Clinical metagenomics of bone and joint infections: a proof of concept study

Bone and joint infections (BJI) are severe infections that require a tailored and protracted antibiotic treatment. Yet, the diagnostic based on culturing samples lacks sensitivity, especially for hardly culturable bacteria. Metagenomic sequencing could potentially address those limitations. Here, we assessed the performances of metagenomic sequencing on 24 BJI samples for the identification of pathogens and the prediction of their antibiotic susceptibility. For monomicrobial samples in culture (n = 8), the presence of the pathogen was confirmed by metagenomics in all cases. For polymicrobial samples (n = 16), 32/55 bacteria (58.2%) were found at the species level (and 41/55 [74.5%] at the genus level). Conversely, 273 bacteria not found in culture were identified, 182 being possible pathogens and 91 contaminants. A correct antibiotic susceptibility could be inferred in 94.1% and 76.5% cases for monomicrobial and polymicrobial samples, respectively. Altogether, we found that clinical metagenomics applied to BJI samples is a potential tool to support conventional culture.

[1]  J. R. Johnson,et al.  Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data , 2013, The Journal of antimicrobial chemotherapy.

[2]  Ole Lund,et al.  Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. , 2013, The Journal of antimicrobial chemotherapy.

[3]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[4]  P. Rosset,et al.  Bone and joint infections in hospitalized patients in France, 2008: clinical and economic outcomes. , 2012, The Journal of hospital infection.

[5]  Daniel J. Wilson,et al.  Prediction of Staphylococcus aureus Antimicrobial Resistance by Whole-Genome Sequencing , 2014, Journal of Clinical Microbiology.

[6]  P. François,et al.  Comparison of DNA Extraction Methods in Analysis of Salivary Bacterial Communities , 2013, PloS one.

[7]  N. Mahlaoui,et al.  Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis. , 2015, Journal of the Pediatric Infectious Diseases Society.

[8]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[9]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[10]  C. Bodemer,et al.  Live rubella virus vaccine long-term persistence as an antigenic trigger of cutaneous granulomas in patients with primary immunodeficiency. , 2014, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[11]  Ole Lund,et al.  Rapid Whole-Genome Sequencing for Detection and Characterization of Microorganisms Directly from Clinical Samples , 2013, Journal of Clinical Microbiology.

[12]  M. Pallen,et al.  Whole-Genome Sequencing for Rapid Susceptibility Testing of M. tuberculosis , 2013 .

[13]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[14]  C. Huttenhower,et al.  Metagenomic microbial community profiling using unique clade-specific marker genes , 2012, Nature Methods.

[15]  Joseph L DeRisi,et al.  Actionable diagnosis of neuroleptospirosis by next-generation sequencing. , 2014, The New England journal of medicine.

[16]  Jacques Corbeil,et al.  The Resistome of Pseudomonas aeruginosa in Relationship to Phenotypic Susceptibility , 2014, Antimicrobial Agents and Chemotherapy.

[17]  J. Schrenzel,et al.  Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients , 2014, Front. Cell. Infect. Microbiol..

[18]  Sanket Patel,et al.  Interconnected microbiomes and resistomes in low-income human habitats , 2016, Nature.

[19]  Phelim Bradley,et al.  Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis , 2015, Nature Communications.

[20]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[21]  Julian Parkhill,et al.  Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. , 2012, The New England journal of medicine.

[22]  Joshua N. Daly,et al.  Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples , 2012, PloS one.

[23]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[24]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[25]  L. Öhrmalm,et al.  Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia , 2016, Scientific Reports.

[26]  R. Knight,et al.  Avoiding Pandemic Fears in the Subway and Conquering the Platypus , 2016, mSystems.

[27]  Paul Turner,et al.  Reagent and laboratory contamination can critically impact sequence-based microbiome analyses , 2014, BMC Biology.

[28]  G. Church,et al.  Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora , 2009, Science.

[29]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[30]  Derrick E. Wood,et al.  Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.

[31]  Paul D. Shaw,et al.  Using Tablet for visual exploration of second-generation sequencing data , 2013, Briefings Bioinform..

[32]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[33]  Sanket Patel,et al.  Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes , 2013, PloS one.

[34]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[35]  J. Schrenzel,et al.  Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia. , 2016, Future microbiology.

[36]  Duy Tin Truong,et al.  MetaPhlAn2 for enhanced metagenomic taxonomic profiling , 2015, Nature Methods.

[37]  Lisa C. Crossman,et al.  Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing , 2017, The Journal of antimicrobial chemotherapy.

[38]  Shaohua Zhao,et al.  WGS accurately predicts antimicrobial resistance in Escherichia coli. , 2015, The Journal of antimicrobial chemotherapy.