Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

Background: Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patients with Salmonella are at high risk, and require a rapid response. We initially investigated this outbreak by whole-genome sequencing using a novel rapid protocol on the Illumina MiSeq; we then integrated these data with whole-genome data from surveillance sequencing, thereby placing the outbreak in a national context. Additionally, we investigated the potential of a newly released sequencing technology, the MinION from Oxford Nanopore Technologies, in the management of a hospital outbreak of Salmonella. Results: We demonstrate that rapid MiSeq sequencing can reduce the time to answer compared to the standard sequencing protocol with no impact on the results. We show, for the first time, that the MinION can acquire clinically relevant information in real time and within minutes of a DNA library being loaded. MinION sequencing permits confident assignment to species level within 20 min. Using a novel streaming phylogenetic placement method samples can be assigned to a serotype in 40 min and determined to be part of the outbreak in less than 2 h. Conclusions: Both approaches yielded reliable and actionable clinical information on the Salmonella outbreak in less than half a day. The rapid availability of such information may facilitate more informed epidemiological investigations and influence infection control practices

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

Background Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications. Methods We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC). Findings In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683–0·717]). Interpretation In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required. Funding British Journal of Surgery Society

Effectiveness of wheat soya blend supplementation during pregnancy and lactation on pregnancy outcomes and nutritional status of their infants at 6 months of age in Thatta and Sujawal districts of Sindh, Pakistan: A cluster randomized-controlled trial

Purpose: We aimed to assess the effectiveness of wheat soya blend plus (WSBP) provided during pregnancy and lactation on weight gain during pregnancy, reduction of low birthweight (LBW), and improvement in nutritional status in infants at 6 months of age in Thatta and Sujawal districts of Sindh, Pakistan.Methods: A cluster randomized-controlled trial was conducted in Thatta and Sujawal districts in Pakistan from August 2014 to December 2016. A total of 2030 pregnant women were enrolled in the study. These women and their infants were followed during pregnancy and first 6 months of life. Pregnant women received a monthly ration of 5 kg (i.e., 165 g/day) of WSB + during pregnancy and the first 6 months of their lactation period.Results: There was no difference in weight gain during pregnancy between the intervention and control groups (n = 496, 326.7 g/week 95% CI 315.2-338.1 vs. (n = 507, 306.9 g/week, 95% CI 279.9-333.9 P = 0.192), after adjustment with different factors. The reduction in the prevalence of LBW was not different between intervention and control groups (n = 325, 34.0%, 95% CI 31.7-36.4, vs. (n = 127, 34.3%, 95% CI 27.2-41.5, P = 0.932). Significant reductions in risk of stunting (n = 1319 RR 0.85, 95% CI 0.73-0.99, P = 0.041), wasting (n = 1330 RR 0.77, 95% CI 0.65-0.91, P = 0.003), and underweight (n = 1295 RR 0.77, 95% CI 0.69-0.87, P \u3c 0.001) were observed in infants at 6 months of age in the intervention as compared to the control group. However, no difference was noted on reduction in the risk of stunting among infants at 6 months of age in the intervention and control group (n = 1318 RR 0.91, 95% CI 0.78-1.07, P = 0.253) after adjustment. A significant reduction in anemia was noted (n = 1328 RR 0.94, 95% CI 0.91-0.98, P = 0.002) in infants at 6 months of age in the intervention as compared to the control group in adjusted analysis.Conclusions: Provision of WSB + during pregnancy and the first 6 months of lactation is effective in reducing the risk of under nutrition and anemia in infants at 6 months of age. This study can potentially guide the government and donor agencies in investing in nutritional programmes, especially for pregnant and lactating women living in vulnerable settings