Skip to main content

Advertisement

Log in

Antibiotic resistance genes in the Actinobacteria phylum

  • Review
  • Published:
European Journal of Clinical Microbiology & Infectious Diseases Aims and scope Submit manuscript

Abstract

The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Nouioui I, Carro L, García-López M, Meier-Kolthoff J, Woyke T, Kyrpides N et al (2018) Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 9:2007. https://doi.org/10.3389/fmicb.2018.02007

  2. Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF et al (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 71(3):495–548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Hasegawa T, Tanida S, Hatano K, Higashide E, Yoneda M (1983) Motile actinomycetes: Actinosynnema pretiosum subsp. pretiosum sp. nov., subsp. nov., and Actinosynnema pretiosum subsp. auranticum subsp. nov. Int J Syst Evol Microbiol 33(2):314–320

    Google Scholar 

  4. Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-i, Ludwig W et al (2012) Bergey’s manual of systematic bacteriology. Volume 5, The Actinobacteria. Part B. New York; Dordrecht; Heidelberg: Springer

  5. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Klenk H-P et al (2016) Taxonomy, physiology, and natural products of Actinobacteria. Microbiol Mol Biol Rev 80(1):1–43

    Article  PubMed  Google Scholar 

  6. Lanéelle M-A, Launay A, Spina L, Marrakchi H, Laval F, Eynard N et al (2012) A novel mycolic acid species defines two novel genera of the Actinobacteria, Hoyosella and Amycolicicoccus. Microbiology 158(3):843–855

    Article  CAS  PubMed  Google Scholar 

  7. Marrakchi H, Lanéelle M-A, Daffé M (2014) Mycolic acids: structures, biosynthesis, and beyond. Chem Biol 21(1):67–85

    Article  CAS  PubMed  Google Scholar 

  8. Fatahi-Bafghi M (2017) Nocardiosis from 1888 to 2017. Microb Pathog 114:369–384

    Article  PubMed  Google Scholar 

  9. Andalibi F, Fatahi-Bafghi M (2017) Gordonia: isolation and identification in clinical samples and role in biotechnology. Folia Microbiol 62(3):245–252

    Article  CAS  Google Scholar 

  10. Safaei S, Fatahi-Bafghi M, Pouresmaeil O (2018) Role of Tsukamurella species in human infections: the first literature review. New Microbes New Infect 22:6–12

  11. Majidzadeh M, Fatahi-Bafghi M (2018) Current taxonomy of Rhodococcus species and their role in infections. Eur J Clin Microbiol Infect Dis 37(11):2045–2062

    Article  CAS  PubMed  Google Scholar 

  12. Barberis C, Almuzara M, Join-Lambert O, Ramírez MS, Famiglietti A, Vay C (2014) Comparison of the Bruker MALDI-TOF mass spectrometry system and conventional phenotypic methods for identification of Gram-positive rods. PLoS One 9(9):e106303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Buckwalter S, Olson S, Connelly B, Lucas B, Rodning A, Walchak R et al (2015) Evaluation of MALDI-TOF mass spectrometry for the identification of Mycobacterium species, Nocardia species and other aerobic actinomycetes. J Clin Microbiol 54(2):376–384

    Article  PubMed  Google Scholar 

  14. Loucif L, Bendjama E, Gacemi-Kirane D, Rolain J-M (2014) Rapid identification of Streptomyces isolates by MALDI-TOF MS. Microbiol Res 169(12):940–947

    Article  CAS  PubMed  Google Scholar 

  15. Seng P, Abat C, Rolain JM, Colson P, Lagier J-C, Gouriet F et al (2013) Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of MALDI-TOF mass spectrometry. J Clin Microbiol 51(7):2182–2194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Ayeni FA, Okwu M (2016) Comparison of ViTEK 2, MALDI-TOF and partial sequencing of 16S rRNA gene in identification of Brevibacterium species with its antibiotic susceptibility pattern. Nig J Pharm Sci 12(1):69–73

    Google Scholar 

  17. Hu Y, Sun F, Liu W (2018) The heat shock protein 70 gene as a new alternative molecular marker for the taxonomic identification of Streptomyces strains. AMB Express 8(1):144

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Sen A, Daubin V, Abrouk D, Gifford I, Berry AM, Normand P (2014) Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol 64(11):3821–3832

    Article  CAS  PubMed  Google Scholar 

  19. Woese CR (1987) Bacterial evolution. Microbiol Rev 51(2):221–271

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Schäfer J, Jäckel U, Kämpfer P (2010) Development of a new PCR primer system for selective amplification of Actinobacteria. FEMS Microbiol Lett 311(2):103–112

    Article  CAS  PubMed  Google Scholar 

  21. Killer J, Sedláček I, Rada V, Havlik J, Kopečný J (2013) Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis. Int J Syst Evol Microbiol 63(11):4350–4353

    Article  CAS  PubMed  Google Scholar 

  22. Subedi S, Kong F, Jelfs P, Gray TJ, Xiao M, Sintchenko V et al (2016) 16S-23S internal transcribed spacer region PCR and sequencer-based capillary gel electrophoresis has potential as an alternative to high performance liquid chromatography for identification of slowly growing nontuberculous Mycobacteria. PLoS One 11(10):e0164138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Stone BB, Nietupski RM, Breton GL, Weisburg WG (1995) Comparison of Mycobacterium 23S rRNA sequences by high-temperature reverse transcription and PCR. Int J Syst Evol Microbiol 45(4):811–819

    CAS  Google Scholar 

  24. Letek M, Ordonez E, Fernández-Natal I, Gil J, Mateos L (2006) Identification of the emerging skin pathogen Corynebacterium amycolatum using PCR-amplification of the essential divIVA gene as a target. FEMS Microbiol Lett 265(2):256–263

    Article  CAS  PubMed  Google Scholar 

  25. Steingrube VA, Wilson RW, Brown BA, Jost K, Blacklock Z, Gibson JL et al (1997) Rapid identification of clinically significant species and taxa of aerobic actinomycetes, including Actinomadura, Gordona, Nocardia, Rhodococcus, Streptomyces, and Tsukamurella isolates, by DNA amplification and restriction endonuclease analysis. J Clin Microbiol 35(4):817–822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57(1):81–91

    Article  CAS  PubMed  Google Scholar 

  27. Stackebrandt E, Goebel B (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44(4):846–849

    Article  CAS  Google Scholar 

  28. Tindall BJ, Rosselló-Mora R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60(1):249–266

    Article  CAS  PubMed  Google Scholar 

  29. Sangal V, Goodfellow M, Jones AL, Schwalbe EC, Blom J, Hoskisson PA et al (2016) Next-generation systematics: an innovative approach to resolve the structure of complex prokaryotic taxa. Sci Rep 6:38392

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC et al (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52(3):1043–1047

    CAS  PubMed  Google Scholar 

  31. Wayne L, Brenner D, Colwell R, Grimont P, Kandler O, Krichevsky M et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37(4):463–464

    Article  Google Scholar 

  32. Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-Møller N et al (2014) Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol 52(1):139–146

    Article  PubMed  PubMed Central  Google Scholar 

  33. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA et al (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39(suppl_2):W339–WW46

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL et al (2012) Multilocus sequence typing of total genome sequenced bacteria. J Clin Microbiol 50(4):1355–1361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kwong JC, McCallum N, Sintchenko V, Howden BP (2015) Whole genome sequencing in clinical and public health microbiology. Pathology 47(3):199–210

    Article  CAS  PubMed  Google Scholar 

  36. http://www.bacterio.net (LPSN-list of prokaryotic names with standing in nomenclature)

  37. Scholz CF, Kilian M (2016) The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int J Syst Evol Microbiol 66(11):4422–4432

    Article  CAS  PubMed  Google Scholar 

  38. Kaleta EJ, Clark AE, Cherkaoui A, Wysocki VH, Ingram EL, Schrenzel J et al (2011) Comparative analysis of PCR–electrospray ionization/mass spectrometry (MS) and MALDI-TOF/MS for the identification of bacteria and yeast from positive blood culture bottles. Clin Chem 57(7):1057–1067

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Beguelin C, Genne D, Varca A, Tritten ML, Siegrist H, Jaton K et al (2011) Actinobaculum schaalii: clinical observation of 20 cases. Clin Microbiol Infect 17(7):1027–1031

  40. van de Sande WW (2013) Global burden of human mycetoma: a systematic review and meta-analysis. PLoS Negl Trop Dis 7(11):e2550

    Article  PubMed  PubMed Central  Google Scholar 

  41. Li J, Li Y, Zhou Y, Wang C, Wu B, Wan J (2018) Actinomyces and alimentary tract diseases: a review of its biological functions and pathology. Biomed Res Int 2018:8. https://doi.org/10.1155/2018/3820215

  42. Pedersen H, Senneby E, Rasmussen M (2017) Clinical and microbiological features of Actinotignum bacteremia: a retrospective observational study of 57 cases. Eur J Clin Microbiol Infect Dis 36(5):791–796

    Article  CAS  PubMed  Google Scholar 

  43. Sridhar S, Wang AY, Chan JF, Yip CC, Lau SK, Woo PC et al (2015) First report of human infection by Agromyces mediolanus, a gram-positive organism found in soil. J Clin Microbiol 53(10):3377–3379

    Article  PubMed  PubMed Central  Google Scholar 

  44. Brown MK, Forbes BA, Stitley K, Doern CD (2016) Defining the clinical significance of Alloscardovia omnincolens in the urinary tract. J Clin Microbiol 54(6):1552–1556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Chesdachai S, Larbcharoensub N, Chansoon T, Chalermsanyakorn P, Santanirand P, Chotiprasitsakul D et al (2014) Arcanobacterium pyogenes endocarditis: a case report and literature review. Southeast Asian J Trop Med Public Health 45(1):142–148

  46. Bernasconi E, Valsangiacomo C, Peduzzi R, Carota A, Moccetti T, Funke G (2004) Arthrobacter woluwensis subacute infective endocarditis: case report and review of the literature. Clin Microbiol Infect 38(4):27–31

  47. Polatti F (2012) Bacterial vaginosis, Atopobium vaginae and nifuratel. Curr Clin Pharmacol 7(1):36–40

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Butta H, Sardana R, Vaishya R, Singh KN, Mendiratta L (2017) Bifidobacterium: an emerging clinically significant metronidazole-resistant anaerobe of Mmixed pyogenic infections. Cureus 9(4):e1134

    PubMed  PubMed Central  Google Scholar 

  49. Tomida J, Sakamoto D, Sugita T, Fujiwara N, Naka T, Hamada M et al (2011) Branchiibius cervicis sp. nov., a novel species isolated from patients with atopic dermatitis. Syst Appl Microbiol 34(7):503–507

  50. Wauters G, Charlier J, Janssens M, Delmée M (2001) Brevibacterium paucivorans sp. nov., from human clinical specimens. Int J Syst Evol Microbiol 51(5):1703–1707

  51. Salas NM, Prevost M, Hofinger D, Fleming H (2014) Cellulomonas, an emerging pathogen: a case report and review of the literature. Scand J Infect Dis 46(1):73–75

