Fungal infections are of increasing incidence and importance in immunocompromised and immunocompetent patients. Timely diagnosis relies on appropriate use of laboratory testing in susceptible ...patients.
The relevant literature related to diagnosis of invasive pulmonary aspergillosis, invasive candidiasis, and the common endemic mycoses was systematically reviewed. Meta-analysis was performed when appropriate. Recommendations were developed using the Grading of Recommendations Assessment, Development, and Evaluation approach.
This guideline includes specific recommendations on the use of galactomannan testing in serum and BAL and for the diagnosis of invasive pulmonary aspergillosis, the role of PCR in the diagnosis of invasive pulmonary aspergillosis, the role of β-d-glucan assays in the diagnosis of invasive candidiasis, and the application of serology and antigen testing in the diagnosis of the endemic mycoses.
Rapid, accurate diagnosis of fungal infections relies on appropriate application of laboratory testing, including antigen testing, serological testing, and PCR-based assays.
Abstract
Background
The yield of next-generation sequencing (NGS) added to a Sanger sequencing–based 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) assay was evaluated in clinical ...practice for diagnosis of bacterial infection.
Methods
PCR targeting the V1 to V3 regions of the 16S rRNA gene was performed, with amplified DNA submitted to Sanger sequencing and/or NGS (Illumina MiSeq) or reported as negative, depending on the cycle threshold value. A total of 2146 normally sterile tissues or body fluids were tested between August 2020 and March 2021. Clinical sensitivity was assessed in 579 patients from whom clinical data were available.
Results
Compared with Sanger sequencing alone (400 positive tests), positivity increased by 87% by adding NGS (347 added positive tests). Clinical sensitivity of the assay that incorporated NGS was 53%, which was higher than culture (42%, P < .001), with an impact on clinical decision-making in 14% of infected cases. Clinical sensitivity in the subgroup that received antibiotics at sampling was 41% for culture and 63% for the sequencing assay (P < .001).
Conclusions
Adding NGS to Sanger sequencing of the PCR-amplified 16S rRNA gene substantially improved test positivity. In the patient population studied, the assay was more sensitive than culture, especially in patients who had received antibiotic therapy.
The addition of next-generation sequencing to 16S ribosomal RNA gene polymerase chain reaction/Sanger sequencing of normally sterile tissues and body fluids increased clinical sensitivity. In the study population, the described targeted metagenomic sequencing–based approach was more sensitive than culture, especially in patients who had received antimicrobial therapy prior to sampling.
species are found worldwide and are opportunistic pathogens of both immunocompromised and immunocompetent hosts. Recent updates to the taxonomy of this genus have indicated that there are more than ...90 recognized species of
with 54 species reported to be clinically relevant. In this paper, we report the species distribution, specimen source distribution, and antimicrobial susceptibility profiles of 2,091 clinical isolates recovered for the years 2011 to 2017 using the updated taxonomy. The most commonly isolated species included
complex,
, and
complex, with an additional 25 species or species complexes recovered from clinical specimens. The antimicrobial susceptibility profile was highly variable between the species, but in general, amikacin, linezolid, and trimethoprim-sulfamethoxazole demonstrated good
activity against most species.
Abstract Methods used for the laboratory diagnosis of tuberculosis are continually evolving in order to achieve more rapid, less expensive, and accurate results. Acid-fast staining and culture for ...mycobacteria remain at the core of any diagnostic algorithm. Following growth in culture, molecular technologies such as nucleic acid hybridization probes, MALDI-TOF MS, and DNA sequencing may be used for definitive species identification. Nucleic acid amplification methods allow for the direct detection of Mycobacterium tuberculosis complex within respiratory specimens without relying on culture growth, leading to more rapid diagnoses and appropriate patient care.
