The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex that contains numerous closely related lineages, which vary in their ability to cause illness in humans and ...animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is thus essential for informing public health and food safety efforts. However, taxonomic classification of these organisms is challenging. Numerous-often conflicting-taxonomic changes to the group have been proposed over the past two decades, making it difficult to remain up to date. In this review, we discuss the major nomenclatural changes that have accumulated in the B. cereus s.l. taxonomic space prior to 2020, particularly in the genomic sequencing era, and outline the resulting problems. We discuss several contemporary taxonomic frameworks as applied to B. cereus s.l., including (i) phenotypic, (ii) genomic, and (iii) hybrid nomenclatural frameworks, and we discuss the advantages and disadvantages of each. We offer suggestions as to how readers can avoid B. cereus s.l. taxonomic ambiguities, regardless of the nomenclatural framework(s) they choose to employ. Finally, we discuss future directions and open problems in the B. cereus s.l. taxonomic realm, including those that cannot be solved by genomic approaches alone.
Izhodišča: Pomembno vlogo pri prehranski obravnavi imata tako presejanje prehranske ogroženosti kot prehranski pregled, na podlagi katerega lahko postavimo diagnozo motnje prehranjenosti ali s ...prehranjenostjo povezane motnje. Ocena posameznikovega prehranskega stanja, ki jo pridobimo s prehransko obravnavo, je namreč ključna za načrtovanje učinkovite prehranske oskrbe. Za razvoj področja je pomembno, da so vsi termini, ki se uporabljajo pri kliničnem delu, usklajeni. Taki terminološki dokumenti v mednarodnem prostoru že obstajajo, smiselni pa so tudi za slovenščino in naše okolje.
Metode: Prispevek temelji na eksplicitnem terminološkem dogovoru skupine 42 relevantnih slovenskih strokovnjakov iz 19 slovenskih ustanov. Osnova oblikovanja terminoloških smernic je terminološki dokument Evropskega združenja za klinično prehrano in presnovo, pri čemer so bili upoštevani tudi novejši izsledki klinične prehrane.
Rezultati: Predstavljeni so slovenski termini in terminološke definicije s področja klinične prehrane. Opredeljeni so osnovni pojmi s področja prehranske obravnave, ki je praviloma del medicinske obravnave. Predstavljena sta pojma prehranska ogroženost in presejanje prehranske ogroženosti, ob čemer so navedeni tudi različni presejalni testi za presejanje prehranskih motenj in s prehranjenostjo povezanih stanj. Podrobno so opredeljeni tudi prehranski pregled in njegovi sestavni deli.
Zaključki: Tako presejanje prehranske ogroženosti kot prehranski pregled sta bistvena za diagnostično obravnavo v okviru klinične prehrane, poenoteno razumevanje terminologije pa omogoča primerno prepoznavo patoloških stanj pri bolnikih in pripravo ustreznega načrta prehranskih ukrepov.
Izhodišča: Prehransko stanje posameznika uvrščamo med ključne dejavnike njegovega zdravja. Za učinkovito individualno in multidisciplinarno obravnavo stanj, povezanih s prehranskim stanjem ...posameznika, moramo dobro poznati terminologijo klinične prehrane. Ker je klinična prehrana kot medicinska stroka razvita tudi pri nas, v tujini pa so tovrstni terminološki dokumenti že na voljo, želimo tudi v Sloveniji na podlagi konsenza oblikovati enotno terminologijo.
Metode: Prispevek je osnovan na podlagi eksplicitnega terminološkega dogovora. K sodelovanju smo povabili obsežno skupino relevantnih slovenskih strokovnjakov s kliničnih, predkliničnih in drugih področij, ki so povezana z dejavnostjo klinične prehrane v medicini, pri oblikovanju pa je sodeloval tudi terminolog s področja medicine. Kot izhodišče smo izbrali terminološke smernice Evropskega združenja za klinično prehrano in presnovo ter ob njih upoštevali najnovejša strokovna priporočila za posamezne pojme. Avtorji so bili v stiku prek osebnih srečanj in elektronske pošte. Pri končnem oblikovanju konsenza je sodelovalo 42 avtorjev iz 19 slovenskih ustanov.
Rezultati: Predstavljamo temeljne pojme, terminološke definicije in pripadajoče slovenske termine s področja klinične prehrane. Opredelili smo osnovne motnje prehranjenosti – podhranjenost, prekomerno hranjenost, neravnovesje mikrohranil in sindrom ponovnega hranjenja. Poleg tega smo opredelili tudi s prehranjenostjo povezana stanja – sarkopenijo in krhkost. Osnovne pojme smo podprli s kliničnim kontekstom, v katerem nastopajo.