    Article  PubMed  Google Scholar 

  52. Kim JS, Lee TW, Ihm CG, Kim YJ, Moon SM, Lee HJ et al (2015) CAPD peritonitis caused by co-infection with Cellulosimicrobium cellulans (Oerskovia xanthineolytica) and Enterobacter cloacae: a case report and literature review. Intern Med 54(6):627–630

    Article  Google Scholar 

  53. Sangal V, Hoskisson PA (2016) Evolution, epidemiology and diversity of Corynebacterium diphtheriae: new perspectives on an old foe. Infect Genet Evol 43:364–370

    Article  PubMed  Google Scholar 

  54. Liu D (2011) Molecular detection of human bacterial pathogens. CRC press

  55. Corvec S (2018) Clinical and biological features of Cutibacterium (formerly Propionibacterium) avidum, an underrecognized microorganism. Clin Microbiol Rev 31(3):e00064–e00017

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  56. Fernández-Natal I, Sáez-Nieto J, Medina-Pascual M, Albersmeier A, Valdezate S, Guerra-Laso J et al (2013) Dermabacter hominis: a usually daptomycin-resistant gram-positive organism infrequently isolated from human clinical samples. New Microbes New Infect 1(3):35–40

  57. Takahashi N, Shinjoh M, Tomita H, Fujino A, Sugita K, Katohno Y et al (2015) Catheter-related blood stream infection caused by Dermacoccus barathri, representing the first case of Dermacoccus infection in humans. J Infect Chemother 21(8):613–616

    Article  PubMed  Google Scholar 

  58. Fournier P-E, Drancourt M, Raoult D (2017) New laboratory tools for emerging bacterial challenges. Clin Infect Dis 65(suppl_1):S39–S49

    Article  CAS  PubMed  Google Scholar 

  59. Koerner RJ, Goodfellow M, Jones AL (2009) The genus Dietzia: a new home for some known and emerging opportunist pathogens. FEMS Immunol Med Microbiol 55(3):296–305

    Article  CAS  PubMed  Google Scholar 

  60. Gardiner B, Tai A, Kotsanas D, Francis M, Roberts S, Ballard SA et al (2015) Clinical and microbiological characteristics of Eggerthella lenta bacteremia. J Clin Microbiol 53(2):626–635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Balashov SV, Mordechai E, Adelson ME, Gygax SE (2014) Identification, quantification and subtyping of Gardnerella vaginalis in noncultured clinical vaginal samples by quantitative PCR. J Med Microbiol 63(2):162–175

    Article  CAS  PubMed  Google Scholar 

  62. Smith B, Ashley D (2015) Next-generation sequencing of culture negative bronchoalveolar lavage reveals the presence of potentially pathogenic microorganisms https://digitalcommons.hsc.unt.edu/theses/840

  63. Woo PC, Teng JL, Lam KK, Cindy W, Leung K-W, Leung AW et al (2010) First report of Gordonibacter pamelaeae bacteremia. J Clin Microbiol 48(1):319–322

    Article  PubMed  Google Scholar 

  64. Pulcrano G, Balzaretti M, Grosini A, Piacentini V, Poddighe D (2017) First report of Kocuria marina bloodstream infection unrelated to a central venous catheter: a mini-review on an emerging and under-recognized opportunistic pathogen. Infez Med 25(1):71–74

    PubMed  Google Scholar 

  65. Cadenas MB, Maggi RG, Diniz PP, Breitschwerdt KT, Sontakke S, Breithschwerdt EB (2007) Identification of bacteria from clinical samples using Bartonella alpha-Proteobacteria growth medium. J Microbiol Methods 71(2):147–155

    Article  CAS  PubMed  Google Scholar 

  66. Liu J, Jenkins D, Malnick H, Kovac J, Szostek J (2012) Kytococcus schroeteri endocarditis successfully managed with daptomycin: a case report and review of the literature. J Med Microbiol 61(5):750–753

  67. Menezes MF, Sousa MJ, Paixão P, Atouguia J, Negreiros I, Simões M (2018) Lawsonella clevelandensis as the causative agent of a breast abscess. IDCases 12:95–96

  68. Han L, J-e L, Wang X, L-t G, Q-y K, He L et al (2013) Septicemia caused by Leifsonia aquatica in a healthy patient after retinal reattachment surgery. J Clin Microbiol 51(11):3886–3888

    Article  PubMed  PubMed Central  Google Scholar 

  69. Valdivia-Arenas MA, Sood N (2008) Micrococcus bloodstream infection in patients with pulmonary hypertension on epoprostenol. Infect Dis Clin Pract 16(5):285–287

    Article  Google Scholar 

  70. Bahar H, Torun MM, Öçer F, Kocazeybek B (2005) Mobiluncus species in gynaecological and obstetric infections: antimicrobial resistance and prevalence in a Turkish population. Int J Antimicrob Agents 25(3):268–271

    Article  CAS  PubMed  Google Scholar 

  71. Hunter RL Jr (2018) The pathogenesis of tuberculosis: the early infiltrate of post-primary (adult pulmonary) tuberculosis—a distinct disease entity. Front Immunol 9:2108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Beau F, Bollet C, Coton T, Garnotel E, Drancourt M (1999) Molecular identification of a Nocardiopsis dassonvillei blood isolate. J Clin Microbiol 37(10):3366–3368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Lang PM, Jacinto RC, Dal Pizzol TS, Ferreira MBC, Montagner F (2016) Resistance profiles to antimicrobial agents in bacteria isolated from acute endodontic infections: systematic review and meta-analysis. Int J Antimicrob Agents 48(5):467–474

    Article  CAS  PubMed  Google Scholar 

  74. Lee M-R, Huang Y-T, Liao C-H, Chuang T-Y, Wang W-J, Lee S-W et al (2012) Clinical and microbiological characteristics of bacteremia caused by Eggerthella, Paraeggerthella and Eubacterium species at a university hospital in Taiwan, 2001-2010. J Clin Microbiol 50(6):2053–2055

    Article  PubMed  PubMed Central  Google Scholar 

  75. Mantzourani M, Fenlon M, Beighton D (2009) Association between Bifidobacteriaceae and the clinical severity of root caries lesions. Oral Microbiol Immunol 24(1):32–37

    Article  CAS  PubMed  Google Scholar 

  76. Mollerup S, Friis-Nielsen J, Vinner L, Hansen TA, Richter SR, Fridholm H et al (2016) Propionibacterium acnes—disease causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing. J Clin Microbiol 54(4):980–987

  77. Oyaert M, De Baere T, Breyne J, De Laere E, Mariën S, Waets P et al (2013) First case of Pseudoclavibacter bifida bacteremia in an immunocompromised host with chronic obstructive pulmonary disease (COPD). J Clin Microbiol 51(6):1973–1976

    Article  PubMed  PubMed Central  Google Scholar 

  78. Navarro-Martínez A, Corominas N, de Baranda CS, Escudero-Jiménez Á, Galán-Ros J, Sáez-Nieto JA et al (2017) Pseudonocardia carboxydivorans in human cerebrospinal fluid: a case report in a patient with traumatic brain injury. BMC Infect Dis 17(1):472

  79. Asdamongkol N, Eswas C, Wongsuk T, Santanirand P, Wattanatranon D, Kiertiburanakul S (2012) Pseudonocardia oroxyli supperative sialadenitis: the first case report in human infection. Int J Infect Dis 16:e247

  80. Saito M, Shinozaki-Kuwahara N, Tsudukibashi O, Hashizume-Takizawa T, Kobayashi R, Kurita-Ochiai T (2018) Pseudopropionibacterium sp. nov., a novel red-pigmented species isolated from human gingival sulcus. Microbiol Immunol 62(6):388–394

    Article  CAS  PubMed  Google Scholar 

  81. Eissa AE, Faisal M (2014) Clinical outbreaks of bacterial kidney disease (BKD) in hatchery-raised brook trout (Salvelinus fontinalis) (Mitchill, 1814): lessons learned. J Aquac Res Dev. 5:242. https://doi.org/10.4172/2155-9546.1000242

  82. Mahobia N, Chaudhary P, Kamat Y (2013) Rothia prosthetic knee joint infection: report and mini-review. New Microbes New Infect 1(1):2–5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Yassin A (2009) Saccharopolyspora rosea sp. nov., isolated from a patient with bronchial carcinoma. Int J Syst Evol Microbiol 59(5):1148–1152

  84. Downes J, Mantzourani M, Beighton D, Hooper S, Wilson MJ, Nicholson A et al (2011) Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata. Int J Syst Evol Microbiol 61(1):25–29

    Article  CAS  PubMed  Google Scholar 

  85. Butler WR, Sheils CA, Brown-Elliott BA, Charles N, Colin AA, Gant MJ et al (2007) First isolations of Segniliparus rugosus from patients with cystic fibrosis. J Clin Microbiol 45(10):3449–3452

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Chander AM, Kaur G, Nair RG, Dhawan DK, Kochhar R, Mayilraj S et al (2016) Genome sequencing of Serinicoccus chungangensis strain CD08_5 isolated from duodenal mucosa of a celiac disease patient. Genome Announc 4(2):e00043–e00016

    PubMed  PubMed Central  Google Scholar 

  87. Kim K-S, Rowlinson M-C, Bennion R, Liu C, Talan D, Summanen P et al (2010) Characterization of Slackia exigua isolated from human wound infections, including abscesses of intestinal origin. J Clin Microbiol 48(4):1070–1075

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Lagier J-C, Raoult D (2018) Whipple’s disease and Tropheryma whipplei infections: when to suspect them and how to diagnose and treat them. Curr Opin Infect Dis 31(6):463–470

    Article  PubMed  Google Scholar 

  89. Lawrence C, Waseem S, Newsholme W, Klein J (2018) Trueperella bernardiae: an unusual cause of septic thrombophlebitis in an intravenous drug user. New Microbes New Infect 26:89–91

  90. de Frutos M, López-Urrutia L, Aragón R, Vegas AM, Vázquez M, Bouza JME (2018) Turicella otitidis, aportaciones a su posible papel en la etiología de la patología infecciosa del oído. Rev Esp Quimioter 31(3):278–281

  91. Barberis C, Budia M, Palombarani S, Rodriguez CH, Ramírez MS, Arias B et al (2017) Antimicrobial susceptibility of clinical isolates of Actinomyces and related genera reveals an unusual clindamycin resistance among Actinomyces urogenitalis strains. J Glob Antimicrob Resist 8:115–120

    Article  PubMed  Google Scholar 

  92. Yassin AF, Lombardi SJ, Fortunato SJ, McNabb PC, Carr MB, Trabue CH (2010) Perinatal sepsis caused by Williamsia serinedens infection in a 31-year-old pregnant woman. J Clin Microbiol 48(7):2626–2629

    Article  PubMed  PubMed Central  Google Scholar 

  93. Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74(3):417–433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Sheldon AT Jr (2005) Antibiotic resistance: a survival strategy. Clin Lab Sci 18(3):170–180

    PubMed  Google Scholar 

  95. D’Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C et al (2011) Antibiotic resistance is ancient. Nature 477:457–461

