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• Krauer, Fabienne & Schmid, Boris Valentijn (2022). Mapping the plague through natural language processing. Epidemics. ISSN 1755-4365. 41. doi: 10.1016/j.epidem.2022.100656. Fulltekst i vitenarkiv Vis sammendrag

  Pandemic diseases such as plague have produced a vast amount of literature providing information about the spatiotemporal extent, transmission, or countermeasures. However, the manual extraction of such information from running text is a tedious process, and much of this information remains locked into a narrative format. Natural Language processing (NLP) is a promising tool for the automated extraction of epidemiological data, and can facilitate the establishment of datasets. In this paper, we explore the utility of NLP to assist in the creation of a plague outbreak dataset. We produced a gold standard list of toponyms by manual annotation of a German plague treatise published by Sticker in 1908. We investigated the performance of five pre-trained NLP libraries (Google, Stanford CoreNLP, spaCy, germaNER and Geoparser) for the automated extraction of location data compared to the gold standard. Of all tested algorithms, spaCy performed best (sensitivity 0.92, F1 score 0.83), followed closely by Stanford CoreNLP (sensitivity 0.81, F1 score 0.87). Google NLP had a slightly lower performance (F1 score 0.72, sensitivity 0.78). Geoparser and germaNER had a poor sensitivity (0.41 and 0.61). We then evaluated how well automated geocoding services such as Google geocoding, Geonames and Geoparser located these outbreaks correctly. All geocoding services performed poorly – particularly for historical regions – and returned the correct GIS information only in 60.4%, 52.7% and 33.8% of all cases. Finally, we compared our newly digitized plague dataset to a re-digitized version of the plague treatise by Biraben and provide an update of the spatio-temporal extent of the second pandemic plague outbreaks. We conclude that NLP tools have their limitations, but they are potentially useful to accelerate the collection of data and the generation of a global plague outbreak database.

• Nilsson, Pernille; Ravinet, Mark; Cui, Yujun; Berg, Paul Ragnar; Zhang, Yujiang & Guo, Rong [Vis alle 17 forfattere av denne artikkelen] (2022). Polygenic plague resistance in the great gerbil uncovered by population sequencing. PNAS Nexus. 1(5). doi: 10.1093/pnasnexus/pgac211. Fulltekst i vitenarkiv
• Carlson, Colin J.; Bevins, Sarah N. & Schmid, Boris V. (2021). Plague risk in the western United States over seven decades of environmental change. Global Change Biology. ISSN 1354-1013. 28(3), s. 753–769. doi: 10.1111/gcb.15966. Fulltekst i vitenarkiv Vis sammendrag

  After several pandemics over the last two millennia, the wildlife reservoirs of plague (Yersinia pestis) now persist around the world, including in the western United States. Routine surveillance in this region has generated comprehensive records of human cases and animal seroprevalence, creating a unique opportunity to test how plague reservoirs are responding to environmental change. Here, we test whether animal and human data suggest that plague reservoirs and spillover risk have shifted since 1950. To do so, we develop a new method for detecting the impact of climate change on infectious disease distributions, capable of disentangling long-term trends (signal) and interannual variation in both weather and sampling (noise). We find that plague foci are associated with high-elevation rodent communities, and soil biochemistry may play a key role in the geography of long-term persistence. In addition, we find that human cases are concentrated only in a small subset of endemic areas, and that spillover events are driven by higher rodent species richness (the amplification hypothesis) and climatic anomalies (the trophic cascade hypothesis). Using our detection model, we find that due to the changing climate, rodent communities at high elevations have become more conducive to the establishment of plague reservoirs—with suitability increasing up to 40% in some places—and that spillover risk to humans at mid-elevations has increased as well, although more gradually. These results highlight opportunities for deeper investigation of plague ecology, the value of integrative surveillance for infectious disease geography, and the need for further research into ongoing climate change impacts.

• Nilsson, Pernille; Solbakken, Monica Hongrø; Schmid, Boris Valentijn; Orr, Russell; Lv, Ruichen & Cui, Yujun [Vis alle 15 forfattere av denne artikkelen] (2020). The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene. Genome Biology and Evolution (GBE). 12(2), s. 3832–3849. doi: 10.1093/gbe/evaa008. Fulltekst i vitenarkiv Vis sammendrag

  Abstract The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.

