Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia

New Research on the Bacillus anthracis Genetic Diversity in Siberia

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.

Whole genome sequencing of Bacillus anthracis isolated from animal in the 1960s, Brazil, belonging to the South America subclade

Bacillus anthracis causes anthrax disease and can affect humans and other animals. This zoonotic disease has an impact on the economic and health aspects. B. anthracis population is divided into three major clades: A (with worldwide distribution), B, and C (restricted to specific regions). Anthrax is most common in agricultural regions of central and southwestern Asia, sub-Saharan Africa, Southern and Eastern Europe, the Caribbean, and Central and South America. Here, we sequenced by short and long reads technologies to generate a hybrid assembly of a lineage of B. anthracis recovered from animal source in the 1960s in Brazil. Isolate identification was confirmed by phenotypic/biochemical tests and MALDI-TOF MS. Antimicrobial susceptibility was performed by in-house broth microdilution. B. anthracis IAL52 was susceptible to penicillin, amoxicillin, doxycycline, levofloxacin, and tetracycline but non-susceptible to ciprofloxacin. IAL52 was classified as sequence type ST2, clade A.Br.069 (V770 group). Sequencing lineages of B. anthracis, especially from underrepresented regions, can help determine the evolution of this critical zoonotic and virulent pathogen.

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].

An Update on Eukaryotic Viruses Revived from Ancient Permafrost

One quarter of the Northern hemisphere is underlain by permanently frozen ground, referred to as permafrost. Due to climate warming, irreversibly thawing permafrost is releasing organic matter frozen for up to a million years, most of which decomposes into carbon dioxide and methane, further enhancing the greenhouse effect. Part of this organic matter also consists of revived cellular microbes (prokaryotes, unicellular eukaryotes) as well as viruses that have remained dormant since prehistorical times. While the literature abounds on descriptions of the rich and diverse prokaryotic microbiomes found in permafrost, no additional report about "live" viruses have been published since the two original studies describing pithovirus (in 2014) and mollivirus (in 2015). This wrongly suggests that such occurrences are rare and that "zombie viruses" are not a public health threat. To restore an appreciation closer to reality, we report the preliminary characterizations of 13 new viruses isolated from seven different ancient Siberian permafrost samples, one from the Lena river and one from Kamchatka cryosol. As expected from the host specificity imposed by our protocol, these viruses belong to five different clades infecting Acanthamoeba spp. but not previously revived from permafrost: Pandoravirus, Cedratvirus, Megavirus, and Pacmanvirus, in addition to a new Pithovirus strain.

Synthesizing the connections between environmental disturbances and zoonotic spillover

Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identification, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region.

New formulation of a recombinant anthrax vaccine stabilised with structurally modified plant viruses

Anthrax is a disease caused by Bacillus anthracis. The most promising approach to the development of anthrax vaccine is use of the anthrax protective antigen (PA). At the same time, recombinant PA is a very unstable protein. Previously, the authors have designed a stable modified recombinant anthrax protective antigen with inactivated proteolytic sites and substituted deamidation sites (rPA83m). As a second approach to recombinant PA stabilisation, plant virus spherical particles (SPs) were used as a stabiliser. The combination of these two approaches was shown to be the most effective. Here, the authors report the results of a detailed study of the stability, immunogenicity and protectiveness of rPA83m + SPs compositions. These compositions were shown to be stable, provided high anti-rPA83m antibody titres in guinea pigs and were able to protect them from a fully virulent 81/1 Bacillus anthracis strain. Given these facts, the formulation of rPA83m + SPs compositions is considered to be a prospective anthrax vaccine candidate.

