A Curated, Comprehensive Database of Plasmid Sequences

Brooks, Lauren; Kaze, Mo; Sistrom, Mark

doi:10.1128/mra.01325-18

Cited by 46 publications

(47 citation statements)

References 8 publications

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“…The profiling of AMR genes took place by aligning the reads using Blast (v2.9.0) against CARD database (v3.0.7) (Supplementary Table 3) 51,52 . Sequenced plasmids were characterized by aligning the contigs of each sample against the database of plasmid sequences (v2) ( Supplementary Table 4) 53 . In addition, plasmid-borne virulence factors and insertion sequences were detected by aligning the reads to the Virulence Factors Database (update 01/24/2020) and ISFinder database (update 09/25/2019), respectively (Supplementary Table 5) 54,55 .…”

Section: Plasmid Extractionmentioning

confidence: 99%

Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

Hassan

Tantawy

Gouda

et al. 2020

Sci Rep

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Infection with multiple drug resistant (MDR) Escherichia coli poses a life threat to immunocompromised pediatric cancer patients. Our aim is to genotypically characterize the plasmids harbored in MDR E. coli isolates recovered from bacteremic patients of Children's Cancer Hospital in Egypt 57357 (CCHE 57357). In this study, 21 carbapenem-resistant E. coli (CRE) isolates were selected that exhibit Quinolones and Aminoglycosides resistance. Plasmid shotgun sequencing was performed using Illumina nextgeneration sequencing platform. Isolates demonstrated resistant to all beta-lactams, carbapenems, aminoglycosides and quinolones. Of the 32 antimicrobial resistant genes identified that exceeded the analysis cutoff coverage, the highest represented genes were aph(6)-Id, sul2, aph(3″)-Ib, aph(3′)-Ia, sul1, dfrA12, TEM-220, NDM-11. Isolates employed a wide array of resistance mechanisms including antibiotic efflux, antibiotic inactivation, antibiotic target replacements and antibiotic target alteration. Sequenced isolates displayed diverse insertion sequences, including IS26, suggesting dynamic reshuffling of the harbored plasmids. Most isolates carried plasmids originating from other bacterial species suggesting a possible horizontal gene transfer. Only two isolates showed virulence factors with iroA gene cluster which was found in only one of them. Outside the realms of nosocomial infections among patients in hospitals, our results indicate a transfer of resistant genes and plasmids across different organisms. Escherichia coli represents the most frequent sources of blood stream and urinary tract infections worldwide. A continual increase in E. coli antibiotic resistance burdens medical facilities throughout the world by causing difficult to treat infections among patients 1,2. There has been a particular concern regarding the increase in Extended-Spectrum Beta-Lactamase (ESBL)-producing and carbapenem-resistant E. coli. carbapenem-resistant E. coli (CRE) have become resistant to the majority of available antibiotics, including carbapenems which are a last-resort treatment for multidrug-resistant pathogens. This is often accompanied by resistance to fluoroquinolones and aminoglycosides 3,4. The increase in antimicrobial resistance (AMR) frequency presents a global healthcare challenge by limiting the choices of antimicrobials that can be used in the treatment of bacterial infections 5,6. Mobile elements like transposons, integrons and plasmids frequently carry Multiple Drug Resistance (MDR) genetic motifs. These elements can be transferred from foodborne pathogens to human pathogens, increasing their virulence 7. This method has enabled the rapid propagation of AMR among several pathogenic bacterial genera to humans, including E. coli 8. CRE-encoding plasmids are now regarded as the primary vector facilitating this transmission between bacteria 9 .