• Cui, Yujun; Schmid, Boris Valentijn; Cao, Hanli; Dai, Xiang; Du, Zhongmin & Easterday, William Ryan [Vis alle 24 forfattere av denne artikkelen] (2020). Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment. Nature Communications. 11, s. 1–8. doi: 10.1038/s41467-019-14099-w. Fulltekst i vitenarkiv Vis sammendrag

  Yersinia pestis is transmitted from fleas to rodents when the bacterium develops an extensive biofilm in the foregut of a flea, starving it into a feeding frenzy, or, alternatively, during a brief period directly after feeding on a bacteremic host. These two transmission modes are in a trade-off regulated by the amount of biofilm produced by the bacterium. Here by investigating 446 global isolated Y. pestis genomes, including 78 newly sequenced isolates sampled over 40 years from a plague focus in China, we provide evidence for strong selection pressures on the RNA polymerase ω-subunit encoding gene rpoZ. We demonstrate that rpoZ variants have an increased rate of biofilm production in vitro, and that they evolve in the ecosystem during colder and drier periods. Our results support the notion that the bacterium is constantly adapting—through extended phenotype changes in the fleas—in response to climate-driven changes in the niche.

• Mahmoudi, Ahmad; Kryštufek, Boris; Sludsky, Alexander; Schmid, Boris Valentijn; Almeida, Alzira M. P. De & Lei, Xu [Vis alle 11 forfattere av denne artikkelen] (2020). Plague reservoir species throughout the world. Integrative Zoology. ISSN 1749-4869. s. 1–14. doi: 10.1111/1749-4877.12511. Fulltekst i vitenarkiv Vis sammendrag

  Plague has been known since ancient times as a re‐emerging infectious disease, causing considerable socioeconomic burden in regional hotspots. To better understand the epidemiological cycle of the causative agent of the plague, its potential occurrence, and possible future dispersion, one must carefully consider the taxonomy, distribution, and ecological requirements of reservoir‐species in relation either to natural or human‐driven changes (e.g. climate change or urbanization). In recent years, the depth of knowledge on species taxonomy and species composition in different landscapes has undergone a dramatic expansion, driven by modern taxonomic methods such as synthetic surveys that take into consideration morphology, genetics, and the ecological setting of captured animals to establish their species identities. Here, we consider the recent taxonomic changes of the rodent species in known plague reservoirs and detail their distribution across the world, with a particular focus on those rodents considered to be keystone host species. A complete checklist of all known plague‐infectable vertebrates living in plague foci is provided as a Supporting Information table.

• Jones, Susan D.; Atshabar, Bakyt; Schmid, Boris Valentijn; Zuk, Marlene; Amramina, Anna & Stenseth, Nils Christian (2019). Living with plague: Lessons from the Soviet Union's antiplague system. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 116(19), s. 9155–9163. doi: 10.1073/pnas.1817339116. Fulltekst i vitenarkiv
• Sun, Zhe; Xu, Lei; Schmid, Boris Valentijn; Dean, Katharine Rose; Zhang, Zhibin & Xie, Yan [Vis alle 14 forfattere av denne artikkelen] (2019). Human plague system associated with rodent diversity and other environmental factors. Royal Society Open Science. 6(6), s. 1–11. doi: 10.1098/rsos.190216. Fulltekst i vitenarkiv Vis sammendrag

  Plague remains a threat to public health and is considered as a re-emerging infectious disease today. Rodents play an important role as major hosts in plague persistence and driving plague outbreaks in natural foci; however, few studies have tested the association between host diversity in ecosystems and human plague risk. Here we use zero-inflated generalized additive models to examine the association of species richness with human plague presence (where plague outbreaks could occur) and intensity (the average number of annual human cases when they occurred) in China during the Third Pandemic. We also account for transportation network density, annual precipitation levels and human population size. We found rodent species richness, particularly of rodent plague hosts, is positively associated with the presence of human plague. Further investigation shows that species richness of both wild and commensal rodent plague hosts are positively correlated with the presence, but only the latter correlated with the intensity. Our results indicated a positive relationship between rodent diversity and human plague, which may provide suggestions for the plague surveillance system.

