The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air

Premkrishnan, Balakrishnan N. V.; Heinle, Cassie E.; Uchida, Akira; Purbojati, Rikky W.; Kushwaha, Kavita K.; Putra, Alexander; Santhi, Puramadathil Sasi; Khoo, Benjamin W. Y.; Wong, Anthony; Vettath, Vineeth Kodengil; Drautz–Moses, Daniela I.; Junqueira, Ana Carolina M.; Schuster, Stephan C.

doi:10.1186/s13099-021-00399-4

Cited by 13 publications

(9 citation statements)

References 52 publications

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“…The detection of acquired antimicrobial resistance genes by two different programs in conjunction with two different databases resulted in a different number of detected genes. Premkrishnan et al also identified discrepancies in the number of detected antimicrobial resistance genes when using different methods for the detection of ARGs ( 42 ). This finding shows the importance of using multiple ARG detection tools to improve the detection of antimicrobial resistance genes ( 42 ).…”

Section: Resultsmentioning

confidence: 99%

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Comparative Analysis of Bacillus cereus Group Isolates' Resistance Using Disk Diffusion and Broth Microdilution and the Correlation between Antimicrobial Resistance Phenotypes and Genotypes

Mills

Sullivan

Kovač

2022

Appl Environ Microbiol

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Bacillus cereus group isolates (n = 85) were screened for phenotypic resistance to 18 antibiotics using broth microdilution and CLSI M45 Bacillus spp. breakpoints. The susceptibility to 9 out of 18 antibiotics was tested also using disk diffusion method and M100 Staphylococcus spp. breakpoints. Overall, a high prevalence of susceptibility to clinically relevant antibiotics was identified using broth microdilution. For most tested antibiotics, a poor correlation was found between zones of inhibition and minimum inhibitory concentrations. Using the broth microdilution results as a reference for comparison, we identified high error rates and low categorical agreement between results produced using disk diffusion and broth microdilution for the seven tested antibiotics with defined breakpoints. This suggests that disk diffusion should be avoided for AST of B. cereus group isolates. Further, we detected antimicrobial resistance genes with ARIBA and ABRIcate to calculate the sensitivity and specificity for predicting phenotypic resistance determined using broth microdilution based on the presence of detected antimicrobial resistance genes (ARGs). ARGs with poor sensitivity and high specificity included rph (rifampicin, 0%, 93%), mph (erythromycin, 0%, 99%), bla1 (penicillin, 29%, 100), and blaZ (penicillin, 56%, 100%). Compared to penicillin, bla1 and blaZ had lower specificity for the prediction of ampicillin resistance. Overall, none of the ARGs had both high sensitivity and specificity, suggesting the need for further study of the mechanisms underlying phenotypic antimicrobial resistance in the B. cereus group. IMPORTANCE Bacillus cereus group includes human pathogens that can cause severe infections requiring antibiotic treatment. Screening of environmental and food isolates for antimicrobial resistance can provide insight into what antibiotics may be more effective therapeutic options based on the lower prevalence of resistance. Currently, the comparison of antimicrobial susceptibility testing results using the disk diffusion method is complicated by the fact that many previous studies have used Staphylococcus spp. breakpoints to interpret their results. In this study, we compared the results of disk diffusion interpreted using the Staphylococcus spp. breakpoints against the results of broth microdilution interpreted using Bacillus spp. breakpoints. We demonstrated that the disk diffusion method does not produce reliable results for B. cereus group isolates and should therefore be avoided. This study also provides new insight into poor associations between the presence of antimicrobial resistance genes and resistance phenotypes for the B. cereus group.

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Section: Resultsmentioning

confidence: 99%

“…Premkrishnan et al also identified discrepancies in the number of detected antimicrobial resistance genes when using different methods for the detection of ARGs ( 42 ). This finding shows the importance of using multiple ARG detection tools to improve the detection of antimicrobial resistance genes ( 42 ).…”

Section: Resultsmentioning

confidence: 99%

Comparative Analysis of Bacillus cereus Group Isolates' Resistance Using Disk Diffusion and Broth Microdilution and the Correlation between Antimicrobial Resistance Phenotypes and Genotypes

Mills

Sullivan

Kovač

2022

Appl Environ Microbiol

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“…These data support the hypothesis that E. amstelodami is a rich resource for mining novel SMs. Similarly, Bacillus species are common gram-positive bacterium detected in the air ( Premkrishnan et al, 2021 ), water ( Mothe and Sultanpuram, 2016 ), soil ( Lim et al, 2016 ), and fermented foods ( Wu et al, 2022 ). Various Bacillus members (e.g., Bacillus licheniformis , Bacillus subtilis , and Bacillus amyloliquefaciens ) are extensively used in the production of bioinsecticides and antibiotics due to their ability to synthesize a number of metabolites with biological activity ( Xu et al, 2014 ; Yang et al, 2016 ; Shahzad et al, 2017 ; Mohamad et al, 2018 ), indicating a great potential for SM synthesis.…”

Section: Introductionmentioning

confidence: 99%

Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis

Wang

Chen²,

Xin³

et al. 2023

Front. Microbiol.