Zaključki: Poenoteno razumevanje osnovnih patoloških stanj, ki jih obravnava klinična prehrana, je izhodišče za nadaljnji razvoj stroke, poleg tega pa je podlaga tudi za prehransko obravnavo in učinkovito prehransko oskrbo.
A facultatively anaerobic, spore-forming Bacillus strain, FSL W8-0169T, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified ...as a Bacillus cereus group species based on a partial sequence of the rpoB gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known B. cereus group species. Pairwise average nucleotide identity blast values obtained for FSL W8-0169T compared to the type strains of existing B. cereus group species were <95 % and predicted DNA-DNA hybridization values were <70 %, suggesting that this strain represents a novel B. cereus group species. We characterized 10 additional strains with the same or closely related rpoB allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C16 : 0 fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169T from other B. cereus group species. FSL W8-0169T is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name Bacillus wiedmannii sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169T (=DSM 102050T=LMG 29269T).
The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. ...alone, whole-genome sequencing (WGS) is not yet routinely employed to characterize
group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the
group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33
group isolates were obtained from human cases (
= 7) and food samples (
= 26). Emetic (
= 30) and diarrheal (
= 3) isolates were most closely related to
(group III) and
(group IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely related and formed a well-supported clade distinct from publicly available emetic group III genomes with an identical sequence type (ST 26). The 30 emetic group III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly available emetic group III ST 26
group genomes by a mean of 301.7-528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain
ATCC 14579. We hypothesize that the outbreak was a single source outbreak caused by emetic group III
belonging to the
species, although food samples were not tested for presence of the emetic toxin cereulide. In addition to showcasing how WGS can be used to characterize
group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by
group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.
Whole-genome sequencing (WGS) is being applied increasingly to Bacillus cereus group species; however, misinterpretation of WGS results may have severe consequences. We report 3 cases, 1 of which was ...an outbreak, in which misinterpretation of B. cereus group WGS results hindered communication within public health and industrial laboratories.
The
group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, ...but it can be particularly challenging due to the high genomic similarity within the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multilocus sequence typing (MLST), (iii)
clade typing, and (iv)
allelic typing to rapidly classify
group isolates using nucleotide sequencing data. BTyper was applied to a set of 662
group genome assemblies to (i) identify anthrax-associated genes in non-
members of the
group, and (ii) identify assemblies from
group strains with emetic potential. With BTyper, the anthrax toxin genes
,
, and
were detected in 8 genomes classified by the NCBI as
that clustered into two distinct groups using
-medoids clustering, while either the
poly-γ-d-glutamate capsule biosynthesis genes
or the hyaluronic acid capsule
gene was detected in an additional 16 assemblies classified as either
or
isolated from clinical, environmental, and food sources. The emetic toxin genes
were detected in 24 assemblies belonging to
clades III and VI that had been isolated from food, clinical, and environmental settings. The command line version of BTyper is available at https://github.com/lmc297/BTyper In addition, BMiner, a companion application for analyzing multiple BTyper output files in aggregate, can be found at https://github.com/lmc297/BMiner
is a foodborne pathogen that is estimated to cause tens of thousands of illnesses each year in the United States alone. Even with molecular methods, it can be difficult to distinguish nonpathogenic
group isolates from their pathogenic counterparts, including the human pathogen
, which is responsible for anthrax, as well as the insect pathogen
By using the variety of typing schemes employed by BTyper, users can rapidly classify, characterize, and assess the virulence potential of any isolate using its nucleotide sequencing data.
The
(
.) species comprises strains of biovar
(
) known for their bioinsecticidal activity, as well as strains with foodborne pathogenic potential.
