Identification and antibiotic resistance of Bacillus spp. isolates from natural samples

Authors

  • Tanja Berić University of Belgrade, Faculty of Biology, Studentski trg 16, 11000 Belgrade http://orcid.org/0000-0002-4860-2225
  • Marjan Biočanin 1. University of Belgrade, Faculty of Biology, Studentski trg 16, 11000 Belgrade, Serbia; 2. Swiss Federal Institute of Technology in Lausanne, School of Life Sciences, Institute for Bioengineering, Laboratory of Systems Biology and Genetics, Lausanne, Switzerland
  • Slaviša Stanković University of Belgrade, Faculty of Biology, Studentski trg 16, 11000 Belgrade
  • Ivica Dimkić University of Belgrade, Faculty of Biology, Studentski trg 16, 11000 Belgrade
  • Tamara Janakiev University of Belgrade, Faculty of Biology, Studentski trg 16, 11000 Belgrade
  • Đorđe Fira University of Belgrade, Faculty of Biology, Studentski trg 16, 11000 Belgrade
  • Jelena Lozo University of Belgrade, Faculty of Biology, Studentski trg 16, 11000 Belgrade

Keywords:

Bacillus, 5' hypervariable 16S rRNA, antibiotic resistance, erythromycin-resistance (erm)

Abstract

Paper description:

  • Non-pathogenic bacteria from the environment as a source of antibiotic resistance determinants are recognized.
  • Identification of 33 Bacillus spp. isolates from different natural samples from Serbia was performed by sequencing the 5' hypervariable section of the 16S rRNA gene. Eight species was determined. This is the first report about antibiotic resistance of natural isolates of Bacillus spp. from Serbian soil, manure and straw.
  • The potential for the presence and spread of resistance determinants in the soil and similar ecosystems exists, and monitoring of antibiotic resistance genes in nonpathogenic Bacillus strains from the environment is advised.


Abstract: Identification of 33 Bacillus spp. isolates from different environmental samples collected from the territory of Serbia was performed by sequencing of the 5'-hypervariable section of 16S rRNA gene. Eight species were identified within four phylogenetic groups: B. pumilus, B. megaterium, B. subtilis and B. cereus. Determination of their antibiotic resistance was performed using the minimum inhibitory concentration (MIC) assay. We found that just one isolate was resistant to gentamicin, 9 were resistant to clindamycin and all were resistant to vancomycin. Based on the profile of resistance, the isolates were categorized into 4 categories. In silico analysis of the erythromycin-resistance (erm) gene for clindamycin resistance showed their distribution between related and nonrelated soil and human isolates including different species of Bacillus genera. This finding indicates that Bacillus spp. from the environment could be a source of resistance to clindamycin. The potential for the presence and spread of resistance determinants in the soil and similar ecosystems exists so that monitoring of antibiotic resistance genes in nonpathogenic Bacillus strains from the environment is advised.

https://doi.org/10.2298/ABS180302019B

Received: March 2, 2018; Revised: April 10, 2018; Accepted: April 23, 2018; Published online: May 14, 2018

How to cite this article: Berić T, Biočanin M, Stanković S, Dimkić I, Janakiev T, Fira Đ, Lozo J. Identification and antibiotic resistance of Bacillus spp. isolates from natural samples. Arch Biol Sci. 2018;70(3):…

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References

. Logan NA, De Vos P. Genus I. Bacillus Cohn 1872, 174AL. In: De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB, editors. Bergey’s Manual of Systematic Bacteriology. Vol. 3 The Firmicutes. 2nd ed. New York: Springer;2009. p.21-128.

Olsen GJ, Woese CR. Ribosomal RNA: a key to phylogeny. FASEB J. 1993;7:113-23.

Janda MJ, Abbott SL. 16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls. J Clin Microbiol. 2007;45(9):2761-4.

Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E. The Prokaryotes. Vol. 3. Firmicutes. 3rd ed. New York: Springer-Verlag; 2006.

Te Giffel MC, Beumer RR, Klijn N, Wagendorp A, Rombouts FM. Discrimination between Bacillus cereus and Bacillus thuringiensis using specific DNA probes based on variable regions of 16S rRNA. FEMS Microbiol Lett. 1997;146:47-51.

