Rapidly growing mycobacteria (RGM) inhabit soil and water but certain strains represent a health risk for human and animals. Both clinical and soil RGM may be under selection pressure for resistance to tetracycline (TET) antibiotics, since tetracyclines are administrated to humans and farm animals, and TET residues enter soil through manuring; however, resistance to TET and the presence of TET-resistance genes have been assessed only in clinical isolates. We were therefore interested in comparing soil and clinical RGM in terms of TET resistance and the presence of TET-resistance genes. We used 44 RGM from grasslands with different exposure to animal manure, and 38 clinical RGM from Czech hospitals. There was no difference between the clinical and soil isolates in TET resistance, with >50% resistant isolates in both groups. otr(A), otr(B), tet(K), tet(L) or tet(M) were not detected in any soil or clinical isolate. In contrast, most isolates harbored tet(V) and tap, both encoding mycobacterial efflux pumps, including species where these genes have never been evidenced before. The phylogeny of tet(V) correlated with isolates' BOX-PCR profiles, suggesting that this gene evolved along with mycobacterial genomes as a part of the intrinsic resistome. In certain cases, tet(V) and/or tap were found in TET-sensitive isolates, or inversely, were not found in resistant strains. Concluding, intrinsic efflux pumps may be more important for TET resistance than horizontally transferred genes in both soil and clinical RGM. Their simple presence, however, does not attest to resistance, and therefore their diversity, function and expression merit further research.

Biology Centre of the Academy of Sciences of the Czech Republic Institute of Soil Biology České Budějovice Czech Republic

See more in PubMed

Aarestrup FM, Agerso Y, Gerner-Smidt P, Madsen M, Jensen LB. Comparison of antimicrobial resistance phenotypes and resistance genes in Enterococcus faecalis and Enterococcus faecium from humans in the community, broilers, and pigs in Denmark. Diagn Microbiol Infect Dis. 2000;37:127–137. PubMed

Adékambi T, Stein A, Carvajal J, Raoult D, Drancourt M. Description of Mycobacterium conceptionense sp. nov., a Mycobacterium fortuitum group organism isolated from a posttraumatic osteitis inflammation. J Clin Microbiol. 2006;44:1268–1273. PubMed PMC

Agersø Y, Jensen LB, Givskov M, Roberts MC. The identification of a tetracycline resistance gene tet M., on a Tn916-like transposon, in the Bacillus cereus group. FEMS Microbiol Lett. 2002;214:251–256. PubMed

Aínsa JA, Blokpoel MC, Otal I, Young DB, De Smet KA, Martí C. Molecular cloning and characterization of Tap, a putative multidrug efflux pump present in Mycobacterium fortuitum and Mycobacterium tuberculosis. J Bacteriol. 180(1998):5836–5843. PubMed PMC

Alexander TW, Reuter T, Sharma R, Yanke LJ, Topp E, McAllister TA. Longitudinal characterization of resistant Escherichia coli in fecal deposits from cattle fed subtherapeutic levels of antimicrobials. Appl Environ Microbiol. 2009;75:7125–7134. PubMed PMC

Aminov RI, Garrigues-Jeanjean N, Mackie RI. Molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins. Appl Environ Microbiol. 2001;67:22–32. PubMed PMC

Aminov RI, Chee-Sanford JC, Garrigues N, Teferedegne B, Krapac IJ, White BA, Mackie RI. Development, validation, and application of PCR primers for detection of tetracycline efflux genes of Gram-negative bacteria. Appl Environ Microbiol. 2002;68:1786–1793. PubMed PMC

Appelgren P, Farnebo F, Dotevall L, Studahl M, Jönsson B, Petrini B. Late-onset posttraumatic skin and soft-tissue infections caused by rapid-growing mycobacteria in tsunami survivors. Clin. Infect. Dis. 2008;47:e11–6. PubMed

Butler MJ, Friend EJ, Hunter IS, Kaczmarek FS, Sugden DA, Warren M. Molecular cloning of resistance genes and architecture of a linked gene cluster involved in biosynthesis of oxytetracycline by Streptomyces rimosus. Mol Gen Genet. 1989;215:231–238. PubMed

Chee-Sanford JC, Mackie RI, Koike S, Krapac IG, Lin Y-F, Yannarell AC, Maxwell S, Aminov RI. Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste. J Environ Qual. 2009;38:1086–1108. PubMed

Chun J, Lee J-H, Jung Y, Kim M, Kim S, Kim BK, Lim YW. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol. 2007;57:2259–2261. PubMed

Coenye T, Spilker T, Martin A, LiPuma JJ. Comparative assessment of genotyping methods for epidemiologic study of Burkholderia cepacia genomovar III. J Clin Microbiol. 2002;40:3300–3307. PubMed PMC

Davelos Baines AL, Xiao K, Kinkel LL. Lack of correspondence between genetic and phenotypic groups amongst soil-borne streptomycetes. FEMS Microbiol Ecol. 2007;59:564–575. PubMed

D’Costa VM, McGrann KM, Hughes DW, Wright GD. Sampling the antibiotic resistome. Science. 2006;311:374–377. PubMed

