Rahul Batra

Rahul Batra
Guy's and St Thomas' NHS Foundation Trust · Department of Infectious Diseases

MD

About

84
Publications
10,769
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3,408
Citations
Citations since 2016
53 Research Items
2915 Citations
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201620172018201920202021202202004006008001,0001,2001,400
Introduction
Skills and Expertise

Publications

Publications (84)
Chapter
Participatory agent-based modelling (ABM) can help bring the benefits of simulation to domain users by actively involving stakeholders in the development process. Collaboration in enterprise modelling can improve the model developer’s understanding of the domain and therefore improve the effectiveness of domain analysis. Where many agent-oriented m...
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The management of COVID-19 has become more complex due to the expansion of available therapies. The presence of SARS-CoV-2 variants and mutations further complicate treatment due to their differing susceptibilities to therapies. Here we outline the use of real-time whole genome sequencing to characterise infections and guide treatment decisions.
Preprint
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Variovorax durovernum nov. sp. was isolated from an infected, prosthetic endovascular graft explanted from a shepherd. Variovorax durovernum nov.sp. was isolated from blood agar, chocolate and MacConkey agar incubated at 37°C in an aerobic environment after 48h of incubation. Variovorax durovernum nov sp. is an aerobic, Gram-negative, motile, curve...
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Background Nosocomial acquisition of influenza is known to occur but the risk after exposure to a known case and the outcomes after acquisition are poorly defined. Methods Prospective observational study of patients exposed to influenza from another patient in a multi-site healthcare organisation, with follow-up of 7 days or until discharge, and P...
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Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the...
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The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May and December 2021. How Delta infection compares with previous variants is unknown. This prospective observational cohort study assessed symptomatic adults participating in the app-based COVID Symptom Study who tested positive for SARS-CoV-2 from May 26 to...
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Numerous studies have shown that a prior SARS-CoV-2 infection can greatly enhance the antibody response to COVID-19 vaccination, with this so called “hybrid immunity” leading to greater neutralization breadth against SARS-CoV-2 variants of concern. However, little is known about how breakthrough infection (BTI) in COVID-19-vaccinated individuals wi...
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Aims/Objectives/Background Patients admitted to hospital via the emergency department (ED) need to be separated by SARS-CoV-2 infection status to prevent transmission. Using clinical criteria alone is not feasible due to the range of symptoms and asymptomatic spread. Turnaround time of laboratory PCR assays (~6–24 hrs) hinders patient movement thro...
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Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was as...
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Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was as...
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Background The Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 emerged and became the dominant circulating variant in the UK in late 2020. Current literature is unclear on whether the Alpha variant is associated with increased severity. We linked clinical data with viral genome sequence data to compare admitted cases between SARS-CoV-2 waves in Londo...
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Background : Viral diversity presents an ongoing challenge for diagnostic tests, which need to accurately detect all circulating variants. The Abbott Global Surveillance program monitors severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants and their impact on diagnostic test performance. Objectives : To evaluate the capacity of Ab...
Preprint
Full-text available
Numerous studies have shown that a prior SARS-CoV-2 infection can greatly enhance the antibody response to COVID-19 vaccination, with this so called 'hybrid immunity' leading to greater neutralization breadth against SARS-CoV-2 variants of concern. However, little is known about how breakthrough infection (BTI) in COVID-19 vaccinated individuals wi...
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Full-text available
Background Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-re...
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COVID-19 vaccine design and vaccination rollout need to take into account a detailed understanding of antibody durability and cross-neutralizing potential against SARS-CoV-2 and emerging variants of concern (VOCs). Analyses of convalescent sera provide unique insights into antibody longevity and cross-neutralizing activity induced by variant spike...
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Background Point-of-care (POC) SARS-CoV-2 lateral-flow antigen detection (LFD) testing in the emergency department (ED) could inform rapid infection control decisions but requirements for safe deployment have not been fully defined Methods Review of LFD test results, laboratory and POC-RT-PCR results and ED-performance metrics during a two-week hi...
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There is a worldwide need for reagents to perform SARS-CoV-2 detection. Some laboratories have implemented kit-free protocols, but many others do not have the capacity to develop these and/or perform manual processing. We provide multiple workflows for SARS-CoV-2 nucleic acid detection in clinical samples by comparing several commercially available...
