The Genetic Mechanism of Resistance to Antibiotics in Bacillus pumilus 3-19 Strain

Danilova, Iuliia V.; Toymentseva, Anna A.; Baranova, Darya S.; Шарипова, М. Р.

doi:10.1007/s12668-016-0295-9

Cited by 3 publications

(5 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Sixteen papers were analysed in depth. Eleven had methodological problems with regard to the identification procedures (Danilova et al., ; Garcia‐Ramon et al., ; Osman et al., ; Joshi et al., ; Shah et al., ,b; Li et al., ; Tsonis et al., ), source attribution (Allam et al., ; Joshi et al., , Shah et al., ,b) or were not food related (Aydin et al., ).…”

Section: Assessmentmentioning

confidence: 99%

Scientific Opinion on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA (2017–2019)

Koutsoumanis¹,

Allende²,

Álvarez‐Ordóñez³

et al. 2020

EFS2

243

207

View full text Add to dashboard Cite

The qualified presumption of safety (QPS) was developed to provide a safety pre‐assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as ‘qualifications’. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS‐recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.

show abstract

Section: Assessmentmentioning

confidence: 99%

Scientific Opinion on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA (2017–2019)

Koutsoumanis¹,

Allende²,

Álvarez‐Ordóñez³

et al. 2020

EFS2

243

207

View full text Add to dashboard Cite

show abstract

“…The presence of the mutation in codon 56 of the rpsL gene (Lys56Asn), which encodes the S12 ribosomal protein, was confirmed. The mutation occurred at the streptomycin binding site, as previously established, and caused resistance to high concentrations (>100 μg/mL) of streptomycin in the 3-19 strain [ 39 ]. The presence of the mutation in the rpoB gene (Asp185Gly), encoding the RNA polymerase β subunit, was also shown.…”

Section: Resultsmentioning

confidence: 97%

“…Prior to this study, comparative analysis of draft genomes of strain 7P and it’s streptomycin-resistant derivative 3-19 showed that B. pumilus 3-19 became streptomycin-resistant due to a mutation of the S12 protein of 30S ribosomal subunit, RpsL K56N [ 39 ]. Here, further analysis of the genomes of B. pumilus strains 7P and 3-19 was carried out by complete sequencing, correct completion and circularization of genomes.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases

Pudova

Toymentseva

Gogoleva

et al. 2022

Genes

Self Cite

View full text Add to dashboard Cite

Whole-genome sequencing of a soil isolate Bacillus pumilus, strain 7P, and its streptomycin-resistant derivative, B. pumilus 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp, respectively. Annotation of the genome showed 3794 CDS (3204 with predicted function) and 3746 CDS (3173 with predicted function) in the genome of strains 7P and 3-19, respectively. In the genomes of both strains, the prophage regions Bp1 and Bp2 were identified. These include 52 ORF of prophage proteins in the Bp1 region and 38 prophages ORF in the Bp2 region. Interestingly, more than 50% of Bp1 prophage proteins are similar to the proteins of the phi105 in B. subtilis. The DNA region of Bp2 has 15% similarity to the DNA of the Brevibacillus Jimmer phage. Degradome analysis of the genome of both strains revealed 148 proteases of various classes. These include 60 serine proteases, 48 metalloproteases, 26 cysteine proteases, 4 aspartate proteases, 2 asparagine proteases, 3 threonine proteases, and 2 unclassified proteases. Likewise, three inhibitors of proteolytic enzymes were found. Comparative analysis of variants in the genomes of strains 7P and 3-19 showed the presence of 81 nucleotide variants in the genome 3-19. Among them, the missense mutations in the rpsL, comA, spo0F genes and in the upstream region of the srlR gene were revealed. These nucleotide polymorphisms may have affected the streptomycin resistance and overproduction of extracellular hydrolases of the 3-19 strain. Finally, a plasmid DNA was found in strain 7P, which is lost in its derivative, strain 3-19. This plasmid contains five coding DNA sequencing (CDS), two regulatory proteins and three hypothetical proteins.

show abstract

“…on the QPS list (Broussolle et al, 2017;Bzdil et al, 2017), one paper because it does not deal with safety concerns (Lakshmi et al, 2017). The remaining five articles were considered relevant as they described potential safety concerns but were not considered: one paper because of methodological shortcomings on source attribution (Allam et al, 2017), two papers because of methodological shortcomings on strain identification (Danilova et al, 2017;Garcia-Ramon et al, 2018), two papers because they are dealing with intrinsic AMR not associated with any known genetic element able to mobilise resistance genes (Glenwright et al, 2016;Jeong et al, 2017) and with strain specific acquired antimicrobial resistance genes (Jeong et al, 2017). The ELS did not come up with any information that would change the Bacillus species included in the QPS list.…”

Section: Propionibacteriummentioning

confidence: 99%

Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 8: suitability of taxonomic units notified to EFSA until March 2018

Ricci¹,

Allende²,

Bolton³

et al. 2018

EFS2

View full text Add to dashboard Cite

The qualified presumption of safety (QPS) was developed to provide a harmonised generic pre‐evaluation procedure to support safety risk assessments of biological agents performed by EFSA's Scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns identified for a taxonomic unit are, where possible and reasonable in number, reflected by ‘qualifications’ which should be assessed at the strain level by the EFSA's Scientific Panels. During the current assessment, no new information was found that would change the previously recommended QPS taxonomic units and their qualifications. The Panel clarified that the qualification ‘for production purpose only’ implies the absence of viable cells of the production organism in the final product and can also be applied for food and feed products based on microbial biomass. Between September 2017 and March 2018, the QPS notification list was updated with 46 microorganisms from applications for market authorisation. From these, 28 biological agents already had QPS status, 15 were excluded of the QPS exercise from the previous QPS mandate (10 filamentous fungi and one bacteriophage) or from further evaluations within the current mandate (two notifications of Streptomyces spp. and one of Escherichia coli), and one was excluded where confirmatory data for the risk assessment of a plant protection product (PPP) was requested (Pseudomonas sp.). Three taxonomic units were (re)evaluated: Paracoccus carotinifaciens and Paenibacillus lentus had been previously evaluated in 2008 and 2014, respectively, and were now re‐evaluated within this mandate, and Yarrowia lipolytica, which was evaluated for the first time. P. carotinifaciens and P. lentus cannot be granted QPS status due to lack of scientific knowledge. Y. lipolytica is recommended for QPS status, but only for production purpose.

show abstract

The Genetic Mechanism of Resistance to Antibiotics in Bacillus pumilus 3-19 Strain

Cited by 3 publications

References 17 publications

Scientific Opinion on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA (2017–2019)

Scientific Opinion on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA (2017–2019)

Comparative Genome Analysis of Two Bacillus pumilus Strains Producing High Level of Extracellular Hydrolases

Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 8: suitability of taxonomic units notified to EFSA until March 2018

Contact Info

Product

Resources

About