Advertisement

Antibiotic resistance genes in the Actinobacteria phylum

  • Mehdi Fatahi-BafghiEmail author
Review
  • 88 Downloads

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.

Keywords

Actinobacteria Antibiotics Antibiotics resistance Antibiotic resistance genes Phylum 

Notes

Compliance with ethical standards

Conflict of interest

The author declares that there is no conflict to interest.

References

  1. 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. 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):495–548Google Scholar
  3. 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):314–320Google Scholar
  4. 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: SpringerGoogle Scholar
  5. 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):1–43Google Scholar
  6. 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):843–855Google Scholar
  7. 7.
    Marrakchi H, Lanéelle M-A, Daffé M (2014) Mycolic acids: structures, biosynthesis, and beyond. Chem Biol 21(1):67–85Google Scholar
  8. 8.
    Fatahi-Bafghi M (2017) Nocardiosis from 1888 to 2017. Microb Pathog 114:369–384Google Scholar
  9. 9.
    Andalibi F, Fatahi-Bafghi M (2017) Gordonia: isolation and identification in clinical samples and role in biotechnology. Folia Microbiol 62(3):245–252Google Scholar
  10. 10.
    Safaei S, Fatahi-Bafghi M, Pouresmaeil O (2018) Role of Tsukamurella species in human infections: the first literature review. New Microbes New Infect 22:6–12Google Scholar
  11. 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):2045–2062Google Scholar
  12. 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):e106303Google Scholar
  13. 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):376–384Google Scholar
  14. 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):940–947Google Scholar
  15. 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):2182–2194Google Scholar
  16. 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):69–73Google Scholar
  17. 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):144Google Scholar
  18. 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):3821–3832Google Scholar
  19. 19.
    Woese CR (1987) Bacterial evolution. Microbiol Rev 51(2):221–271Google Scholar
  20. 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):103–112Google Scholar
  21. 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):4350–4353Google Scholar
  22. 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):e0164138Google Scholar
  23. 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):811–819Google Scholar
  24. 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):256–263Google Scholar
  25. 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):817–822Google Scholar
  26. 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):81–91Google Scholar
  27. 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):846–849Google Scholar
  28. 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):249–266Google Scholar
  29. 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 6:38392Google Scholar
  30. 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):1043–1047Google Scholar
  31. 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):463–464Google Scholar
  32. 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):139–146Google Scholar
  33. 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–WW46Google Scholar
  34. 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):1355–1361Google Scholar
  35. 35.
    Kwong JC, McCallum N, Sintchenko V, Howden BP (2015) Whole genome sequencing in clinical and public health microbiology. Pathology 47(3):199–210Google Scholar
  36. 36.
    http://www.bacterio.net (LPSN-list of prokaryotic names with standing in nomenclature)
  37. 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):4422–4432Google Scholar
  38. 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):1057–1067Google Scholar
  39. 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):1027–1031Google Scholar
  40. 40.
    van de Sande WW (2013) Global burden of human mycetoma: a systematic review and meta-analysis. PLoS Negl Trop Dis 7(11):e2550Google Scholar
  41. 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. 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):791–796Google Scholar
  43. 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):3377–3379Google Scholar
  44. 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):1552–1556Google Scholar
  45. 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):142–148Google Scholar
  46. 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):27–31Google Scholar
  47. 47.
    Polatti F (2012) Bacterial vaginosis, Atopobium vaginae and nifuratel. Curr Clin Pharmacol 7(1):36–40Google Scholar
  48. 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):e1134Google Scholar
  49. 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):503–507Google Scholar
  50. 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):1703–1707Google Scholar
  51. 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):73–75Google Scholar
  52. 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):627–630Google Scholar
  53. 53.
    Sangal V, Hoskisson PA (2016) Evolution, epidemiology and diversity of Corynebacterium diphtheriae: new perspectives on an old foe. Infect Genet Evol 43:364–370Google Scholar
  54. 54.
    Liu D (2011) Molecular detection of human bacterial pathogens. CRC pressGoogle Scholar
  55. 55.
    Corvec S (2018) Clinical and biological features of Cutibacterium (formerly Propionibacterium) avidum, an underrecognized microorganism. Clin Microbiol Rev 31(3):e00064–e00017Google Scholar
  56. 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):35–40Google Scholar
  57. 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):613–616Google Scholar
  58. 58.