strains are identified (i) based on the production ...of insecticidal crystal proteins, also known as Bt toxins, or (ii) based on the presence of
,
, and
genes, which encode Bt toxins. Multiple bioinformatics tools have been developed for the detection of crystal protein-encoding genes based on whole-genome sequencing (WGS) data. However, the performance of these tools is yet to be evaluated using phenotypic data. Thus, the goal of this study was to assess the performance of four bioinformatics tools for the detection of crystal protein-encoding genes. The accuracy of sequence-based identification of
was determined in reference to phenotypic microscope-based screening for the production of crystal proteins. A total of 58 diverse
strains isolated from clinical, food, environmental, and commercial biopesticide products underwent WGS. Isolates were examined for crystal protein production using phase contrast microscopy. Crystal protein-encoding genes were detected using BtToxin_Digger, BTyper3, IDOPS (identification of pesticidal sequences), and Cry_processor. Out of 58 isolates, the phenotypic production of crystal proteins was confirmed for 18 isolates. Specificity and sensitivity of
identification based on sequences were 0.85 and 0.94 for BtToxin_Digger, 0.97 and 0.89 for BTyper3, 0.95 and 0.94 for IDOPS, and 0.88 and 1.00 for Cry_processor, respectively. Cry_processor predicted crystal protein production with the highest specificity, and BtToxin_Digger and IDOPS predicted crystal protein production with the highest sensitivity. Three out of four tested bioinformatics tools performed well overall, with IDOPS achieving high sensitivity and specificity (>0.90).IMPORTANCEStrains of
(
.) biovar
(
) are used as organic biopesticides
is differentiated from the foodborne pathogen
. by the production of insecticidal crystal proteins. Thus, reliable genomic identification of biovar
is necessary to ensure food safety and facilitate risk assessment. This study assessed the accuracy of whole-genome sequencing (WGS)-based identification of
compared to phenotypic microscopy-based screening for crystal protein production. Multiple bioinformatics tools were compared to assess their performance in predicting crystal protein production. Among them, identification of pesticidal sequences performed best overall at WGS-based
identification.
The Bacillus cereus group, also known as B. cereus sensu lato (s.l.), is a species complex comprising numerous closely related lineages, which vary in their ability to cause illness in humans and ...animals. The classification of B. cereus s.l. isolates into species-level taxonomic units is essential for facilitating communication between and among microbiologists, clinicians, public health officials, and industry professionals, but is not always straightforward. A recently proposed genomospecies-subspecies-biovar taxonomic framework aims to provide a standardized nomenclature for this species complex but relies heavily on whole-genome sequencing (WGS). It thus is unclear whether popular, low-cost typing methods (e.g., single- and multi-locus sequence typing) remain congruent with the proposed taxonomy. Here, we characterize 2,231 B. cereus s.l. genomes using a combination of in silico (i) average-nucleotide identity (ANI)-based genomospecies assignment, (ii) ANI-based subspecies assignment, (iii) seven-gene multi-locus sequence typing (MLST), (iv) single-locus panC group assignment, (v) rpoB allelic typing, and (vi) virulence factor detection. We show that sequence types (STs) assigned using MLST can be used for genomospecies assignment, and we provide a comprehensive list of ST/genomospecies associations. For panC group assignment, we show that an adjusted, eight-group framework is largely, albeit not perfectly, congruent with the proposed eight-genomospecies taxonomy, as panC alone may not distinguish (i) B. luti from Group II B. mosaicus and (ii) B. paramycoides from Group VI B. mycoides. We additionally provide a list of loci that capture the topology of the whole-genome B. cereus s.l. phylogeny that may be used in future sequence typing efforts. For researchers with access to WGS, MLST, and/or panC data, we showcase how our recently released software, BTyper3 (https://github.com/lmc297/BTyper3), can be used to assign B. cereus s.l. isolates to taxonomic units within this proposed framework with little-to-no user intervention or domain-specific knowledge of B. cereus s.l. taxonomy. We additionally outline a novel method for assigning B. cereus s.l. genomes to pseudo-gene flow units within proposed genomospecies. The results presented here highlight the backward-compatibility and accessibility of the recently proposed genomospecies-subspecies-biovar taxonomic framework and illustrate that WGS is not a necessity for microbiologists who want to use the proposed nomenclature effectively.
In this trial of a recombinant VZV glycoprotein E subunit vaccine with the adjuvant AS01
B
, the risk of herpes zoster and postherpetic neuralgia is shown to be significantly lower in association ...with the vaccine than with placebo among persons 70 years of age or older.
Herpes zoster, or shingles, results from the reactivation of latent varicella–zoster virus (VZV) and typically manifests as a vesicular, painful dermatomal rash.
1
,
2
The most common complication of herpes zoster, postherpetic neuralgia, manifests as chronic neuropathic pain that can greatly limit daily activities.
1
,
3
–
6
The overall incidence of herpes zoster is 2.0 to 4.6 cases per 1000 person-years but increases with age to 10.0 to 12.8 per 1000 person-years among persons 80 years of age or older.
7
–
10
Similarly, the incidence of postherpetic neuralgia also increases with age.
10
–
13
Antiviral therapy can reduce the duration of herpes zoster rash . . .
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