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Inference on extended-spectrum beta-lactamase Escherichia coli and Klebsiella pneumoniae data through SMC2

Rimella, L, Alderton, S, Sammarro, Melodie, Rowlingson, B, Cocker, Derek, Feasey, Nicholas ORCID:, Fearnhead, P and Jewell, C (2023) 'Inference on extended-spectrum beta-lactamase Escherichia coli and Klebsiella pneumoniae data through SMC2'. Journal of the Royal Statistical Society Series C: Applied Statistics, Vol 72, Issue 5, pp. 1435-1451.

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We propose a novel stochastic model for the spread of antimicrobial-resistant bacteria in a population, together with an efficient algorithm for fitting such a model to sample data. We introduce an individual-based model for the epidemic, with the state of the model determining which individuals are colonised by the bacteria. The transmission rate of the epidemic takes into account both individuals’ locations, individuals’ covariates, seasonality, and environmental effects. The state of our model is only partially observed, with data consisting of test results from individuals from a sample of households. Fitting our model to data is challenging due to the large state space of our model. We develop an efficient SMC2 algorithm to estimate parameters and compare models for the transmission rate. We implement this algorithm in a computationally efficient manner by using the scale invariance properties of the underlying epidemic model. Our motivating application focuses on the dynamics of community-acquired extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae, using data collected as part of the Drivers of Resistance in Uganda and Malawi project. We infer the parameters of the model and learn key epidemic quantities such as the effective reproduction number, spatial distribution of prevalence, household cluster dynamics, and seasonality.

Item Type: Article
Subjects: WA Public Health > WA 105 Epidemiology
WC Communicable Diseases > Infection. Bacterial Infections > Bacterial Infections > WC 202 Pneumonia (General or not elsewhere classified)
WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 290 Escherichia coli infections
Faculty: Department: Clinical Sciences & International Health > Clinical Sciences Department
Digital Object Identifer (DOI):
SWORD Depositor: JISC Pubrouter
Depositing User: JISC Pubrouter
Date Deposited: 14 Jul 2023 09:32
Last Modified: 05 Feb 2024 10:59


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