Predicting the Herd Immunity Threshold during an Outbreak: A Recursive Approach

BACKGROUND: The objective was to develop a novel algorithm that can predict, based on field survey data, the minimum vaccination coverage required to reduce the mean number of infections per infectious individual to less than one (the Outbreak Response Immunization Threshold or ORIT) from up to six days in the advance. METHODOLOGY/PRINCIPAL FINDINGS: First, the relationship between the rate of immunization and the ORIT was analyzed to establish a link. This relationship served as the basis for the development of a recursive algorithm that predicts the ORIT using survey data from two consecutive days. The algorithm was tested using data from two actual measles outbreaks. The prediction day difference (PDD) was defined as the number of days between the second day of data input and the day of the prediction. The effects of different PDDs on the prediction error were analyzed, and it was found that a PDD of 5 minimized the error in the prediction. In addition, I developed a model demonstrating the relationship between changes in the vaccination coverage and changes in the individual reproduction number. CONCLUSIONS/SIGNIFICANCE: The predictive algorithm for the ORIT generates a viable prediction of the minimum number of vaccines required to stop an outbreak in real time. With this knowledge, the outbreak control agency may plan to expend the lowest amount of funds required stop an outbreak, allowing the diversion of the funds saved to other areas of medical need

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

2018 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1005/thumbnail.jp

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Breast cancer management pathways during the COVID-19 pandemic: outcomes from the UK ‘Alert Level 4’ phase of the B-MaP-C study

Abstract: Background: The B-MaP-C study aimed to determine alterations to breast cancer (BC) management during the peak transmission period of the UK COVID-19 pandemic and the potential impact of these treatment decisions. Methods: This was a national cohort study of patients with early BC undergoing multidisciplinary team (MDT)-guided treatment recommendations during the pandemic, designated ‘standard’ or ‘COVID-altered’, in the preoperative, operative and post-operative setting. Findings: Of 3776 patients (from 64 UK units) in the study, 2246 (59%) had ‘COVID-altered’ management. ‘Bridging’ endocrine therapy was used (n = 951) where theatre capacity was reduced. There was increasing access to COVID-19 low-risk theatres during the study period (59%). In line with national guidance, immediate breast reconstruction was avoided (n = 299). Where adjuvant chemotherapy was omitted (n = 81), the median benefit was only 3% (IQR 2–9%) using ‘NHS Predict’. There was the rapid adoption of new evidence-based hypofractionated radiotherapy (n = 781, from 46 units). Only 14 patients (1%) tested positive for SARS-CoV-2 during their treatment journey. Conclusions: The majority of ‘COVID-altered’ management decisions were largely in line with pre-COVID evidence-based guidelines, implying that breast cancer survival outcomes are unlikely to be negatively impacted by the pandemic. However, in this study, the potential impact of delays to BC presentation or diagnosis remains unknown

The Acceptability and Impact of a Weekly Text-Messaging Program to Support HIV Treatment Adherence in KwaZulu-Natal, South Africa

Introduction: In randomized controlled trials, short message service (SMS) programs have improved adherence to HIV antiretroviral therapy (ART). In response, the World Health Organization recommended use of SMS programs to support ART. However, there is limited data on real-world implementations of SMS programs. Methods: We conducted two studies to assess the acceptability and impact of an SMS program implementation into clinical care at an HIV clinic in KwaZulu-Natal, South Africa. Study 1 included structured interviews with a cross-sectional convenience sample of 100 adult patients who were invited to join the program, 88 of whom had received a program SMS. Study 2 was a retrospective cohort study. We analyzed data from all adult patients who 1) enrolled at the clinic before the observation period (July 2013 through June 2014), 2) had ≥1 ART prescriptions in the observation period, and 3) had data on phone number availability (N = 2,255). Our primary exposure was whether or not the patient had been sent SMS, which was based on availability of phone numbers recorded at the patients’ initial clinic enrollments. Our main outcome measure was prescription coverage, defined as the presence of a valid ART prescription for each day observed. Using an intention-to-treat approach, we fit generalized linear mixed models adjusted for pre- program prescription coverage, demographics, and ART duration, dosing, and regimen. Results: In study 1, 81 (92%) of respondents who had received an SMS would recommend the program to a friend. Sixty-eight (77%) felt the program helped them remember clinic appointments, a response associated with male gender [adjusted odds ratio (AOR) 5.88, 95% confidence interval (CI) 1.52 – 23.26, P=0.011] and HIV disclosure outside the home [AOR 3.40, 95%CI 1.00 – 11.60, P=0.050]. In study 2, exposure to the SMS program was independently associated with greater prescription coverage (AOR = 1.23, 95%CI 1.13 – 1.34, P<0.001) compared with non-exposure, although the absolute increase in prescription coverage was small (4.7 days of ART prescription coverage per average patient per year). Among a subset of patients (n=725) whose pre-program prescription coverage was <100%, the corresponding mean expected absolute increase in prescription coverage was 8.2 days per year. Conclusions: This clinical SMS adherence program was found to have high patient- perceived usefulness and a positive impact on prescription coverage of uncertain clinical significance

To begin to understand the trends in the changes in the Outbreak Response Immunization Threshold (ORIT), I calculate the ORIT, using the Threshold Model, at several points during the 2003 RMI measles outbreak.

<p>I also graph the fraction of the population immunized during the outbreak.</p

Data demonstrating the two key relationships concerning RPORITA prediction error for the 2006 Fiji measles outbreak.

<p>The prediction day difference (PDD) is the difference between the second day of direct input on which the prediction is based and the day of the prediction. The Days since Start of Immunization (DSI) is the number of days between the day of prediction and the start of the Outbreak Response Immunization. This data presents a numerical depiction of the two critical relationships with regard to Recursive Prediction of the Outbreak Response Immunization Threshold Algorithm (RPORITA) error: 1) between DSI and prediction error, and 2) between PDD and prediction error.</p