BACKGROUND Salmonella enterica serotype Napoli (S Napoli), a non-typhoidal Salmonella serotype that has been emerging in Italy, Switzerland, and France since the mid-1990s, has an unusual epidemiological profile that suggests a role for the environment in the transmission of these bacteria. The genomics of S Napoli has been inadequately characterised; we, therefore, aimed to provide a robust genomic framework for S Napoli surveillance. METHODS In this genomic epidemiology study, we performed short-read sequencing of 1145 S Napoli isolates from national surveillance in four European countries (Italy, Switzerland, France, and Spain) and complemented this dataset with 175 additional genomes (174 published and one unpublished). We used the EnteroBase core genome multilocus sequence typing (cgMLST) scheme and its associated Hierarchical Clustering algorithm, along with other genome-based bioinformatics approaches such as single nucleotide variant-based phylogenetic analyses, ResFinder, PlasmidFinder, and RefSeq genomes, to characterise population structure, antimicrobial resistance (AMR) prevalence, and differences in gene content among genetic lineages. FINDINGS We analysed 1320 S Napoli genomes, collected between April, 1945, and September 14, 2022, from human (n=1088, 82·4%) and non-human (n=232, 17·6%) sources in Italy (n=317, 24%), Switzerland (n=181, 13·7%), France (n=773, 58·5%), and Spain (n=48, 3·6%), confirming that the rising prevalence of S Napoli is driven by a single monophyletic serotype within cgMLST superlineage HC2000_1289. However, this serotype displays considerable genetic diversity (15 lineages falling into 12 HC900 clusters), strong spatial structuring, and a low frequency (2%) of AMR determinants. We also detected genetic introgression between S Napoli and the sympatric, closely related Salmonella enterica serotype Veneziana. INTERPRETATION Unlike successful non-typhoidal Salmonella serotypes, for which globalisation has had a homogenising effect, S Napoli forms distinct lineages isolated by geographical distance. This study suggests that the persistence of S Napoli as a geographically structured metapopulation, causing localised human infections, could reflect the natural ecology of Salmonella before the rise of agribusiness. Future research should investigate the environmental reservoirs and transmission pathways of S Napoli. FUNDING Fondation Le Roch-Les Mousquetaires, Institut Pasteur, Santé publique France, Investissement d'Avenir programme, Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases', and Institute of Health Carlos III 'Acción Estratégica de Salud Intramural'.
BACKGROUND Global antibiotic use during the COVID-19 pandemic and its impact remain unclear. This study analysed antibiotic use, bacterial co-infections, and the association between antibiotic use and in-hospital mortality among patients hospitalised for COVID-19, using a WHO database. METHODS We conducted a multicountry cohort study using anonymised patient-level data from The WHO Global Clinical Platform for COVID-19. Data were collected across 64 countries in all six WHO regions between January, 2020, and October, 2023. The study included hospitalised patients of all ages with suspected or confirmed SARS-CoV-2 infection. We obtained patient-level data from standardised WHO case report forms completed prospectively or retrospectively and from harmonised national registries, research studies, and hospital databases. Patients without a suspected or confirmed COVID-19 diagnosis or missing information on hospital admission date, antibiotic use, or outcome were excluded from the analysis. Patients were followed up from hospital admission until death, discharge, transfer, or 28 days, whichever occurred first. Follow-up data were collected at hospital discharge or death by the treating facility and entered into the platform. The primary outcome was 28-day in-hospital mortality, and we analysed this outcome using Cox proportional hazards models with a shared frailty term to account for country-level clustering. FINDINGS The median age of the study population was 61·9 years (±21·7), with 198 223 women and 251 990 men with data available on antibiotic use. Of the 592 898 patients enrolled, 451 291 (76·1%) had data on antibiotic use and were included in the descriptive analysis; 122 854 had complete data on empirical treatment type, of whom 47 359 (38·5%) were included in the regression analysis. Among the 451 291 patients with data on antibiotic use, 341 125 (75·6%) received antibiotics, more frequently in severe to critical cases than in mild to moderate cases (80·5% vs 71·6%). Prescribing was highest in the Eastern Mediterranean (83·0%) and African (82·7%) regions and lowest in the Western Pacific region (32·8%), declining in the European region and region of the Americas but increasing in the African region between 2020 and 2022. Treatment was predominantly empirical and involved Watch antibiotics of the WHO Access, Watch, and Reserve classification. Clinically suspected co-infections were reported in 47 050 (7·9%) of the 592 898 patients; among those with positive cultures, 1815 (42·8%) of 4237 had multidrug-resistant bacteria. In the unadjusted analyses, empirical antibiotic use was associated with higher mortality across severity strata. After adjustment for age, sex, comorbidities, and disease severity, empirical antibiotic use remained associated with increased mortality in mild to moderate cases (adjusted hazard ratio 1·80, 95% CI 1·36-2·38) and severe to critical cases (1·16, 1·08-1·24). INTERPRETATION Despite clinically suspected co-infections being reported in only 47 050 (7·9%) of the 592 898 enrolled patients, 341 125 (75·6%) of the 451 291 patients with data on antibiotic use received antibiotic therapy, predominantly broad-spectrum agents. As antibiotic use was not associated with improved clinical outcomes and is known to increase antimicrobial resistance, it should be rationalised through strengthened antimicrobial stewardship and behavioural interventions, particularly during respiratory viral epidemics. FUNDING None.
