scholarly journals Predictive Antibiotic Susceptibility Testing by Next-Generation Sequencing for Periprosthetic Joint Infections: Potential and Limitations

Biomedicines ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 910
Author(s):  
Lukas Lüftinger ◽  
Ines Ferreira ◽  
Bernhard J. H. Frank ◽  
Stephan Beisken ◽  
Johannes Weinberger ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antibiotic Susceptibility ◽  
Susceptibility Testing ◽  
Multidrug Resistant ◽  
Antibiotic Susceptibility Testing ◽  
Next Generation ◽  
Joint Infections ◽  
Prosthetic Joint ◽  
Prosthetic Joint Infections ◽  
Generation Sequencing

Joint replacement surgeries are one of the most frequent medical interventions globally. Infections of prosthetic joints are a major health challenge and typically require prolonged or even indefinite antibiotic treatment. As multidrug-resistant pathogens continue to rise globally, novel diagnostics are critical to ensure appropriate treatment and help with prosthetic joint infections (PJI) management. To this end, recent studies have shown the potential of molecular methods such as next-generation sequencing to complement established phenotypic, culture-based methods. Together with advanced bioinformatics approaches, next-generation sequencing can provide comprehensive information on pathogen identity as well as antimicrobial susceptibility, potentially enabling rapid diagnosis and targeted therapy of PJIs. In this review, we summarize current developments in next generation sequencing based predictive antibiotic susceptibility testing and discuss potential and limitations for common PJI pathogens.

scholarly journals Presence of the neonatal Staphylococcus capitis outbreak clone (NRCS-A) in prosthetic joint infections

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Staffan Tevell ◽  
Sharmin Baig ◽  
Bengt Hellmark ◽  
Patricia Martins Simoes ◽  
Thierry Wirth ◽  
...  
Keyword(s):  
Neonatal Intensive Care ◽  
Bloodstream Infections ◽  
Multidrug Resistant ◽  
Coagulase Negative Staphylococcus ◽  
Nasal Carrier ◽  
Joint Infections ◽  
Staphylococcus Capitis ◽  
Prosthetic Joint ◽  
Strain Collection ◽  
Prosthetic Joint Infections

AbstractStaphylococcus capitis is a coagulase-negative staphylococcus that has been described primarily as causing bloodstream infections in neonatal intensive care units (NICUs), but has also recently been described in prosthetic joint infections (PJIs). The multidrug-resistant S. capitis subsp. urealyticus clone NRCS-A, comprising three sublineages, is prevalent in NICUs across the world, but its impact on other patient groups such as those suffering from PJIs or among adults planned for arthroplasty is unknown. Genome sequencing and subsequent analysis were performed on a Swedish collection of PJI isolates (n = 21), nasal commensals from patients planned to undergo arthroplasty (n = 20), NICU blood isolates (n = 9), operating theatre air isolates (n = 4), and reference strains (n = 2), in conjunction with an international strain collection (n = 248). The NRCS-A Outbreak sublineage containing the composite type V SCCmec-SCCcad/ars/cop element was present in PJIs across three Swedish hospitals. However, it was not found among nasal carrier strains, where the less virulent S. capitis subsp. capitis was most prevalent. The presence of the NRCS-A Outbreak clone in adult patients with PJIs demonstrates that dissemination occurs beyond NICUs. As this clone has several properties which facilitate invasive infections in patients with medical implants or immunosuppression, such as biofilm forming ability and multidrug resistance including heterogeneous glycopeptide-intermediate susceptibility, further research is needed to understand the reservoirs and distribution of this hospital-associated pathogen.

Rare case of Ureaplasma parvum septic arthritis in an immunocompetent patient

2020 ◽  
Vol 13 (9) ◽  
pp. e236396
Author(s):  
Abuzar Ali Asif ◽  
Moni Roy ◽  
Sharjeel Ahmad
Keyword(s):  
Septic Arthritis ◽  
Rare Case ◽  
Immunocompetent Patient ◽  
Next Generation ◽  
Ureaplasma Parvum ◽  
Urogenital Infections ◽  
Joint Infections ◽  
Prosthetic Joint ◽  
Prosthetic Joint Infections ◽  
Diagnostic Modalities