Allelic Polymorphism of Anthrax Pathogenicity Factor Genes as a Means of Estimating Microbiological Risks Associated with Climate Change

Abstract

Climate change brings new risks of emergence of especially dangerous diseases. The paper reports the possibility of assessing the pathogenic potential of bacteria as demonstrated by studying the allelic polymorphism of anthrax bacterium pathogenicity factor genes, which is a prerequisite for assessing the associated microbiological risks. The allelic polymorphism of the capBCADE operon (capB, capC, capA, capD, and capE genes) encoding the capsule biosynthesis proteins of Bacillus anthracis, and the acpA and acpB genes encoding the expression regulators of this operon have been studied for the first time. A number of single nucleotide polymorphisms (SNPs) were described in the strains of the studied sample, including 5 SNPs in the capB gene, 3 in capC, 4 in capA, 14 in capD, 2 in capE, and 15 in acpB, as well as 7 SNPs and one insertion in the acpA gene. As a result, the sample has been divided into sequence types for each gene and 17 genotypes, which are combinations of the identified sequence types. In silico translation of the detected alleles of the studied genes revealed three isoforms of the CapB and CapA proteins, two isoforms of the CapC and CapE proteins, six isoforms of the CapD protein, five isoforms of the AcpA protein, and four isoforms in the AcpB protein. It has been demonstrated that the SNP in the 351A → G position of capC is a marker of A.Br.Aust94 group strains. Based on the results, A.Br.Vollum group strains were divided into two subgroups. The strains in the evolutionary lines B and C differed from the line A strains by the presence of an 853G → A SNP in the acpA gene. In addition, a previously unknown variable number tandem repeat (VNTR), has been found in the acpA gene and the possibility of using it for differentiating and genotyping of B. anthracis strains has been demonstrated.

Some Peculiarities of Anthrax Epidemiology in Herbivorous and Carnivorous Animals

Anthrax is an especially dangerous zooanthroponosis caused by the Gram-positive spore-forming bacterium Bacillus anthracis. A notable feature of this disease is the difference in susceptibility to it among different groups of animals. Anthrax primarily affects herbivorous ungulate mammals; they are easily infected, and their disease often leads to rapid, even sudden, death. However, predators and scavengers are extremely resistant to anthrax, and if they become infected, they usually become mildly ill. As the result of the increased sensitivity of ungulates to anthrax and the possibility of disease transmission from them to humans, most studies of anthrax have focused on the diagnosis, prevention, and treatment of infection in farm animals and humans. The issues of anthrax in other animals, such as predators, and the peculiarities of anthrax epidemiology in wild ungulates have not been sufficiently detailed in the literature. In this article, we provide a review of literature sources that describe the differential susceptibility to infection of various groups of animals to anthrax and some epidemiological features of anthrax in animals that are not the main hosts of B. anthracis.

Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques

Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining long- and short-read next-generation sequencing techniques, highly accurate genomes were reconstructed, enabling detailed in silico genotyping. Thus, the strains could be assigned to the Tsiankovskii subgroup of the “TransEurAsia” clade, which is commonly found in this region. Their high genetic similarity suggests that the four strains are members of the endemic population whose progenitor was once introduced in the Ukraine and bordering regions. This study provides information on B. anthracis strains from a region where there is little knowledge of the local population, thereby adding to the picture of global B. anthracis genotype distribution. We also emphasize the importance of surveillance and prevention methods regarding anthrax outbreaks, as other studies predicted a higher number of cases in the future due to global warming.

Bacillus anthracis Phylogeography: New Clues From Kazakhstan, Central Asia

This article describes Bacillus anthracis strains isolated in Kazakhstan since the 1950s until year 2016 from sixty-one independent events associated with anthrax in humans and animals. One hundred and fifty-four strains were first genotyped by Multiple Locus VNTR (variable number of tandem repeats) Analysis (MLVA) using 31 VNTR loci. Thirty-five MLVA31 genotypes were resolved, 28 belong to the A1/TEA group, five to A3/Sterne-Ames group, one to A4/Vollum and one to the B clade. This is the first report of the presence of the B-clade in Kazakhstan. The MLVA31 results and epidemiological data were combined to select a subset of seventy-nine representative strains for draft whole genome sequencing (WGS). Strains from Kazakhstan significantly enrich the known phylogeny of the Ames group polytomy, including the description of a new branch closest to the Texas, United States A.Br.Ames sublineage stricto sensu. Three among the seven currently defined branches in the TEA polytomy are present in Kazakhstan, “Tsiankovskii”, “Heroin”, and “Sanitary Technical Institute (STI)”. In particular, strains from the STI lineage are largely predominant in Kazakhstan and introduce numerous deep branching STI sublineages, demonstrating a high geographic correspondence between “STI” and Kazakhstan, Central Asia. This observation is a strong indication that the TEA polytomy emerged after the last political unification of Asian steppes in the fourteenth century of the Common Era. The phylogenetic analysis of the Kazakhstan data and of currently available WGS data of worldwide origin strengthens our understanding of B. anthracis geographic expansions in the past seven centuries.