    Article  CAS  PubMed  Google Scholar 

  96. Warinner C, Rodrigues JFM, Vyas R, Trachsel C, Shved N, Grossmann J et al (2014) Pathogens and host immunity in the ancient human oral cavity. Nat Genet 46:336–344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Köser CU, Ellington MJ, Peacock SJ (2014) Whole-genome sequencing to control antimicrobial resistance. Trends Genet 30(9):401–407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O et al (2012) Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67(11):2640–2644

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Aarestrup FM, Agerso Y, Gerner–Smidt P, Madsen M, Jensen LB (2000) 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 37(2):127–137

    Article  CAS  PubMed  Google Scholar 

  100. Batchelor M, Hopkins KL, Liebana E, Slickers P, Ehricht R, Mafura M et al (2008) Development of a miniaturised microarray-based assay for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria. Int J Antimicrob Agents 31(5):440–451

    Article  CAS  PubMed  Google Scholar 

  101. Levy SB, Marshall B (2004) Antibacterial resistance worldwide: causes, challenges and responses. Nat Med 10(12s):S122

    Article  CAS  PubMed  Google Scholar 

  102. Andersson DI, Hughes D (2010) Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol 8(4):260–271

    Article  CAS  PubMed  Google Scholar 

  103. Eriksen N, Blanco J (1992) Extended-spectrum (second-and third-generation) cephalosporins. Obstet Gynecol Clin N Am 19(3):461–474

    CAS  Google Scholar 

  104. Courvalin P (2008) Predictable and unpredictable evolution of antibiotic resistance. J Intern Med 264(1):4–16

    Article  CAS  PubMed  Google Scholar 

  105. Jiang X, Ellabaan MMH, Charusanti P, Munck C, Blin K, Tong Y et al (2017) Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat Commun 8:15784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Perry J, Wright G (2013) The antibiotic resistance “mobilome”: searching for the link between environment and clinic. Front Microbiol 4:138

    Article  PubMed  PubMed Central  Google Scholar 

  107. D'costa VM, McGrann KM, Hughes DW, Wright GD (2006) Sampling the antibiotic resistome. Science 311(5759):374–377

    Article  PubMed  Google Scholar 

  108. Nikaido H (2009) Multidrug resistance in bacteria. Annu Rev Biochem 78:119–146

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. https://www.uniprot.org/uniprot/G8SB60

  110. https://www.uniprot.org/uniprot/A0A174EUX3

  111. https://www.uniprot.org/uniprot/A0A0E3KTL6

  112. Van Hoek AH, Mevius D, Guerra B, Mullany P, Roberts AP, Aarts HJ (2011) Acquired antibiotic resistance genes: an overview. Front Microbiol 2:203

    PubMed  PubMed Central  Google Scholar 

  113. Brunton LL (2014) Goodman and Gilman’s manual of pharmacology and therapeutics. McGraw-Hill, New York

    Google Scholar 

  114. Chambers HF, Deck D (2007) Beta-lactam and other cell wall and membrane active antibiotics. Basic and clinical pharmacology, 10th edn. McGraw-Hill Companies Inc, New York, pp 726–744

    Google Scholar 

  115. Carroll KC, Butel JS, Morse SA (2015) Jawetz Melnick & Adelbergs Medical Microbiology 27 E: McGraw-Hill Education / Medical; 27 edition

  116. Walsh C (2003) Antibiotics: actions, origins, resistance: American society for. Microbiology (ASM)

  117. Sköld O (2011) Antibiotics and antibiotic resistance. John Wiley & Sons. https://doi.org/10.1002/9781118075609

  118. Durand GA, Raoult D, Dubourg G (2018) Antibiotic discovery: history, methods and perspectives. Int J Antimicrob Agents 53(4):371–382

    Article  CAS  PubMed  Google Scholar 

  119. Gallagher JC, MacDougall C (2016) Antibiotics simplified, Fourth edn. Jones & Bartlett Learning

  120. Sauvage E, Kerff F, Terrak M, Ayala JA, Charlier P (2008) The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol Rev 32(2):234–258

    Article  CAS  PubMed  Google Scholar 

  121. Abraham EP, Chain E (1940) An enzyme from bacteria able to destroy penicillin. Nature 146:837

    Article  CAS  Google Scholar 

  122. Bush K, Jacoby GA (2010) Updated functional classification of β-lactamases. Antimicrob Agents Chemother 54(3):969–976

    Article  CAS  PubMed  Google Scholar 

  123. Ogawara H (1981) Antibiotic resistance in pathogenic and producing bacteria, with special reference to beta-lactam antibiotics. Microbiol Rev 45(4):591–619

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Nakazawa H, Ogawara H (1982) Mechanisms of acquired penicillin-resistance in Streptomyces cacaoi. J Antibiot 35(12):1683–1691

  125. Carattoli A (2009) Resistance plasmid families in Enterobacteriaceae. Antimicrob Agents Chemother 53(6):2227–2238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Schröder J, Maus I, Meyer K, Wördemann S, Blom J, Jaenicke S et al (2012) Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. BMC Genomics 13:141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Smith T, Wolff KA, Nguyen L (2013) Molecular biology of drug resistance in Mycobacterium tuberculosis. Pathogenesis of Mycobacterium tuberculosis and its interaction with the host organism.Curr Top Microbiol Immunol 374:53-80

  128. Nasiri MJ, Haeili M, Ghazi M, Goudarzi H, Pormohammad A, Imani Fooladi AA et al (2017) New insights in to the intrinsic and acquired drug resistance mechanisms in mycobacteria. Front Microbiol 8:681

    Article  PubMed  PubMed Central  Google Scholar 

  129. Laviad S, Lapidus A, Copeland A, Reddy T, Huntemann M, Pati A et al (2015) High quality draft genome sequence of Leucobacter chironomi strain MM2LB T (DSM 19883 T) isolated from a Chironomus sp. egg mass. Stand Genomic Sci 10(1):21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. http://ardb.cbcb.umd.edu/cgi/ssquery.cgi?db=G&gn=a&ge=1988

  131. Philippon A, Slama P, Dény P, Labia R (2016) A structure-based classification of class A β-lactamases, a broadly diverse family of enzymes. Clin Microbiol Rev 29(1):29–57

    Article  CAS  PubMed  Google Scholar 

  132. Zhang AN, Hou C-J, Li L-G, Zhang T (2018) ARGs-OSP: online searching platform for antibiotic resistance genes distribution in metagenomic database and bacterial whole genome database. bioRxiv 337675

  133. Adesoji AT, Ogunjobi AA (2016) Detection of extended spectrum beta-lactamases resistance genes among bacteria isolated from selected drinking water distribution channels in southwestern Nigeria. Biomed Res Int. 2016:7149295 https://doi.org/10.1155/2016/7149295

  134. Poirel L, Laurent F, Naas T, Labia R, Boiron P, Nordmann P (2001) Molecular and biochemical analysis of AST-1, a class A β-lactamase from Nocardia asteroides sensu stricto. Antimicrob Agents Chemother 45(3):878–882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Leiros H-KS, Kozielski-Stuhrmann S, Kapp U, Terradot L, Leonard GA, McSweeney SM (2004) Structural basis of 5-nitroimidazole antibiotic resistance the crystal structure of NimA from Deinococcus radiodurans. J Biol Chem 279(53):55840–55849

    Article  CAS  PubMed  Google Scholar 

  136. Zhou Q, Wang M, Zhong X, Liu P, Xie X, Wangxiao J et al (2019) Dissemination of resistance genes in duck/fish polyculture ponds in Guangdong Province: correlations between Cu and Zn and antibiotic resistance genes. Environ Sci Pollut Res Int 26(8):8182–8193

    Article  CAS  PubMed  Google Scholar 

  137. Roberts MC (2008) Update on macrolide–lincosamide–streptogramin, ketolide, and oxazolidinone resistance genes. FEMS Microbiol Lett 282(2):147–159

  138. Chopra I, Roberts M (2001) Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev 65(2):232–260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Martel A, Meulenaere V, Devriese L, Decostere A, Haesebrouck F (2003) Macrolide and lincosamide resistance in the gram-positive nasal and tonsillar flora of pigs. Microb Drug Resist 9(3):293–297

    Article  CAS  PubMed  Google Scholar 

  140. Barraud O, Isnard C, Lienhard R, Guérin F, Couvé-Deacon E, Martin C et al (2016) Sulphonamide resistance associated with integron derivative Tn 6326 in Actinotignum schaalii. J Antimicrob Chemother 71(9):2670–2671

    Article  CAS  PubMed  Google Scholar 

  141. Hays C, Lienhard R, Auzou M, Barraud O, Guérin F, Ploy M-C et al (2014) Erm (X)-mediated resistance to macrolides, lincosamides and streptogramins in Actinobaculum schaalii. J Antimicrob Chemother 69(8):2056–2060

    Article  CAS  PubMed  Google Scholar 

  142. Malandain D J-LO, Auzou M,Cattoir V (2016) Antimicrobial susceptibility and molecular mechanisms of acquired resistance in Actinotignum (Actinobaculum) schaalii isolated in patients with hidradenitis suppurativa ECCMID

  143. Li D, Yu T, Zhang Y, Yang M, Li Z, Liu M et al (2010) Antibiotic resistance characteristics of environmental bacteria from an oxytetracycline production wastewater treatment plant and the receiving river. Appl Environ Microbiol 76(11):3444–3451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. https://www.genome.jp/kegg/annotation/br01555.html

  145. Khan S, Knapp CW, Beattie TK (2016) Antibiotic resistant bacteria found in municipal drinking water. Environ Process 3(3):541–552

    Article  CAS  Google Scholar 

  146. Xu L, Shi W, Zeng X-C, Yang Y, Zhou L, Mu Y et al (2017) Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin. China Stand Genomic Sci 12(1):11

    Article  CAS  PubMed  Google Scholar 

  147. Wang N, Hang X, Zhang M, Liu X, Yang H (2017) Analysis of newly detected tetracycline resistance genes and their flanking sequences in human intestinal bifidobacteria. Sci Rep 7(1):6267

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. van Hoek AH, Mayrhofer S, Domig KJ, Aarts HJ (2008) Resistance determinant erm (X) is borne by transposon Tn5432 in Bifidobacterium thermophilum and Bifidobacterium animalis subsp. lactis. Int J Antimicrob Agents 31(6):544–548

  149. Ammor MS, Flórez AB, Van Hoek AH, Clara G, Aarts HJ, Margolles A et al (2008) Molecular characterization of intrinsic and acquired antibiotic resistance in lactic acid bacteria and bifidobacteria. J Mol Microbiol Biotechnol 14(1–3):6–15

    Article  CAS  PubMed  Google Scholar 

  150. Wang N, Hang X, Zhang M, Peng X, Yang H (2017) New genetic environments of the macrolide-lincosamide-streptogramin resistance determinant erm (X) and their influence on potential horizontal transferability in bifidobacteria. Int J Antimicrob Agents 50(4):572–580

