Advancing monitoring of antimicrobial resistance trajectories using flexible spatiotemporal modelling: a change-point analysis

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This paper proposes flexible spatiotemporal modeling for tracking antimicrobial resistance trajectories over space and time, using change-point analysis to identify when statistically significant shifts occur. The approach is framed at a methodological level, integrating flexible modeling of resistance dynamics with formal detection of temporal change points while leveraging spatiotemporal structure. The main limitation is that, as presented, the framework’s performance depends on data availability and suitability for modeling spatiotemporal variation and change points, with practical constraints not fully detailed in the excerpt provided. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

Background: Detecting changes in infectious disease trends, including antimicrobial resistance (AMR), is critical for developing effective public health strategies and surveillance systems. However, many statistical methods struggle to detect gradual shifts as they primarily rely on mean-level shift estimates. Methods We examined AMR prevalence among Enterobacterales isolates, primarily carbapenem-resistance (CRE), in bloodstream and urinary tract infections from 24 European countries and 45 US-states (2004-2022) leveraging Pfizer’s ATLAS dataset. We applied spatiotemporal generalised additive models (GAMs) with intrinsic Gaussian Markov Random Fields to estimate AMR prevalence and included country/state-time interactions. We used restricted maximum likelihood to estimate AMR prevalence growth rates and their corresponding first derivatives (increase/decrease rate) and second derivatives (acceleration/deceleration rate), which were used to identify change-points marking significant trend shifts in AMR dynamics. We performed biological sex and age-group-specific GAMs, and evaluated the association between growth rates and carbapenem usage. Carbapenem use was obtained from the European surveillance of antimicrobial consumption Network. Results We observed a consistent increase in CRE prevalence over time in Europe and the US. In Europe, the rate of change increased in 2007 (first-derivative change-point), with deceleration in 2012 and 2019 and acceleration in 2015 (second-derivative change-points), followed by a decline in 2020 (first-derivative change-point), particularly in Central and Eastern Europe, including France as an exemplar. Conversely, the US showed fewer change-points, with New York (exemplar) marking a substantial acceleration change-point after 2008. Subgroup analyses showed that population change points were largely driven by males over 18, reflecting both their larger numbers and more pronounced, often earlier, shifts. We found a positive association between carbapenem use and CRE growth rates in Europe. Conclusions Employing GAMs could improve AMR surveillance by detecting changes in trends in the overall population as well as in subgroups.
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