• Dean, Katharine Rose; Krauer, Fabienne & Schmid, Boris Valentijn (2019). Epidemiology of a bubonic plague outbreak in Glasgow, Scotland in 1900. Royal Society Open Science. 6(181695), s. 1–11. doi: 10.1098/rsos.181695. Fulltekst i vitenarkiv Vis sammendrag

  On 3 August 1900, bubonic plague (Yersinia pestis) broke out in Glasgow for the first time during the Third Pandemic. The local sanitary authorities rigorously tracked the spread of the disease and they found that nearly all of the 35 cases could be linked by contact with a previous case. Despite trapping hundreds of rats in the area, there was no evidence of a rat epizootic and the investigators speculated that the outbreak could be due to human-to-human transmission of bubonic plague. Here we use a likelihood-based method to reconstruct transmission trees for the outbreak. From the description of the outbreak and the reconstructed trees, we infer several epidemiological parameters. We found that the estimated mean serial interval was 7.4–9.2 days and the mean effective reproduction number dropped below 1 after implementation of control measures. We also found a high rate of secondary transmissions within households and observations of transmissions from individuals who were not terminally septicaemic. Our results provide important insights into the epidemiology of a bubonic plague outbreak during the Third Pandemic in Europe.

• Bramanti, Barbara; Namouchi, Amine; Schmid, Boris Valentijn; Dean, Katharine Rose & Stenseth, Nils Christian (2019). Reply to Barbieri et al.: Out of the Land of Darkness: Plague on the fur trade routes. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 116(16). doi: 10.1073/pnas.1902274116. Fulltekst i vitenarkiv
• Jones, Susan D.; Schmid, Boris Valentijn; Zuk, Marlene & Stenseth, Nils Christian (2019). Reply to McLean et al.: Collections are critical. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 116(29), s. 1–1. doi: 10.1073/pnas.1909035116. Fulltekst i vitenarkiv
• Namouchi, Amine; Guellil, Meriam; Kersten, Oliver; Hänsch, Stephanie; Ottoni, Claudio & Schmid, Boris Valentijn [Vis alle 16 forfattere av denne artikkelen] (2018). Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 115(50), s. E11790–E11797. doi: 10.1073/pnas.1812865115. Fulltekst i vitenarkiv Vis sammendrag

  Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.

• Dean, Katharine Rose; Krauer, Fabienne; Walløe, Lars; Lingjærde, Ole Christian; Bramanti, Barbara & Stenseth, Nils Christian [Vis alle 7 forfattere av denne artikkelen] (2018). Human ectoparasites and the spread of plague in Europe during the Second Pandemic. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 115(6), s. 1304–1309. doi: 10.1073/pnas.1715640115. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn; Büntgen, Ulf; Easterday, William Ryan; Ginzler, Christian; Walløe, Lars & Bramanti, Barbara [Vis alle 7 forfattere av denne artikkelen] (2015). Climate-driven introduction of the Black Death and successive plague reintroductions into Europe. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 112(10), s. 3020–3025. doi: 10.1073/pnas.1412887112. Fulltekst i vitenarkiv
• Xu, Lei; Schmid, Boris Valentijn; Liu, Jun; Si, Xiaoyan; Stenseth, Nils Christian & Zhang, Zhibin (2015). The trophic responses of two different rodent–vector–plague systems to climate change. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 282(1800). doi: 10.1098/rspb.2014.1846. Fulltekst i vitenarkiv
• Wit, G. Ardine De; Over, Eelco A.B.; Schmid, Boris Valentijn; Bergen, Jan E.A.M. Van; Broek, Ingrid V.F. Van Den & Sande, Marianne A.B. Van Der [Vis alle 9 forfattere av denne artikkelen] (2015). Chlamydia screening is not cost-effective at low participation rates: Evidence from a repeated register-based implementation study in the Netherlands. Sexually Transmitted Infections. ISSN 1368-4973. 91(6), s. 423–429. doi: 10.1136/sextrans-2014-051677. Fulltekst i vitenarkiv
• Xu, Lei; Stige, Leif Christian; Kausrud, Kyrre Linné; Ari, Tamara Myriam Ben; Wang, Shuchun & Fang, Xiye [Vis alle 10 forfattere av denne artikkelen] (2014). Wet climate and transportation routes accelerate spread of human plague. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 281(1780). doi: 10.1098/rspb.2013.3159. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn; Over, Eelco AB; Broek, Ingrid VF van den; Coul, Eline LM Op de; Bergen, Jan EAM van & Fennema, Johan SA [Vis alle 11 forfattere av denne artikkelen] (2013). Effects of Population Based Screening for Chlamydia Infections in The Netherlands Limited by Declining Participation Rates. PLOS ONE. 8(3). doi: 10.1371/journal.pone.0058674. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn; Jesse, Marieke; Wilschut, Liesbeth; Viljugrein, Hildegunn & Heesterbeek, Hans (2012). Local persistence and extinction of plague in a metapopulation of great gerbil burrows, Kazakhstan. Epidemics. ISSN 1755-4365. 4(4), s. 211–218. doi: 10.1016/j.epidem.2012.12.003. Fulltekst i vitenarkiv Vis sammendrag