Sequence Variability of pXO1-Located Pathogenicity Genes of Bacillus anthracis Natural Strains of Different Geographic Origin

The main pathogenic factor of Bacillus anthracis is a three-component toxin encoded by the pagA, lef, and cya genes, which are located on the pXO1 plasmid. The atxA gene, which encodes the primary regulator of pathogenicity factor expression, is located on the same plasmid. In this work, we evaluated the polymorphism of the pagA, lef, cya, and atxA genes for 85 B. anthracis strains from different evolutionary lineages and canSNP groups. We have found a strong correlation of 19 genotypes with the main evolutionary lineages, but the correlation with the canSNP group of the strain was not as strong. We have detected several genetic markers indicating the geographical origin of the strains, for example, their source from the steppe zone of the former USSR. We also found that strains of the B.Br.001/002 group caused an anthrax epidemic in Russia in 2016 and strains isolated during paleontological excavations in the Russian Arctic have the same genotype as the strains of the B.Br.CNEVA group circulating in Central Europe. This data could testify in favor of the genetic relationship of these two groups of strains and hypothesize the ways of distribution of their ancestral forms between Europe and the Arctic.

Risk factors and spatio-temporal patterns of livestock anthrax in Khuvsgul Province, Mongolia

Anthrax is a worldwide zoonotic disease. Anthrax has long been a public health and socio-economic issue in Mongolia. Presently, there is no spatial information on carcass burial sites as a potential hazard of future anthrax outbreaks and possible risk factors associated with anthrax occurrences in Mongolia. Here, we analyze retrospective data (1986-2015) on the disposal sites of livestock carcasses to describe historical spatio-temporal patterns of livestock anthrax in Khuvsgul Province, which showed the highest anthrax incidence rate in Mongolia. From the results of spatial mean and standard deviational ellipse analyses, we found that the anthrax spatial distribution in livestock did not change over the study period, indicating a localized source of exposure. The multi-distance spatial cluster analysis showed that carcass sites distributed in the study area are clustered. Using kernel density estimation analysis on carcass sites, we identified two anthrax hotspots in low-lying areas around the south and north regions. Notably, this study disclosed a new hotspot in the northern part that emerged in the last decade of the 30-year study period. The highest proportion of cases was recorded in cattle, whose prevalence per area was highest in six districts (i.e., Murun, Chandmani-Undur, Khatgal, Ikh-Uul, Tosontsengel, and Tsagaan-Uul), suggesting that vaccination should prioritize cattle in these districts. Furthermore, size of outbreaks was influenced by the annual summer mean air temperature of Khuvsgul Province, probably by affecting the permafrost freeze-thawing activity.

Reindeer Anthrax in the Russian Arctic, 2016: Climatic Determinants of the Outbreak and Vaccination Effectiveness

