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Timofeev V, Bakhteeva I, Khlopova K, Mironova R, Titareva G, Goncharova Y, Solomentsev V, Kravchenko T, Dyatlov I, Vergnaud G. New Research on the Bacillus anthracis Genetic Diversity in Siberia. Pathogens 2023; 12:1257. [PMID: 37887773 PMCID: PMC10610006 DOI: 10.3390/pathogens12101257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
Anthrax is a particularly dangerous infection of humans and ungulates caused by the Gram-positive spore-forming bacterium Bacillus anthracis. The highly monomorphic and clonal species B. anthracis is commonly divided into three main lineages, A, B, and C, which in turn are divided into several canSNP groups. We report here a phylogenetic analysis based on the whole-genome sequence (WGS) data of fifteen strains isolated predominantly in Siberia or Central and Southern Russia. We confirm the wide distribution of the cluster of strains of the B.Br.001/002 group, endemic to the Russian Arctic, which is also present in the steppe zone of Southern Siberia. We characterize additional branches within the major A.Br.001/002 polytomy comprising the A.Br.Ames and A.Br.Sterne lineages, one of which is identified in the Arctic.
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Affiliation(s)
- Vitalii Timofeev
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Irina Bakhteeva
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Kseniya Khlopova
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Raisa Mironova
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Galina Titareva
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Yulia Goncharova
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Viktor Solomentsev
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Tatiana Kravchenko
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Ivan Dyatlov
- State Research Center for Applied Microbiology and Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
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2
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Metrailer MC, Hoang TTH, Jiranantasak T, Luong T, Hoa LM, Ngoc DB, Pham QT, Pham VK, Hung TTM, Huong VTL, Pham TL, Ponciano JM, Hamerlinck G, Dang DA, Norris MH, Blackburn JK. Spatial and phylogenetic patterns reveal hidden infection sources of Bacillus anthracis in an anthrax outbreak in Son La province, Vietnam. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 114:105496. [PMID: 37678701 DOI: 10.1016/j.meegid.2023.105496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Bacillus anthracis, the bacterial cause of anthrax, is a zoonosis affecting livestock and wildlife often spilling over into humans. In Vietnam, anthrax has been nationally reportable since 2015 with cases occurring annually, mostly in the northern provinces. In April 2022, an outbreak was reported in Son La province following the butchering of a water buffalo, Bubalus bubalis. A total of 137 humans from three villages were likely exposed to contaminated meat from the animal. Early epidemiological investigations suggested a single animal was involved in all exposures. Five B. anthracis isolates were recovered from human clinical cases along with one from the buffalo hide, another from associated maggots, and one from soil at the carcass site. The isolates were whole genome sequenced, allowing global, regional, and local molecular epidemiological analyses of the outbreak strains. All recovered B. anthracis belong to the A.Br.001/002 lineage based on canonical single nucleotide polymorphism analysis (canSNP). Although not previously identified in Vietnam, this lineage has been identified in the nearby countries of China, India, Indonesia, Thailand, as well as Australia. A twenty-five marker multi-locus variable number tandem repeat analysis (MLVA-25) was used to investigate the relationship between human, soil, and buffalo strains. Locally, four MLVA-25 genotypes were identified from the eight isolates. This level of genetic diversity is unusual for the limited geography and timing of cases and differs from past literature using MLVA-25. The coupled spatial and phylogenetic data suggest this outbreak originated from multiple, likely undetected, animal sources. These findings were further supported by local news reports that identified at least two additional buffalo deaths beyond the initial animal sampled in response to the human cases. Future outbreak response should include intensive surveillance for additional animal cases and additional molecular epidemiological traceback to identify pathogen sources.
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Affiliation(s)
- Morgan C Metrailer
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | - Treenate Jiranantasak
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Tan Luong
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Luong Minh Hoa
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Do Bich Ngoc
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Quang Thai Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Van Khang Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | | | | | | | | | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Michael H Norris
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Jason K Blackburn
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
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Luong T, Nguyen TT, Trinh VB, Walker MA, Ha Hoang TT, Pham QT, Tran TMH, Pham VK, Nguyen VL, Pham TL, Blackburn JK. Informing One Health Anthrax Surveillance and Vaccination Strategy from Spatial Analysis of Anthrax in Humans and Livestock in Ha Giang Province, Vietnam (1999-2020). Am J Trop Med Hyg 2023; 108:492-502. [PMID: 36689942 PMCID: PMC9978550 DOI: 10.4269/ajtmh.22-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/29/2022] [Indexed: 01/24/2023] Open
Abstract
Anthrax, caused by Bacillus anthracis, has a nearly global distribution but is understudied in Southeast Asia, including Vietnam. Here, we used historical data from 1999 to 2020 in Ha Giang, a province in northern Vietnam. The objectives were to describe the spatiotemporal patterns and epidemiology of human and livestock anthrax in the province and compare livestock vaccine coverage with human and livestock anthrax incidence. Annual incidence rates (per 10,000) for humans, buffalo/cattle, and goats were used to explore anthrax patterns and for comparison with livestock annual vaccine variations. A data subset describes anthrax epidemiology in humans by gender, age, source of infection, type of anthrax, admission site, and season. Zonal statistics and SaTScan were used to identify spatial and space-time clusters of human anthrax. SaTScan revealed space-time clusters in 1999, 2004, and 2007-2008 in the province, including in the northeastern, eastern, and western areas. Most human anthrax was reported between July and October. Most patients were male, aged 15-59 years, who had handled sick animals and/or consumed contaminated meat. High case-fatality rates were reported with gastrointestinal or respiratory cases. Our data suggest that vaccination in buffalo and cattle reduces the disease burden in humans and vaccinated animals but does not reduce the incidence in unvaccinated animals (goats). This study identified spatial areas of high risk for anthrax and can inform One Health surveillance and livestock vaccination planning in contextual settings similar to Ha Giang province.