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Background: Reports indicate that COVID-19 patients have more bloodstream infections (BSI) on the intensive care unit (ICU) potentially due to lapses in infection control practice or other factors. Methods: Retrospective single-site study of ICU-BSIs in mechanically ventilated (MV) COVID-19 patients during the first pandemic year. Clinical, demogr...
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Objectives Analysis of nosocomial transmission in the early stages of the pandemic at a large multi-site healthcare institution. Nosocomial incidence is linked with infection control interventions.. Methods Viral genome sequence and epidemiological data were analysed for 574 consecutive SARS-CoV-2 PCR-positive patients including 86 nosocomial case...
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As SARS–CoV–2 variants continue to emerge globally, a major challenge for COVID–19 vaccination is the generation of a durable antibody response with cross–neutralizing activity against both current and newly emerging viral variants. Cross–neutralizing activity against major variants of concern (B.1.1.7, P.1 and B.1.351) has been observed following...
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Objectives : Assess the feasibility and impact of nanopore-based 16S rRNA gene sequencing (Np16S) service on antibiotic treatment for acute severe pneumonia on the intensive care unit (ICU). Methods : Speciation and sequencing accuracy of Np16S on isolates with bioinformatics pipeline optimisation, followed by technical evaluation including qualit...
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Background Lateral flow devices (LFDs) for rapid antigen testing are set to become a cornerstone of SARS-CoV-2 mass community testing, although their reduced sensitivity compared with PCR has raised questions of how well they identify infectious cases. Understanding their capabilities and limitations is, therefore, essential for successful implemen...
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Background Antimicrobial resistance (AMR) in Enterobacterales is a global health threat. Capacity for individual-level surveillance remains limited in many countries, whilst population-level surveillance approaches could inform empiric antibiotic treatment guidelines. Methods In this exploratory study, a novel approach to population-level predicti...
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Background Viral diversity presents an ongoing challenge for diagnostic tests, which need to accurately detect all circulating variants. The Abbott Global Surveillance program monitors severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants and their impact on diagnostic test performance. Objectives To evaluate the capacity of Abbott...
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Full-text available
During the first wave of the global COVID-19 pandemic the clinical utility and indications for SARS-CoV-2 serological testing were not clearly defined. The urgency to deploy serological assays required rapid evaluation of their performance characteristics. We undertook an internal validation of a CE marked lateral flow immunoassay (LFIA) (SureScree...
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Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the associatio...
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Introduction: A second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of social distancing policies and implementation of mass vaccination, highlights the need for real-time integration of detailed patient clinic...
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Background: Rapid antigen lateral flow devices (LFDs) are set to become a cornerstone of SARS-CoV-2 mass community testing. However, their reduced sensitivity compared to PCR has raised questions of how well they identify infectious cases. Understanding their capabilities and limitations is therefore essential for successful implementation. To addr...
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Full-text available
Background Clinical metagenomics (CMg) is being evaluated for translation from a research tool into routine diagnostic service, but its potential to significantly improve management of acutely unwell patients has not been demonstrated. The SARS-CoV-2 pandemic provides impetus to determine that benefit given increased risk of secondary infection and...
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Antibody responses to SARS-CoV-2 can be detected in most infected individuals 10–15 d after the onset of COVID-19 symptoms. However, due to the recent emergence of SARS-CoV-2 in the human population, it is not known how long antibody responses will be maintained or whether they will provide protection from reinfection. Using sequential serum sample...
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Many healthcare facilities report SARS-CoV-2 outbreaks but transmission analysis is complicated by the high prevalence of infection and limited viral genetic diversity. The contribution of different vectors to nosocomial infection or the effectiveness of interventions is therefore currently unclear. Detailed epidemiological and viral nanopore seque...
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Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability o...
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There is a clear requirement for an accurate SARS-CoV-2 antibody test, both as a complement to existing diagnostic capabilities and for determining community seroprevalence. We therefore evaluated the performance of a variety of antibody testing technologies and their potential use as diagnostic tools. Highly specific in-house ELISAs were developed...