De Groote MA, Huitt G. Infections due to rapidly growing mycobacteria. Clin Infect Dis. 2006;42:1756–1763. PubMed

De Groote MA, Pace NR, Fulton K, Falkinham JO., III Relationships between Mycobacterium isolates from patients with pulmonary mycobacterial infection and potting soils. Appl Environ Microbiol. 2006;72:7602–7606. PubMed PMC

De Rossi E, Aínsa JA, Riccardi G. Role of mycobacterial efflux transporters in drug resistance: an unresolved question. FEMS Microbiol Rev. 2005;30:36–52. PubMed

De Rossi E, Arrigo P, Bellinzoni M, Silva PEA, Martín C, Aínsa JA, Guglierame P, Riccardi G. The multidrug transporters belonging to major facilitator superfamily (MFS) in Mycobacterium tuberculosis. Mol Med. 2002;8:714–724. PubMed PMC

De Rossi E, Blokpoel MCJ, Cantoni R, Branzoni M, Riccardi G, Young DB, De Smet KAL, Ciferri O. Molecular cloning and functional analysis of a novel tetracycline resistance determinant, tet(V), from Mycobacterium smegmatis. Antimicrob Agents Chemother. 1998;42:1931–1937. PubMed PMC

Donoghue HD, Overend E, Stanford JL. A longitudinal study of environmental mycobacteria on a farm in south-west England. J Appl Microbiol. 1997;82:57–67. PubMed

Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989;17:7843–7853. PubMed PMC

Esteban J, Martín-de-Hijas NZ, Ortiz A, Kinnari TJ, Bodas Sánchez A, Gadea I, Fernández-Roblas R. Detection of lfrA and tap efflux pump genes among clinical isolates of non-pigmented rapidly growing mycobacteria. Int. J. Antimicrob Agents. 2009;34:454–456. PubMed

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

Han XY, Dé I, Jacobson KL. Rapidly growing mycobacteria: clinical and microbiologic studies of 115 cases. Am J Clin Pathol. 2007;128:612–621. PubMed

Hartmans S, De Bont JAM, Stackebrandt E. The genus Mycobacterium—nonmedical. In: Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, Dworkin M, editors. The Prokaryotes. Vol. 3. Springer-Verlag; New York: 2006. pp. 889–918.

Hindler JF, Munro S. Disk diffusion test. In: Garcia LS, Isenberg HD, editors. Clinical Microbiology Procedures Handbook. 3rd ed. Vol. 2. ASM Press; Washington, DC: 2010. pp. 5.1.1–5.1.13.

Iivanainen E. Isolation of mycobacteria from acidic forest soil samples: comparison of culture methods. J Appl Bacteriol. 1995;78:663–668. PubMed

Jirout J, Tříska J, Růžičková K, Elhottová D. Disturbing impact of outdoor cattle husbandry on community of arbuscular mycorrhizal fungi in upland pasture soil. Commun Soil Sci Plant Anal. 2009;40:736–745.

Lamy B, Marchandin H, Hamitouche K, Laurent F. Mycobacterium setense sp. nov., a Mycobacterium fortuitum-group organism isolated from a patient with soft tissue infection and osteitis. Int J Syst Evol Microbiol. 2008;58:486–490. PubMed

Lane DJ, Pace B, Olsen GJ, Stahl DA, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Nat Acad Sci USA. 1985;82:6955–6959. PubMed PMC

Lanoot B, Vancanneyt M, Dawyndt P, Cnockaert MC, Zhang J, Huang Y, Liu Z, Swings J. BOX-PCR fingerprinting as a powerful tool to reveal synonymous names in the genus Streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentous, S. vinaceus and S. phaeopurpureus. Syst Appl Microbiol. 2004;27:84–92. PubMed

Levy SB, McMurry LM, Barbosa TM, Burdett V, Courvalin P, Hillen W, Roberts MC, Rood JI, Taylor DE. Nomenclature for new tetracycline resistance determinants. Antimicrob Agents Chemother. 1999;43:1523–1524. PubMed PMC

Louw GE, Warren RM, Gey van Pittius NC, McEvoy CRE, Van Helden PD, Victor TC. A balancing act: efflux/ influx in mycobacterial drug resistance. Antimicrob Agents Chemother. 2009;53:3181–3189. PubMed PMC

Martin P, Trieu-Cuot P, Courvalin P. Nucleotide sequence of the tetM tetracycline resistance determinant of the streptococcal conjugative shuttle transposon Tn1545. Nucleic Acids Res. 1986;14:7047–7058. PubMed PMC

Nash KA, Andini N, Zhang Y, Brown-Elliott BA, Wallace RJ., Jr Intrinsic macrolide resistance in rapidly growing mycobacteria. Antimicrob Agents Chemother. 2006;50:3476–3478. PubMed PMC

Nguyen L, Thompson CJ. Foundations of antibiotic resistance in bacterial physiology: the mycobacterial paradigm. Trends Microbiol. 2006;14:304–312. PubMed

