scholarly journals Putative plasmid prophages of Bacillus cereus sensu lato may hold the key to undiscovered phage diversity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Emma G. Piligrimova ◽  
Olesya A. Kazantseva ◽  
Andrey N. Kazantsev ◽  
Nikita A. Nikulin ◽  
Anna V. Skorynina ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Bacterial Species ◽  
Experimental Studies ◽  
Host Population ◽  
Whole Genome ◽  
Actual Number ◽  
Host Cytoplasm ◽  
Bacterial Viruses ◽  
Biological Entities ◽  
Bacillus Cereus Sensu Lato

AbstractBacteriophages are bacterial viruses and the most abundant biological entities on Earth. Temperate bacteriophages can form prophages stably maintained in the host population: they either integrate into the host genome or replicate as plasmids in the host cytoplasm. As shown, tailed temperate bacteriophages may form circular plasmid prophages in many bacterial species of the taxa Firmicutes, Gammaproteobacteria and Spirochaetes. The actual number of such prophages is thought to be underestimated for two main reasons: first, in bacterial whole genome-sequencing assemblies, they are difficult to distinguish from actual plasmids; second, there is an absence of experimental studies which are vital to confirm their existence. In Firmicutes, such prophages appear to be especially numerous. In the present study, we identified 23 genomes from species of the Bacillus cereus group that were deposited in GenBank as plasmids and may belong to plasmid prophages with little or no homology to known viruses. We consider these putative prophages worth experimental assays since it will broaden our knowledge of phage diversity and suggest that more attention be paid to such molecules in all bacterial sequencing projects as this will help in identifying previously unknown phages.

scholarly journals Cereulide synthetase acquisition and loss events within the evolutionary history of Group III Bacillus cereus sensu lato facilitate the transition between emetic and diarrheal foodborne pathogen

2020 ◽  
Author(s):  
Laura M. Carroll ◽  
Martin Wiedmann
Keyword(s):  
Bacillus Cereus ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Reference Genome ◽  
Foodborne Pathogen ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Group Iii ◽  
History Of ◽  
Bacillus Cereus Sensu Lato

AbstractCereulide-producing members of Bacillus cereus sensu lato (B. cereus s.l.) Group III, also known as “emetic B. cereus”, possess cereulide synthetase, a plasmid-encoded, non-ribosomal peptide synthetase encoded by the ces gene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by “emetic B. cereus” has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize Group III B. cereus s.l. genomes which possess ces (ces-positive) alongside their closely related ces-negative counterparts to (i) assess the genomic diversity encompassed by “emetic B. cereus”, and (ii) identify potential ces loss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly available ces-positive Group III B. cereus s.l. genomes and the ces-negative genomes interspersed among them (n = 150), we show that “emetic B. cereus” is not clonal; rather, multiple lineages within Group III harbor cereulide-producing strains, all of which share a common ancestor incapable of producing cereulide (posterior probability [PP] 0.86-0.89). The ST 26 common ancestor was predicted to have emerged as ces-negative (PP 0.60-0.93) circa 1904 (95% highest posterior density [HPD] interval 1837.1-1957.8) and first acquired the ability to produce cereulide before 1931 (95% HPD 1893.2-1959.0). Three subsequent ces loss events within ST 26 were observed, including among isolates responsible for B. cereus s.l. toxicoinfection (i.e., “diarrheal” illness).Importance“B. cereus” is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., “emetic” syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., “diarrheal” syndrome). Here, we show that “emetic B. cereus” is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some Group III B. cereus s.l. populations to oscillate between diarrheal and emetic foodborne pathogen over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereus s.l. outbreaks, as some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.

scholarly journals Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Sara L. Loo ◽  
Anna Ong ◽  
Wunna Kyaw ◽  
Loïc M. Thibaut ◽  
Ruiting Lan ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Negative Selection ◽  
Bacterial Species ◽  
Host Population ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Chronic Infections ◽  
Snp Data ◽  
Sequencing Studies