Background. The sensitivity of the MVista Histoplasma antigen enzyme immunoassay (MiraVista Diagnostics) has been evaluated in disseminated histoplasmosis in patients with AIDS and in the "epidemic" ...form of acute pneumonia. Moreover, there has been no evaluation of the sensitivity of antigenemia detection in disseminated histoplasmosis after the implementation of methods to dissociate immune complexes and denature released antibodies. The goal of this study was to determine the sensitivity of the current antigen assay in different categories of histoplasmosis. Methods. Urine and serum specimens obtained from 218 patients with histoplasmosis and 229 control subjects, including 30 with blastomycosis, were tested. Results. Antigenuria was detected in 91.8% of 158 patients with disseminated histoplasmosis, 83.3% of 6 patients with acute histoplasmosis, 30.4% of 46 patients with subacute histoplasmosis, and 87.5% of 8 patients with chronic pulmonary histoplasmosis; antigenemia was present in 100% of 31 tested cases of disseminated histoplasmosis. Among patients with disseminated cases, antigenuria was detected more often and at higher concentrations in immunocompromised patients and those with severe disease. Specificity was 99.0% for patients with nonfungal infections (n = 130) and in healthy subjects (n = 69), but cross-reactivity occurred in 90% of patients with blastomycosis. Conclusions. The sensitivity of antigen detection in disseminated histoplasmosis is higher in immunocompromised patients than in immunocompetent patients and in patients with more severe illness. The sensitivity for detection of antigenemia is similar to that for antigenuria in disseminated infection.
Abstract Objectives To determine the incidence and clinical characteristics of cutaneous nontuberculous mycobacterial (NTM) infection during the past 30 years and whether the predominant species have ...changed. Patients and Methods Using Rochester Epidemiology Project data, we identified Olmsted County, Minnesota, residents with cutaneous NTM infections between January 1, 1980, and December 31, 2009, examining the incidence of infection, patient demographic and clinical features, the mycobacterium species, and therapy. Results Forty patients (median age, 47 years; 58% female 23 of 40) had positive NTM cultures plus 1 or more clinical signs. The overall age- and sex-adjusted incidence of cutaneous NTM infection was 1.3 per 100,000 person-years (95% CI, 0.9-1.7 per 100,000 person-years). The incidence increased with age at diagnosis ( P =.003) and was higher in 2000 to 2009 (2.0 per 100,000 person-years; 95% CI, 1.3-2.8 per 100,000 person-years) than in 1980 to 1999 (0.7 per 100,000 person-years; 95% CI, 0.3-1.1 per 100,000 person-years) ( P =.002). The distal extremities were the most common sites of infection (27 of 39 patients 69%). No patient had human immunodeficiency virus infection, but 23% (9 of 39) were immunosuppressed. Of the identifiable causes, traumatic injuries were the most frequent (22 of 29 patients 76%). The most common species were Mycobacterium marinum (17 of 38 patients 45%) and Mycobacterium chelonae/Mycobacterium abscessus (12 of 38 patients 32%). In the past decade (2000-2009), 15 of 24 species (63%) were rapidly growing mycobacteria compared with only 4 of 14 species (29%) earlier (1980-1999) ( P =.04). Conclusion The incidence of cutaneous NTM infection increased nearly 3-fold during the study period. Rapidly growing mycobacteria were predominant during the past decade.
Background. Prosthetic joint infection (PJI) due to rapidly growing mycobacteria (RGM) is only occasionally encountered in clinical practice. Therefore, the optimal clinical management for this ...condition is unknown. Methods. The medical records of patients who had PJI due to RGM during 1969–2006 were reviewed to summarize its clinical characteristics, treatment, and outcome. Results. Eight patients developed 9 episodes of PJI (7 episodes involving the knee and 1 each involving the hip or elbow) due to RGM at a median of 312 weeks (range, 1–170 weeks) after prosthesis implantation. Patients presented with joint pain (7 patients), joint swelling (7 patients), and fever (3 patients), accompanied by an elevated erythrocyte sedimentation rate (median, 70.5 mm/h) and C-reactive protein level (median, 6 mg/dL). Mycobacterium chelonae (n = 3), Mycobacterium abscessus (n = 2), Mycobacterium fortuitum (n = 3), and Mycobacterium smegmatis (n = 1) were isolated from the 9 infected joints. Seven of 9 prostheses were resected, whereas 2 were retained after surgical debridement. Six of 8 patients received ⩾1 active antimicrobial agent for at least 6 months. During a median follow-up period of 33 weeks (range, 2.6–326 weeks) after surgical intervention, no clinical or microbiological relapses were observed. Reimplantation was performed successfully for 2 of 6 patients who underwent resection arthroplasty. The 2 patients with retained prosthesis continued to receive prolonged courses of suppressive antimicrobial therapy. Conclusions. RGM is a rare cause of PJI that should be suspected in patients with negative results of routine bacterial cultures. The combination of resection arthroplasty and antimicrobial therapy is the preferred approach. However, in cases involving retained prosthetic components, RGM infection may be suppressed with lifelong courses of effective antibiotic therapy.
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