Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer; Seyfarth, Anne Mette; Agersø, Yvonne; Lund, Ole; Larsen, Mette Voldby; Aarestrup, Frank Møller

doi:10.1093/jac/dks496

Cited by 280 publications

(207 citation statements)

References 32 publications

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“…Pure cultures were stored for WGS at Ϫ80°C in cryotubes containing 30% glycerol. Antimicrobial susceptibility testing was performed as MIC testing using microtiter plates (10).…”

Section: Clinical Samples the Clinical Microbiological Laboratory Atmentioning

confidence: 99%

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Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

et al. 2014

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c Whole-genome sequencing (WGS) is becoming available as a routine tool for clinical microbiology. If applied directly on clinical samples, this could further reduce diagnostic times and thereby improve control and treatment. A major bottleneck is the availability of fast and reliable bioinformatic tools. This study was conducted to evaluate the applicability of WGS directly on clinical samples and to develop easy-to-use bioinformatic tools for the analysis of sequencing data. Thirty-five random urine samples from patients with suspected urinary tract infections were examined using conventional microbiology, WGS of isolated bacteria, and direct sequencing on pellets from the urine samples. A rapid method for analyzing the sequence data was developed. Bacteria were cultivated from 19 samples but in pure cultures from only 17 samples. WGS improved the identification of the cultivated bacteria, and almost complete agreement was observed between phenotypic and predicted antimicrobial susceptibilities. Complete agreement was observed between species identification, multilocus sequence typing, and phylogenetic relationships for Escherichia coli and Enterococcus faecalis isolates when the results of WGS of cultured isolates and urine samples were directly compared. Sequencing directly from the urine enabled bacterial identification in polymicrobial samples. Additional putative pathogenic strains were observed in some culture-negative samples. WGS directly on clinical samples can provide clinically relevant information and drastically reduce diagnostic times. This may prove very useful, but the need for data analysis is still a hurdle to clinical implementation. To overcome this problem, a publicly available bioinformatic tool was developed in this study.

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“…Pure cultures were stored for WGS at Ϫ80°C in cryotubes containing 30% glycerol. Antimicrobial susceptibility testing was performed as MIC testing using microtiter plates (10).…”

Section: Clinical Samples the Clinical Microbiological Laboratory Atmentioning

confidence: 99%

“…Its great value in describing and improving our understanding of bacterial evolution, outbreaks, and transmission events has been shown in a number of recent studies, including studies of Staphylococcus aureus (4)(5)(6), Vibrio cholerae (7), Escherichia coli (8), and Mycobacterium tuberculosis (9) and surveillance of antimicrobial resistance (10).…”

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confidence: 99%

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

et al. 2014

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“…The search for antibiotic resistance and virulence genes was performed with ResFinder version 2.1 [31] and VirulenceFinder version 1.5 [32] web services. The identity threshold was set to 85% and the minimum length to 40% for both tools.…”

Section: Methodsmentioning

confidence: 99%

Ancient permafrost staphylococci carry antibiotic resistance genes

Kashuba

Dmitriev

Kamal

et al. 2017

Microbial Ecology in Health and Disease

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Background: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years.Objective: To cultivate bacterial strains from permafrost.Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40–60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences.Results: Genomic sequence analysis revealed the close relation of the isolated ancient bacteria to the modern bacteria of this species. Moreover, several genes associated with resistance to different groups of antibiotics were found in the S. hominis MMP2 genome.Conclusions: These findings supports a hypothesis that antibiotic resistance has an ancient origin. The enrichment of cultivated bacterial communities with ancient permafrost strains is essential for the analysis of bacterial evolution and antibiotic resistance.

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“…Currently, the majority of the routine microbiology laboratories still screen for MDR based on phenotypic susceptibility testing, which not only is subject to guidelines and breakpoints but also is time-consuming as it depends on pathogen growth. Previous NGS-based studies have demonstrated high concordance between in silico-predicted and phenotypic antimicrobial susceptibility (24,36). Nonetheless, sequence-based predictions of phenotypic resistance for clinical purposes need to be made with caution.…”

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confidence: 99%

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

et al. 2016

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The unrestricted use of antibiotics has resulted in rapid acquisition of antibiotic resistance (AR) and spread of multidrug-resistant (MDR) bacterial pathogens. With the advent of next-generation sequencing technologies and their application in understanding MDR pathogen dynamics, it has become imperative to unify AR gene data resources for easy accessibility for researchers. However, due to the absence of a centralized platform for AR gene resources, availability, consistency, and accuracy of information vary considerably across different databases. In this article, we explore existing AR gene data resources in order to make them more visible to the clinical microbiology community, to identify their limitations, and to propose potential solutions.

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Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

Abstract: High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.

Cited by 280 publications

References 32 publications

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples

Ancient permafrost staphylococci carry antibiotic resistance genes

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

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