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Affiliation(s)
- Tan Luong
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | - Tat Thang Nguyen
- Ha Giang Provincial Center for Disease Control, Ha Giang City, Vietnam
| | - Van Binh Trinh
- Ha Giang Provincial Sub-Department of Husbandry and Animal Health, Ha Giang City, Vietnam
| | - Morgan A. Walker
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | | | - Quang Thai Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- School of Preventive Medicine and Public Health, Hanoi Medical University, Hanoi, Vietnam
| | | | - Van Khang Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Van Long Nguyen
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Thanh Long Pham
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Jason K. Blackburn
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
- Address correspondence to Jason Blackburn, Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, 3141 Turlington Hall, Gainesville, FL 32611-7011.
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Tan LM, Hung DN, My DT, Walker MA, Ha HTT, Thai PQ, Hung TTM, Blackburn JK. Spatial analysis of human and livestock anthrax in Dien Bien province, Vietnam (2010-2019) and the significance of anthrax vaccination in livestock. PLoS Negl Trop Dis 2022; 16:e0010942. [PMID: 36538536 PMCID: PMC9767330 DOI: 10.1371/journal.pntd.0010942] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Anthrax is a serious zoonosis caused by Bacillus anthracis, which primarily affects wild herbivorous animals with spillover into humans. The disease occurs nearly worldwide but is poorly reported in Southeast Asian countries. In Vietnam, anthrax is underreported, and little is known about its temporal and spatial distributions. This paper examines the spatio-temporal distribution and epidemiological characteristics of human and livestock anthrax from Dien Bien province, Vietnam from 2010 to 2019. We also aim to define the role of livestock vaccination in reducing human cases. Historical anthrax data were collected by local human and animal health sectors in the province. Spatial rate smoothing and spatial clustering analysis, using Local Moran's I in GeoDa and space-time scan statistic in SaTScan, were employed to address these objectives. We found temporal and spatial overlap of anthrax incidence in humans and livestock with hotspots of human anthrax in the east. We identified three significant space-time clusters of human anthrax persisting from 2010 to 2014 in the east and southeast, each with high relative risk. Most of the human cases were male (69%), aged 15-59 years (80%), involved in processing, slaughtering, or eating meat of sick or dead livestock (96.9%) but environmental and unknown exposure were reported. Animal reports were limited compared to humans and at coarser spatial scale, but in areas with human case clusters. In years when livestock vaccination was high (>~25%), human incidence was reduced, with the opposite effect when vaccine rates dropped. This indicates livestock vaccination campaigns reduce anthrax burden in both humans and livestock in Vietnam, though livestock surveillance needs immediate improvement. These findings suggest further investigation and measures to strengthen the surveillance of human and animal anthrax for other provinces of Vietnam, as well as in other countries with similar disease context.
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Affiliation(s)
- Luong Minh Tan
- Spatial Epidemiology and Ecology Research Laboratory (SEER Lab), Department of Geography, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Doan Ngoc Hung
- Provincial Center for Disease Control, Dien Bien Phu City, Dien Bien, Vietnam
| | - Do Thai My
- Provincial Sub-Department of Animal Health, Dien Bien Phu City, Dien Bien, Vietnam
| | - Morgan A. Walker
- Spatial Epidemiology and Ecology Research Laboratory (SEER Lab), Department of Geography, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | | | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
- School of Preventive medicine and public health, Hanoi Medical University, Hanoi, Vietnam
| | | | - Jason K. Blackburn
- Spatial Epidemiology and Ecology Research Laboratory (SEER Lab), Department of Geography, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Walker MA, Tan LM, Dang LH, Van Khang P, Ha HTT, Hung TTM, Dung HH, Anh DD, Duong TN, Hadfield T, Thai PQ, Blackburn JK. Spatiotemporal Patterns of Anthrax, Vietnam, 1990–2015. Emerg Infect Dis 2022; 28:2206-2213. [PMID: 36285873 PMCID: PMC9622238 DOI: 10.3201/eid2811.212584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Anthrax is a priority zoonosis for control in Vietnam. The geographic distribution of anthrax remains to be defined, challenging our ability to target areas for control. We analyzed human anthrax cases in Vietnam to obtain anthrax incidence at the national and provincial level. Nationally, the trendline for cases remained at ≈61 cases/year throughout the 26 years of available data, indicating control efforts are not effectively reducing disease burden over time. Most anthrax cases occurred in the Northern Midlands and Mountainous regions, and the provinces of Lai Chau, Dien Bien, Lao Cai, Ha Giang, Cao Bang, and Son La experienced some of the highest incidence rates. Based on spatial Bayes smoothed maps, every region of Vietnam experienced human anthrax cases during the study period. Clarifying the distribution of anthrax in Vietnam will enable us to better identify risk areas for improved surveillance, rapid clinical care, and livestock vaccination campaigns.
