Comparison of broad-range polymerase chain reaction and metagenomic next-generation sequencing for the diagnosis of prosthetic joint infection

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

“…Pneumocystis jirovecii is the predominant fungus reported (~25% of the fungi detected), followed by Aspergillus species (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively~5%) (Figure 2). Excluding P. jirovecii, which is generally unculturable, out of the remaining 274 fungi detected by NGS, only 105 (~38%) were recovered by fungal culture from the same or different specimens from the respective patients [26,[29][30][31][32][33][34][35][36][37][38][39]43,45,46,49,52,54,57,59,62,64,66,67,71,73,76,77]. cies (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively ~5%) (Figure 2).…”

“…cies (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively ~5%) (Figure 2). Excluding P. jirovecii, which is generally unculturable, out of the remaining 274 fungi detected by NGS, only 105 (~38%) were recovered by fungal culture from the same or different specimens from the respective patients [26,[29][30][31][32][33][34][35][36][37][38][39]43,45,46,49,52,54,57,59,62,64,66,67,71,73,76,77]. The majority of P. jirovecii infections diagnosed by NGS were reported in case series [34,36,39,41,48,53,55,58,62,64,65,67,72,75].…”

“…Lastly, publications were searched using specific fungal names and after manual examination five extra articles were added. Therefore, in total 52 articles were included in this review [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ].…”

“…It was a case of allergic bronchopulmonary mycosis where A. fumigatus and Schizophyllum commune sequences were detected in the homogenised sputum and mucoid plugs of the patient [ 26 ]. Since then, up to the time of writing, a total of 319 cases of fungal infections diagnosed by NGS were described in the literature, with some in case reports and others in case series or cohorts [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ]. In 40 out of the 319 cases (12.5%), more than 1 fungus was detected by NGS [ 26 , ...…”

Precision Medicine in the Diagnosis and Management of Orthopedic Biofilm Infections

“…Outcome was defined as control of the infection and absence of recurrence during follow-up ( 45 ). Compared to PCR-based assays, mNGS is a relatively young technique with plenty of potential that will inevitably improve, as demonstrated by four recent studies where its sensitivity to diagnose PJI was above 90% in one of them and 95% in three of them, respectively ( 29 – 32 ) ( Table 1 ). A same-day NGS diagnostic result may significantly increase precision and efficiency while reducing the cost of PJI care.…”