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Section: Plasmid Extractionmentioning

confidence: 99%

Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

Hassan

Tantawy

Gouda

et al. 2020

Sci Rep

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“…5). Sequencing reads containing bla CTX-M genes were recognized as plasmid-borne when BLAST search of these reads against the plasmid database from Brooks et al 19 yielded positive hits (Fig. 3).…”

Section: Resultsmentioning

confidence: 99%

“…Plasmid detection. Raw sequencing reads (≥ 300 bp) were searched against the comprehensive plasmid sequences database from Brooks et al 19 using BLAST (downloaded March2019), Only hits with ≥ 80% similarity, E-value ≤ 10 −6 and with ≥ 80% coverage of the query were kept. Assembled contigs were initially searched against the NCBI plasmid database using the PlasmidFinder v.2.0.2 27 and positive hits were additionally confirmed through the search against the PLSDB plasmid database v.2019_06_03 28 .…”

Section: Inoculation and Incubation Of Blood Cultures For Incubationmentioning

confidence: 99%

Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

Taxt

Avershina

Frye

et al. 2020

Sci Rep

114

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Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1-2 days for identification of bacterial agent and an additional 2-3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and bla CTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes. Bloodstream infections (BSIs) and sepsis are major causes of morbidity and mortality worldwide. Epidemiological data are scarce, but a recent estimate indicated that 31.5 million cases of sepsis and 5.3 million sepsis attributable deaths occur annually 1. This estimate is only based on data collected from high-income countries, and it therefore likely underestimates the true burden of disease worldwide, especially in low-and-middle-income countries 2. Most studies on sepsis and BSIs report an increasing incidence over the last two decades 3 , particularly among the immunocompromised, multimorbid, and elderly patients, or due to failure of empiric antibiotic regimens as result of antimicrobial resistance (AMR) 4. With multi drug resistant pathogens spreading at an alarming rate, widely adopted empirical antibiotic treatment regimens for sepsis based on penicillin (or aminopenicillin) in combination with gentamicin 5 are being challenged. In particular, the escalating burden of infections due to extended-spectrum β-lactamase (ESBL) producing Gram negative bacteria represents a major health concern. These bacteria, mainly Escherichia coli and Klebsiella pneumoniae, are not only resistant to all penicillins and third generation cephalosporins, but also frequently express co-resistance to gentamicin. Consequently, treatment failure may occur, and clinicians increasingly prescribe last-resort antibiotics such as carbapenems as initial antibiotic treatment of sepsis. This in turn contributes to development and spread of AMR and to a further increase in the burden of infections caused by resistant bacteria. Current state-of-...

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“…04. 2019; https://doi.org/10.15146/R33X2J) [66], and blast runs performed using the same elements as in the ariba search as input. To account for less closely related organisms, we accepted hits with over 99% similarity.…”

Section: Plasmid/integron Analysesmentioning

confidence: 99%

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

et al. 2019

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Background: Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing patterns of disease caused by these two pathogens is based on studies with limited timeframes that provide few insights into their population dynamics or the dynamics in AMR elements that they can carry. Results: We investigate the population dynamics of two priority AMR pathogens over 7 years between 2007 and 2012 in a major UK hospital, spanning changes made to UK national antimicrobial prescribing policy in 2007. Between 2006 and 2012, K. pneumoniae showed epidemiological cycles of multi-drug-resistant (MDR) lineages being replaced approximately every 2 years. This contrasted E. cloacae where there was no temporally changing pattern, but a continuous presence of the mixed population. Conclusions: The differing patterns of clonal replacement and acquisition of mobile elements shows that the flux in the K. pneumoniae population was linked to the introduction of globally recognized MDR clones carrying drug resistance markers on mobile elements. However, E. cloacae carries a chromosomally encoded ampC conferring resistance to front-line treatments and shows that MDR plasmid acquisition in E. cloacae was not indicative of success in the hospital. This led to markedly different dynamics in the AMR populations of these two pathogens and shows that the mechanism of the resistance and its location in the genome or mobile elements is crucial to predict population dynamics of opportunistic pathogens in clinical settings.

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A Curated, Comprehensive Database of Plasmid Sequences

Cited by 46 publications

References 8 publications

Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

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