Temporal and spatial distribution characteristics in the natural plague foci of Chinese Mongolian gerbils based on spatial autocorrelation

Yersinia pestis and Plague: some knowns and unknowns

Since its first identification in 1894 during the third pandemic in Hong Kong, there has been significant progress of understanding the lifestyle of Yersinia pestis, the pathogen that is responsible for plague. Although we now have some understanding of the pathogen's physiology, genetics, genomics, evolution, gene regulation, pathogenesis and immunity, there are many unknown aspects of the pathogen and its disease development. Here, we focus on some of the knowns and unknowns relating to Y. pestis and plague. We notably focus on some key Y. pestis physiological and virulence traits that are important for its mammal-flea-mammal life cycle but also its emergence from the enteropathogen Yersinia pseudotuberculosis. Some aspects of the genetic diversity of Y. pestis, the distribution and ecology of plague as well as the medical countermeasures to protect our population are also provided. Lastly, we present some biosafety and biosecurity information related to Y. pestis and plague.

Interrelationship of soil moisture and temperature to sylvatic plague cycle among prairie dogs in the Western United States

Plague, caused by Yersinia pestis, is a flea-borne disease that is endemic in areas throughout the world due to its successful maintenance in a sylvatic cycle, mainly in areas with temperate climates. Burrowing rodents are thought to play a key role in the enzootic maintenance as well as epizootic outbreaks of plague. In the United States, prairie dogs (Cynomys), rodents (Muridae), and ground squirrels (Spermophilus) are susceptible to infection and are parasitized by fleas that transmit plague. In particular, prairie dogs can experience outbreaks that rapidly spread, which can lead to extirpation of colonies. A number of ecological parameters, including climate, are associated with these epizootics. In this study, we asked whether soil parameters, primarily moisture and temperature, are associated with outbreaks of plague in black-tailed prairie dogs and Gunnison's prairie dogs in the Western United States, and at what depth these associations were apparent. We collected publicly available county-level information on the occurrence of population declines or colony extirpation, while historical soil data was collected from SCAN and USCRN stations in counties and states where prairie dogs have been located. The analysis suggests that soil moisture at lower depths correlates with colony die-offs, in addition to temperature near the surface, with key differences within the landscape ecology that impact the occurrence of plague. Overall, the model suggests that the burrow environment may play a significant role in the epizootic spread of disease amongst black-tailed and Gunnison's prairie dogs.

Yersinia pestis: the Natural History of Plague

The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Transmission dynamics of brucellosis: Mathematical modelling and applications in China

Brucellosis, the most common zoonotic disease worldwide, represents a great threat to animal husbandry with the potential to cause enormous economic losses. Meanwhile, brucellosis is one of the major public-health problems in China, and the number of human brucellosis cases has increased dramatically in recent years. In order to show the main features of brucellosis transmission in China, we give a systematic review on the transmission dynamics of brucellosis including a series of mathematical models and their applications in China. For different situations, dynamical models of brucellosis transmission in single population and multiple populations are devised based on ordinary differential equations. Furthermore, we revealed the spatial-temporal characteristics and effective control measures of brucellosis transmission. The results may provide new perspectives for the prevention and control of other types of zoonoses.

Spatial inequality, characteristics of internal migration, and pulmonary tuberculosis in China, 2011-2017: a spatial analysis

Background

Human migration facilitate the spread of tuberculosis (TB). Migrants face an increased risk of TB infection. In this study, we aim to explore the spatial inequity of sputum smear-positive pulmonary TB (SS + PTB) in China; and the spatial heterogeneity between SS + PTB and internal migration.

Methods

Notified SS + PTB cases in 31 provinces in mainland China were obtained from the national web-based PTB surveillance system database. Internal migrant data were extracted from the report on China’s migrant population development. Spatial autocorrelations were explored using the global Moran’s statistic and local indicators of spatial association. The spatial variation in temporal trends was performed using Kulldorff’s scan statistic. Fixed effect and spatial autoregressive models were used to explore the spatial inequity between SS + PTB and internal migration.

Results

A total of 2 380 233 SS + PTB cases were reported in China between 2011 and 2017, of which, 1 716 382 (72.11%) were male and 663 851 (27.89%) were female. Over 70% of internal migrants were from rural households and had lower income and less education. The spatial variation in temporal trend results showed that there was an 9.9% average annual decrease in the notification rate of SS + PTB from 2011 to 2017; and spatial clustering of SS + PTB cases was mainly located in western and southern China. The spatial autocorrelation results revealed spatial clustering of internal migration each year (2011–2017), and the clusters were stable within most provinces. Internal emigration, urban-to-rural migration and GDP per capita were significantly associated with SS + PTB, further, internal emigration could explain more variation in SS + PTB in the eastern region in mainland. However, internal immigration and rural-to-urban migration were not significantly associated with SS + PTB across China.

Conclusions

Our study found the spatial inequity between SS + PTB and internal migration. Internal emigration, urban-to-rural migration and GDP per capita were statistically associated with SS + PTB; the negative association was identified between internal emigration, urban-to-rural migration and SS + PTB. Further, we found those migrants with lower income and less education, and most of them were from rural households. These findings can help stakeholders to implement effective PTB control strategies for areas at high risk of PTB and those with high rates of internal migration.