    Article  CAS  PubMed  Google Scholar 

  151. https://www.uniprot.org/uniprot/B3DS16

  152. Rahman MH, Sakamoto KQ, Nonaka L, Suzuki S (2008) Occurrence and diversity of the tetracycline resistance gene tet(M) in enteric bacteria of Antarctic Adelie penguins. J Antimicrob Chemother 62(3):627–628

    Article  CAS  PubMed  Google Scholar 

  153. Tak EJ, Kim PS, Hyun D-W, Kim HS, Lee J-Y, Kang W et al (2018) Phenotypic and genomic properties of Brachybacterium vulturis sp. nov. and Brachybacterium avium sp. nov. Front Microbiol 9:1809

    Article  PubMed  PubMed Central  Google Scholar 

  154. Taft DH, Liu J, Maldonado-Gomez MX, Akre S, Huda MN, Ahmad S, et al (2018) Bifidobacterial dominance of the gut in early life and acquisition of antimicrobial resistance. mSphere 3(5):e00441–18

  155. Kenzaka T, Ishimoto Y, Tani K (2017) Draft genome sequence of multidrug-resistant Cellulosimicrobium sp. strain KWT-B, isolated from feces of Hirundo rustica. Genome Announc 5(28):e00641–e00617

    Article  PubMed  PubMed Central  Google Scholar 

  156. Zhang N, Lu Z, Ma Y (2017) Draft genome sequences of three multidrug-resistant Cutibacterium (formerly Propionibacterium) acnes strains isolated from acne patients, China. J Glob Antimicrob Resist 11:114–115

    Article  PubMed  Google Scholar 

  157. Oprica C, Löfmark S, Lund B, Edlund C, Emtestam L, Nord CE (2005) Genetic basis of resistance in Propionibacterium acnes strains isolated from diverse types of infection in different European countries. Anaerobe 11(3):137–143

    Article  CAS  PubMed  Google Scholar 

  158. Stinear TP, Olden DC, Johnson PD, Davies JK, Grayson ML (2001) Enterococcal vanB resistance locus in anaerobic bacteria in human faeces. Lancet 357(9259):855–856

    Article  CAS  PubMed  Google Scholar 

  159. Ballard SA, Pertile KK, Lim M, Johnson PD, Grayson ML (2005) Molecular characterization of vanB elements in naturally occurring gut anaerobes. Antimicrob Agents Chemother 49(5):1688–1694

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Sanakal RD, Kaliwal BB (2011) Vancomycin resistance genes in various organisms-an Insilico study. Bioinformatics 5:111–129

    Google Scholar 

  161. Seo JY, Kim P-W, Lee J-H, Song J-H, Peck K-R, Chung D-R et al (2011) Evaluation of PCR-based screening for vancomycin-resistant enterococci compared with a chromogenic agar-based culture method. J Med Microbiol 60(7):945–949

    Article  PubMed  Google Scholar 

  162. Domingo M-C, Huletsky A, Bernal A, Giroux R, Boudreau D, Picard F et al (2005) Characterization of a Tn 5382-like transposon containing the vanB 2 gene cluster in a Clostridium strain isolated from human faeces. Antimicrob Chemother 55(4):466–474

  163. https://www.genome.jp/kegg-bin/show_pathway?aym01501

  164. https://www.uniprot.org/uniprot/M5A2P3

  165. https://www.genome.jp/dbget-bin/www_bget?ica:Intca_0490

  166. https://www.genome.jp/kegg-bin/show_pathway?org_name=ica&mapno=01502&mapscale=&show_description=hide

  167. http://www.bio.nite.go.jp/mifup/microbes/view/function_potential/56

  168. Chander AM, Kochhar R, Dhawan DK, Bhadada SK, Mayilraj S (2018) Genome sequence and comparative genomic analysis of a clinically important strain CD11-4 of Janibacter melonis isolated from celiac disease patient. Gut Pathog 10(1):2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Hwang JY, Kim SH, Oh HR, Cho Y-J, Chun J, Chung YR et al (2014) Draft genome sequence of Kitasatospora cheerisanensis KCTC 2395, which produces plecomacrolide against phytopathogenic fungi. Genome Announc 2(3):e00604–e00614

    Article  PubMed  PubMed Central  Google Scholar 

  170. Takarada H, Sekine M, Kosugi H, Matsuo Y, Fujisawa T, Omata S et al (2008) Complete genome sequence of the soil actinomycete Kocuria rhizophila. J Bacteriol 190(12):4139–4146

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Whon TW, Kim HS, Bae J-W (2018) Complete genome sequence of Kocuria rhizophila BT304, isolated from the small intestine of castrated beef cattle. Gut Pathog 10(1):42

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. http://www.bio.nite.go.jp/mifup/microbes/view/nbrc/103217

  173. Liebl W, Kloos WE, Ludwig W (2002) Plasmid-borne macrolide resistance in Micrococcus luteusa. Microbiology 148(8):2479–2487

    Article  CAS  PubMed  Google Scholar 

  174. McGuire J, Bunch R, Anderson R, Boaz H, Flynn E, Powell H et al (1952) Ilotycin, a new antibiotic. Antibiot Chemother (Northfield, Ill) 2(6):281–283

    CAS  Google Scholar 

  175. Brown CT, Sharon I, Thomas BC, Castelle CJ, Morowitz MJ, Banfield JF (2013) Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome 1(1):30

    Article  PubMed  PubMed Central  Google Scholar 

  176. Roberts MC (1995) Distribution of tetracycline and macrolide-lincosamide-streptogramin B resistance genes in anaerobic bacteria. Clin Infect Dis:S367–S3S9

  177. https://ardb.cbcb.umd.edu/cgi/ssquery.cgi?db=O&gn=a&sp=383372

  178. https://www.uniprot.org/uniprot/A5UTP3

  179. Jacoby GA, Hooper DC (2013) Phylogenetic analysis of chromosomally determined qnr and related proteins. Antimicrob Agents Chemother 57(4):1930–1934

  180. https://www.uniprot.org/uniprot/A4FAX1

  181. Ruppé E, Lazarevic V, Girard M, Mouton W, Ferry T, Laurent F et al (2017) Clinical metagenomics of bone and joint infections: a proof of concept study. Sci Rep 7(1):7718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. https://www.genome.jp/kegg-bin/show_pathway?sti01501

  183. Binda E, Cappelletti P, Marinelli F, Marcone G (2018) Specificity of induction of glycopeptide antibiotic resistance in the producing actinomycetes. Antibiotics 7(2):36

    Article  CAS  PubMed Central  Google Scholar 

  184. Hong HJ, Hutchings MI, Neu JM, Wright GD, Paget MS, Buttner MJ (2004) Characterization of an inducible vancomycin resistance system in Streptomyces coelicolor reveals a novel gene (vanK) required for drug resistance. Mol Microbiol 52(4):1107–1121

  185. Hu H, Zhang Q, Ochi K (2002) Activation of antibiotic biosynthesis by specified mutations in the rpoB gene (encoding the RNA polymerase β subunit) of Streptomyces lividans. J Bacteriol 184(14):3984–3991

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. https://www.uniprot.org/uniprot/A0A089X3A0

  187. Kaur P, Peterson E (2018) Antibiotic resistance mechanisms in bacteria: relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front Microbiol 9:2928

    Article  PubMed  PubMed Central  Google Scholar 

  188. Koteva K, Cox G, Kelso JK, Surette MD, Zubyk HL, Ejim L et al (2018) Rox, a rifamycin resistance enzyme with an unprecedented mechanism of action. Cell Chem Biol 25(4):403–412

    Article  CAS  PubMed  Google Scholar 

  189. https://www.uniprot.org/uniprot/Q1RQK2

  190. Wang N, Yang X, Jiao S, Zhang J, Ye B, Gao S (2014) Sulfonamide-resistant bacteria and their resistance genes in soils fertilized with manures from Jiangsu Province, Southeastern China. PLoS One 9(11):e112626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Nardelli M, Scalzo PM, Ramírez MS, Quiroga MP, Cassini MH, Centrón D (2012) Class 1 integrons in environments with different degrees of urbanization. PLoS One 7(6):e39223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Park Y-J, Yu JK, Kim S-I, Lee K, Arakawa Y (2009) Accumulation of plasmid-mediated fluoroquinolone resistance genes, qepA and qnrS1, in Enterobacter aerogenes co-producing RmtB and class A β-lactamase LAP-1. Ann Clin Lab Sci 39(1):55–59

    CAS  PubMed  Google Scholar 

  193. https://www.uniprot.org/uniprot/Q59830

  194. https://www.uniprot.org/uniprot/P50074

  195. https://www.uniprot.org/uniprot/P81173

  196. Spanogiannopoulos P, Thaker M, Koteva K, Waglechner N, Wright GD (2012) Characterization of a rifampin inactivating glycosyltransferase from a screen of environmental Actinomycetes. Antimicrob Agents Chemother 56:5061–5069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. http://www.bio.nite.go.jp/mifup/microbes/view/nbrc/15933

  198. Masselot F, Boulos A, Maurin M, Rolain J, Raoult D (2003) Molecular evaluation of antibiotic susceptibility: Tropheryma whipplei paradigm. Antimicrob Agents Chemother 47(5):1658–1664

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Zhao K-L, Liu Y, Zhang X-Y, Wang H-N, Yue B-S (2011) Detection and characterization of antibiotic-resistance genes in Arcanobacterium pyogenes strains from abscesses of forest musk deer. J Med Microbiol 60(12):1820–1826

    Article  CAS  PubMed  Google Scholar 

  200. Dong W-L, Kong L-C, Wang Y, Gou C-L, Xu B, GAO Y-H (2017) Aminoglycoside resistance of Trueperella pyogenes isolated from pigs in China. J Vet Med Sci 79(11):1836–1839

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Feßler AT, Schwarz S (2017) Antimicrobial resistance in Corynebacterium spp., Arcanobacterium spp., and Trueperella pyogenes. Microbiol Spectr 5(6)

  202. Tamai IA, Mohammadzadeh A, Salehi TZ, Mahmoodi P (2018) Genomic characterisation, detection of genes encoding virulence factors and evaluation of antibiotic resistance of Trueperella pyogenes isolated from cattle with clinical metritis. Antonie Van Leeuwenhoek 111(12):2441–2453

    Article  CAS  Google Scholar 

  203. Goldstone RJ, Amos M, Talbot R, Schuberth H-J, Sandra O, Sheldon IM et al (2014) Draft genome sequence of Trueperella pyogenes, isolated from the infected uterus of a postpartum cow with metritis. Genome Announc 2(2):e00194–e00114

    Article  PubMed  PubMed Central  Google Scholar 

  204. Billington SJ, Jost BH (2006) Multiple genetic elements carry the tetracycline resistance gene tet (W) in the animal pathogen Arcanobacterium pyogenes. Antimicrob Agents Chemother 50(11):3580–3587

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  205. Jost BH, Field AC, Trinh HT, Songer JG, Billington SJ (2003) Tylosin resistance in Arcanobacterium pyogenes is encoded by an Erm X determinant. Antimicrob Agents Chemother 47(11):3519–3524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Boumghar-Bourtchai L, Chardon H, Malbruny B, Mezghani S, Leclercq R, Dhalluin A (2009) Resistance to macrolides by ribosomal mutation in clinical isolates of Turicella otitidis. Int J Antimicrob Agents 34(3):274–277