Goto K, Omura T, Hara Y, Sadaie Y. Application of the partial 16S rDNA sequence as an index for rapid identification of species in the genus Bacillus. J Gen Appl Microbiol. 2000;46:1-8.

Cote CK, Welkos SL. Anthrax toxins in context of Bacillus anthracis spores and spore germination. Toxins (Basel). 2015;7:3167-78.

Lacey LA, Grzywacz D, Shapiro-Ilan DI, Frutos R, Brownbridge M, Goettel MS. Insect pathogens as biological control agents: Back to the future. J Invertebr Pathol. 2015;132:1-41.9. Logan NA. Bacillus and relatives in foodborne illness. J Appl Microbiol. 2012;112:417-29.

Bartelt-Hunt S, Snow DD, Damon-Powell T, Miesbach D. Occurrence of steroid hormones and antibiotics in shallow groundwater impacted by livestock waste control facilities. J Contam Hydrol. 2011;123:94-103.

Heuer H, Schmitt H, Smalla K. Antibiotic resistance gene spread due to manure application on agricultural fields. Curr Opin Microbiol. 2011;14:236-43.

D’Costa VM, Griffiths E, Wright GD. Expanding the soil antibiotic resistome: exploring environmental diversity. Curr Opin Microbiol. 2007;10:481-9.

Witte W. Ecological impact of antibiotic use in animals on different complex microflora: Environment. Int J Antimicrob Agents. 2000;14:321-5.

Benveniste R, Davies J. Aminoglycoside antibiotic-inactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria. Proc Natl Acad Sci USA. 1973;70:2276-80.

Canton R. Antibiotic resistance genes from the environment: a perspective through newly identified antibiotic resistance mechanisms in the clinical setting. Clin Microbiol Infect. 2009;15(Suppl. 1):20-5.

Tenson T, Lovmar M, Ehrenberg, M. The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome. J Mol Biol. 2003;330:1005-14.

Leclercq R. Mechanisms of Resistance to Macrolides and Lincosamides: Nature of the Resistance Elements and Their Clinical Implications. Clin Infect Dis. 2002;34(4):482-92.

Eitel Z, Sóki J, Urbán E, Nagy E. The prevalence of antibiotic resistance genes in Bacteroides fragilis group strains isolated in different European countries. Anaerobe. 2013;21:43-9.

Brisson-Noël A, Courvalin P. Nucleotide sequence of gene linA encoding resistance to lincosamides in Staphylococcus haemolyticus. Gene (Amst.). 1986;43(3):247-53.

Dimkić I, Živković S, Berić T, Ivanović Ž, Gavrilović V, Stanković S, Fira Đ. Characterization and evaluation of two Bacillus strains, SS-12.6 and SS-13.1, as potential agents for the control of phytopathogenic bacteria and fungi. Biol Control. 2013;65(3):312-21.

Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673-80.

Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999;41:95-8.

Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schäffer AA. Database indexing for production MegaBLAST searches. Bioinformatics. 2008:24;1757-64.

Altschul S, Gish W, Miller W. Basic Local Alignment Search Tool. J Mol Biol. 1990:215;403-10.

Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725-9.

CLSI. Methods for Antimicrobial Dilution and Disk Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria: Proposed Guideline. CLSI document M45-P. Wayne, PA: Clinical and Laboratory Standards Institute; 2006.

Draganić V, Lozo J, Biočanin M, Dimkić I, Garalejić E, Fira Đ, Stanković S, Berić T. Genotyping of Bacillus spp. isolate collection from natural samples. Genetika. 2017;49(2):445-56.

Wu XY, Walker MJ, Hornitzky M, Chin J. Development of a group-specific PCR combined with ARDRA for the identification of Bacillus species of environmental significance. J Microbiol Methods. 2006;64:107-19.

Helgason E, Økstad OA, Caugant DA, Johansen HA, Fouet A, Mock M, Hegna I, Kolstø AB. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis - one species on the basis of genetic evidence. Appl Environ Microbiol. 2000:66;2627-30.

