A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infections
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PROVIDER: PRJEB87803 | ENA |
REPOSITORIES: ENA
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Project description:Objectives: To evaluate the performance of metagenomic next generation sequencing (mNGS) using adequate criteria for the detection of pathogens in lower respiratory tract (LRT) samples with a paired comparison to conventional microbiology tests (CMT). Methods: One hundred sixty-seven patients were reviewed from four different intensive care units (ICUs) in mainland China during 2018 with both mNGS and CMT results of LRT samples available. The reads per million ratio (RPMsample/RPMnon-template-control ratio) and standardized strictly mapped reads number (SDSMRN) were the two criteria chosen for identifying positive pathogens reported from mNGS. A McNemar test was used for a paired comparison analysis between mNGS and CMT. Results: One hundred forty-nine cases were counted into the final analysis. The RPMsample/RPMNTC ratio criterion performed better with a higher accuracy for bacteria, fungi, and virus than SDSMRN criterion [bacteria (RPMsample/RPMNTC ratio vs. SDSMRN), 65.1 vs. 55.7%; fungi, 75.8 vs. 71.1%; DNA virus, 86.3 vs. 74.5%; RNA virus, 90.9 vs. 81.8%]. The mNGS was also superior in bacteria detection only if an SDSMRN ≥3 was used as a positive criterion with a paired comparison to culture [SDSMRN positive, 92/149 (61.7%); culture positive, 54/149 (36.2%); p < 0.001]; however, it was outperformed with significantly more fungi and DNA virus identification when choosing both criteria for positive outliers [fungi (RPMsample/RPMNTC ratio vs. SDSMRN vs. culture), 23.5 vs. 29.5 vs. 8.7%, p < 0.001; DNA virus (RPMsample/RPMNTC ratio vs. SDSMRN vs. PCR), 14.1 vs. 20.8 vs. 11.8%, p < 0.05]. Conclusions: Metagenomic next generation sequencing may contribute to revealing the LRT infection etiology in hospitalized groups of potential fungal infections and in situations with less access to the multiplex PCR of LRT samples from the laboratory by choosing a wise criterion like the RPMsample/RPMNTC ratio.
| S-EPMC8526841 | biostudies-literature
Project description:BackgroundPatients with solid tumors frequently undergo surgical procedures and develop procedure-related infections. We sought to describe the current microbiologic spectrum of infections at various sites following common surgical procedures.MethodsThis was a retrospective review of microbiologic data between January 2011 and February 2012. The sites studied were those associated with breast cancer surgery, thoracotomy, craniotomy, percutaneous endoscopic gastrostomy (PEG) tube insertion, and abdominal/pelvic surgery. Only patients with solid tumors were included.ResultsA total of 368 surgical site infections (SSIs) were identified (68 breast cancer related; 91 thoracotomy related; 45 craniotomy related; 75 PEG-tube insertion related; and 89 abdominal/pelvic surgery related). Of these, 58% were monomicrobial and 42% were polymicrobial. Overall, 85% of the 215 monomicrobial infections were caused by Gram-positive organisms and 13% by Gram-negative bacilli (GNB). Staphylococcus aureus was the predominant pathogen in monomicrobial infections (150 of 215, 70%). Sixty (40%) of these staphylococcal isolates were methicillin resistant (MRSA), and 65% had a vancomycin minimal inhibitory concentration (MIC) ≥1.0 µg/ml. Pseudomonas aeruginosa was the predominant GNB pathogen (19 of 27, 70%). Staphylococci were also the predominant pathogens in polymicrobial infections, while P. aeruginosa and Escherichia coli were the predominant GNB. Overall, 35% of isolates from polymicrobial infections were GNB. Cephalosporins (e.g., cefazolin) or amoxicillin/clavulanate was used most often for surgical prophylaxis, and 47% of organisms from monomicrobial infections (MRSA, P. aeruginosa) were resistant to them. A similar resistance pattern was observed in polymicrobial infections.ConclusionStaphylococcus species were isolated most often from the sites studied. Polymicrobial infections (42%) and GNB monomicrobial infections (13%) were relatively frequent causes of SSIs. Many of these infections were caused by organisms that are resistant to agents commonly used for surgical prophylaxis. Additionally, 65% of staphylococcal isolates had a vancomycin MIC ≥1.0 µg/ml, suggesting the need for alternative therapeutic agents.
