Non-Toxin-Producing
            <i>Bacillus cereus</i>
            Strains Belonging to the
            <i>B. anthracis</i>
            Clade Isolated from the International Space Station

Venkateswaran, Kasthuri; Singh, Nitin Kumar; Sielaff, Aleksandra Checinska; Pope, Robert K.; Bergman, Nicholas H.; Tongeren, Sandra P. van; Patel, Niyati; Lawson, Paul A.; Satomi, Masataka; Williamson, Charles H. D.; Sahl, Jason W.; Keim, Paul; Pierson, Duane L.; Perry, Jay L.

doi:10.1128/msystems.00021-17

Cited by 31 publications

(38 citation statements)

References 75 publications

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“…Clade III includes the B. anthracis Ames ancestor and 9 dairy isolates. No genes encoding B. anthracis plasmid-encoded virulence factors (e.g., lef , cya , and capsular genes capABCDE ) were identified in any of the 9 dairy isolates in this clade; it has been shown previously that isolates in clade III ( B. anthracis / B. cereus sensu lato ) do not always carry the anthrax-associated plasmid-encoded virulence factors and hence cannot always be identified as B. anthracis ( 16 , 51 , 52 ).…”

Section: Resultsmentioning

confidence: 91%

Intraclade Variability in Toxin Production and Cytotoxicity of Bacillus cereus Group Type Strains and Dairy-Associated Isolates

Miller

Jian

Beno

et al. 2018

Appl Environ Microbiol

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While some species in the Bacillus cereus group are well-characterized human pathogens (e.g., B. anthracis and B. cereus sensu stricto), the pathogenicity of other species (e.g., B. pseudomycoides) either has not been characterized or is presently not well understood. To provide an updated characterization of the pathogenic potential of species in the B. cereus group, we classified a set of 52 isolates, including 8 type strains and 44 isolates from dairy-associated sources, into 7 phylogenetic clades and characterized them for (i) the presence of toxin genes, (ii) phenotypic characteristics used for identification, and (iii) cytotoxicity to human epithelial cells. Overall, we found that B. cereus toxin genes are broadly distributed but are not consistently present within individual species and/or clades. After growth at 37°C, isolates within a clade did not typically show a consistent cytotoxicity phenotype, except for isolates in clade VI (B. weihenstephanensis/B. mycoides), where none of the isolates were cytotoxic, and isolates in clade I (B. pseudomycoides), which consistently displayed cytotoxic activity. Importantly, our study highlights that B. pseudomycoides is cytotoxic toward human cells. Our results indicate that the detection of toxin genes does not provide a reliable approach to predict the pathogenic potential of B. cereus group isolates, as the presence of toxin genes is not always consistent with cytotoxicity phenotype. Overall, our results suggest that isolates from multiple B. cereus group clades have the potential to cause foodborne illness, although cytotoxicity is not always consistently found among isolates within each clade.IMPORTANCE Despite the importance of the Bacillus cereus group as a foodborne pathogen, characterizations of the pathogenic potential of all B. cereus group species were lacking. We show here that B. pseudomycoides (clade I), which has been considered a harmless environmental microorganism, produces toxins and exhibits a phenotype consistent with the production of pore-forming toxins. Furthermore, B. mycoides/B. weihenstephanensis isolates (clade VI) did not show cytotoxicity when grown at 37°C, despite carrying multiple toxin genes. Overall, we show that the current standard methods to characterize B. cereus group isolates and to detect the presence of toxin genes are not reliable indicators of species, phylogenetic clades, or an isolate's cytotoxic capacity, suggesting that novel methods are still needed for differentiating pathogenic from nonpathogenic species within the B. cereus group. Our results also contribute data that are necessary to facilitate risk assessments and a better understanding as to which B. cereus group species are likely to cause foodborne illness.

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Section: Resultsmentioning

confidence: 91%

Intraclade Variability in Toxin Production and Cytotoxicity of Bacillus cereus Group Type Strains and Dairy-Associated Isolates

Miller

Jian

Beno

et al. 2018

Appl Environ Microbiol

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“…We performed a whole genome SNP analysis comparison of these ten genomes and also included archive reads and assemblies downloaded from EBI-ENA. We used B. cereus strain ISSFR-23F representative of one B. cereus lineage closest to B. anthracis as outgroup to root the tree [31]. Figure 1 shows the relative position of the Yamal and Yakut strains within the global B. anthracis population represented by a selection of 50 strains among 650.…”

Section: Resultsmentioning

confidence: 99%

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

Timofeev

Bahtejeva

Mironova

et al. 2018

Preprint

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20This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on 21 the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common 22 feature of these strains is their conservation in permafrost, from which they were extracted either 23 due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations 24 (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage 2 25 B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In 26 contrast, during the excavations in Yakutia, three genetically different strains were recovered from 27 a single pit. One strain belongs to B.Br.001/002, as the Yamal strains. Despite the remoteness of 28 Yamal from Yakutia, whole genome sequence analysis showed that the B.Br.001/002 strains are 29 very closely related. The two other strains contribute to two different branches of A.Br.008/011, 30 one of the remarkable polytomies described so far in B. anthracis population. The geographic 31 distribution of the strains belonging to this polytomy is suggesting that this polytomy emerged in 32 the thirteenth century, in combination with the constitution of a unified Mongol empire extending 33 from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution 34 in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage 35 except in some geographically isolated areas.36

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“…To demonstrate typical use of a first-pass taxonomic classification program, we analyzed all simulated reads from the B. cereus JEM-2 genome ( Venkateswaran et al, 2017a , 2017b ) with Kraken. The majority of the reads (79%) were assigned to the B. cereus group; of these, only 32% of the reads were assigned more specifically to B. cereus .…”

Section: Resultsmentioning

confidence: 99%

BLAST-based validation of metagenomic sequence assignments

Bazinet¹,

Ondov

Sommer³

et al. 2018

PeerJ

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When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by “first-pass” classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a BLAST-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of BLAST results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available.

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Non-Toxin-Producing Bacillus cereus Strains Belonging to the B. anthracis Clade Isolated from the International Space Station

Cited by 31 publications

References 75 publications

Intraclade Variability in Toxin Production and Cytotoxicity of Bacillus cereus Group Type Strains and Dairy-Associated Isolates

Intraclade Variability in Toxin Production and Cytotoxicity of Bacillus cereus Group Type Strains and Dairy-Associated Isolates

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

BLAST-based validation of metagenomic sequence assignments

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