    Fournier P-E, Drancourt M, Raoult D (2017) New laboratory tools for emerging bacterial challenges. Clin Infect Dis 65(suppl_1):S39–S49Google Scholar
  59. 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):296–305Google Scholar
  60. 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):626–635Google Scholar
  61. 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):162–175Google Scholar
  62. 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. 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):319–322Google Scholar
  64. 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):71–74Google Scholar
  65. 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):147–155Google Scholar
  66. 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):750–753Google Scholar
  67. 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 12:95–96Google Scholar
  68. 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):3886–3888Google Scholar
  69. 69.
    Valdivia-Arenas MA, Sood N (2008) Micrococcus bloodstream infection in patients with pulmonary hypertension on epoprostenol. Infect Dis Clin Pract 16(5):285–287Google Scholar
  70. 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):268–271Google Scholar
  71. 71.
    Hunter RL Jr (2018) The pathogenesis of tuberculosis: the early infiltrate of post-primary (adult pulmonary) tuberculosis—a distinct disease entity. Front Immunol 9:2108Google Scholar
  72. 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):3366–3368Google Scholar
  73. 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):467–474Google Scholar
  74. 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):2053–2055Google Scholar
  75. 75.
    Mantzourani M, Fenlon M, Beighton D (2009) Association between Bifidobacteriaceae and the clinical severity of root caries lesions. Oral Microbiol Immunol 24(1):32–37Google Scholar
  76. 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):980–987Google Scholar
  77. 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):1973–1976Google Scholar
  78. 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):472Google Scholar
  79. 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:e247Google Scholar
  80. 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):388–394Google Scholar
  81. 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. 82.
    Mahobia N, Chaudhary P, Kamat Y (2013) Rothia prosthetic knee joint infection: report and mini-review. New Microbes New Infect 1(1):2–5Google Scholar
  83. 83.
    Yassin A (2009) Saccharopolyspora rosea sp. nov., isolated from a patient with bronchial carcinoma. Int J Syst Evol Microbiol 59(5):1148–1152Google Scholar
  84. 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):25–29Google Scholar
  85. 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):3449–3452Google Scholar
  86. 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–e00016Google Scholar
  87. 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):1070–1075Google Scholar
  88. 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):463–470Google Scholar
  89. 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 26:89–91Google Scholar
  90. 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):278–281Google Scholar
  91. 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 8:115–120Google Scholar
  92. 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):2626–2629Google Scholar
  93. 93.
    Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74(3):417–433Google Scholar
  94. 94.
    Sheldon AT Jr (2005) Antibiotic resistance: a survival strategy. Clin Lab Sci 18(3):170–180Google Scholar
  95. 95.
    D’Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C et al (2011) Antibiotic resistance is ancient. Nature 477:457–461Google Scholar
  96. 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 46:336–344Google Scholar
  97. 97.
    Köser CU, Ellington MJ, Peacock SJ (2014) Whole-genome sequencing to control antimicrobial resistance. Trends Genet 30(9):401–407Google Scholar
  98. 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):2640–2644Google Scholar
  99. 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):127–137Google Scholar
  100. 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):440–451Google Scholar
  101. 101.
    Levy SB, Marshall B (2004) Antibacterial resistance worldwide: causes, challenges and responses. Nat Med 10(12s):S122Google Scholar
  102. 102.
    Andersson DI, Hughes D (2010) Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol 8(4):260–271Google Scholar
  103. 103.
    Eriksen N, Blanco J (1992) Extended-spectrum (second-and third-generation) cephalosporins. Obstet Gynecol Clin N Am 19(3):461–474Google Scholar
  104. 104.
    Courvalin P (2008) Predictable and unpredictable evolution of antibiotic resistance. J Intern Med 264(1):4–16Google Scholar
  105. 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 8:15784Google Scholar
  106. 106.
    Perry J, Wright G (2013) The antibiotic resistance “mobilome”: searching for the link between environment and clinic. Front Microbiol 4:138Google Scholar
  107. 107.
    D'costa VM, McGrann KM, Hughes DW, Wright GD (2006) Sampling the antibiotic resistome. Science 311(5759):374–377Google Scholar
  108. 108.
    Nikaido H (2009) Multidrug resistance in bacteria. Annu Rev Biochem 78:119–146Google Scholar
  109. 109.
  110. 110.
  111. 111.
  112. 112.
    Van Hoek AH, Mevius D, Guerra B, Mullany P, Roberts AP, Aarts HJ (2011) Acquired antibiotic resistance genes: an overview. Front Microbiol 2:203Google Scholar
  113. 113.
    Brunton LL (2014) Goodman and Gilman’s manual of pharmacology and therapeutics. McGraw-Hill, New YorkGoogle Scholar
  114. 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 726–744Google Scholar
  115. 115.
    Carroll KC, Butel JS, Morse SA (2015) Jawetz Melnick & Adelbergs Medical Microbiology 27 E: McGraw-Hill Education / Medical; 27 editionGoogle Scholar
