No abstract

Respiratory tract infections (RTI) are more commonly caused by viral pathogens in children than in adults. Surprisingly, little is known about antibiotic use in children as compared to adults with RTI. This prospective study aimed to determine antibiotic misuse in children and adults with RTI, using an expert panel reference standard, in order to prioritise the target age population for antibiotic stewardship interventions. We recruited children and adults who presented at the emergency department or were hospitalised with clinical presentation of RTI in The Netherlands and Israel. A panel of three experienced physicians adjudicated a reference standard diagnosis (i.e. bacterial or viral infection) for all the patients using all available clinical and laboratory information, including a 28-day follow-up assessment. The cohort included 284 children and 232 adults with RTI (median age, 1.3 years and 64.5 years, respectively). The proportion of viral infections was larger in children than in adults (209(74%) versus 89(38%), p < 0.001). In case of viral RTI, antibiotics were prescribed (i.e. overuse) less frequently in children than in adults (77/209 (37%) versus 74/89 (83%), p < 0.001). One (1%) child and three (2%) adults with bacterial infection were not treated with antibiotics (i.e. underuse); all were mild cases. This international, prospective study confirms major antibiotic overuse in patients with RTI. Viral infection is more common in children, but antibiotic overuse is more frequent in adults with viral RTI. Together, these findings support the need for effective interventions to decrease antibiotic overuse in RTI patients of all ages. Electronic supplementary material The online version of this article (10.1007/s10096-018-03454-2) contains supplementary material, which is available to authorized users.

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies—ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies—ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies—ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable.

This is the first prospective international multicenter RSV study using an expert panel as reference standard to identify children with and without bacterial coinfection. All cases of bacterial coinfections are treated, whereas as many as one-third of all children with RSV LRTI are treated unnecessarily with antibiotics.

BackgroundThe emergence and spread of antibiotic resistant micro-organisms is a global concern, which is largely attributable to inaccurate prescribing of antibiotics to patients presenting with non-bacterial infections. The use of ‘omics’ technologies for discovery of novel infection related biomarkers combined with novel treatment algorithms offers possibilities for rapidly distinguishing between bacterial and viral infections. This distinction can be particularly important for patients suffering from lower respiratory tract infections (LRTI) and/or sepsis as they represent a significant burden to healthcare systems. Here we present the study details of the TAILORED-Treatment study, an observational, prospective, multi-centre study aiming to generate a multi-parametric model, combining host and pathogen data, for distinguishing between bacterial and viral aetiologies in children and adults with LRTI and/or sepsis.MethodsA total number of 1200 paediatric and adult patients aged 1 month and older with LRTI and/or sepsis or a non-infectious disease are recruited from Emergency Departments and hospital wards of seven Dutch and Israeli medical centres. A panel of three experienced physicians adjudicate a reference standard diagnosis for all patients (i.e., bacterial or viral infection) using all available clinical and laboratory information, including a 28-day follow-up assessment. Nasal swabs and blood samples are collected for multi-omics investigations including host RNA and protein biomarkers, nasal microbiota profiling, host genomic profiling and bacterial proteomics. Simplified data is entered into a custom-built database in order to develop a multi-parametric model and diagnostic tools for differentiating between bacterial and viral infections. The predictions from the model will be compared with the consensus diagnosis in order to determine its accuracy.DiscussionThe TAILORED-Treatment study will provide new insights into the interplay between the host and micro-organisms. New host- or pathogen-related biomarkers will be used to generate a multi-parametric model for distinguishing between bacterial and viral infections. This model will be helpful to better guide antimicrobial therapy for patients with LRTI and sepsis. This study has the potential to improve patient care, reduce unnecessary antibiotic prescribing and will contribute positively to institutional, national and international healthcare economics.Trial RegistrationNCT02025699. Registration Date: January, 1, 2014.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3300-9) contains supplementary material, which is available to authorized users.

No abstract

BackgroundBacterial and viral infections are often clinically indistinguishable, particularly in upper respiratory tract infections (URTI), which leads to antibiotic misuse. A novel assay (ImmunoXpert™) that integrates measurements of three host-response proteins (TRAIL, IP-10, CRP) was recently developed to assist in differentiation between bacterial and viral etiologies. We evaluated the assay performance in URTI patients and compared it with standard laboratory measures.MethodsWe performed a sub-analysis of 464 patients with clinical suspicion of URTI enrolled in three previously conducted multi-center clinical studies that evaluated the assay performance in patients with acute infections: ‘Curiosity’ study (NCT01917461), ‘Opportunity’ study (NCT01931254), and ‘Pathfinder’ study (NCT01911143). Comparator method was predetermined criteria combined with expert panel adjudication, which was blinded to the test results. Diagnostic performance was evaluated by comparing test and comparator method outcomes.ResultsA unanimous panel adjudication was attained for 61 bacterial (13%) and 241 viral (52%) patients (162 patients (35%) had an indeterminate diagnosis). The assay distinguished between bacterial and viral infected patients with a sensitivity of 92% (95% CI: 82%- 98%) and specificity of 93% (88%-96%) with 11% equivocal test results. Overall the assay outperformed other routine laboratory tests (FIG 1), including: white blood cell count (WBC; cutoff 15,000 cells/µL, sensitivity 48% (35%-60%), P < 10-−6; specificity 85% (80%-90%), P < 0.05); CRP (cutoff 40 mg/L, sensitivity 82% (72%–92%), P = 0.16, specificity 79% (74%–84%), P < 10-4); Procalcitonin (PCT; cutoff 0.5 ng/mL, sensitivity 22% (11%–32%), P < 10–14, specificity 80% (74%–85%), P < 0.001); absolute neutrophil count (ANC; cutoff 10,000 cells/µL, sensitivity 58% (45%–71%), P < 10-−4, specificity 94% (91%–97%), P = 0.7).ConclusionThe novel assay demonstrated superior performance compared with routine laboratory tests (WBC, ANC) and biomarkers (CRP, PCT), in distinguishing bacterial from viral etiologies in patients with URTI. It has the potential to help clinicians avoid missing bacterial infections or prescribing unwarranted antibiotics for viral URTIs.Disclosures K. Oved, MeMed Diagnostics: Board Member, Employee and Shareholder, Salary E. Eden, MeMed Diagnostics: Board Member, Employee and Shareholder, Salary T. Gottlieb, MeMed Diagnostics: Employee, Salary R. Navon, MeMed Diagnostics: Employee, Salary A. Cohen, MeMed Diagnostics: Employee, Salary O. Boico, MeMed Diagnostics: Employee, Salary M. Paz, MeMed Diagnostics: Employee, Salary L. Etshtein, MeMed Diagnostics: Employee, Salary G. Kronenfeld, MeMed Diagnostics: Employee, Salary T. Friedman, MeMed Diagnostics: Employee, Salary E. Bamberger, MeMed Diagnostics: Employee, Salary I. Chistyakov, MeMed Diagnostics: Consultant, Consulting fee I. Potasman, MeMed Diagnostics: Holding stock options, stock options

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME and an in house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 and R9.2 were compared.