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Introduction: Antibodies to SARS-CoV-2 serve as critical diagnostic markers for determining how broadly the COVID-19 pandemic has spread, confirming patient recovery, monitoring potential long-term effects of infection, and evaluating potential protection from reinfection. As new antibody tests become available, it is important to evaluate their p...
Preprint
Objectives: Determine indications and clinical utility of SARS-CoV-2 serology testing in adults and children. Design: Prospective evaluation of initial three weeks of a daily Monday to Friday pilot SARS-CoV-2 serology service for patients. Setting: Early post 'first-wave' SARS-CoV-2 transmission period at single centre London teaching hospital that...
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Antibody (Ab) responses to SARS-CoV-2 can be detected in most infected individuals 10-15 days following the onset of COVID-19 symptoms. However, due to the recent emergence of this virus in the human population it is not yet known how long these Ab responses will be maintained or whether they will provide protection from re-infection. Using sequent...
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An evaluation of a rapid portable gold- nanotechnology measuring SARS-CoV-2 IgM, IgA and IgG antibody concentrations against spike 1 (S1), spike 2 (S) and nucleocapsid (N) was conducted using serum samples from 74 patients tested for SARS-CoV-2 RNA on admission to hospital, and 47 historical control patients from March 2019. 59 patients were RNA(+)...
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There is a clear requirement for an accurate SARS−CoV−2 antibody test, both as a complement to existing diagnostic capabilities and for determining community seroprevalence. We therefore evaluated the performance of a variety of antibody testing technologies and their potential as diagnostic tools. A highly specific in−house ELISA was developed for...
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Full-text available
There is a worldwide shortage of reagents to perform detection of SARS-2. Many clinical diagnostic laboratories rely on commercial platforms that provide integrated end-to-end solutions. While this provides established robust pipelines, there is a clear bottleneck in the supply of reagents given the current situation of extraordinary high demand. S...
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Background: Studies estimating excess length of stay (LoS) attributable to nosocomial infections have failed to address time-varying confounding, likely leading to overestimation of their impact. We present a methodology based on inverse probability-weighted (IPW) survival curves to address this limitation. Methods: A case-study focusing on inte...
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Antimicrobial resistance (AMR) is a global health threat, especially in low-/middle-income countries (LMICs), where there is limited surveillance to inform empiric antibiotic treatment guidelines. Enterobacterales are amongst the most important causes of drug-resistant bacterial infections. We developed a novel AMR surveillance approach for Enterob...
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Background Rapid and accurate identification of bacteria is the basis of appropriate antibiotic treatment and effective clinical decision-making. Next-generation sequencing (NGS) platforms such as Oxford Nanopore Technologies (ONT) holds the promise of a diagnostic revolution by overcoming the limitations of culture-based identification with rapid...
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Background Methicillin-Resistant Staphylococcus aureus (MRSA) and C. difficile infection have reduced across the UK National Health Service in the last decade following implementation of an infection control campaign. The national impact on hospital-acquired infections in the ICU however has not been comprehensively documented. Methods Data on MRS...
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Objectives: We evaluated risk factors for gastrointestinal carriage of Enterobacteriaceae which produce extended-spectrum β-lactamases (ESBL-E), including individual-level variables such as antibiotic use and foreign travel, and community-level variables such as housing and deprivation. Methods: In an observational study in 2015, all patients ad...
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Background Despite the escalating level of concern regarding the spread of Carbapenem resistant and Extended spectrum β-lactamase (ESBL) producing Enterobacteriaceae (CR-E and ESBL-E), little is still known about their dissemination within households. In this small cohort study, four households were followed-up for 6 months, to track their carriage...
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Background Individual risk factors such as antibiotic use and foreign travel are typically associated with ESBL-producing Enterobacteriaceae (ESBL-E) carriage. Few studies have evaluated variations in community demographics or social and material deprivation as risk factors for ESBL-E carriage. Methods All admissions to a London hospital group wer...
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Background: Studies often ignore time-varying confounding or use inappropriate methodology to adjust for time-varying confounding. Aim: We estimated the effect of ICU-acquired bacteraemia on ICU mortality and discharge using appropriate methodology. Methods: Marginal structural models with inverse probability weighting were used to estimate th...