ABSTRACT Genomic data reveal single-nucleotide polymorphisms (SNPs) that may carry information about the evolutionary history of bacteria. However, it remains unclear what inferences about selection can be made from genomic SNP data. Bacterial species are often sampled during epidemic outbreaks or within hosts during the course of chronic infections. SNPs obtained from genomic analysis of these data are not necessarily fixed. Treating them as fixed during analysis by using measures such as the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS) may lead to incorrect inferences about the strength and direction of selection. In this study, we consider data from a range of whole-genome sequencing studies of bacterial pathogens and explore patterns of nonsynonymous variation to assess whether evidence of selection can be identified by investigating SNP counts alone across multiple WGS studies. We visualize these SNP data in ways that highlight their relationship to neutral baseline expectations. These neutral expectations are based on a simple model of mutation, from which we simulate SNP accumulation to investigate how SNP counts are distributed under alternative assumptions about positive and negative selection. We compare these patterns with empirical SNP data and illustrate the general difficulty of detecting positive selection from SNP data. Finally, we consider whether SNP counts observed at the between-host population level differ from those observed at the within-host level and find some evidence that suggests that dynamics across these two scales are driven by different underlying processes. IMPORTANCE Identifying selection from SNP data obtained from whole-genome sequencing studies is challenging. Some current measures used to identify and quantify selection acting on genomes rely on fixed differences; thus, these are inappropriate for SNP data where variants are not fixed. With the increase in whole-genome sequencing studies, it is important to consider SNP data in the context of evolutionary processes. How SNPs are counted and analyzed can help in understanding mutation accumulation and trajectories of strains. We developed a tool for identifying possible evidence of selection and for comparative analysis with other SNP data. We propose a model that provides a rule-of-thumb guideline and two new visualization techniques that can be used to interpret and compare SNP data. We quantify the expected proportion of nonsynonymous SNPs in coding regions under neutrality and demonstrate its use in identifying evidence of positive and negative selection from simulations and empirical data.

Sidrophore Production and Phosphate Solubilization by Bacillus cereus and Pseudomonas fluorescens Isolated from Iraqi Soils and Soil Characterization

2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Zaid Raad Abbas ◽  
Aqeel Mohammed Majeed Al-Ezee ◽  
Sawsan H
Keyword(s):  
Bacillus Cereus ◽  
Pseudomonas Fluorescens ◽  
Phosphate Solubilization ◽  
Bacterial Species ◽  
Nutrient Status ◽  
Bacterial Count ◽  
Soil Samples ◽  
Phosphate Solubilizing Bacteria ◽  
Clear Zone ◽  
Zone Formation

This study was conducted to explore the ability of Pseudomonas fluorescens and Bacillus cereus to solubilizing a phosphate in soil for enhancing the planting growth and, its relation with soill characterization. The isolates were identified as P.fluorescens and B. cereus using convential analysis and, its phosphate solubilization ability and sidrophore was shown by the clear zone formation on National Botanical Research Institute���s Phosphate medium. Moreover, Pseudomonas fluorescens isolates (n = 9) and three of B. cereus isolated from agricultural area in Baghdad university, Mustansiriyah university and Diyala bridge. Results displayed that bacterial count were varied in soil samples according to their region, and ranging from 30 to 60 *10 2 CFU/g in Baghdad university soil to 10���20 *10 2 CFU/g in Mustansiriyah university soil, the Baghdad soil macronutrient which included: NH4, NO3, P, and K were, 8.42, 20.53, 19.09, 218.73 respectively, While the physio analysis revealed that the mean of pH was 7.3 and EC was 8.63. on the other hand the micronutrient analysis indicated that the soil samples were included Ca, Fe, Mn, Zn and Cu which gave their mean 5025.9, 8.9, 4.9, 0.5 and 1.5 respectevily. Results revealed that all isolated bacteria (9 isolates of P.fluorescens and three isolates of B. cereus gave ahalo zone which mean their ability to be phosphate solubilizing bacteria at 100%. Results revealed that all isolated bacteria were detected a ability to produce high levels from chelating agents (siderophores)) by P.fluorescens and. B cereus at 100%, when appeared ahalo clear zone. Furthermore, the high levels of phosphate solubilization and siderophore production were grouped in bacterial species isolated from Iraqi soils. might be attributed to many soil factors such as soil nutrient status, soil acidity, water content, organic matter and soil enzyme activities.

scholarly journals Comparison of whole genome sequences of three Bacillus cereus strains reveals the food safety risks of Apostichopus japonicus in China

2021 ◽  
Vol 20 ◽  
pp. 100649
Author(s):  
Xiaoran Zhao ◽  
Ruijun Li ◽  
Huifeng Dang ◽  
Luo Wang ◽  
Songzhe Fu ◽  
...  
Keyword(s):  
Food Safety ◽  
Bacillus Cereus ◽  
Apostichopus Japonicus ◽  
Whole Genome ◽  
Genome Sequences ◽  
Safety Risks

scholarly journals A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kathy E. Raven ◽  
Sophia T. Girgis ◽  
Asha Akram ◽  
Beth Blane ◽  
Danielle Leek ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Dna Extraction ◽  
Genome Sequencing ◽  
Clinical Microbiology ◽  
Bacterial Species ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Library Preparation ◽  
Simultaneous Processing ◽  
Antimicrobial Resistance Gene