    Article  CAS  PubMed  Google Scholar 

  207. Yang H, Byelashov OA, Geornaras I, Goodridge L, Nightingale KK, Belk KE, et al. (n.d.) Screening for antibiotic resistance genes and class 1 integrons in commensal bacteria in agricultural and other environments and their potential transfer to pathogenic bacteria

  208. Paul C, Bayrychenko Z, Junier T, Filippidou S, Beck K, Bueche M et al (2018) Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater. PeerJ 6:e4989

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Adesoji AT, Ogunjobi AA, Olatoye IO, Douglas DR (2015) Prevalence of tetracycline resistance genes among multi-drug resistant bacteria from selected water distribution systems in southwestern Nigeria. Ann Clin Microbiol Antimicrob 14:35

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Adesoji AT, Ogunjobi AA, Olatoye IO (2017) Characterization of integrons and sulfonamide resistance genes among bacteria from drinking water distribution systems in southwestern Nigeria. Chemotherapy 62(1):34–42

  211. http://ardb.cbcb.umd.edu/cgi/ssquery.cgi?db=O&gn=a&sp=269800

  212. Serafini F, Bottacini F, Viappiani A, Baruffini E, Turroni F, Foroni E et al (2011) Insights into physiological and genetic mupirocin susceptibility in bifidobacteria. Appl Environ Microbiol 77(9):3141–3146

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  213. https://www.uniprot.org/uniprot/A0A2R4FVI6

  214. https://www.uniprot.org/uniprot/E6SA16

  215. Szemraj M, Kwaszewska A, Szewczyk EM (2018) New gene responsible for resistance of clinical Corynebacteria to macrolide, lincosamide and streptogramin B. Pol J Microbiol 67(2):237–240

  216. https://www.uniprot.org/uniprot/Q79RV0

  217. https://ardb.cbcb.umd.edu/cgi/ssquery.cgi?db=S&gn=a&sp=1717

  218. Barraud O, Badell E, Denis F, Guiso N, Ploy M-C (2011) Antimicrobial drug resistance in Corynebacterium diphtheriae mitis. Emerg Infect Dis 17(11):2078–2080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  219. https://www.ncbi.nlm.nih.gov/protein/WP_076773831.1

  220. https://www.ncbi.nlm.nih.gov/protein/CAI40608220.

  221. Ekizoğlu M, Koike S, Krapac I, Sultan MN, Mackie R (2013) Phenotypic and genotypic characterization of antibiotic-resistant soil and manure bacteria adjacent to swine production facilities. Turk J Vet Anim Sci 37(5):504–511

    Article  Google Scholar 

  222. Kim H-J, Kim Y, Lee M-S, Lee H-S (2001) Gene ImrB of Corynebacterium glutamicum confers efflux-mediated resistance to lincomycin. Mol Cell 12(1):112–116

  223. Tauch A, Götker S, Pühler A, Kalinowski J, Thierbach G (2002) The 27.8-kb R-plasmid pTET3 from Corynebacterium glutamicum encodes the aminoglycoside adenyltransferase gene cassette aadA9 and the regulated tetracycline efflux system Tet33 flanked by active copies of the widespread insertion sequence IS6100. Plasmid 48(2):117–129

    Article  CAS  PubMed  Google Scholar 

  224. http://tagc.univ-mrs.fr/rsa-tools/data/genomes/Corynebacterium_glutamicum_ATCC_13032_uid61611/genome/feature.tab

  225. https://www.uniprot.org/uniprot/Q9X544

  226. Isabel F-N HM, Martin-Quijada N, Temprano M A, Marrodan-Ciordia T, Rodriguez-Lazaro D, Soriano F (2017) Genetic elements associated with antimicrobial resistance among Corynebacterium urealyticum isolates from a University Hospital in León (Spain). The congress of ESCMID(P0720). (22-25 April)

  227. Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A et al (2008) The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing. J Biotechnol 136(1–2):11–21

    Article  CAS  PubMed  Google Scholar 

  228. https://ardb.cbcb.umd.edu/cgi/ssquery.cgi?db=504474

  229. Soriano F, Tauch A (2008) Microbiological and clinical features of Corynebacterium urealyticum: urinary tract stones and genomics as the Rosetta Stone. Clin Microbiol Infect 14(7):632–643

    Article  CAS  PubMed  Google Scholar 

  230. Alibi S, Ferjani A, Boukadida J, Cano ME, Fernández-Martínez M, Martínez-Martínez L et al (2017) Occurrence of Corynebacterium striatum as an emerging antibiotic-resistant nosocomial pathogen in a Tunisian hospital. Sci Rep 7(1):9704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  231. Ramos JN, Rodrigues IdS, Baio PVP, Veras JFC, Ramos RTJ, Pacheco LG, et al (2018) Genome sequence of a multidrug-resistant Corynebacterium striatum isolated from bloodstream infection from a nosocomial outbreak in Rio de Janeiro, Brazil. Mem Inst Oswaldo Cruz 113(9):e180051. https://doi.org/10.1590/0074-02760180051

  232. Li W, Zhang Z (2013) Implication of ermCX gene of Corynebacterium striatum in macrolide resistance in Beijing, China. Bangladesh J Pharmacol 8(1):54–57

    Google Scholar 

  233. Nudel K, Zhao X, Basu S, Dong X, Hoffmann M, Feldgarden M et al (2018) Genomics of Corynebacterium striatum, an emerging multidrug-resistant pathogen of immunocompromised patients. Clin Microbiol Infect 24(9):1016.e7–1016.e13

  234. Tauch A, Zheng Z, Pühler A, Kalinowski J (1998) Corynebacterium striatum chloramphenicol resistance transposon Tn5564: genetic organization and transposition in Corynebacterium glutamicum. Plasmid 40(2):126–139

  235. Rosato AE, Lee BS, Nash KA (2001) Inducible Macrolide Resistance inCorynebacterium jeikeium. Antimicrob Agents Chemother 45(7):1982–1989

  236. Brown-Elliott BA, Nash KA, Wallace RJ (2012) Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. Clin Microbiol Rev 25(3):545–582

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  237. Maurer FP, Castelberg C, Quiblier C, Böttger EC, Somoskövi A (2014) Erm (41)-dependent inducible resistance to azithromycin and clarithromycin in clinical isolates of Mycobacterium abscessus. J Antimicrob Chemother 69(6):1559–1563

    Article  CAS  PubMed  Google Scholar 

  238. Esteban J, Martín-de-Hijas N, García-Almeida D, Bodas-Sánchez Á, Gadea I, Fernández-Roblas R (2009) Prevalence of erm methylase genes in clinical isolates of non-pigmented, rapidly growing mycobacteria. Clin Microbiol Infect 15(10):919–923

    Article  CAS  PubMed  Google Scholar 

  239. van Ingen J, Boeree MJ, van Soolingen D, Mouton JW (2012) Resistance mechanisms and drug susceptibility testing of nontuberculous mycobacteria. Drug Resist Updat 15(3):149–161

    Article  CAS  PubMed  Google Scholar 

  240. Soroka D, Dubée V, Soulier-Escrihuela O, Cuinet G, Hugonnet J-E, Gutmann L et al (2013) Characterization of broad-spectrum Mycobacterium abscessus class A β-lactamase. J Antimicrob Chemother 69(3):691–696

    Article  CAS  PubMed  Google Scholar 

  241. Unissa AN, Hanna LE (2017) Molecular mechanisms of action, resistance, detection to the first-line anti tuberculosis drugs: rifampicin and pyrazinamide in the post whole genome sequencing era. Tuberculosis 105:96–107

    Article  CAS  Google Scholar 

  242. Campus S (2010) jefA (Rv2459), a drug efflux gene in Mycobacterium tuberculosis confers resistance to isoniazid & ethambutol. Indian J Med Res 132:176–188

    Google Scholar 

  243. Rossi ED, Aínsa JA, Riccardi G (2006) Role of mycobacterial efflux transporters in drug resistance: an unresolved question. FEMS Microbiol Rev 30(1):36–52

    Article  CAS  PubMed  Google Scholar 

  244. Bhembe NL, Nwodo UU, Govender S, Hayes C, Ndip RN, Okoh AI et al (2014) Molecular detection and characterization of resistant genes in Mycobacterium tuberculosis complex from DNA isolated from tuberculosis patients in the Eastern Cape province South Africa. BMC Infect Dis 14(1):479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  245. Dookie N, Rambaran S, Padayatchi N, Mahomed S, Naidoo K (2018) Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care. J Antimicrob Chemother 73(5):1138–1151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  246. Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P et al (2016) Genetic determinants of drug resistance in Mycobacterium tuberculosis and their diagnostic value. Am J Respir Crit Care Med 194(5):621–630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  247. Farhat MR, Freschi L, Calderon R, Ioerger T, Snyder M, Meehan CJ, et al (2018) Genome wide association with quantitative resistance phenotypes in Mycobacterium tuberculosis reveals novel resistance genes and regulatory regions. bioRxiv https://doi.org/10.1101/429159

  248. Cui Z-J, Yang Q-Y, Zhang H-Y, Zhu Q, Zhang Q-Y (2016) Bioinformatics identification of drug resistance-associated gene pairs in Mycobacterium tuberculosis. Int J Mol Sci 17(9):1417

    Article  PubMed Central  Google Scholar 

  249. Maus CE, Plikaytis BB, Shinnick T (2005) Mutation of tlyA confers capreomycin resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 49(2):571–577

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  250. Nazir T, Abraham S, Islam A (2012) Emergence of potential superbug Mycobacterium tuberculosis, lessons from New Delhi mutant-1 bacterial strains. IJHS 6(1):87

    Article  PubMed  PubMed Central  Google Scholar 

  251. Cole S, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D et al (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393(6685):537–544

    Article  CAS  PubMed  Google Scholar 

  252. Hackbarth CJ, Unsal I, Chambers HF (1997) Cloning and sequence analysis of a class A beta-lactamase from Mycobacterium tuberculosis H37Ra. Antimicrob Agents Chemother 41(5):1182–1185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  253. Nash KA (2003) Intrinsic macrolide resistance in Mycobacterium smegmatis is conferred by a novel erm gene, erm (38). Antimicrob Agents Chemother 47(10):3053–3060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  254. Montero C, Mateu G, Rodriguez R, Takiff H (2001) Intrinsic resistance of Mycobacterium smegmatis to fluoroquinolones may be influenced by new pentapeptide protein MfpA. Antimicrob Agents Chemother 45(12):3387–3392

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  255. Sander P, De Rossi E, Böddinghaus B, Cantoni R, Branzoni M, Böttger EC et al (2000) Contribution of the multidrug efflux pump LfrA to innate mycobacterial drug resistance. FEMS Microbiol Lett 193(1):19–23

    Article  CAS  PubMed  Google Scholar 

  256. De Rossi E, Blokpoel MC, Cantoni R, Branzoni M, Riccardi G, Young DB et al (1998) Molecular cloning and functional analysis of a novel tetracycline resistance determinant, tet (V), from Mycobacterium smegmatis. Antimicrob Agents Chemother 42(8):1931–1937