Soil salinity and aridity specify plague foci in the United States of America

Plague is a deadly zoonosis that periodically reemerges as small outbreaks in geographically limited foci where the causative agent Yersinia pestis may reside in soil. We analyzed a dataset of 1.005 carefully documented plague cases that were georeferenced over 113 years in peer-reviewed literature in the contiguous United States. Plotting outbreaks by counties defined as plague foci on geographical maps, we observed a significant co-localization of plague outbreaks with high soil salinity measured by an electric conductivity of >4 dS/ m^-1 and aridity measured by an aridity index <0.5. Thus, we identified aridity and soil salinity as significantly associated with ecological risk factors for relapsing plague in the contiguous United States. These results reveal two evolutive parameters that are partially associated with anthropic activities, complicating the epidemiology of plague in the contiguous United States. Exploiting aridity and soil salinity data may help in the surveillance of evolving plague foci in the contiguous United States.

The association between internal migration and pulmonary tuberculosis in China, 2005-2015: a spatial analysis

BACKGROUND

Internal migration places individuals at high risk of contracting tuberculosis (TB). However, there is a scarcity of national-level spatial analyses regarding the association between TB and internal migration in China. In our research, we aimed to explore the spatial variation in cases of sputum smear-positive pulmonary TB (SS + PTB) in China; and the associations between SS + PTB, internal migration, socioeconomic factors, and demographic factors in the country between 2005 and 2015.

METHODS

Reported cases of SS + PTB were obtained from the national PTB surveillance system database; cases were obtained at the provincial level. Internal migration data were extracted from the national population sampling survey and the census. Spatial autocorrelations were explored using the global Moran's statistic and local indicators of spatial association. The spatial temporal analysis was performed using Kulldorff's scan statistic. Fixed effects regression was used to explore the association between SS + PTB and internal migration.

RESULTS

A total of 4 708 563 SS + PTB cases were reported in China between 2005 and 2015, of which 3 376 011 (71.7%) were male and 1 332 552 (28.3%) were female. There was a trend towards decreasing rates of SS + PTB notifications between 2005 and 2015. The result of global spatial autocorrelation indicated that there were significant spatial correlations between SS + PTB rate and internal migration each year (2005-2015). Spatial clustering of SS + PTB cases was mainly located in central and southern China and overlapped with the clusters of emigration. The proportions of emigrants and immigrants were significantly associated with SS + PTB. Per capita GDP and education level were negatively associated with SS + PTB. The internal migration flow maps indicated that migrants preferred neighboring provinces, with most migrating for work or business.

CONCLUSIONS

This study found a significant spatial autocorrelation between SS + PTB and internal migration. Both emigration and immigration were statistically associated with SS + PTB, and the association with emigration was stronger than that for immigration. Further, we found that SS + PTB clusters overlapped with emigration clusters, and the internal migration flow maps suggested that migrants from SS + PTB clusters may influence the TB epidemic characteristics of neighboring provinces. These findings can help stakeholders to implement effective PTB control strategies for areas at high risk of PTB and those with high rates of internal migrants.

Spatial and temporal clustering analysis of tuberculosis in the mainland of China at the prefecture level, 2005-2015

Background

Tuberculosis (TB) is still one of the most serious infectious diseases in the mainland of China. So it was urgent for the formulation of more effective measures to prevent and control it.

Methods

The data of reported TB cases in 340 prefectures from the mainland of China were extracted from the China Information System for Disease Control and Prevention (CISDCP) during January 2005 to December 2015. The Kulldorff’s retrospective space-time scan statistics was used to identify the temporal, spatial and spatio-temporal clusters of reported TB in the mainland of China by using the discrete Poisson probability model. Spatio-temporal clusters of sputum smear-positive (SS+) reported TB and sputum smear-negative (SS-) reported TB were also detected at the prefecture level.

Results

A total of 10 200 528 reported TB cases were collected from 2005 to 2015 in 340 prefectures, including 5 283 983 SS- TB cases and 4 631 734 SS + TB cases with specific sputum smear results, 284 811 cases without sputum smear test. Significantly TB clustering patterns in spatial, temporal and spatio-temporal were observed in this research. Results of the Kulldorff’s scan found twelve significant space-time clusters of reported TB. The most likely spatio-temporal cluster (RR = 3.27, P <  0.001) was mainly located in Xinjiang Uygur Autonomous Region of western China, covering five prefectures and clustering in the time frame from September 2012 to November 2015. The spatio-temporal clustering results of SS+ TB and SS- TB also showed the most likely clusters distributed in the western China. However, the clustering time of SS+ TB was concentrated before 2010 while SS- TB was mainly concentrated after 2010.

Conclusions

This study identified the time and region of TB, SS+ TB and SS- TB clustered easily in 340 prefectures in the mainland of China, which is helpful in prioritizing resource assignment in high-risk periods and high-risk areas, and to formulate powerful strategy to prevention and control TB.

Electronic supplementary material

The online version of this article (10.1186/s40249-018-0490-8) contains supplementary material, which is available to authorized users.