Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach

Thoendel, Matthew; Jeraldo, Patricio; Greenwood‐Quaintance, Kerryl E.; Yao, Jingwen; Chia, Nicholas; Hanssen, Arlen D.; Abdel, Matthew P.; Patel, Robin

doi:10.1093/cid/ciy303

Cited by 204 publications

(203 citation statements)

References 27 publications

Supporting

Mentioning

192

Contrasting

Order By: Relevance

“…Other sources that have either been validated or are close to clinical validation for metagenomics include respiratory specimens [64,74] and prosthetic joint specimens [75][76][77], respectively. Studies in these sample types also detect a number of questionable or insignificant positive results, highlighting the need for careful clinical interpretation.…”

Section: Next-generation Sequencing and Clinical Metagenomicsmentioning

confidence: 99%

Appropriate Use and Future Directions of Molecular Diagnostic Testing

Graf

Pancholi

2020

Curr Infect Dis Rep

View full text Add to dashboard Cite

Purpose of Review Major technologic advances in two main areas of molecular infectious disease diagnostics have resulted in accelerated adoption or ordering, outpacing implementation, and clinical utility studies. Physicians must understand the limitations to and appropriate utilization of these technologies in order to provide cost-effective and well-informed care for their patients. Recent Findings Rapid molecular testing and, to a lesser degree, clinical metagenomics are now being routinely used in clinical practice. While these tests allow for a breadth of interrogation not possible with conventional microbiology, they pose new challenges for diagnostic and antimicrobial stewardship programs. This review will summarize the most recent literature on these two categories of technologic advances and discuss the few studies that have looked at utilization and stewardship approaches. This review also highlights the future directions for both of these technologies. Summary The appropriate utilization of rapid molecular testing and clinical metagenomics has not been well established. More studies are needed to assess their prospective impacts on patient management and antimicrobial stewardship efforts as the future state of infectious disease diagnostics will see continued expansion of these technologic advances.

show abstract

Section: Next-generation Sequencing and Clinical Metagenomicsmentioning

confidence: 99%

Appropriate Use and Future Directions of Molecular Diagnostic Testing

Graf

Pancholi

2020

Curr Infect Dis Rep

View full text Add to dashboard Cite

show abstract

“…Clinical metagenomics is an emerging field in which the microbiological diagnosis of complex, polymicrobial infections is determined from sequencing of DNA extracted directly from clinical specimens 6,5,7 . The ability to reassemble plasmids and detect combinations of antimicrobial resistance elements is an important step for molecular surveillance of high impact antimicrobial resistance genes such as carbapenemases as they disseminate and recombine between mobile Purified DNA was quantified by Qubit dsDNA BR assay (Q32853, Thermo Fisher Scientific).…”

Section: Discussionmentioning

confidence: 99%

“…Illumina short reads 18 (SRR2822454) and Illumina synthetic long reads 18 (SRR2822457) were downloaded for the HMP staggered mock community from the SRA database (https://www.ncbi.nlm.nih.gov/sra). As PacBio sequencing data for the HMP staggered mock community was not available, we downloaded the PacBio HMP even mock community dataset (https://s3.amazonaws.com/datasets.pacb.com/Human_microbiome_mockB/hmp_set5.tar.gz/hm p_set [5][6][7].tar.gz) and generated a staggered version using the following protocol: i) mapping reads to the reference genome using GraphMap (v0.2.2, default parameters), ii) computing for each genome the ratio € of observed abundances versus expected abundances, iii) subsampling reads to obtain the same ratio € for observed versus expected abundances in the staggered community.…”

Section: Hmp Mock Community Datasetsmentioning

confidence: 99%

“…Studies of the transmission of antibiotic resistant organisms between hosts and the environment have primarily relied on cultured isolates, though increasingly metagenomic techniques are being applied to this problem [4][5][6][7] . By avoiding culture bias, shotgun metagenomic sequencing promises a more complete view of the gut microbiome, including antibiotic resistant bacteria or fungi and corresponding genes.…”

Section: Introductionmentioning

confidence: 99%

“…genetic elements and bacterial species, and for rational antibiotic selection in this treatment paradigm. The enhanced resolution of OPERA-MS assembly thus has the potential to accelerate the implementation of metagenomics into outbreak investigations and surveillance programs where culture-independent approaches speed-up detection of unknown pathogens, novel antimicrobial resistance combinations and virulence mechanisms6,5,7 .MethodsHigh molecular weight DNA extraction for stool metagenomicsMetagenomic DNA extraction was carried out using Phenol-Chloroform extraction and various commercial kits (i.e. QIAamp DNA Stool Mini Kit, PowerSoil® DNA Isolation Kit, and PowerFecal® DNA Isolation Kit).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome

Bertrand

Shaw

Kalathiappan

et al. 2018

Preprint

View full text Add to dashboard Cite

The analysis of information rich whole-metagenome datasets acquired from complex microbial communities is often restricted by the fragmented nature of assembly from short-read sequencing.The availability of long-reads from third-generation sequencing technologies (e.g. PacBio or Oxford Nanopore) can help improve assembly quality in principle, but high error rates and low throughput have limited their application in metagenomics. In this work, we describe the first hybrid metagenomic assembler which combines the advantages of short and long-read technologies, providing an order of magnitude improvement in contiguity compared to short read assemblies, and high base-pair level accuracy. The proposed approach (OPERA-MS) integrates a novel assembly-based metagenome clustering technique with an exact scaffolding algorithm that can efficiently assemble repeat rich sequences. Based on evaluations with defined in vitro communities and virtual gut microbiomes, we show that it is possible to assemble near complete genomes from metagenomes with as little as 9× long read coverage, thus enabling high quality assembly of lowly abundant species (<1%). Furthermore, OPERA-MS's fine-grained clustering is able to deconvolute and assemble multiple genomes of the same species in a single sample, allowing us to study the complex dynamics of the human microbiome at the sub-species level.Applying nanopore sequencing to gut metagenomes of patients undergoing antibiotic treatment, we show that long reads can be obtained from stool samples in clinical studies to produce more meaningful metagenomic assemblies (up to 200× improvement over short-read assemblies), including the closed assembly of >80 putative plasmid/phage sequences and a 263kbp jumbo phage. Our results highlight that high-quality hybrid assemblies provide an unprecedented view of the gut resistome in these patients, including strain dynamics and identification of novel plasmid sequences.

show abstract

Introduction

Zimmerli¹

2021

Bone and Joint Infections

View full text Add to dashboard Cite

Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach

Abstract: Metagenomic shotgun sequencing is a powerful tool to identify a wide range of PJI pathogens, including difficult-to-detect pathogens in culture-negative infections.

Cited by 204 publications

References 27 publications

Appropriate Use and Future Directions of Molecular Diagnostic Testing

Appropriate Use and Future Directions of Molecular Diagnostic Testing

Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome

Introduction

Contact Info

Product

Resources

About