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As an important source of new drug molecules, secondary metabolites (SMs) produced by microorganisms possess important biological activities, such as antibacterial, anti-inflammatory, and hypoglycemic effects. However, the true potential of microbial synthesis of SMs has not been fully elucidated as the SM gene clusters remain silent under laboratory culture conditions. Herein, we evaluated the inhibitory effect of Staphylococcus aureus by co-culture of Eurotium amstelodami and three Bacillus species, including Bacillus licheniformis, Bacillus subtilis, and Bacillus amyloliquefaciens. In addition, a non-target approach based on ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) was used to detect differences in extracellular and intracellular metabolites. Notably, the co-culture of E. amstelodami and Bacillus spices significantly improved the inhibitory effect against S. aureus, with the combination of E. amstelodami and B. licheniformis showing best performance. Metabolomics data further revealed that the abundant SMs, such as Nummularine B, Lucidenic acid E2, Elatoside G, Aspergillic acid, 4-Hydroxycyclohexylcarboxylic acid, Copaene, and Pipecolic acid were significantly enhanced in co-culture. Intracellularly, the differential metabolites were involved in the metabolism of amino acids, nucleic acids, and glycerophospholipid. Overall, this work demonstrates that the co-culture strategy is beneficial for inducing biosynthesis of active metabolites in E. amstelodami and B. licheniformis.

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“…The detection of acquired antimicrobial resistance genes by two different programs in conjunction with two different databases resulted in a different number of detected genes. Premkrishnan et al also identified discrepancies in the number of detected antimicrobial resistance genes when using different methods for the detection of genes (38). This finding shows the importance of using multiple AMR gene detection tools to improve the detection of antimicrobial resistance genes (38).…”

Section: Resultsmentioning

confidence: 98%

“…Premkrishnan et al also identified discrepancies in the number of detected antimicrobial resistance genes when using different methods for the detection of genes (38). This finding shows the importance of using multiple AMR gene detection tools to improve the detection of antimicrobial resistance genes (38).…”

Section: Resultsmentioning

confidence: 98%

Comparative analysis of Bacillus cereus group isolates’ resistance using disk diffusion and broth microdilution and the correlation between resistance phenotypes and genotypes

Mills¹,

Sullivan²,

Kovač³

2021

Preprint

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A collection of 85 Bacillus cereus group isolates were screened for phenotypic resistance to nine antibiotics using disk diffusion and broth microdilution. The broth microdilution antimicrobial results were interpreted using the CLSI M45 breakpoints for Bacillus spp. Due to the lack of Bacillus spp. disk diffusion breakpoints, the results obtained with the disk diffusion assay were interpreted using the CLSI M100 breakpoints for Staphylococcus spp. We identified significant (p < 0.05) discrepancies in resistance interpretation between the two methods for ampicillin, gentamicin, rifampicin, tetracycline, and trimethoprim/sulfamethoxazole. Antimicrobial resistance genes were detected using unassembled and assembled whole-genome sequences with Ariba and Abricate, respectively, to assess the sensitivity and specificity for predicting phenotypic resistance based on the presence of antimicrobial resistance genes. We found antimicrobial resistance gene presence to be a poor indicator for phenotypic resistance, calling for further investigation of mechanisms underlying antimicrobial resistance in the B. cereus group. Genes with poor sensitivity and/or specificity, as determined based on broth microdilution results included rph (rifampicin, 0%, 95%), mph genes (erythromycin, 0%, 96%), and all van genes (vancomycin, 100%, 35%). However, Bc (ampicillin, 64%, 100%) and tet genes (tetracycline, 67%, 100%) were highly specific, albeit moderately sensitive indicators of phenotypic resistance based on broth microdilution results. Only beta-lactam resistance genes (Bc, BcII, and blaTEM) were highly sensitive (94%) and specific (100%) markers of resistance to ceftriaxone based on the disk diffusion results, providing further evidence of these beta-lactams’ role in nonsusceptibility of Bacillus cereus group isolates to ceftriaxone.IMPORTANCEBacillus cereus group includes human pathogens that can cause severe infections requiring antibiotic treatment. Screening of environmental and food isolates for antimicrobial resistance can provide insight into what antibiotics may be more effective therapeutic options based on the lower prevalence of resistance. Currently, interpretation of antimicrobial susceptibility testing results using the disk diffusion method is complicated by the fact that there are no standard disk diffusion resistance breakpoints defined for Bacillus spp. Hence, the breakpoints for Staphylococcus are often used in research studies. By comparing the results of disk diffusion interpreted using the Staphylococcus spp. breakpoints against broth microdilution interpreted using Bacillus spp. breakpoints, this study demonstrated that disk diffusion results interpretation with Staphylococcus spp. breakpoints are inconsistent. This study also provides new insight into the poor associations between antimicrobial resistance genotypes and phenotypes for the B. cereus group.

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The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air

Cited by 13 publications

References 52 publications

Comparative Analysis of Bacillus cereus Group Isolates' Resistance Using Disk Diffusion and Broth Microdilution and the Correlation between Antimicrobial Resistance Phenotypes and Genotypes

Comparative Analysis of Bacillus cereus Group Isolates' Resistance Using Disk Diffusion and Broth Microdilution and the Correlation between Antimicrobial Resistance Phenotypes and Genotypes

Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis

Comparative analysis of Bacillus cereus group isolates’ resistance using disk diffusion and broth microdilution and the correlation between resistance phenotypes and genotypes

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