The Yamal Peninsula in the Russian Federation experienced a massive outbreak of anthrax in reindeer (Rangifer tarandus) in July–August 2016, with 2,650 (6.46% of the total susceptible population) animals infected, of which 2,350 died (case fatality rate of 88.67%). In our study, we analyzed climatic and epidemiological factors that could have triggered the outbreak. The cancelation of reindeer vaccination against anthrax in 2007 resulted in an increase in population susceptibility. In response to the outbreak, total vaccination of all susceptible animals was resumed. To assess the vaccination effectiveness, we tested 913 samples of blood serum taken from vaccinated reindeer using an antigenic erythrocyte diagnostic kit to detect specific anti-anthrax antibodies via an indirect hemagglutination assay (IHA) 9 months after vaccination. We found that 814 samples had sufficiently high levels of anti-anthrax antibodies to indicate a protection level of 89% (95% confidence interval: 87–91%) of the whole reindeer population. Abnormally high ambient temperature in the summer of 2016 contributed to the thawing of permafrost and viable Bacillus anthracis spores could have become exposed to the surface; the monthly average air temperatures in June, July, and August 2016 were 20–100% higher than those of the previous 30-year period, while the maximum air temperatures were 16–75% higher. Using the projected climate data for 2081–2100 according to the “worst case” RCP8.5 scenario, we demonstrated that the yearly air temperature may average above 0°C across the entire Yamal Peninsula, while the yearly number of days with a mean temperature above 0°C may rise by 49 ± 6 days, which would provide conditions for reactivation of soil anthrax reservoirs. Our results showed that the outbreak of anthrax occurred under conditions of a significant increase in air temperature in the study area, underlined the importance of vaccination for controlling the epidemic process, and demonstrated the effectiveness of monitoring studies using the IHA diagnostic kit for detecting erythrocyte anthrax antigens.

Climatic Factors Influencing the Anthrax Outbreak of 2016 in Siberia, Russia

In 2016, an outbreak of anthrax killing thousands of reindeer and affecting dozens of humans occurred on the Yamal peninsula, Northwest Siberia, after 70 years of epidemiological situation without outbreaks. The trigger of the outbreak has been ascribed to the activation of spores due to permafrost thaw that was accelerated during the summer heat wave. The focus of our study is on the dynamics of local environmental factors in connection with the observed anthrax revival. We show that permafrost was thawing rapidly for already 6 years before the outbreak. During 2011-2016, relatively warm years were followed by cold years with a thick snow cover, preventing freezing of the soil. Furthermore, the spread of anthrax was likely intensified by an extremely dry summer of 2016. Concurrent with the long-term decreasing trend in the regional annual precipitation, the rainfall in July 2016 was less than 10% of its 30-year mean value. We conclude that epidemiological situation of anthrax in the previously contaminated Arctic regions requires monitoring of climatic factors such as warming and precipitation extremes.

Climate change, melting cryosphere and frozen pathogens: Should we worry…?

Permanently frozen environments (glaciers, permafrost) are considered as natural reservoirs of huge amounts of microorganisms, mostly dormant, including human pathogens. Due to global warming, which increases the rate of ice-melting, approximately 4 × 1021 of these microorganisms are released annually from their frozen confinement and enter natural ecosystems, in close proximity to human settlements. Some years ago, the hypothesis was put forward that this massive release of potentially-pathogenic microbes-many of which disappeared from the face of the Earth thousands and even millions of years ago-could give rise to epidemics. The recent anthrax outbreaks that occurred in Siberia, and the presence of bacterial and viral pathogens in glaciers worldwide, seem to confirm this hypothesis. In that context, the present review summarizes the currently available scientific evidence that allows us to imagine a near future in which epidemic outbreaks, similar to the abovementioned, could occur as a consequence of the resurrection and release of microbes from glaciers and permafrost.

Supplementary Information

The online version of this article (10.1007/s42398-021-00184-8) contains supplementary material, which is available to authorized users.

