Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods

Weaver, Abigail A.; Hasan, Nur A.; Klaassen, Mark A.; Karathia, Hiren; Colwell, Rita R.; Shrout, Joshua D.

doi:10.1099/jmm.0.001068

Cited by 15 publications

(17 citation statements)

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“…Secondly, the manifestation of PJI can be highly variable and the presence of other infecting organisms and the host microbiome can influence the relative abundances of various pathogens. Weaver et al 24 also showed that discordance between genomical analysis and culture results was possible and reported positive cultures of organisms falling below their whole genome shotgun sequencing thresholds. Furthermore, mNGS also identified five additional pathogens from CP-PJI cases, as well as ten pathogens from CN-PJI cases.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic next-generation sequencing of synovial fluid demonstrates high accuracy in prosthetic joint infection diagnostics

Huang

Lee

et al. 2020

Bone & Joint Research

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Aims The aim of this study was to evaluate the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens from synovial fluid of prosthetic joint infection (PJI) patients. Methods A group of 75 patients who underwent revision knee or hip arthroplasties were enrolled prospectively. Ten patients with primary arthroplasties were included as negative controls. Synovial fluid was collected for mNGS analysis. Optimal thresholds were determined to distinguish pathogens from background microbes. Synovial fluid, tissue, and sonicate fluid were obtained for culture. Results A total of 49 PJI and 21 noninfection patients were finally included. Of the 39 culture-positive PJI cases, mNGS results were positive in 37 patients (94.9%), and were consistent with culture results at the genus level in 32 patients (86.5%) and at the species level in 27 patients (73.0%). Metagenomic next-generation sequencing additionally identified 15 pathogens from five culture-positive and all ten culture-negative PJI cases, and even one pathogen from one noninfection patient, while yielding no positive findings in any primary arthroplasty. However, seven pathogens identified by culture were missed by mNGS. The sensitivity of mNGS for diagnosing PJI was 95.9%, which was significantly higher than that of comprehensive culture (79.6%; p = 0.014). The specificity is similar between mNGS and comprehensive culture (95.2% and 95.2%, respectively; p = 1.0). Conclusion Metagenomic next-generation sequencing can effectively identify pathogens from synovial fluid of PJI patients, and demonstrates high accuracy in diagnosing PJI. Cite this article: Bone Joint Res 2020;9(7):440–449.

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Section: Discussionmentioning

confidence: 99%

Metagenomic next-generation sequencing of synovial fluid demonstrates high accuracy in prosthetic joint infection diagnostics

Huang

Lee

et al. 2020

Bone & Joint Research

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“…Corynebacterium striatum is oen resistant to several antibiotics, and it is associated with wound infections, pneumonia, and meningitis. 23,24 As with Staphylococcus aureus USA300, the growth of Corynebacterium striatum was considerably inhibited by phage-mimicking ANPs with increasing silver coating on the gold nanospheres (Fig. 4C).…”

Section: Enterococcus Faecalismentioning

confidence: 86%

“…Staphylococcus aureus USA300; 22 Corynebacterium striatum; 23,24 Enterococcus faecalis; 24,25 Pseudomonas aeruginosa FRD1; 26 200 proof ethanol (VWR); 20% w/v ammonium hydroxide (NH 4 OH; BDH); tetraethyl orthosilicate (TEOS; Sigma Aldrich, 99% GC grade); 3-aminopropyltriethoxysilane (APTES; Sigma Aldrich, 99%); sodium hydroxide (NaOH; Sigma Aldrich, >97%); sodium citrate dihydrate (C 6 H 5 Na 3 O 7 $2H 2 O; Sigma Aldrich, >99%); tetrakis(hydroxymethyl)phosphonium chloride (80% purity) (THPC; Sigma Aldrich, 80% in water); gold chloride (anhydrous; Sigma Aldrich); silver nitrate (AgNO 3 ; Sigma Aldrich, 99% ACS grade); hydroquinone (Sigma Aldrich, >99% reagent grade); deionized water (DI water); 16% w/v paraformaldehyde (Beantown Chemical); Dulbecco's Modied Eagle's Medium (DMEM; Gibco); heat-inactivated fetal bovine serum (FBS); phosphate buffered saline (pH 7.4; Gibco); ethidium homodimer (Molecular Probes); 0.1% (w/v) saponin (Sigma).…”

Section: Methodsmentioning

confidence: 99%

“…Enterococcus faecalis can cause endocarditis, septicemia, urinary tract infections, and meningitis. 24,25 As an opportunistic nosocomial pathogen representing a high risk for immunocompromised patients in the clinical environment, Enterococcus faecalis was observed to be the most sensitive to the phage-mimicking ANP treatment. MS phagemimicking ANPs containing 31-47 mg ml À1 silver (factoring dilution) inhibited the growth of Enterococcus faecalis and inhibited the maximum cell count 3-fold in comparison to the normal/healthy growth of the culture (Fig.…”

Section: Enterococcus Faecalismentioning

confidence: 99%

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Phage-mimicking antibacterial core–shell nanoparticles

et al. 2019

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“…Weaver et al 57 demonstrated, in the synovial fluid from seven PJIs, that whole-genome shotgun sequencing (WGSS) is an ideal tool to detect strains when culture did not, notably for dormant, culture-resistant and rare microbes. Interestingly, in all their samples, multiple microorganisms with multiple virulent factors were present.…”

Section: Introductionmentioning

confidence: 99%

Next generation sequencing for pathogen detection in periprosthetic joint infections

et al. 2021

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Periprosthetic joint infections (PJI) represent one of the most catastrophic complications following total joint arthroplasty (TJA). The lack of standardized diagnostic tests and protocols for PJI is a challenge for arthroplasty surgeons. Next generation sequencing (NGS) is an innovative diagnostic tool that can sequence microbial deoxyribonucleic acids (DNA) from a synovial fluid sample: all DNA present in a specimen is sequenced in parallel, generating millions of reads. It has been shown to be extremely useful in a culture-negative PJI setting. Metagenomic NGS (mNGS) allows for universal pathogen detection, regardless of microbe type, in a 24–48-hour timeframe: in its nanopore-base variation, mNGS also allows for antimicrobial resistance characterization. Cell-free DNA (cfDNA) NGS, characterized by lack of the cell lysis step, has a fast run-time (hours) and, together with a high sensitivity and specificity in microorganism isolation, may provide information on the presence of antimicrobial resistance genes. Metagenomics and cfDNA testing have reduced the time needed to detect infecting bacteria and represent very promising technologies for fast PJI diagnosis. NGS technologies are revolutionary methods that could disrupt the diagnostic paradigm of PJI, but a comprehensive collection of clinical evidence is still needed before they become widely used diagnostic tools. Cite this article: EFORT Open Rev 2021;6:236-244. DOI: 10.1302/2058-5241.6.200099

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Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods

Cited by 15 publications

References 50 publications

Metagenomic next-generation sequencing of synovial fluid demonstrates high accuracy in prosthetic joint infection diagnostics

Metagenomic next-generation sequencing of synovial fluid demonstrates high accuracy in prosthetic joint infection diagnostics

Phage-mimicking antibacterial core–shell nanoparticles

Next generation sequencing for pathogen detection in periprosthetic joint infections

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