BACKGROUND Effective cholera outbreak response requires accurate bedside rapid diagnostic tests (RDTs) because of poor laboratory access. Formative studies suggest that cholera diagnostics have multiple vulnerabilities, including target degradation by virulent bacteriophage (phage) specific to Vibrio cholerae and antibiotics. Our study objectives were to evaluate the performance of RDTs as a function of these antimicrobials to improve deployment and guide future diagnostic development. METHODS In this prospective longitudinal study, participants were enrolled at seven hospitals across Bangladesh from March 13, 2018, to April 9, 2019. Inclusion criteria were participants aged 2 months or older with uncomplicated diarrhoeal disease. Exclusion criteria were the presence of severe comorbidity or the absence of participant or guardian consent or assent. Stool samples were analysed using culture, quantitative PCR (qPCR), and mass spectrometry. The primary outcome was RDT performance (eg, sensitivity and specificity) as a function of phage detection. Exploratory outcomes were the effects of antibiotics and disease severity on RDT performance. FINDINGS 2574 participants were enrolled, and for 2078 samples, all assays were completed for analysis of the primary outcome. 394 samples without RDT data and 102 samples without qPCR data were excluded. Using the current gold standard of culture or qPCR positivity for V cholerae, we found that phage detection had no effect on RDT performance. When the diagnostic criteria were expanded to include phage detection, RDT sensitivity decreased from 0·46 (95% CI 0·41-0·51) to 0·38 (0·34-0·43), and the odds of RDT positivity among patients with cholera decreased with phage exposure (odds ratio 0·428; 95% CI 0·296-0·613). Antibiotics were detected in more than 80% of samples using liquid chromatography-tandem mass spectrometry, limiting assessment of their effects on RDT performance. Among patients with moderate and severe dehydration, large increases in sensitivity and specificity were observed. We estimated that restricting RDT use to patients with severe dehydration and no reported antibiotic exposure increased sensitivity by 50% compared with unrestricted RDT use. If the presence of phage is considered a diagnostic proxy for V cholerae infection, then RDTs might not detect an additional 17% of cholera cases. INTERPRETATION Cholera RDTs have limitations that require consideration during global deployments. Inclusion of phage detection in diagnostic criteria might improve case detection, although this requires further research in diverse settings. The implications of these findings likely extend to other diseases in which diagnostics share similar vulnerabilities. FUNDING Wellcome Trust (DFID grant), NIH, and Thrasher Research Fund.
BACKGROUND The current practice of empirical antifungal treatment for suspected invasive Candida infection in the intensive care unit (ICU) leads to overtreatment. Biomarkers might better target treatment; however, their diagnostic accuracy in this patient group is uncertain. This study aimed to evaluate whether a biomarker or a combination of biomarkers has sufficiently high negative predictive value (NPV) to enable early cessation of empirical antifungal treatment in patients in ICUs. METHODS In this prospective, multicentre, diagnostic test accuracy study, we recruited patients who had been started on empirical antifungal treatment for suspected candidiasis and had blood cultures drawn within 24 h of starting treatment from 43 UK ICUs. We tested a research blood sample, collected within 24 h of the standard-of-care care blood culture (ie, within 48 h of starting empirical antifungal treatment), with three DNA detection tests (Fungiplex, T2Candida, and CandID) and one (1,3)-β-D-glucan test (Fungitell). We assessed the accuracy of these tests against an international consensus definition of proven invasive Candida infection and a constructed reference standard for proven or probable infection. The primary outcome was NPV for exclusion of proven Candida infection; we also reported sensitivity, specificity, and likelihood ratios. FINDINGS Among 4005 patients screened, 1251 were enrolled. A total of 1225 participants, recruited between April, 2018 and Feb, 2023, were evaluable, among whom 54 (4·4%) had proven invasive Candida infection. The median duration of antifungal treatment was 9 days (IQR 5-15), and survival at 28 days was 76·8%. The index tests had similar NPVs: 96·6% (95·3-97·6) for Fungiplex, 97·1% (94·7-98·6) for T2Candida, 96·7% (95·4-97·8) for CandID, and 97·2% (95·5-98·4) for Fungitell; however, sensitivity varied widely among the tests, from 27·5% to 68·6%. The optimal test combination was Fungitell and CandID, which had an NPV of 97·5% (95·7-98·7) and a sensitivity of 75·0%. Combining these biomarkers with standard-of-care blood culture testing further increased the NPV to 98·6% (97·0-99·4), with a sensitivity of 85·1%. INTERPRETATION No single biomarker had sufficiently high sensitivity to justify stopping empirical antifungal treatment. Combining Fungitell and CandID with standard-of-care blood culture testing could provide a sufficiently high NPV to allow early cessation of empirical antifungal treatment in this patient group, thereby reducing overtreatment, although this gain in sensitivity is accompanied by a reduction in specificity. Randomised trials are needed to confirm the clinical and cost-effectiveness of this diagnostic strategy before it is adopted in practice. FUNDING UK National Institute for Health and Care Research Health Technology Assessment Programme and the Research Charitable Trust Fund of the Belfast Health & Social Care Trust.