| S-EPMC4269616 | biostudies-literature
Project description:Necrotizing soft tissue infections (NSTIs) represent similar pathophysiological features, but the clinical course might range from subacute to a rapidly progressive, fulminant sepsis. Initial wound microbiology is the base for the Guiliano classification. The timeline of microbiological colonization has not been described during the clinical course. The role of the different microbiological pathogens on the outcome and mortality is unclear. One hundred eighty patients were included with septic inflammation response syndrome on admission. Initial wound microbiology and the changes in wound microbiology were analysed during the clinical course and correlated with outcome and risk indicators. Overall mortality was 35%. Higher age, a high Charlson Comorbidity Index or ASA score and truncal infections were highly prognostic for a lethal outcome. Microbiological findings revealed significant differences in the persistence of bacteria during the course of disease. Streptococci were only detectable within the first 5 days, whereas other bacteria persisted over a longer period of time. Initial microbiological findings correlated with better prognosis when no causative agent was identified and for gram-negative rods. Varying survival rates were observed for different Streptococci, Staphylococci, Enterococci and other bacteria. The highest odds ratio for a lethal outcome was observed for Enterococci and fungi. Microbiological colonization changes during the clinical course of NSTIs and some microbiologic pathogens are predictive for worsening the outcome and survival. Streptococcus pyogenes is only detectable in the very early phase of NSTI and after 6 days not anymore detectable. Later Enterococci and fungi showed the highest odds ratios for a lethal outcome. Enterococci bacteria and fungi have yet not been considered of clinical relevance in NSTI or even as indicator for worsening the outcome.
| S-EPMC10681420 | biostudies-literature
Project description:BackgroundOsteoarticular infections (OAIs) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children.MethodsThis was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children's hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon's discretion per standard care (fluid or tissue) and based on imaging and operative findings. We compared mNGS to culture and usual care testing (culture and polymerase chain reaction [PCR]) from the same site.ResultsWe recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In 4 subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS.ConclusionsIn this single-site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens.
| S-EPMC8314938 | biostudies-literature
Project description:PurposeTo assess the in vitro efficacy of common antimicrobial agents used empirically for methicillin- resistant and sensitive Staphylococcus aureus (MRSA and MSSA) infections of the lacrimal system.MethodsA retrospective review of culture-proven S. aureus isolates retrieved from lacrimal system samples collected between January 2013-December 2022 was performed. Microbiologic characteristics such as in vitro susceptibility as well as clinical characteristics including history of recent ocular surgery, presence of lacrimal biomaterial implant, anti-microbial regimen, and treatments outcome were collected.ResultsOne hundred and sixteen S. aureus isolates (patients = 116) were identified. Thirty-one (27.4%) and 22 (19.5%) patients had recent ocular procedure and lacrimal intubation, respectively. Fifty (44.2%) patients received a combination of oral and topical antibiotics as first line of treatment. The most common empirically utilized antibiotics were β-lactams (38.9%) and polymyxin B/ trimethoprim (31.0%). The antibiotic regimen was changed at least once in 20.5% of patients due to ineffectiveness. Of the patients with positive cultures from the lacrimal excretory apparatus, 37.3% underwent surgery as part of the treatment approach. Of all isolates identified 44.8% were MRSA. Among the fluoroquinolones, the resistance rate was 38.8% for ciprofloxacin and 30.4% for moxifloxacin, with significantly higher resistance rates in MRSA (P-value <0.0001). The resistance rates for trimethoprim/sulfamethoxazole (TMP/SXT) and gentamicin were 8.6% and 3.4%, retrospectively.ConclusionsThere is low in vitro efficacy of commonly used antimicrobials such as β-lactams and fluoroquinolones in our study population; thus, we recommend opting for trimethoprim/sulfamethoxazole and gentamicin for systemic and topical single-agent treatments.