    Article  PubMed  PubMed Central  Google Scholar 

  257. Li X-Z, Zhang L, Nikaido H (2004) Efflux pump-mediated intrinsic drug resistance in Mycobacterium smegmatis. Antimicrob Agents Chemother 48(7):2415–2423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  258. Brandt C, Braun SD, Stein C, Slickers P, Ehricht R, Pletz MW et al (2017) In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species. Sci Rep 7:43232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  259. Maeda S, Matsuoka M, Nakata N, Kai M, Maeda Y, Hashimoto K et al (2001) Multidrug resistant Mycobacterium leprae from patients with leprosy. Antimicrob Agents Chemother 45(12):3635–3639

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  260. Pang Y, Brown B, Steingrube V, Wallace R, Roberts M (1994) Tetracycline resistance determinants in Mycobacterium and Streptomyces species. Antimicrob Agents Chemother 38(6):1408–1412

  261. Nash KA, Zhang Y, Brown-Elliott BA, Wallace RJ Jr (2005) Molecular basis of intrinsic macrolide resistance in clinical isolates of Mycobacterium fortuitum. J Antimicrob Chemother 55(2):170–177

    Article  CAS  PubMed  Google Scholar 

  262. Ramón-García S, Otal I, Martín C, Gómez-Lus R, Aínsa JA (2006) Novel streptomycin resistance gene from Mycobacterium fortuitum. Antimicrob Agents Chemother 50(11):3920–3922

  263. Kim HY, Kim BJ, Kook Y, Yun YJ, Shin JH, Kim BJ et al (2010) Mycobacterium massiliense is differentiated from Mycobacterium abscessus and Mycobacterium bolletii by erythromycin ribosome methyltransferase gene (erm) and clarithromycin susceptibility patterns. Microbiol Immunol 54(6):347–353

  264. https://www.uniprot.org/uniprot/A0A239VBJ5

  265. Nash KA, Inderlied CB (1995) Genetic basis of macrolide resistance in Mycobacterium avium isolated from patients with disseminated disease. Antimicrob Agents Chemother 39(12):2625–2630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  266. Valdezate S, Garrido N, Carrasco G, Villalón P, Medina-Pascual MJ, Saéz-Nieto JA (2015) Resistance gene pool to co-trimoxazole in non-susceptible Nocardia strains. Front Microbiol 6:376

  267. Laurent F, Poirel L, Naas T, Chaibi EB, Labia R, Boiron P et al (1999) Biochemical-genetic analysis and distribution of FAR-1, a class A β-lactamase from Nocardia farcinica. Antimicrob Agents Chemother 43(7):1644–1650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  268. Ishikawa J, Chiba K, Kurita H, Satoh H (2006) Contribution of rpoB2 RNA polymerase β subunit gene to rifampin resistance in Nocardia species. Antimicrob Agents Chemother 50(4):1342–1346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  269. Ishikawa J, Yamashita A, Mikami Y, Hoshino Y, Kurita H, Hotta K et al (2004) The complete genomic sequence of Nocardia farcinica IFM 10152. Proc Natl Acad Sci 101(41):14925–14930

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  270. Abdelwahab H, Del Campo JSM, Dai Y, Adly C, El-Sohaimy S, Sobrado P (2016) Mechanism of rifampicin inactivation in Nocardia farcinica. PLoS One 11(10):e0162578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  271. Yasuike M, Nishiki I, Iwasaki Y, Nakamura Y, Fujiwara A, Shimahara Y et al (2017) Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: the first reference genome sequence of the fish pathogenic Nocardia species. PLoS One 12(3):e0173198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  272. Yazawa K, Mikami Y, Maeda A, Akao M, Morisaki N, Iwasaki S (1993) Inactivation of rifampin by Nocardia brasiliensis. Antimicrob Agents Chemother 37(6):1313–1317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  273. DeLorenzo DM, Rottinghaus AG, Henson WR, Moon TS (2018) Molecular toolkit for gene expression control and genome modification in Rhodococcus opacus PD630. ACS Synth Biol 7(2):727–738

    Article  CAS  PubMed  Google Scholar 

  274. Andersen SJ, Quan S, Gowan B, Dabbs ER (1997) Monooxygenase-like sequence of a Rhodococcus equi gene conferring increased resistance to rifampin by inactivating this antibiotic. Antimicrob Agents Chemother 41(1):218–221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  275. Niwa H, Lasker BA (2010) Mutant selection window and characterization of allelic diversity for ciprofloxacin-resistant mutants of Rhodococcus equi. Antimicrob Agents Chemother 54(8):3520–3523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  276. Liu H, Wang Y, Yan J, Wang C, He H (2014) Appearance of multidrug-resistant virulent Rhodococcus equi clinical isolates obtained in China. J Clin Microbiol 52(2):703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  277. Anastasi E, Giguère S, Berghaus LJ, Hondalus MK, Willingham-Lane JM, MacArthur I et al (2015) Novel transferable erm (46) determinant responsible for emerging macrolide resistance in Rhodococcus equi. J Antimicrob Chemother 70(12):3184–3190

    CAS  PubMed  Google Scholar 

  278. Gressler LT, ACd V, MMd C, Pötter L, BPd S, Sangioni LA et al (2014) Genotypic and phenotypic detection of efflux pump in Rhodococcus equi. Braz J Microbiol 45(2):661–665

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  279. Desomer J, Vereecke D, Crespi M, Van Montagu M (1992) The plasmid-encoded chloramphenicol-resistance protein of Rhodococcus fascians is homologous to the transmembrane tetracycline efflux proteins. Mol Microbiol 6(16):2377–2385

    Article  CAS  PubMed  Google Scholar 

  280. https://www.uniprot.org/uniprot/A0A165LRG1

  281. https://ardb.cbcb.umd.edu/cgi/ssquery.cgi?db=T&gn=tetw

  282. McCormick MH (1956) Vancomycin, a new antibiotic. I. Chemical and biologic properties. Antibiot Annu 3:606–611

    CAS  Google Scholar 

  283. Grayson ML, Cosgrove SE, Crowe S, Hope W, McCarthy JS, Mills J et al (2017) Kucers’ the use of antibiotics: a clinical review of antibacterial, antifungal, antiparasitic, and antiviral drugs, -three volume set. CRC Press

  284. Yao RC, Crandall LSW (1994) Glycopeptides: classification, occurrence and discovery,” in Glycopeptide Atibiotics, ed. R. Nagarajan (New York: Taylor & Francis Group), 1–28.

  285. Faron ML, Ledeboer NA, Buchan BW (2016) Resistance mechanisms, epidemiology, and approaches to screening for vancomycin resistant Enterococcus (VRE) in the health care setting. J Clin Microbiol 54(10):2436–2447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  286. Leavis HL, Willems RJ, Van Wamel WJ, Schuren FH, Caspers MP, Bonten MJ (2007) Insertion sequence–driven diversification creates a globally dispersed emerging multiresistant subspecies of E. faecium. PLoS Pathog 3(1):e7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  287. Power EG, Abdulla YH, Talsania HG, Spice W, Aathithan S, French GL (1995) van A genes in vancomycin-resistant clinical isolates of Oerskovia turbata and Arcanobacterium (Corynebacterium) haemolyticum. J Antimicrob Chemother 36(4):595–606

  288. Arif M, Busot GY, Mann R, Rodoni B, Liu S, Stack JP (2016) Emergence of a new population of Rathayibacter toxicus: an ecologically complex, geographically isolated bacterium. PLoS One 11(5):e0156182

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  289. Chander AM, Nair RG, Kaur G, Kochhar R, Mayilraj S, Dhawan DK et al (2016) Genome sequence of Kocuria palustris strain CD07_3 isolated from the duodenal mucosa of a celiac disease patient. Genome Announc 4(2):e00210–e00216

    PubMed  PubMed Central  Google Scholar 

  290. Schatz A, Waksman SA (1944) Effect of streptomycin and other antibiotic substances upon Mycobacterium tuberculosis and related organisms. Proc Soc Exp Biol Med 57(2):244–248

    Article  CAS  Google Scholar 

  291. Davies J, Wright GD (1997) Bacterial resistance to aminoglycoside antibiotics. Trends Microbiol 5(6):234–240

    Article  CAS  PubMed  Google Scholar 

  292. Umezawa H (1957) Production and isolation of a new antibiotic, kanamycin. J Antibiot 10(5):181–188

    CAS  Google Scholar 

  293. Waksman SA, Lechevalier HA, Harris DA (1949) Neomycin—production and antibiotic properties. J Clin Invest 28(5):934–939

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  294. Vakulenko SB, Mobashery S (2003) Versatility of aminoglycosides and prospects for their future. Clin Microbiol Rev 16(3):430–450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  295. de Lima Procópio RE, da Silva IR, Martins MK, de Azevedo JL, de Araújo JM (2012) Antibiotics produced by Streptomyces. Braz J Infect Dis 16(5):466–471

    Article  Google Scholar 

  296. Waglechner N, Wright GD (2017) Antibiotic resistance: it’s bad, but why isn’t it worse? BMC Biol 15(1):84

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  297. https://www.uniprot.org/uniprot/W7IY03

  298. van Overbeek LS, Wellington EM, Egan S, Smalla K, Heuer H, Collard J-M et al (2002) Prevalence of streptomycin-resistance genes in bacterial populations in European habitats. FEMS Microbiol Ecol 42(2):277–288

  299. https://www.uniprot.org/uniprot/A0A0A0J3N0

  300. Kelemen GH, Cundliffe E, Financsek I (1991) Cloning and characterization of gentamicin-resistance genes from Micromonospora purpurea and Micromonospora rosea. Gene 98(1):53–60

    Article  CAS  PubMed  Google Scholar 

  301. Goldberg SL, Romero JG, DEO YM (1990) Cloning and characterization of the sisomicin-resistance gene from Micromonospora inyoensis. J Antibiot 43(8):992–999

    Article  CAS  Google Scholar 

  302. Derewacz DK, Goodwin CR, McNees CR, McLean JA, Bachmann BO (2013) Antimicrobial drug resistance affects broad changes in metabolomic phenotype in addition to secondary metabolism. Proc Soc Exp Biol Med 110(6):2336–3341

    CAS  Google Scholar 

  303. https://www.uniprot.org/uniprot/A0A0Q6G031

  304. Schwarz S, Kehrenberg C, Doublet B, Cloeckaert A (2004) Molecular basis of bacterial resistance to chloramphenicol and florfenicol. FEMS Microbiol Rev 28(5):519–542

    Article  CAS  PubMed  Google Scholar 

  305. https://www.dsmz.de

  306. Weisblum B (1995) Erythromycin resistance by ribosome modification. Antimicrob Agents Chemother 39(3):577–585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  307. Roberts MC, Sutcliffe J, Courvalin P, Jensen LB, Rood J, Seppala H (1999) Nomenclature for macrolide and macrolide-lincosamide-streptogramin B resistance determinants. Antimicrob Agents Chemother 43(12):2823–2830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  308. Fernández-Natal I, Sáez-Nieto J, Rodríguez-Lázaro D, Valdezate-Ramos S, Parras-Padilla T, Medina M et al (2016) Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples. New Microbes New Infect 10:116–121