Phylogenetics of Bacillus anthracis isolates from Russia and bordering countries

Anthrax is a concern for public health and veterinary medicine in Russia. The available phylogenetic data on isolates from Russia and neighboring CIS countries are clearly not enough to gain a better understanding of their position in the global phylogenetic population structure of this pathogen. In this study, we analyzed the genomes of 66 Bacillus anthracis strains, which were isolated between 1935 and 2019 from different sources in Russia, as well as in Ukraine, Azerbaijan, Georgia, Armenia and Moldova. Whole genome SNP analysis of genomes of 66 strains obtained in this study along with 222 B. anthracis genomes available in the GenBank database revealed 7242 SNPs used to construct a phylogenetic reconstruction with the method of Maximum Likelihood. Studied strains belong to 6 different genetic groups: A.Br.008(A.Br.008/009), A.Br.081(Ames), A.Br.014(A.Br.Aust94), A.Br.082(A.Br.001/002), A.Br.034(A.Br.005/006, Ancient A) and B.Br.002 (B.Br.001/002). Within the group A.Br.014(A.Br.Aust94) a subcluster A.Br.029 of strains isolated in Georgia, Armenia, Azerbaijan, Russia (Republic of Dagestan) and Turkey, named Caucasus-East Anatolia (CEA), was identified. In the subgroup A.Br.105(Tsiankovskii) the cluster A.Br.117 of strains from Russia, Ukraine and Slovakia are assigned, in the subgroup A.Br118 (STI) - cluster A.Br.123 with strains from Russia and Georgia and cluster A.Br.125 with strains from Republic of Dagestan. New subclusters B.Br.017("EUROPE") were identified in the B.Br.002(B.Br.001/002) cluster, represented by strains from the European part of Russia, as well as from South Korea and Finland. For 8 clusters and subclusters, the SNP markers were identified. The study confirmed a significant genetic diversity of the strains isolated in Russia and border countries and clarified their position in the phylogenetic structure of the global B. anthracis population. New genetic clusters A.Br.029 (CEA), A.Br.117, A.Br.123, A.Br.125, and B.Br.017 («EUROPE») were defined. 96 marker SNPs specific for these clusters were identified.

Implications of Zoonoses From Hunting and Use of Wildlife in North American Arctic and Boreal Biomes: Pandemic Potential, Monitoring, and Mitigation

The COVID-19 pandemic has re-focused attention on mechanisms that lead to zoonotic disease spillover and spread. Commercial wildlife trade, and associated markets, are recognized mechanisms for zoonotic disease emergence, resulting in a growing global conversation around reducing human disease risks from spillover associated with hunting, trade, and consumption of wild animals. These discussions are especially relevant to people who rely on harvesting wildlife to meet nutritional, and cultural needs, including those in Arctic and boreal regions. Global policies around wildlife use and trade can impact food sovereignty and security, especially of Indigenous Peoples. We reviewed known zoonotic pathogens and current risks of transmission from wildlife (including fish) to humans in North American Arctic and boreal biomes, and evaluated the epidemic and pandemic potential of these zoonoses. We discuss future concerns, and consider monitoring and mitigation measures in these changing socio-ecological systems. While multiple zoonotic pathogens circulate in these systems, risks to humans are mostly limited to individual illness or local community outbreaks. These regions are relatively remote, subject to very cold temperatures, have relatively low wildlife, domestic animal, and pathogen diversity, and in many cases low density, including of humans. Hence, favorable conditions for emergence of novel diseases or major amplification of a spillover event are currently not present. The greatest risk to northern communities from pathogens of pandemic potential is via introduction with humans visiting from other areas. However, Arctic and boreal ecosystems are undergoing rapid changes through climate warming, habitat encroachment, and development; all of which can change host and pathogen relationships, thereby affecting the probability of the emergence of new (and re-emergence of old) zoonoses. Indigenous leadership and engagement in disease monitoring, prevention and response, is vital from the outset, and would increase the success of such efforts, as well as ensure the protection of Indigenous rights as outlined in the United Nations Declaration on the Rights of Indigenous Peoples. Partnering with northern communities and including Indigenous Knowledge Systems would improve the timeliness, and likelihood, of detecting emerging zoonotic risks, and contextualize risk assessments to the unique human-wildlife relationships present in northern biomes.