Nikolakopoulou TL, Egan S, van Overbeek LS, et al. PCR detection of oxytetracycline resistance genes otr(A) and otr(B) in tetracycline-resistant streptomycete isolates from diverse habitats. Curr Microbiol. 2005;51:211–216. PubMed

Pang Y, Brown BA, Steingrube VA, Wallace RJ, Jr, Roberts MC. Tetracycline resistance determinants in Mycobacterium and Streptomyces species. Antimicrob Agents Chemother. 1994;38:1408–1412. PubMed PMC

Redemaker JLW, Hoste B, Louws FJ, Kersters K, Swings J, Vauterin L, Vauterin P, van Bruijn JF. Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system. Int J Syst Evol Microbiol. 2000;50:665–677. PubMed

Roberts MC. Update on acquired tetracycline resistance genes. FEMS Microbiol Lett. 2005;245:195–203. PubMed

Rossi-Fedele G, Scott W, Spratt D, Gulabivala K, Roberts AP. Incidence and behaviour of Tn916-like elements within tetracycline-resistant bacteria isolated from root canals. Oral Microbiol Immunol. 2006;21:218–222. PubMed

Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol. 1966;16:313–340.

Šula L. WHO co-operative studies on a simple culture technique for the isolation of mycobacteria. 1. Preparation, lyophilization and reconstitution of a simple semi-synthetic concentrated liquid medium; culture technique, growth pattern of different mycobacteria. Bull World Health Organ. 1963;29:589–606. PubMed PMC

Swenson JM, Wallace RJ, Jr, Silcox VA, Thornsberry C. Antimicrobial susceptibility of five subgroups of Mycobacterium fortuitum and Mycobacterium chelonae. Antimicrob Agents Chemother. 1985;28:807–811. PubMed PMC

Swindell SR, Plasterer TN. SEQMAN. Contig assembly. Methods Mol Biol. 1997;70:75–89. PubMed

Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–1599. PubMed

Thioulouse J, Chessel D, Dolédec S, Olivier JM. ADE-4: a multivariate analysis and graphical display software. Stat Comput. 1997;7:75–83.

Tortoli E. Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev. 2003;16:319–354. PubMed PMC

Vaerewijck MJM, Huys G, Palomino JC, Swings J, Portaels F. Mycobacteria in drinking water distribution systems: ecology and significance for human health. FEMS Microbiol Rev. 2005;29:911–934. PubMed

van Ingen J, Boeree MJ, Dekhuijzen PNR, van Soolingen D. Environmental sources of rapid growing nontuberculous mycobacteria causing disease in humans. Clin Microbiol Infect. 2009;15:888–893. PubMed

Versalovic J, Schneider M, de Bruijn FJ, Lupski JR. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol. 1994;5:25–40.

Wallace RJ, Dalovisio JR, Pankey GA. Disk diffusion testing of susceptibility of Mycobacterium fortuitum and Mycobacterium chelonei to antibacterial agents. Antimicrob Agents Chemoter. 1979;16:611–614. PubMed PMC

Yamamura H, Harayma S. Method for selective isolation of mycobacteria using olive oil emulsified with SDS. Biosci Biotechnol Biochem. 2007;71:1553–1556. PubMed

Millipede gut-derived microbes as a potential source of cellulolytic enzymes

Nontuberculous Mycobacteria as Sapronoses: A Review

Evolution of cyclizing 5-aminolevulinate synthases in the biosynthesis of actinomycete secondary metabolites: outcomes for genetic screening techniques

Microbial environment affects innate immunity in two closely related earthworm species Eisenia andrei and Eisenia fetida

See more in PubMed

GENBANK
JF290326, JF290327, JF290328, JF290329, JF290330, JF290331, JF290332, JF290333, JF290334, JF290335, JF290336, JF290337, JF290338, JF290339, JF290340, JF290341, JF290342, JF290343, JF290344, JF290345, JF290346, JF290347, JF290348, JF290349, JF290350, JF290351, JF290352, JF290353, JF290354, JF290355, JF290356, JF290357, JF290358, JF290359, JF290360, JF290361, JF290362, JF290363, JF290364, JF290365, JF304573, JF304574, JF304575, JF304576, JF304577, JF304578, JF304579, JF304580, JF304581, JF304582, JF304583, JF304584, JF304585, JF304586, JF304587, JF304588, JF304589, JF304590, JF304591, JF304592, JF304593, JF304594, JF304595, JF304596, JF304597, JF304598, JF304599, JF304600, JF304601, JF304602, JF304603, JF304604, JF304605, JF304606, JF304607, JF304608, JF304609, JF304610, JQ348076, JQ348077, JQ348078, JQ348079, JQ348080, JQ348081, JQ348082, JQ348083, JQ348084, JQ348085, JQ348086, JQ348087, JQ348088, JQ348089, JQ348090, JQ348091, JQ348092, JQ348093, JQ348094, JQ348095, JQ348096, JQ348097, JQ348098, JQ348099, JQ348100, JQ348101, JQ348102, JQ348103, JQ348104, JQ348105, JQ348106, JQ348107, JQ348108, JQ348109, JQ348110, JQ348111