Emerging patterns of fluoroquinolone resistance in Campylobacter jejuni in the UK [1998-2018].

Campylobacter jejuni (C.jejuni) is the most common causative agent of bacterial food poisoning worldwide and is known to be genetically highly diverse. C. jejuni is increasingly resistant to fluoroquinolone antibiotics, but very few studies have investigated variant-specific patterns of resistance across time. Here we use statistical modelling and clustering techniques to investigate patterns of fluoroquinolone resistance amongst 10,359 UK isolates from human disease sampled over 20 years. We observed six distinct patterns of fluoroquinolone sensitivity/resistance in C. jejuni across time, grouping by clonal complex (CC). Some CCs were fully resistant, some shifted from susceptible to resistant following a sigmoidal shape, and some remained susceptible over time. Our findings indicate that the fluoroquinolone resistance patterns of C. jejuni are complicated and cannot be analysed as a single species but divided into variant dynamics so that the factors driving resistance can be thoroughly investigated.

How and When to End the COVID-19 Lockdown: An Optimization Approach.

Countries around the world are in a state of lockdown to help limit the spread of SARS-CoV-2. However, as the number of new daily confirmed cases begins to decrease, governments must decide how to release their populations from quarantine as efficiently as possible without overwhelming their health services. We applied an optimal control framework to an adapted Susceptible-Exposure-Infection-Recovery (SEIR) model framework to investigate the efficacy of two potential lockdown release strategies, focusing on the UK population as a test case. To limit recurrent spread, we find that ending quarantine for the entire population simultaneously is a high-risk strategy, and that a gradual re-integration approach would be more reliable. Furthermore, to increase the number of people that can be first released, lockdown should not be ended until the number of new daily confirmed cases reaches a sufficiently low threshold. We model a gradual release strategy by allowing different fractions of those in lockdown to re-enter the working non-quarantined population. Mathematical optimization methods, combined with our adapted SEIR model, determine how to maximize those working while preventing the health service from being overwhelmed. The optimal strategy is broadly found to be to release approximately half the population 2-4 weeks from the end of an initial infection peak, then wait another 3-4 months to allow for a second peak before releasing everyone else. We also modeled an "on-off" strategy, of releasing everyone, but re-establishing lockdown if infections become too high. We conclude that the worst-case scenario of a gradual release is more manageable than the worst-case scenario of an on-off strategy, and caution against lockdown-release strategies based on a threshold-dependent on-off mechanism. The two quantities most critical in determining the optimal solution are transmission rate and the recovery rate, where the latter is defined as the fraction of infected people in any given day that then become classed as recovered. We suggest that the accurate identification of these values is of particular importance to the ongoing monitoring of the pandemic.

The impact of environmental change on the use of early pottery by East Asian hunter-gatherers.

The invention of pottery was a fundamental technological advancement with far-reaching economic and cultural consequences. Pottery containers first emerged in East Asia during the Late Pleistocene in a wide range of environmental settings, but became particularly prominent and much more widely dispersed after climatic warming at the start of the Holocene. Some archaeologists argue that this increasing usage was driven by environmental factors, as warmer climates would have generated a wider range of terrestrial plant and animal resources that required processing in pottery. However, this hypothesis has never been directly tested. Here, in one of the largest studies of its kind, we conducted organic residue analysis of >800 pottery vessels selected from 46 Late Pleistocene and Early Holocene sites located across the Japanese archipelago to identify their contents. Our results demonstrate that pottery had a strong association with the processing of aquatic resources, irrespective of the ecological setting. Contrary to expectations, this association remained stable even after the onset of Holocene warming, including in more southerly areas, where expanding forests provided new opportunities for hunting and gathering. Nevertheless, the results indicate that a broader array of aquatic resources was processed in pottery after the start of the Holocene. We suggest this marks a significant change in the role of pottery of hunter-gatherers, corresponding to an increased volume of production, greater variation in forms and sizes, the rise of intensified fishing, the onset of shellfish exploitation, and reduced residential mobility.