Molecular genotyping of 15 B. anthracis strains isolated in Eastern Siberia and Far East

Bacillus anthracis is a pathogenic bacterium, which causes anthrax disease. The ability of this bacterium to form spores, which can be preserved in soil for decades and cause outbreaks later on, makes this pathogen a serious problem for veterinary and health services of many countries. Siberia is one of the most anthrax-influenced regions of Russia. In this research we report on the results of genotyping based on whole genome SNP analysis of 15 strains, isolated on the territory of Eastern Siberia and the Far East in 1956-2018. In this research, we sequenced 15 genomes of B. anthracis strains isolated from infected humans and animals, and from soil samples from the territory of Eastern Siberia and the Far East in the period from 1956 to 2018. We used genomic sequences obtained in this study and 219 B. anthracis genomes available in the international GenBank database to perform a comparative analysis. As a result we detected 6400 chromosomal SNPs which allowed to differentiate the studied strains. We built phylogenetic reconstruction of the global B. anthracis population based on the detected SNPs using the Maximum Likelihood Method and described genetic diversity of the strains isolated on the territory of Eastern Siberia and the Far East. Strains, isolated on this territory from 1956 to 2018 belong to 5 different genetic groups: "Ames", "STI", "Tsiankovskii", "Siberia" and "Asia". The greatest diversity of the strains is registered for two regions of the southern part of Eastern Siberia - Tyva and Buryatia. This research expands current understanding of genetic diversity of B. anthracis strains circulating on the territory of Russia.

First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core

Despite the unique physiology and metabolic pathways of microbiomes from cold environments providing key evolutionary insights and promising leads for discovering new bioactive compounds, cultivable bacteria entrapped in perennial ice from caves remained a largely unexplored life system. In this context, we obtained and characterized bacterial strains from 13,000-years old ice core of Scarisoara Ice Cave, providing first isolates from perennial ice accumulated in caves since Late Glacial, and first culture-based evidences of bacterial resistome and antimicrobial compounds production. The 68 bacterial isolates belonged to 4 phyla, 34 genera and 56 species, with 17 strains representing putative new taxa. The Gram-negative cave bacteria (Proteobacteria and Bacteroidetes) were more resistant to the great majority of antibiotic classes than the Gram-positive ones (Actinobacteria, Firmicutes). More than 50% of the strains exhibited high resistance to 17 classes of antibiotics. Some of the isolates inhibited the growth of clinically important Gram-positive and Gram-negative resistant strains and revealed metabolic features with applicative potential. The current report on bacterial strains from millennia-old cave ice revealed promising candidates for studying the evolution of environmental resistome and for obtaining new active biomolecules for fighting the antibiotics crisis, and valuable cold-active biocatalysts.

Retrospective Analysis of the Relationship between Two Anthrax Outbreaks in Kazakhstan Based on Genomic Data

We present a retrospective analysis of strains from two anthrax outbreaks in western Kazakhstan in 2009. The outbreaks occurred during the same period and in the same area located close to main roads, favoring a single source of infection. However, multilocus variable-number tandem-repeat analysis (MLVA), canonical single-nucleotide polymorphism (CanSNP) analysis, and genome-wide analysis demonstrated that the outbreaks were not connected.

We present a retrospective analysis of strains from two anthrax outbreaks in western Kazakhstan in 2009. The outbreaks occurred during the same period and in the same area located close to main roads, favoring a single source of infection. However, multilocus variable-number tandem-repeat analysis (MLVA), canonical single-nucleotide polymorphism (CanSNP) analysis, and genome-wide analysis demonstrated that the outbreaks were not connected.

Quantification of endospores in ancient permafrost using time-resolved terbium luminescence

We describe herein a simple procedure for quantifying endospore abundances in ancient and organic-rich permafrost. We repeatedly (10x) extracted and fractionated permafrost using a tandem filter assembly composed of 3 and 0.2 μm filters. Then, the 0.2 μm filter was washed (7x), autoclaved, and the contents eluted, including dipicolinic acid (DPA). Time-resolved luminescence using Tb(EDTA) yielded a LOD of 1.46 nM DPA (6.55 × 10³ endospores/mL). In review, DPA/endospore abundances were ~2.2-fold greater in older 33 ky permafrost (258 ± 36 pmol DPA gdw^-1; 1.15 × 10⁶ ± 0.16 × 10⁶ spores gdw^-1) versus younger 19 ky permafrost (p = 0.007297). This suggests that dormancy increases with permafrost age.