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Objective: Several studies showed that a substantial decline in the use of co-trimoxazole did not result in a decline in resistance rates among Escherichia coli isolates. Since mathematical models have shown that it may take decades before resistance rates start to decline to relevant levels, we performed a new analysis using more recently collect...
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Background: Conflicting results have been found regarding outcomes of intensive care unit (ICU)-acquired Enterobacteriaceae bacteraemia and the potentially modifying effect of appropriate empiric antibiotic therapy. Aim: To evaluate these associations while adjusting for potential time-varying confounding using methods from the causal inference...
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Protocol for defining MRSA importation and acquisition events. (PDF)
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TW and non-TW MRSA importation and acquisition events under different assumptions. The baseline assumption classifies all episodes where MRSA was recovered from an isolate taken within 48 hours of admission as importations. The SA1 assumption uses a 24 hour cutoff instead. See protocol S1 in supporting material for full details of baseline and SA1...
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Estimates of the daily transmission probability (q) from one exposed to one susceptible patient under SA1 and SA2 assumptions. Estimates of the daily transmission probability (q) from one exposed to one susceptible patient under assumptions SA1 and SA2. See protocol S1 in supporting material for details of the SA1 and SA2 assumptions used in thesse...
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Single admission reproduction numbers () estimated using method 2. Estimates (95% CIs) of the ward-level reproduction number, , according to study phase, MRSA type and ward obtained using method 2 and assuming complete bacterial interference and no interaction between ICU 1 and ICU 2. (PDF)
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Estimated ward-level reproduction numbers (s.e.) for TW and non-TW MRSA clones under alternative assumptions. Phase-specific estimates of ward-level reproduction numbers for TW MRSA and Non-TW MRSA derived using Method 1 under baseline assumptions with perfect ward coupling (applies to combined ICU estimates only) and under SA1 assumptions (see pro...
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Estimates of the daily transmission probability (q) from one exposed to one susceptible patient and from background transmission sources. ‘Patient to patient’ estimates corresponds to the daily transmission probability (q) from one exposed to one susceptible patient. Background estimates corresponds to the daily probability of acquisition from back...
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estimates for TW and non-TW combined under SA1 and SA2 assumptions. Sensitivity analysis for phase-specific estimates for , the daily probability of a susceptible patient acquiring MRSA from an MRSA positive patient in the same ward, for ICU 1 and ICU 2 (without distinguishing between TW and non-TW strains). In the Combined row, the estimates are c...
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An important determinant of a pathogen's success is the rate at which it is transmitted from infected to susceptible hosts. Although there are anecdotal reports that methicillin-resistant Staphylococcus aureus (MRSA) clones vary in their transmissibility in hospital settings, attempts to quantify such variation are lacking for common subtypes, as a...
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Antimicrobial resistance and bacterial virulence factors may increase the risk of hematogenous complications during methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection (BSI). This study reports on the impact of increasing vancomycin minimum inhibitory concentrations (V-MICs) and MRSA clone type on risk of hematogenous complicat...
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Appendix 3: analysis without uncertainty, and scenario analyses
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Table A2.2: unadjusted daily probabilities of discharge and death
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Table A3.1: evaluation of cost effectiveness frontier of screening and decolonisation policies
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Appendix 1: model simulating transmission of MRSA in intensive care unit setting
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Table A2.1: values and sources of all parameters
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Table A2.3: unit costs in sterling
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Appendix 2: estimation of parameters used in transmission model
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Table A3.2: evaluation of cost effectiveness frontier of screening and isolation policies
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To assess the cost effectiveness of screening, isolation, and decolonisation strategies in the control of meticillin resistant Staphylococcus aureus (MRSA) in intensive care units. Economic evaluation based on a dynamic transmission model. England and Wales. Population Theoretical population of patients on an intensive care unit. Infections, deaths...
Article
Antibiotics and antiseptics have the potential to influence carriage and transmission of meticillin-resistant Staphylococcus aureus (MRSA), although effects are likely to be complex, particularly in a setting where multiple agents are used. Here admission and weekly MRSA screens and daily antibiotic and antiseptic prescribing data from 544 MRSA car...