La Duc MT, Satomi M, Agata N, Venkateswaram K. gyrB as a phylogenetic discrimination for members of the Bacillus anthracis-cereus-thuringiensis group. J Microbial Methods. 2004:56;383-94.

Ogawa H, Fujikura D, Ohnuma M, Ohnishi N, Hang'ombe BM, Mimuro H, Ezaki T, Mweene AS, Higashi H. A Novel Multiplex PCR Discriminates Bacillus anthracis and Its Genetically Related Strains from Other Bacillus cereus Group Species. PLoS One. 2015;10(3):e0122004. 32. Miranda CA, Martins OB, Clementino MM. Species-level identification of Bacillus strains isolates from marine sediments by conventional biochemical, 16S rRNA gene sequencing and inter-tRNA gene sequence lengths analysis. Antonie Van Leeuwenhoek. 2008;93:297-304.

Amin M, Rakhisi Z, Ahmady AZ. Isolation and identification of Bacillus Species from soil and evaluation of their antibacterial properties. Avicenna J Clin Microb Infec. 2015;2:e23233.

Chaves JQ, Pires ES, Vivoni AM. Genetic diversity, antimicrobial resistance and toxigenic profiles of Bacillus cereus isolated from food in Brazil over three decades. Int J Food Microbiol. 2011;147:12-6.

Gigantelli JW, Torres Gomez J, Osato MS. In vitro susceptibilities of ocular Bacillus cereus isolates to clindamycin, gentamicin, and vancomycin alone or in combination. Antimicrob Agents Chemother. 1991;35:201-2.

Aslim B, Saglam N, Beyatli Y. Determination of Some Properties of Bacillus Isolated from Soil. Turk J Biol. 2002;26:41-8.

Martínez JL. Antibiotics and antibiotic resistance genes in natural environments. Science. 2008;321:365-7.

Yim G, Wang HH, Davies J. Antibiotics as signalling molecules. Philos Trans R Soc Lond B Biol Sci. 2007;362:1195-200.

Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol. 2007;5:175-86.

Goh EB, Yim G, Tsui W, McClure J, Surette MG, Davies J. Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics. Proc Natl Acad Sci USA. 2002;99:17025-30.

Riesenfeld CS, Goodman RM, Handelsman J. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol. 2004;6:981-9.

Christie PJ, Korman RZ, Zahler SA, Adsit JC, Dunny GM. Two conjugation systems associated with Streptococcus faecalis plasmid pCF10: Identification of a conjugative transposon that transfers between S. faecalis and Bacillus subtilis. J Bacteriol. 1987;169:2529-36.

Mullany P, Wilks M, Lamb I, Clayton C, Wren B, Tabaqchali S. Genetic analysis of a tetracycline resistance element from Clostridium difficile and its conjugal transfer to and from Bacillus subtilis. J Gen Microbiol. 1990;136:1343-9.

Hächler H, Berger-Bachi B, Kayser FH. Genetic Characterization of a Clostridium difficile Erythromycin- Clindamycin Resistance Determinant That Is Transferable to Staphylococcus aureus. Microbiology. 1987;31:1039-45.

Eitel Z, Sóki J, Urbán E, Nagy E. The prevalence of antibiotic resistance genes in Bacteroides fragilis group strains isolated in different European countries. Anaerobe. 2013;21:43-9.

Nwosu VC. Antibiotic resistance with particular reference to soil microorganisms. Res Microbiol. 2001;152:421-30.

Cooper AJ, Shoemaker NB, Salyers AA. The erythromycin resistance gene from the Bacteroides conjugal transposon Tcr Emr 7853 is nearly identical to ermG from Bacillus sphaericus. Antimicrob Agents Chemother. 1996;40(2):506-8.

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Published

2018-08-20

How to Cite

1.
Berić T, Biočanin M, Stanković S, Dimkić I, Janakiev T, Fira Đorđe, Lozo J. Identification and antibiotic resistance of Bacillus spp. isolates from natural samples. Arch Biol Sci [Internet]. 2018Aug.20 [cited 2024Dec.22];70(3):581-8. Available from: https://serbiosoc.org.rs/arch/index.php/abs/article/view/2720

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Vol. 70 No. 3 (2018)

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