AbstractWhole-genome sequencing is likely to become increasingly used by local clinical microbiology laboratories, where sequencing volume is low compared with national reference laboratories. Here, we describe a universal protocol for simultaneous DNA extraction and sequencing of numerous different bacterial species, allowing mixed species sequence runs to meet variable laboratory demand. We assembled test panels representing 20 clinically relevant bacterial species. The DNA extraction process used the QIAamp mini DNA kit, to which different combinations of reagents were added. Thereafter, a common protocol was used for library preparation and sequencing. The addition of lysostaphin, lysozyme or buffer ATL (a tissue lysis buffer) alone did not produce sufficient DNA for library preparation across the species tested. By contrast, lysozyme plus lysostaphin produced sufficient DNA across all 20 species. DNA from 15 of 20 species could be extracted from a 24-h culture plate, while the remainder required 48–72 h. The process demonstrated 100% reproducibility. Sequencing of the resulting DNA was used to recapitulate previous findings for species, outbreak detection, antimicrobial resistance gene detection and capsular type. This single protocol for simultaneous processing and sequencing of multiple bacterial species supports low volume and rapid turnaround time by local clinical microbiology laboratories.

Parasite infection and host dynamics in a naturally fluctuating rodent population

2012 ◽  
Vol 90 (9) ◽  
pp. 1149-1160 ◽  
Author(s):  
J.C. Winternitz ◽  
M.J. Yabsley ◽  
S.M. Altizer
Keyword(s):  
Population Density ◽  
Experimental Studies ◽  
Host Density ◽  
Positive Association ◽  
Population Cycles ◽  
Host Population ◽  
Reproductive Status ◽  
Vole Cycles ◽  
Host Infection ◽  
The Impact

Parasites can both influence and be affected by host population dynamics, and a growing number of case studies support a role for parasites in causing or amplifying host population cycles. In this study, we examined individual and population predictors of gastrointestinal parasitism on wild cyclic montane voles ( Microtus montanus (Peale, 1848)) to determine if evidence was consistent with theory implicating parasites in population cycles. We sampled three sites in central Colorado for the duration of a multiannual cycle and recorded the prevalence and intensity of directly transmitted Eimeria Schneider, 1875 and indirectly transmitted cestodes from a total of 267 voles. We found significant associations between host infection status, individual traits (sex, age, and reproductive status) and population variables (site, trapping period, and population density), including a positive association between host density and cestode prevalence, and a negative association between host density and Eimeria prevalence. Both cestode and Eimeria intensity correlated positively with host age, reproductive status, and population density, but neither parasite was associated with poorer host condition. Our findings suggest that parasites are common in this natural host, but determining their potential to influence montane vole cycles requires future experimental studies and long-term monitoring to determine the fitness consequences of infection and the impact of parasite removal on host dynamics.

scholarly journals Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer

2018 ◽  
Vol 62 (9) ◽  
Author(s):  
Eva Hong ◽  
Ala-Eddine Deghmane ◽  
Muhamed-Kheir Taha
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Sequencing ◽  
Meningococcal Disease ◽  
Bacterial Species ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Content Type ◽  
Beta Lactamases ◽  
Lactamase Gene

ABSTRACT We report the detection in France of a beta-lactamase-producing invasive meningococcal isolate. Whole-genome sequencing of the isolate revealed a ROB-1-type beta-lactamase gene that is frequently encountered in Haemophilus influenzae, suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci, with no reports for more than 2 decades. This report is worrying, as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.

scholarly journals Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland

BMJ Open ◽  
2018 ◽  
Vol 8 (2) ◽  
pp. e021823 ◽  
Author(s):  
Tanja Stadler ◽  
Dominik Meinel ◽  
Lisandra Aguilar-Bultet ◽  
Jana S Huisman ◽  
Ruth Schindler ◽  
...  
Keyword(s):  
Observational Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Mobile Genetic Elements ◽  
University Hospital ◽  
Whole Genome ◽  
Hospital Acquired Infections ◽  
Genetic Elements ◽  
Hospital Acquired

IntroductionExtended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producingEscherichia coliwas increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control.Methods and analysisThis protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment.Ethics and disseminationThis study has been approved by the local ethics committee (Ethikkommission Nordwest-und Zentralschweiz) as a quality control project (Project-ID 2017–00100). The results of this study will be published in peer-reviewed medical journals, communicated to participants, the general public and all relevant stakeholders.

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