Mycoplasmatacea family comprises two genera: Mycoplasma and Ureaplasma. Ureaplasma parvum (previously known as U. urealyticum biovar 1) commonly colonises the urogenital tract in humans. Although Ureaplasma species have well-established pathogenicity in urogenital infections, its involvement in septic arthritis has been limited to prosthetic joint infections and immunocompromised individuals. We present a rare case of native right knee infection due to U. parvum identified using next-generation sequencing of microbial cell-free DNA testing and confirmed with PCR assays. This rare case of Ureaplasma septic arthritis was diagnosed using newer next-generation DNA sequencing diagnostic modalities and a literature review of prior cases, antibiotic coverage and antimicrobial resistance is incorporated as part of the discussion.

scholarly journals Use of Next Generation Sequencing and Synergy Susceptibility Testing in Diagnosis and Treatment of Carbapenem-Resistant Klebsiella pneumoniae Blood Stream Infection

2018 ◽  
Vol 2018 ◽  
pp. 1-4
Author(s):  
Yuetian Yu ◽  
Fupin Hu ◽  
Cheng Zhu ◽  
Erzhen Chen ◽  
Liangjing Lu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Klebsiella Pneumoniae ◽  
Lupus Erythematosus ◽  
Susceptibility Testing ◽  
Blood Stream Infection ◽  
Blood Stream ◽  
Next Generation ◽  
Carbapenem Resistant ◽  
Appropriate Treatment ◽  
Generation Sequencing

Early diagnosis and appropriate treatment for carbapenem-resistant Klebsiella pneumoniae (CR-Kp) infection is a big challenge for clinicians due to its high mortality. Every effort has been made to improve its clinical outcomes. However, treatment according to synergy susceptibility testing has never been reported in the literature. We reported a 29-year-old systemic lupus erythematosus female with CR-Kp blood stream infection. We highlighted the identification by next generation sequencing and treatment according to synergy susceptibility testing in the case.

scholarly journals Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

2015 ◽  
Vol 60 (3) ◽  
pp. 1249-1257 ◽  
Author(s):  
Hajime Kanamori ◽  
Christian M. Parobek ◽  
David J. Weber ◽  
David van Duin ◽  
William A. Rutala ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acinetobacter Baumannii ◽  
Resistance Genes ◽  
Reference Genome ◽  
Index Case ◽  
Multidrug Resistant ◽  
Next Generation ◽  
The Third ◽  
Burn Center ◽  
Generation Sequencing

Next-generation sequencing (NGS) analysis has emerged as a promising molecular epidemiological method for investigating health care-associated outbreaks. Here, we used NGS to investigate a 3-year outbreak of multidrug-resistantAcinetobacter baumannii(MDRAB) at a large academic burn center. A reference genome from the index case was generated usingde novoassembly of PacBio reads. Forty-six MDRAB isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and sequenced using an Illumina platform. After mapping to the index case reference genome, four samples were excluded due to low coverage, leaving 42 samples for further analysis. Multilocus sequence types (MLST) and the presence of acquired resistance genes were also determined from the sequencing data. A transmission network was inferred from genomic and epidemiological data using a Bayesian framework. Based on single-nucleotide variant (SNV) differences, this MDRAB outbreak represented three sequential outbreaks caused by distinct clones. The first and second outbreaks were caused by sequence type 2 (ST2), while the third outbreak was caused by ST79. For the second outbreak, the MLST and PFGE results were discordant. However, NGS-based SNV typing detected a recombination event and consequently enabled a more accurate phylogenetic analysis. The distribution of resistance genes varied among the three outbreaks. The first- and second-outbreak strains possessed ablaOXA-23-likegroup, while the third-outbreak strains harbored ablaOXA-40-likegroup. NGS-based analysis demonstrated the superior resolution of outbreak transmission networks for MDRAB and provided insight into the mechanisms of strain diversification between sequential outbreaks through recombination.

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

2020 ◽  
Vol 9 (7) ◽  
pp. 440-449 ◽  
Author(s):  
Zida Huang ◽  
Wenbo Li ◽  
Gwo-Chin Lee ◽  
Xinyu Fang ◽  
Li Xing ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Synovial Fluid ◽  
Prosthetic Joint Infection ◽  
Joint Infection ◽  
High Accuracy ◽  
Next Generation ◽  
Primary Arthroplasty ◽  
Prosthetic Joint ◽  
Culture Positive ◽  
Generation Sequencing

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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