    Article  PubMed  PubMed Central  Google Scholar 

  309. https://www.genome.jp/dbget-bin/www_bget?pbo:PACID_32300

  310. http://www.bio.nite.go.jp/mifup/microbes/view/nbrc/105200

  311. McNeil MB, Dennison DD, Shelton CD, Parish T (2017) In vitro isolation and characterization of oxazolidinone-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 61(10):e01296–e01217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  312. Watanabe T (1963) Infective heredity of multiple drug resistance in bacteria. Bacteriol Rev 27(1):87–115

    CAS  PubMed  PubMed Central  Google Scholar 

  313. Leng Z, Riley D, Berger R, Krieger J, Roberts M (1997) Distribution and mobility of the tetracycline resistance determinant tetQ. J Antimicrob Chemother 40(4):551–559

    Article  CAS  PubMed  Google Scholar 

  314. Roberts MC, Moncla B, Hillier S (1991) Characterization of unusual tetracycline-resistant gram-positive bacteria. Antimicrob Agents Chemother 35(12):2655–2657

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  315. http://ardb.cbcb.umd.edu/cgi/ssquery.cgi?db=L&gn=a&ge=157920

  316. https://www.uniprot.org/uniprot/E1VS65

  317. Hooper DC (1995) Quinolone mode of action. Drugs 49(2):10–15

    Article  CAS  PubMed  Google Scholar 

  318. Domagk G (1935) Ein beitrag zur chemotherapie der bakteriellen infektionen. DMW- Dtsch Med Wochenschr 61(07):250–253

    Article  CAS  Google Scholar 

  319. Sköld O (2001) Resistance to trimethoprim and sulfonamides. Vet Res 32(3–4):261–273

    Article  PubMed  Google Scholar 

  320. Ma X, Wang H, Deng Y, Liu Z, Xu Y, Pan X et al (2006) rpoB gene mutations and molecular characterization of rifampin-resistant Mycobacterium tuberculosis isolates from Shandong Province, China. J Clin Microbiol 44(9):3409–3412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  321. Stogios PJ, Cox G, Spanogiannopoulos P, Pillon MC, Waglechner N, Skarina T et al (2016) Rifampin phosphotransferase is an unusual antibiotic resistance kinase. Nat Commun 7:11343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  322. Agrawal P, Miryala S, Varshney U (2015) Use of Mycobacterium smegmatis deficient in ADP-ribosyltransferase as surrogate for Mycobacterium tuberculosis in drug testing and mutation analysis. PLoS One 10(4):e0122076

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  323. Tribuddharat C, Fennewald M (1999) Integron-mediated rifampin resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 43(4):960–962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  324. Yazawa K, Mikami Y, Maeda A, Morisaki N, Iwasaki S (1994) Phosphorylative inactivation of rifampicin by Nocardia otitidiscaviarum. J Antimicrob Chemother 33(6):1127–1135

    Article  CAS  PubMed  Google Scholar 

  325. Dabbs ER (1987) Rifampicin inactivation by Rhodococcus and Mycobacterium species. FEMS Microbiol Lett 44(3):395–399

    Article  CAS  Google Scholar 

  326. Dabbs ER, Yazawa K, Mikami Y, Miyaji M, Morisaki N, Iwasaki S, Furihata K (1995) Ribosylation by mycobacterial strains as a new mechanism of rifampin inactivation. Antimicrob Agents Chemother 39(4):1007–1009

  327. Tanaka Y, Yazawa K, Dabbs ER, Nishikawa K, Komaki H, Mikami Y et al (1996) Different rifampicin inactivation mechanisms in Nocardia and related taxa. Microbiol Immunol 40(1):1–4

    Article  CAS  PubMed  Google Scholar 

  328. Quan S, Venter H, Dabbs ER (1997) Ribosylative inactivation of rifampin by Mycobacterium smegmatis is a principal contributor to its low susceptibility to this antibiotic. Antimicrob Agents Chemother 41(11):2456–2460

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  329. Barr J (2010) A short history of dapsone, or an alternative model of drug development. J Hist Med Allied Sci 66(4):425–467

    Article  PubMed  Google Scholar 

  330. Williams DL, Araujo S, Stryjewska BM, Scollard D (2018) Dapsone resistance in leprosy patients originally from American Samoa, United States, 2010–2012. Emerg Infect Dis 24(8):1584–1585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  331. Cambau E, Carthagena L, Chauffour A, Ji B, Jarlier V (2006) Dihydropteroate synthase mutations in the folP1 gene predict dapsone resistance in relapsed cases of leprosy. Clin Infect Dis 42(2):238–241

    Article  CAS  PubMed  Google Scholar 

  332. Aminov R (2017) History of antimicrobial drug discovery: major classes and health impact. Biochem Pharmacol 133:4–19

    Article  CAS  PubMed  Google Scholar 

  333. Prosser GA, de Carvalho LPS (2013) Kinetic mechanism and inhibition of Mycobacterium tuberculosis d-alanine: d-alanine ligase by the antibiotic d-cycloserine. FEBS J 280(4):1150–1166

    Article  CAS  PubMed  Google Scholar 

  334. Noda M, Kawahara Y, Ichikawa A, Matoba Y, Matsuo H, Lee D-G et al (2004) Self-protection mechanism in D-cycloserine-producing Streptomyces lavendulae: gene cloning, characterization, and kinetics of its alanine racemase and D-alanyl-D-alanine ligase. Which are traget enyzmes of D-cycloserine. J Biol Chem 279(44):46143–46152

  335. WHO GotPMoD-R (n.d.) Tuberculosis Aahwwip, 2006/9241546956_eng.pdf

  336. Chen J, Zhang S, Cui P, Shi W, Zhang W, Zhang Y (2017) Identification of novel mutations associated with cycloserine resistance in Mycobacterium tuberculosis. J Antimicrob Chemother 72(12):3272–3276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  337. Engohang-Ndong J, Baillat D, Aumercier M, Bellefontaine F, Besra GS, Locht C et al (2004) EthR, a repressor of the TetR/CamR family implicated in ethionamide resistance in mycobacteria, octamerizes cooperatively on its operator. Mol Microbiol 51(1):175–188

    Article  CAS  PubMed  Google Scholar 

  338. Morlock GP, Metchock B, Sikes D, Crawford JT, Cooksey RC (2003) ethA, inhA, and katG loci of ethionamide-resistant clinical Mycobacterium tuberculosis isolates. Antimicrob Agents Chemother 47(12):3799–3805

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  339. Wang F, Langley R, Gulten G, Dover LG, Besra GS, Jacobs WR et al (2007) Mechanism of thioamide drug action against tuberculosis and leprosy. J Exp Med 204(1):73–78

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  340. Banerjee A, Dubnau E, Quemard A, Balasubramanian V, Um KS, Wilson T et al (1994) inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis. Science 263(5144):227–230

  341. Wilson TM, de Lisle GW, Collins DM (1995) Effect of inhA and katG on isoniazid resistance and virulence of Mycobacterium bovis. Mol Microbiol 15(6):1009–1015

  342. Belanger AE, Besra GS, Ford ME, Mikusová K, Belisle JT, Brennan PJ et al (1996) The embAB genes of Mycobacterium avium encode an arabinosyl transferase involved in cell wall arabinan biosynthesis that is the target for the antimycobacterial drug ethambutol. Proc Natl Acad Sci 93(21):11919–11924

  343. Telenti A, Philipp WJ, Sreevatsan S, Bernasconi C, Stockbauer KE, Wieles B et al (1997) The emb operon, a gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol. Nat Med 3(5):567–570

  344. Lety M, Nair S, Berche P, Escuyer V (1997) A single point mutation in the embB gene is responsible for resistance to ethambutol in Mycobacterium smegmatis. Antimicrob Agents Chemother 41(12):2629–2633

  345. Alcaide F, Pfyffer GE, Telenti A (1997) Role of embB in natural and acquired resistance to ethambutol in mycobacteria. Antimicrob Agents Chemother 41(10):2270–2273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  346. Arbiser JL, Moschella SL (1995) Clofazimine: a review of its medical uses and mechanisms of action. J Am Acad Dermatol 32(2):241–247

    Article  CAS  PubMed  Google Scholar 

  347. Cholo MC, Steel HC, Fourie PB, Germishuizen WA, Anderson R (2011) Clofazimine: current status and future prospects. J Antimicrob Chemother 67(2):290–298

    Article  CAS  PubMed  Google Scholar 

  348. Almeida D, Ioerger T, Tyagi S, Li S-Y, Mdluli K, Andries K et al (2016) Mutations in pepQ confer low-level resistance to bedaquiline and clofazimine in Mycobacterium tuberculosis. Antimicrob Agents Chemother 60(8):4590–4599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  349. Chen Y, Chen J, Zhang S, Shi W, Zhang W, Zhu M et al (2018) Novel mutations associated with clofazimine resistance in Mycobacterium abscessus. Antimicrob Agents Chemother 62(7):e00544–e00518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  350. Somoskovi A, Parsons LM, Salfinger M (2001) The molecular basis of resistance to isoniazid, rifampin, and pyrazinamide in Mycobacterium tuberculosis. Respir Res 2(3):164

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  351. Timmins GS, Deretic V (2006) Mechanisms of action of isoniazid. Mol Microbiol 62(5):1220–1227

    Article  CAS  PubMed  Google Scholar 

  352. Tekwu EM, Sidze LK, Assam J-PA, Tedom J-C, Tchatchouang S, Makafe GG et al (2014) Sequence analysis for detection of drug resistance in Mycobacterium tuberculosis complex isolates from the Central Region of Cameroon. BMC Microbiol 14(1):1

    Article  CAS  Google Scholar 

  353. Seifert M, Catanzaro D, Catanzaro A, Rodwell TC (2015) Genetic mutations associated with isoniazid resistance in Mycobacterium tuberculosis: a systematic review. PLoS One 10(3):e0119628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  354. Pasca MR, Guglierame P, De Rossi E, Zara F, Riccardi G (2005) mmpL7 gene of Mycobacterium tuberculosis is responsible for isoniazid efflux in Mycobacterium smegmatis. Antimicrob Agents Chemother 49(11):4775–4777

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  355. Heym B, Cole S (1992) Isolation and characterization of isoniazid-resistant mutants of Mycobacterium smegmatis and M. aurum. Res Microbiol 143(7):721–730

    Article  CAS  PubMed  Google Scholar 

  356. Mdluli K, Swanson J, Fischer E, Lee RE, Barry Iii CE (1998) Mechanisms involved in the intrinsic isoniazid resistance of Mycobacterium avium. Mol Microbiol 27(6):1223–1233

    Article  CAS  PubMed  Google Scholar 

  357. Singh P, Mishra A, Malonia S, Chauhan D, Sharma V, Venkatesan K et al (2006) The paradox of pyrazinamide: an update on the molecular mechanisms of pyrazinamide resistance in mycobacteria. J Commun Disord 38(3):288–298