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Abstract
PURPOSE OF REVIEW The advancement of molecular techniques such as whole-genome sequencing (WGS) has revolutionized the field of bacterial strain typing, with important implications for epidemiological surveillance and outbreak investigations. This review summarizes state-of-the-art techniques in strain typing and examines barriers faced by clinical and public health laboratories in implementing these new methodologies. RECENT FINDINGS WGS-based methodologies are on track to become the new 'gold standards' in bacterial strain typing, replacing traditional methods like pulsed-field gel electrophoresis and multilocus sequence typing. These new techniques have an improved ability to identify genetic relationships among organisms of interest. Further, advances in long-read sequencing approaches will likely provide a highly discriminatory tool to perform pangenome analyses and characterize relevant accessory genome elements, including mobile genetic elements carrying antibiotic resistance determinants in real time. Barriers to widespread integration of these approaches include a lack of standardized workflows and technical training. SUMMARY Genomic bacterial strain typing has facilitated a paradigm shift in clinical and molecular epidemiology. The increased resolution that these new techniques provide, along with epidemiological data, will facilitate the rapid identification of transmission routes with high confidence, leading to timely and effective deployment of infection control and public health interventions in outbreak settings.
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Hai Y, Wang WR, Hua Y, Guo WD, Song J, Han S, Zhang YG, Jiang XF, Zhang XH, Li ZJ, Li W, Liang XD, Han RL, Wei JC, Liu ZG. Changed epidemiology of anthrax and molecular characteristics of Bacillus anthracis in Inner Mongolia Autonomous Region, China. Transbound Emerg Dis 2020; 68:2250-2260. [PMID: 33048441 DOI: 10.1111/tbed.13877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/11/2020] [Accepted: 10/06/2020] [Indexed: 10/23/2022]
Abstract
Anthrax is a natural foci disease in Inner Mongolia, which poses a severe threat to public health. In this study, the incidence number, rate and constituent ratio were used to describe the epidemiological characteristics of anthrax in the region from 1956-2018. The molecular correlation and genetic characteristics of the strains were investigated using canonical single nucleotide polymorphisms (CanSNP), multiple-locus variable-number tandem repeat analysis (MLVA-15) and whole genome sequencing (WGS). The epidemiological characteristics of anthrax in Inner Mongolia have altered significantly. The incidence of anthrax has decreased annually without vaccination, and the regional distribution of anthrax gradually transferred from central and western regions to the eastern. Moreover, the occupation distribution evolved from multiple early occupations to predominated by farmers and herdsmen. This change is closely related to policy factors and to changes in the means of production and the living habits of the local population. This indicates that reformulating the control and prevention strategies is essential. Both A. Br. Ames and A. Br. 001/002 subgroups were the predominant CanSNP genotypes of Bacillus anthracis in Inner Mongolia. A total of 36 strains constituted six shared MLVA-15 genotypes, suggesting an epidemiological link between the strains of each shared genotype. The six shared genotypes ([GT1, 9, 11 and 15] and [GT8 and 12]) consisting of 2-7 strains confirmed the occurrence of multiple point outbreaks and cross-regional transmission caused by multiple common sources of infection. Phylogenetic analysis based on the WGS core genome showed that strains from this study formed an independent clade (C.V.), and they were positioned close to each other, suggesting a common origin. Further comparison analysis should be performed to ascertain the geographic origin of these strains.
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Affiliation(s)
- Yan Hai
- College of Veterinary Medicine, Inner Mongolia Agriculture University, Huhhot, China.,Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Wen-Rui Wang
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Yue Hua
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Wei-Dong Guo
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Jian Song
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Song Han
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Yu-Geng Zhang
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Xiao-Feng Jiang
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Xiu-Hong Zhang
- Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China
| | - Zhen-Jun Li
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Wei Li
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xu-Dong Liang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Run-Lin Han
- College of Veterinary Medicine, Inner Mongolia Agriculture University, Huhhot, China
| | - Jian-Chun Wei
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhi-Guo Liu
- College of Veterinary Medicine, Inner Mongolia Agriculture University, Huhhot, China.,Inner Mongolia Autonomous Region Center for Comprehensive Disease Control and Prevention, Huhhot, China.,State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
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