  Speculation on how the bacterium Yersinia pestis re-emerges after years of absence in the Prebalkhash region in Kazakhstan has been ongoing for half a century, but the mechanism is still unclear. One of the theories is that plague persists in its reservoir host (the great gerbil) in so-called hotspots, i.e. small regions in which the conditions remain favourable for plague to persist during times where the conditions in the Prebalkhash region as a whole have become unfavourable for plague persistence. In this paper we use a metapopulation model that describes the dynamics of the great gerbil. With this model we study the minimum size of an individual hotspot and the combined size of multiple hotspots in the Prebalkhash region that would be required for Y. pestis to persist through an inter-epizootic period. We show that the combined area of hotspots required for plague persistence is so large that it would be unlikely to have been missed by existing plague surveillance. This suggests that persistence of plague in that region cannot solely be explained by the existence of hotspots, and therefore other hypotheses, such as survival in multiple host species, and persistence in fleas or in the soil should be considered as well.

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• Schmid, Boris Valentijn (2021). The environmental and societal factors that led to the disappearance of plague from the mostly-rural societies that were the Nordic countries. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn; Lynters, Christos & Royan, Nicola (2021). Poetry, Pestilence, Prescriptions: Plague Biology in Sixteenth Century Scottish Poetry and Medical Manuscripts. An interdisciplinary discussion on plagues and poetry. Fulltekst i vitenarkiv
• Namouchi, Amine; Guellil, Meriam; Kersten, Oliver Sven; Hänsch, Stephanie; Ottoni, Claudio & Schmid, Boris Valentijn [Vis alle 16 forfattere av denne artikkelen] (2020). Correction for Namouchi et al., Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 17(22). doi: 10.1073/pnas.2007983117. Fulltekst i vitenarkiv
• Bramanti, Barbara; Namouchi, Amine; Schmid, Boris Valentijn; Dean, Katharine Rose & Stenseth, Nils Christian (2019). Out of the land of darkness: Plague on the fur trade routes. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 116(16), s. 7622–7623. doi: 10.1073/pnas.1902274116. Fulltekst i vitenarkiv
• Dean, Katharine Rose; Krauer, Fabienne; Walløe, Lars; Lingjærde, Ole Christian; Bramanti, Barbara & Stenseth, Nils Christian [Vis alle 7 forfattere av denne artikkelen] (2018). Reply to Park et al.: Human ectoparasite transmission of plague during the Second Pandemic is still plausible. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 115(34), s. E7894–E7895. doi: 10.1073/pnas.1810221115. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn (2017). Plague in Roscoff. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn (2017). Plague in Oslo. Fulltekst i vitenarkiv
• Stenseth, Nils Christian & Schmid, Boris Valentijn (2015). The climate pulse of Asia: the Black Death and successive plague reintroductions into Europe. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn (2015). The climatic pulse of Asia, the Black Death and successive plague reintroductions into Europe. Fulltekst i vitenarkiv
• Nilsson, Pernille; Easterday, William Ryan; Schmid, Boris Valentijn; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Zhange, Yujiang [Vis alle 8 forfattere av denne artikkelen] (2014). Plague and the Chinese experience – how to collaborate and work in China. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn (2014). Climate effects on host and vector population dynamics leads to Darwinian Selection on the pathogen Yersinia pestis. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn; Buntgen, U; Easterday, William Ryan; Ginzler, Christian; Walløe, Lars & Bramanti, Barbara [Vis alle 7 forfattere av denne artikkelen] (2013). The pulse of Asia: The Black Death and successive reintroductions of plague into Europe. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn (2013). The Black Death and successive reintroductions of plague into Europe. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn (2013). The climate pulse of Asia: the Black Death and the successive plague epidemics in Europe. Fulltekst i vitenarkiv
• Schmid, Boris Valentijn (2001). Climate factors in the dissemination of Plague. Fulltekst i vitenarkiv

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