    Google Scholar 

  358. Zhang S, Chen J, Shi W, Cui P, Zhang J, Cho S et al (2017) Mutation in clpC1 encoding an ATP-dependent ATPase involved in protein degradation is associated with pyrazinamide resistance in Mycobacterium tuberculosis. Emerg Microbes Infect 6(2):e8

    CAS  PubMed  PubMed Central  Google Scholar 

  359. Konno K, Feldmann FM, McDermott W (1967) Pyrazinamide susceptibility and amidase activity of tubercle bacilli. Am Rev Respir Dis 95(3):461–469

    CAS  PubMed  Google Scholar 

  360. Ramirez-Busby SM, Valafar F (2015) A systematic review of mutations in pyrazinamidase associated with pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates. Antimicrob Agents Chemother 59(9):5267–5277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  361. Sun Z, Zhang Y (1999) Reduced pyrazinamidase activity and the natural resistance of Mycobacterium kansasii to the antituberculosis drug pyrazinamide. Antimicrob Agents Chemother 43(3):537–542

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  362. Feuerriegel S, Köser CU, Richter E, Niemann S (2013) Mycobacterium canettii is intrinsically resistant to both pyrazinamide and pyrazinoic acid. J Antimicrob Chemother 68(6):1439–1440

  363. Raynaud C, Lanéelle M-A, Senaratne RH, Draper P, Lanéelle G, Daffé M (1999) Mechanisms of pyrazinamide resistance in mycobacteria: importance of lack of uptake in addition to lack of pyrazinamidase activity. Microbiology 145(6):1359–1367

    Article  CAS  PubMed  Google Scholar 

  364. Sun Z, Scorpio A, Zhang Y (1997) The pncA gene from naturally pyrazinamide-resistant Mycobacterium avium encodes pyrazinamidase and confers pyrazinamide susceptibility to resistant M. tuberculosis complex organisms. Microbiology 143(10):3367–3373

    Article  CAS  PubMed  Google Scholar 

  365. https://www.uniprot.org/uniprot/A4E883

  366. Lubbe MM, Stanley K, Chalkley LJ (1999) Prevalence of nim genes in anaerobic/facultative anaerobic bacteria isolated in South Africa. FEMS Microbiol Lett 172(1):79–83

    Article  CAS  PubMed  Google Scholar 

  367. https://www.uniprot.org/uniprot/R9S0R0

  368. Kon K, Rai M (2016) Antibiotic resistance: mechanisms and new antimicrobial approaches. Academic press. 1 edition

  369. https://www.uniprot.org/uniprot/A0A099D695

  370. https://www.uniprot.org/uniprot/K7S0J6

  371. https://www.uniprot.org/uniprot/A0A2S6GES8

  372. https://www.uniprot.org/uniprot/A0A2U1FQI5

  373. https://www.uniprot.org/uniprot/C7PVF0

  374. https://www.uniprot.org/uniprot/C7MNS5

  375. https://www.uniprot.org/uniprot/D2PKM1

  376. https://www.uniprot.org/uniprot/A0A1H1TIX2

  377. https://www.uniprot.org/uniprot/A0A1B1N7U4

  378. https://www.uniprot.org/uniprot/A0A077M7Q0

  379. https://www.uniprot.org/uniprot/A0A0K1FEI1

  380. https://www.genome.jp/kegg-bin/get_htext?bcv00001+Bcav_2818

  381. https://www.uniprot.org/uniprot/Q0RR17

  382. https://www.uniprot.org/uniprot/F6EHX1

  383. https://www.uniprot.org/uniprot/A0A0K1JHP7

  384. https://www.uniprot.org/uniprot/W2EVC8

  385. https://www.uniprot.org/uniprot/A0A1E8VWJ6

  386. https://www.uniprot.org/uniprot/A1R9Q1

  387. Oliynyk M, Samborskyy M, Lester JB, Mironenko T, Scott N, Dickens S et al (2007) Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338. Nat Biotechnol 25(4):447

    Article  CAS  PubMed  Google Scholar 

  388. Saleh O, Flinspach K, Westrich L, Kulik A, Gust B, Fiedler H-P et al (2012) Mutational analysis of a phenazine biosynthetic gene cluster in Streptomyces anulatus 9663. Beilstein J Org Chem 8:501–513

  389. Leangapichart T, Gautret P, Nguyen TT, Armstrong N, Rolain J-M (2018) Genome sequence of “Leucobacter massiliensis” sp. nov. isolated from human pharynx after travel to the 2014 Hajj. New Microbes New Infect 21:42–48

    Article  CAS  PubMed  Google Scholar 

  390. https://www.uniprot.org/uniprot/F5XK18

  391. https://www.uniprot.org/uniprot/A0A3E2EHP6

  392. Duranti S, Lugli GA, Mancabelli L, Turroni F, Milani C, Mangifesta M et al (2017) Prevalence of antibiotic resistance genes among human gut-derived bifidobacteria. Appl Environ Microbiol 83(3):e02894–e02816

    Article  PubMed  PubMed Central  Google Scholar 

  393. https://www.uniprot.org/uniprot/A0A1W2EWA8

  394. https://www.uniprot.org/uniprot/A0A0F0H5N7

  395. McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C et al (2006) The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci 103(42):15582–15587

    Article  PubMed  PubMed Central  Google Scholar 

  396. https://www.uniprot.org/uniprot/A0A1H7J985

  397. https://www.uniprot.org/uniprot/A0A172RZ18

  398. https://www.uniprot.org/uniprot/A0A172RX44

  399. De Carvalho CC, Costa SS, Fernandes P, Couto I, Viveiros M (2014) Membrane transport systems and the biodegradation potential and pathogenicity of genus Rhodococcus. Front Physiol 5:133

    PubMed  PubMed Central  Google Scholar 

  400. Lim YW, Schmieder R, Haynes M, Furlan M, Matthews TD, Whiteson K et al (2013) Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data. PLoS One 8(5):e64285

  401. https://www.uniprot.org/uniprot/D6Y5J3

  402. https://www.uniprot.org/uniprot/A0A168E827

  403. https://www.genome.jp/kegg-bin/get_htext?ido00001+I598_2717

  404. Ju F, Li B, Ma L, Wang Y, Huang D, Zhang T (2016) Antibiotic resistance genes and human bacterial pathogens: co-occurrence, removal, and enrichment in municipal sewage sludge digesters. Water Res 91:1–10

    Article  CAS  PubMed  Google Scholar 

  405. Stokes H, Hall RM (1989) A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol 3(12):1669–1683

    Article  CAS  PubMed  Google Scholar 

  406. Gillings MR (2014) Integrons: past, present, and future. Microbiol Mol Biol Rev 78(2):257–277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  407. Domingues S, da Silva GJ, Nielsen KM (2012) Integrons: vehicles and pathways for horizontal dissemination in bacteria. Mob Genet Elem 2(5):211–223

    Article  Google Scholar 

  408. Cambray G, Guerout A-M, Mazel D (2010) Integrons. Annu Rev Genet 44:141–166

    Article  CAS  PubMed  Google Scholar 

  409. Boucher Y, Labbate M, Koenig JE, Stokes H (2007) Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol 15(7):301–309

    Article  CAS  PubMed  Google Scholar 

  410. Gillings MR, Xuejun D, Hardwick SA, Holley MP, Stokes HW (2009) Gene cassettes encoding resistance to quaternary ammonium compounds: a role in the origin of clinical class 1 integrons? ISME J 3(2):209–215

  411. Toleman MA, Walsh TR (2011) Combinatorial events of insertion sequences and ICE in Gram-negative bacteria. FEMS Microbiol Rev 35(5):912–935

    Article  CAS  PubMed  Google Scholar 

  412. Martin C, Timm J, Rauzier J, Gomez-Lus R, Davies J, Gicquel B (1990) Transposition of an antibiotic resistance element in mycobacteria. Nature 345(6277):739–743

    Article  CAS  PubMed  Google Scholar 

  413. https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/

  414. Aarts HJ, Guerra B, Malorny B (2006) Molecular methods for detection of antibiotic resistance. Antimicrobial resistance in bacteria of animal origin. Am Soc Microbiol. https://doi.org/10.1128/microbiolspec.ARBA-0011-2017

  415. Schürch AC, Schaik W (2017) Challenges and opportunities for whole-genome sequencing–based surveillance of antibiotic resistance. Ann N Y Acad Sci 1388(1):108–120

    Article  CAS  PubMed  Google Scholar 

  416. Harris SR, Okoro CK (2014) Whole-genome sequencing for rapid and accurate identification of bacterial transmission pathways. Methods Microbiol 41:123–152

    Article  CAS  Google Scholar 

  417. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9(1):75

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  418. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L et al (2014) ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 58(1):212–220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  419. Scaria J, Chandramouli U, Verma SK (2005) Antibiotic resistance genes online (ARGO): a database on vancomycin and β lactam resistance genes. Bioinformation 1(1):5–7

    Article  PubMed  PubMed Central  Google Scholar 

  420. Liu B, Pop M (2008) ARDB—antibiotic resistance genes database. Nucleic Acids Res 37(suppl_1):D443–D4D7

    PubMed  PubMed Central  Google Scholar 

  421. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ et al (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57(7):3348–3357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  422. Zhou C, Smith J, Lam M, Zemla A, Dyer MD, Slezak T (2006) MvirDB—a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Res 35(suppl_1):D391–D3D4

    PubMed  PubMed Central  Google Scholar 

  423. Call DR, Bakko MK, Krug MJ, Roberts MC (2003) Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob Agents Chemother 47(10):3290–3295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  424. Thaker MN, Wang W, Spanogiannopoulos P, Waglechner N, King AM, Medina R et al (2013) Identifying producers of antibacterial compounds by screening for antibiotic resistance. Nat Biotechnol 31(10):922

    Article  CAS  PubMed  Google Scholar 

  425. Yim G, Huimi Wang H, Davies Frs J (2007) Antibiotics as signalling molecules. Philos Trans R Soc Lond Ser B Biol Sci 362(1483):1195–1200

    Article  CAS  Google Scholar 

  426. Ogawara H (2016) Self-resistance in Streptomyces, with special reference to β-lactam antibiotics. Molecules 21(5):605

  427. Walker MS, Walker JB (1970) Streptomycin biosynthesis and metabolism enzymatic phosphorylation of dihydrostreptobiosamine moieties of dihydrostreptomycin-(streptidino) phosphate and dihydrostreptomycin by streptomyces extracts. J Biol Chem 245(24):6683–6689

    CAS  PubMed  Google Scholar 

  428. Benveniste R, Davies J (1973) Aminoglycoside antibiotic-inactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria. Proc Natl Acad Sci 70(8):2276–2280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Mehdi Fatahi-Bafghi.

Ethics declarations

Conflict of interest

The author declares that there is no conflict to interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fatahi-Bafghi, M. Antibiotic resistance genes in the Actinobacteria phylum. Eur J Clin Microbiol Infect Dis 38, 1599–1624 (2019). https://doi.org/10.1007/s10096-019-03580-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10096-019-03580-5

Keywords

Navigation