data from 33 multidrug-resistant E. coli isolates obtained over the course of 7 months from an individual patient in the United States. Two E. coli sequence types causing invasive infection in the same patient and harboring the blaNDM-5 gene, encoded on the IncX3 plasmid and the IncFII plasmid, were identified. This study highlights the emergence of multidrug-resistant bacteria on antibiotic therapy and the necessity of adequate neutrophil number and function in the clearance of bacteremia.

scholarly journals Fate and Persistence of a Pathogenic NDM-1-Positive Escherichia coli Strain in Anaerobic and Aerobic Sludge Microcosms

2017 ◽  
Vol 83 (13) ◽  
Author(s):  
David Mantilla-Calderon ◽  
Pei-Ying Hong
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Liquid Fraction ◽  
Antibiotic Resistance Gene ◽  
Treated Wastewater ◽  
Anaerobic Sludge ◽  
Decay Kinetics ◽  
Content Type ◽  
E Coli ◽  
Aerobic Sludge

ABSTRACT The presence of emerging biological pollutants in treated wastewater effluents has gained attention due to increased interest in water reuse. To evaluate the effectiveness of the removal of such contaminants by the conventional wastewater treatment process, the fate and decay kinetics of NDM-1-positive Escherichia coli strain PI7 and its plasmid-encoded antibiotic resistance genes (ARGs) were assessed in microcosms of anaerobic and aerobic sludge. Results showed that E. coli PI7 decayed at a significantly lower rate under anaerobic conditions. Approximate half-lives were 32.4 ± 1.4 h and 5.9 ± 0.9 h in the anaerobic and aerobic microcosms, respectively. In the aerobic microcosms, after 72 h of operation, E. coli PI7 remained detectable, but no further decay was observed. Instead, 1 in every 10,000 E. coli cells was identified to be recalcitrant to decay and persist indefinitely in the sludge. ARGs associated with the E. coli PI7 strain were detected to have transferred to other native microorganisms in the sludge or were released to the liquid fraction upon host decay. Extracellular DNA quickly degraded in the liquid fraction of the aerobic sludge. In contrast, no DNA decay was detected in the anaerobic sludge water matrix throughout the 24-h sampling period. This study suggests an increased likelihood of environmental dispersion of ARGs associated with anaerobically treated wastewater effluents and highlights the potential importance of persister cells in the dissemination of E. coli in the environment during reuse events of treated wastewater. IMPORTANCE This study examines the decay kinetics of a pathogenic and antibiotic resistant strain of Escherichia coli in microcosms simulating biological treatment units of aerobic and anaerobic sludge. The results of this study point at a significantly prolonged persistence of the E. coli and the associated antibiotic resistance gene in the anaerobic sludge. However, horizontal transfer of the plasmid encoding the antibiotic resistance gene was detected in the aerobic sludge by a cultivation method. A subpopulation of persister E. coli cells was also detected in the aerobic sludge. The findings of this study suggest potential areas of concern arising from pathogenic and antibiotic-resistant E. coli during both anaerobic and aerobic sludge treatment processes.

scholarly journals Identification and Characterization of Integron-Mediated Antibiotic Resistance among Shiga Toxin-Producing Escherichia coli Isolates

2001 ◽  
Vol 67 (4) ◽  
pp. 1558-1564 ◽  
Author(s):  
Shaohua Zhao ◽  
David G. White ◽  
Beilei Ge ◽  
Sherry Ayers ◽  
Sharon Friedman ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Shiga Toxin ◽  
Antibiotic Resistance Gene ◽  
Gene Encoding ◽  
Gene Cassettes ◽  
E Coli ◽  
Class 1 Integrons ◽  
Class 1

ABSTRACT A total of 50 isolates of Shiga toxin-producing Escherichia coli (STEC), including 29 O157:H7 and 21 non-O157 STEC strains, were analyzed for antimicrobial susceptibilities and the presence of class 1 integrons. Seventy-eight (n = 39) percent of the isolates exhibited resistance to two or more antimicrobial classes. Multiple resistance to streptomycin, sulfamethoxazole, and tetracycline was most often observed. Class 1 integrons were identified among nine STEC isolates, including serotypes O157:H7, O111:H11, O111:H8, O111:NM, O103:H2, O45:H2, O26:H11, and O5:NM. The majority of the amplified integron fragments were 1 kb in size with the exception of one E. coli O111:H8 isolate which possessed a 2-kb amplicon. DNA sequence analysis revealed that the integrons identified within the O111:H11, O111:NM, O45:H2, and O26:H11 isolates contained the aadA gene encoding resistance to streptomycin and spectinomycin. Integrons identified among the O157:H7 and O103:H2 isolates also possessed a similaraadA gene. However, DNA sequencing revealed only 86 and 88% homology, respectively. The 2-kb integron of the E. coli O111:H8 isolate contained three genes, dfrXII,aadA2, and a gene of unknown function, orfF, which were 86, 100, and 100% homologous, respectively, to previously reported gene cassettes identified in integrons found inCitrobacter freundii and Klebsiella pneumoniae. Furthermore, integrons identified among the O157:H7 and O111:NM strains were transferable via conjugation to another strain of E. coli O157:H7 and to several strains of Hafnia alvei. To our knowledge, this is the first report of integrons and antibiotic resistance gene cassettes in STEC, in particular E. coliO157:H7.

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