Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance

2017 ◽  
Vol 1388 (1) ◽  
pp. 108-120 ◽  
Author(s):  
Anita C. Schürch ◽  
Willem van Schaik
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Challenges And Opportunities

scholarly journals Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Ellen N. Kersh ◽  
Cau D. Pham ◽  
John R. Papp ◽  
Robert Myers ◽  
Richard Steece ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Content Type ◽  
Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

scholarly journals Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates

2019 ◽  
Vol 17 (2) ◽  
pp. 169-182 ◽  
Author(s):  
Valentina Galata ◽  
Cédric C. Laczny ◽  
Christina Backes ◽  
Georg Hemmrich-Stanisak ◽  
Susanne Schmolke ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Isolates ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

scholarly journals Whole Genome Sequencing as a Diagnostic Test: Challenges and Opportunities

2014 ◽  
Vol 60 (5) ◽  
pp. 724-733 ◽  
Author(s):  
Caitlin C Chrystoja ◽  
Eleftherios P Diamandis
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Test ◽  
Whole Genome ◽  
Clinical Implementation ◽  
Technological Advances ◽  
Challenges And Opportunities ◽  
Patient Health ◽  
Therapeutic Decision Making ◽  
The Cost

Abstract BACKGROUND Extraordinary technological advances and decreases in the cost of DNA sequencing have made the possibility of whole genome sequencing (WGS) as a highly accessible clinical test for numerous indications feasible. There have been many recent, successful applications of WGS in establishing the etiology of complex diseases and guiding therapeutic decision-making in neoplastic and nonneoplastic diseases and in various aspects of reproductive health. However, there are major, but not insurmountable, obstacles to the increased clinical implementation of WGS, such as hidden costs, issues surrounding sequencing and analysis, quality assurance and standardization protocols, ethical dilemmas, and difficulties with interpretation of the results. CONTENT The widespread use of WGS in routine clinical practice remains a distant proposition. Prospective trials will be needed to establish if, and for whom, the benefits of WGS will outweigh the likely substantial costs associated with follow-up tests, the risks of overdiagnosis and overtreatment, and the associated emotional distress. SUMMARY WGS should be carefully implemented in the clinic to allow the realization of its potential to improve patient health in specific indications. To minimize harm the use of WGS for all other reasons must be carefully evaluated before clinical implementation.

The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae

2015 ◽  
Vol 68 (10) ◽  
pp. 835-838 ◽  
Author(s):  
Björn A Espedido ◽  
Borce Dimitrijovski ◽  
Sebastiaan J van Hal ◽  
Slade O Jensen
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
De Novo ◽  
Antibiotic Resistance Genes ◽  
Whole Genome ◽  
Antimicrobial Surveillance ◽  
Metropolitan Hospital ◽  
Genetic Context

AimsTo characterise the resistome of a multi-drug resistant Klebsiella pneumoniae (Kp0003) isolated from an Australian traveller who was repatriated to a Sydney Metropolitan Hospital from Myanmar with possible prosthetic aortic valve infective endocarditis.MethodsKp0003 was recovered from a blood culture of the patient and whole genome sequencing was performed. Read mapping and de novo assembly of reads facilitated in silico multi-locus sequence and plasmid replicon typing as well as the characterisation of antibiotic resistance genes and their genetic context. Conjugation experiments were also performed to assess the plasmid (and resistance gene) transferability and the effect on the antibiotic resistance phenotype.ResultsImportantly, and of particular concern, the carbapenem-hydrolysing β-lactamase gene blaNDM-4 was identified on a conjugative IncX3 plasmid (pJEG027). In this respect, the blaNDM-4 genetic context is similar (at least to some extent) to what has previously been identified for blaNDM-1 and blaNDM-4-like variants.ConclusionsThis study highlights the potential role that IncX3 plasmids have played in the emergence and dissemination of blaNDM-4-like variants worldwide and emphasises the importance of resistance gene surveillance.

scholarly journals Challenges and opportunities for strain verification by whole-genome sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jenna E. Gallegos ◽  
Sergei Hayrynen ◽  
Neil R. Adames ◽  
Jean Peccoud
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Challenges And Opportunities

scholarly journals Marine Plastics from Norwegian West Coast Carry Potentially Virulent Fish Pathogens and Opportunistic Human Pathogens Harboring New Variants of Antibiotic Resistance Genes

2020 ◽  
Vol 8 (8) ◽  
pp. 1200 ◽  
Author(s):  
Vera Radisic ◽  
Priyank S. Nimje ◽  
André Marcel Bienfait ◽  
Nachiket P. Marathe
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
West Coast ◽  
Antibiotic Resistance Genes ◽  
Whole Genome ◽  
Human Pathogens ◽  
Morganella Morganii ◽  
Fish Pathogens

To our best knowledge this is the first study characterizing fish pathogens isolated from marine plastics from the West coast of Norway for their potential for pathogenicity using whole genome sequencing. Marine plastic polymers identified as polyethylene, polyethylene/ethylene vinyl acetate copolymer and polypropylene, yielded a total of 37 bacterial isolates dominated by Pseudomonas spp. (70%). Six isolates representing either fish pathogens or opportunistic human pathogens were selected for whole genome sequencing (WGS). These included four isolates belonging to Aeromonas spp., one Acinetobacter beijerinckii isolate and one Morganella morganii isolate. Three Aeromonas salmonicida isolates were potentially virulent and carried virulence factors involved in attachment, type II and type VI secretion systems as well as toxins such as aerA/act, ahh1, ast, hlyA, rtxA and toxA. A. salmonicida and Acinetobacter beijerinckii carried new variants of antibiotic resistance genes (ARGs) such as β-lactamases and chloramphenicol acetyltransferase (catB), whereas Morganella morganii carried several clinically relevant ARGs. Our study shows that marine plastics carry not only potentially virulent fish pathogens but also multidrug resistant opportunistic human pathogens like M. morganii and may serve as vectors for transport of these pathogens in the marine environment.

scholarly journals Whole-Genome Sequencing of the Fungus Penicillium citrinum Reveals the Biosynthesis Gene Cluster for the Mycotoxin Citrinin

2019 ◽  
Vol 8 (4) ◽  
Author(s):  
Markus Schmidt-Heydt ◽  
Dominic Stoll ◽  
Rolf Geisen
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Gene Cluster ◽  
Genome Sequencing ◽  
Penicillium Citrinum ◽  
Whole Genome ◽  
Biosynthesis Gene Cluster ◽  
Content Type ◽  
Biosynthesis Gene

Penicillium citrinum is a food-contaminating ascomycete that consistently produces large amounts of the mycotoxin citrinin. Citrinin exhibits, besides its toxicity, antibiotic effects and thus potentially forces antibiotic resistance.

Sign in / Sign up

Export Citation Format

Share Document