A Review of Arguments for the Existence of Latent Infections of Bacillus anthracis, and Research Needed to Understand their Role in the Outbreaks of Anthrax

Hugh-Jones and Blackburn and Turnbull’s collective World Health Organization (WHO) report did literature reviews of the theories and the bases for causes of anthrax outbreaks. Both comment on an often-mentioned suspicion that, even though unproven, latent infections are likely involved. Hugh-Jones suggested Gainer do an updated review of our present-day knowledge of latent infections, which was the basis for Gainer’s talk at the Biology of Anthrax Conference in Bari, Italy 2019. At the Conference Gainer met Vergnaud who presented anthrax genome studies that implied that the disease might have spread throughout Asia and from Europe to North America in a short time span of three or four centuries. Vergnaud wondered if latent infections might have played a role in the process. Several other presenters at the Conference also mentioned results that might suggest the existence of latent infections. Vergnaud subsequently looked into some of the old French literature about related observations, results, and discussions of early Pasteur vaccine usage (late 1800′s) and found mentions of suspected latent infections. The first part of the paper is a focused summary and interpretation of Hugh-Jones and Blackburn’s and Turnbull’s reviews specifically looking for suggestions of latent infections, a few additional studies with slightly different approaches, and several mentions made of presentations and posters at the Conference in Italy. In general, many different investigators in different areas and aspects of the anthrax study at the Conference found reasons to suspect the existence of latent infections. The authors conclude that the affected species most studied, including Homo sapiens, provide circumstantial evidence of latent infections and modified host resistance. The last part of the review explores the research needed to prove or disprove the existence of latent infections.

A Rare Glimpse into the Past of the Anthrax Pathogen Bacillus anthracis

The bacterium Bacillus anthracis is the causative agent of the zoonotic disease anthrax. While genomics of extant B. anthracis isolates established in-depth phylogenomic relationships, there is scarce information on the historic genomics of the pathogen. Here, we characterized the oldest documented B. anthracis specimen. The inactive 142-year-old material originated from a bovine diseased in Chemnitz (Germany) in 1878 and is contemporary with the seminal studies of Robert Koch on B. anthracis. A specifically developed isolation method yielded high-quality DNA from this specimen for genomic sequencing. The bacterial chromosome featuring 242 unique base-characters placed it into a major phylogenetic clade of B. anthracis (B.Branch CNEVA), which is typical for central Europe today. Our results support the notion that the CNEVA-clade represents part of the indigenous genetic lineage of B. anthracis in this part of Europe. This work emphasizes the value of historic specimens as precious resources for reconstructing the past phylogeny of the anthrax pathogen.

Genetic characterization of Bacillus anthracis strains circulating in Italy from 1972 to 2018

In Italy anthrax is an endemic disease, with a few outbreaks occurring almost every year. We surveyed 234 B. anthracis strains from animals (n = 196), humans (n = 3) and the environment (n = 35) isolated during Italian outbreaks in the years 1972-2018. Despite the considerable genetic homogeneity of B. anthracis, the strains were effectively differentiated using canonical single nucleotide polymorphisms (CanSNPs) assay and multiple-locus variable-number tandem repeat analysis (MLVA). The phylogenetic identity was determined through the characterization of 14 CanSNPs. In addition, a subsequent 31-loci MLVA assay was also used to further discriminate B. anthracis genotypes into subgroups. The analysis of 14 CanSNPs allowed for the identification of four main lineages: A.Br.011/009, A.Br.008/011 (respectively belonging to A.Br.008/009 sublineage, also known Trans-Eurasian or TEA group), A.Br.005/006 and B.Br.CNEVA. A.Br.011/009, the most common subgroup of lineage A, is the major genotype of B. anthracis in Italy. The MLVA analysis revealed the presence of 55 different genotypes in Italy. Most of the genotypes are genetically very similar, supporting the hypothesis that all strains evolved from a local common ancestral strain, except for two genotypes representing the branch A.Br.005/006 and B.Br.CNEVA. The genotyping analysis applied in this study remains a very valuable tool for studying the diversity, evolution, and molecular epidemiology of B. anthracis.