| S-EPMC11584140 | biostudies-literature
Project description:ObjectivesOveruse of antibiotics and antibiotic resistance are global healthcare problems. In pediatric patients with respiratory infections, viral and bacterial etiologies are challenging to distinguish, leading to irrational antibiotic use. Rapid and accurate molecular diagnostic testing methods for respiratory pathogens has been shown to facilitate effective clinical decision-making and guide antibiotic stewardship interventions in the developed regions, but its impacts on pediatric patient care in the developing countries remain unclear.MethodsIn this single-center, retrospective case-control study, we compared demographics, clinical characteristics, especially microbiological findings, and antibiotic usage between pediatric patients with respiratory infection receiving FilmArray Respiratory Panel (FilmArray RP) testing and a matched routine testing control group. Our primary outcome was the duration of intravenous antibiotics treatment (DOT) during hospitalization.ResultsEach group consisted of 346 children with a respiratory infection. In the FilmArray RP testing group, the DOT was shorter than that in the routine testing group (6.41 ± 3.67 days versus 7.23 ± 4.27 days; p = 0.006). More patients in the FilmArray RP testing group de-escalated antibiotic treatments within 72 hours of hospitalization (7.80%, 27/346 versus 2.60%, 9/346; p = 0.002). By contrast, fewer patients in the FilmArray RP testing group had escalated antibiotic treatments between 72 hours and seven days (7.80% versus 14.16%; p = 0.007). The cost of hospitalization was significantly lower in the FilmArray RP testing group ($ 1413.51 ± 1438.01 versus $ 1759.37 ± 1929.22; p = 0.008). Notably, the subgroup analyses revealed that the FilmArray RP test could shorten the DOT, improve early de-escalation of intravenous antibiotics within 72 hours of hospitalization, decline the escalation of intravenous antibiotics between 72 hours and seven days, and reduce the cost of hospitalization for both patient populations with or without underlying diseases.ConclusionsMolecular point-of-care testing for respiratory pathogens could help to reduce intravenous antibiotic use and health care costs of pediatric patients with respiratory infections in developing countries.
| S-EPMC8640230 | biostudies-literature
Project description:BACKGROUND:This study represents the first Scottish retrospective analysis of the microbiology of diabetic foot infections (DFIs). The aims were to compare the microbiological profile of DFIs treated at a Scottish tertiary hospital to that in the literature, gather data regarding antimicrobial resistance and investigate potential trends between the microbiological results and nature or site of the clinical sample taken and age or gender of the patients. METHODS:A retrospective analysis of wound microbiology results was performed, data were obtained from one multidisciplinary outpatient foot clinic during the 12?months of the year 2017. Seventy-three patients and 200 microbiological investigations were included. In cases of soft tissue infection, the deepest part of a cleansed and debrided wound was sampled. In cases of osteomyelitis a bone biopsy was obtained. Factors influencing the pattern of microbial growth or prevalence of Staphylococcus aureus were investigated. RESULTS:Of the 200 microbiological investigations, 62% were culture positive, of which 37.9% were polymicrobial and 62.1% monomicrobial. Among the monomicrobial results (n =?77), most were Gram positive isolates (96.1%) and the most frequently isolated bacteria was S. aureus (84.4%). No methicillin-resistant S. aureus was reported. The prevalence of S. aureus in DFIs was associated with increasing age (p =?0.021), but no evidence of association with gender, anatomical sample site or sample material was found. CONCLUSION:The microbiological profile of DFIs in Scotland resembles that reported elsewhere in the UK. In this context, Gram positive organisms, primarily S. aureus, are most frequently isolated from DFIs. The S. aureus isolates identified were largely susceptible to antibiotic therapy. An association between increasing patient age and the prevalence of S. aureus in DFIs was observed.
| S-EPMC7068857 | biostudies-literature
Project description:The recent development of commercial panel-based molecular diagnostics for the rapid detection of pathogens in positive blood culture bottles, respiratory specimens, stool, and cerebrospinal fluid has resulted in a paradigm shift in clinical microbiology and clinical practice. This review focuses on U.S. Food and Drug Administration (FDA)-approved/cleared multiplex molecular panels with more than five targets designed to assist in the diagnosis of bloodstream, respiratory tract, gastrointestinal, or central nervous system infections. While these panel-based assays have the clear advantages of a rapid turnaround time and the detection of a large number of microorganisms and promise to improve health care, they present certain challenges, including cost and the definition of ideal test utilization strategies (i.e., optimal ordering) and test interpretation.
| S-EPMC5740973 | biostudies-literature
Project description:BackgroundMetagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens.MethodsWe conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing.ResultsHuman DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa.ConclusionsWe demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.
| S-EPMC6882222 | biostudies-literature