Sporadic human cutaneous anthrax outbreak in Shaanxi Province, China: report of two cases from 2018

China’s compulsory annual livestock anthrax vaccination policy has remarkably reduced but not completely eradicated human anthrax infections. Herein we describe a sporadic human cutaneous anthrax outbreak involving two cases in 2018 in Shaanxi Province, both involving herdsman who dealt with unvaccinated and potentially sick cattle. Both patients showed Bacillus anthracis-positive blister smear and blood culture. Treatment with penicillin was followed by uneventful recovery for both. The prompt performance of the prophylactic measures successfully interrupted the further transmission of this sporadic human cutaneous anthrax outbreak.

Phylogenetic analysis of Bacillus anthracis strains from Western Siberia reveals a new genetic cluster in the global population of the species

Background

Anthrax is a zoonotic disease caused by the gram-positive bacterium Bacillus anthracis. The most anthrax-endemic regions of Russia are Siberia and North Caucasus. Previously, genotyping of Russian B.anthracis isolates was carried out using canSNP and MLVA data; these methods yield lower resolution results compared to whole genome SNP analysis (wgSNP). In this research, we have used wgSNP method for genotyping of 10 B.anthracis isolates, obtained during 1961–2016 in Russia on territory of Western Siberia.

Results

We have analyzed 185 B.anthracis genomes available in GenBank database and genomes of 10 isolates obtained in this study to determine the place of Russian isolates in the global phylogeny of B.anthracis. For the studied genomes we have detected 7203 SNPs, which were used for building a phylogenetic reconstruction with Maximum Likelihood Method. Results of the phylogenetic analysis indicate that Russian strains belong to three different genetic groups. Three strains belong to genetic group “Ames”, two strains – to “STI” group. Five strains belong to the main genetic line B, and four of them form a subcluster, described for the first time, which we have named “Siberia”.

Conclusions

In this study, the data on genetic diversity of B.anthracis strains on the territory of Western Siberia is presented for the first time. As a result of complex phylogenetic analysis, the place of these isolates was determined in the global phylogenetic structure of the B.anthracis population. We describe a new cluster in the main genetic line B for the first time.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6060-z) contains supplementary material, which is available to authorized users.

Genotyping and phylogenetic location of one clinical isolate of Bacillus anthracis isolated from a human in Russia

Background

Anthrax is a zoonotic disease caused by the Gram-positive bacterium Bacillus anthracis. In Russia, there are more than 35 thousand anthrax stationary unfavourable sites. At the same time, there is very little published information about the isolates of B. anthracis from the territory of Russia. In this study, we report the use of whole genome sequencing (WGS) and bioinformatics analysis to characterize B. anthracis 81/1 strain isolated in Russia in 1969 from a person during an outbreak of the disease in the Stavropol region.

Results

We used 232 B. anthracis genomes, which are currently available in the GenBank database, to determine the place of the Russian isolate in the global phylogeny of B. anthracis. The studied strain was characterized by PCR-based genetic methods, such as Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA), canonical single nucleotide polymorphisms (canSNP), as well as the method of full-genomic analysis of nucleotide polymorphisms (wgSNP). The results indicate that the Russian B. anthracis 81/1 strain belongs to Trans-Eurasion (TEA) group, the most representative in the world.

Conclusions

In this study, the full genomic sequence of virulent B. anthracis strain from Russia was characterized for the first time. As a result of complex phylogenetic analysis, the place of this isolate was determined in the global phylogenetic structure of the B. anthracis population, expanding our knowledge of anthrax phylogeography in Russia.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1542-3) contains supplementary material, which is available to authorized users.