  116. 116.
    Walsh C (2003) Antibiotics: actions, origins, resistance: American society for. Microbiology (ASM)Google Scholar
  117. 117.
    Sköld O (2011) Antibiotics and antibiotic resistance. John Wiley & Sons.  https://doi.org/10.1002/9781118075609
  118. 118.
    Durand GA, Raoult D, Dubourg G (2018) Antibiotic discovery: history, methods and perspectives. Int J Antimicrob Agents 53(4):371–382Google Scholar
  119. 119.
    Gallagher JC, MacDougall C (2016) Antibiotics simplified, Fourth edn. Jones & Bartlett LearningGoogle Scholar
  120. 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):234–258Google Scholar
  121. 121.
    Abraham EP, Chain E (1940) An enzyme from bacteria able to destroy penicillin. Nature 146:837Google Scholar
  122. 122.
    Bush K, Jacoby GA (2010) Updated functional classification of β-lactamases. Antimicrob Agents Chemother 54(3):969–976Google Scholar
  123. 123.
    Ogawara H (1981) Antibiotic resistance in pathogenic and producing bacteria, with special reference to beta-lactam antibiotics. Microbiol Rev 45(4):591–619Google Scholar
  124. 124.
    Nakazawa H, Ogawara H (1982) Mechanisms of acquired penicillin-resistance in Streptomyces cacaoi. J Antibiot 35(12):1683–1691Google Scholar
  125. 125.
    Carattoli A (2009) Resistance plasmid families in Enterobacteriaceae. Antimicrob Agents Chemother 53(6):2227–2238Google Scholar
  126. 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 13:141Google Scholar
  127. 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 374:53-80Google Scholar
  128. 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 8:681Google Scholar
  129. 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):21Google Scholar
  130. 130.
  131. 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):29–57Google Scholar
  132. 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 337675Google Scholar
  133. 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. 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):878–882Google Scholar
  135. 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):55840–55849Google Scholar
  136. 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):8182–8193Google Scholar
  137. 137.
    Roberts MC (2008) Update on macrolide–lincosamide–streptogramin, ketolide, and oxazolidinone resistance genes. FEMS Microbiol Lett 282(2):147–159Google Scholar
  138. 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):232–260Google Scholar
  139. 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):293–297Google Scholar
  140. 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):2670–2671Google Scholar
  141. 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):2056–2060Google Scholar
  142. 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 ECCMIDGoogle Scholar
  143. 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):3444–3451Google Scholar
  144. 144.
  145. 145.
    Khan S, Knapp CW, Beattie TK (2016) Antibiotic resistant bacteria found in municipal drinking water. Environ Process 3(3):541–552Google Scholar
  146. 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):11Google Scholar
  147. 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):6267Google Scholar
  148. 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):544–548Google Scholar
  149. 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):6–15Google Scholar
  150. 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):572–580Google Scholar
  151. 151.
  152. 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):627–628Google Scholar
  153. 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 9:1809Google Scholar
  154. 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):e00441–18Google Scholar
  155. 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–e00617Google Scholar
  156. 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 11:114–115Google Scholar
  157. 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):137–143Google Scholar
  158. 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):855–856Google Scholar
  159. 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):1688–1694Google Scholar
  160. 160.
    Sanakal RD, Kaliwal BB (2011) Vancomycin resistance genes in various organisms-an Insilico study. Bioinformatics 5:111–129Google Scholar
  161. 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):945–949Google Scholar
  162. 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):466–474Google Scholar
  163. 163.
  164. 164.
  165. 165.
  166. 166.
  167. 167.
  168. 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):2Google Scholar
  169. 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–e00614Google Scholar
  170. 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):4139–4146Google Scholar
  171. 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):42Google Scholar
  172. 172.
  173. 173.
    Liebl W, Kloos WE, Ludwig W (2002) Plasmid-borne macrolide resistance in Micrococcus luteusa. Microbiology 148(8):2479–2487Google Scholar
  174. 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):281–283Google Scholar
  175. 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):30Google Scholar
  176. 176.
    Roberts MC (1995) Distribution of tetracycline and macrolide-lincosamide-streptogramin B resistance genes in anaerobic bacteria. Clin Infect Dis:S367–S3S9Google Scholar
  177. 177.
  178. 178.
  179. 179.
    Jacoby GA, Hooper DC (2013) Phylogenetic analysis of chromosomally determined qnr and related proteins. Antimicrob Agents Chemother 57(4):1930–1934Google Scholar
  180. 180.
  181. 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):7718Google Scholar
  182. 182.
  183. 183.
    Binda E, Cappelletti P, Marinelli F, Marcone G (2018) Specificity of induction of glycopeptide antibiotic resistance in the producing actinomycetes. Antibiotics 7(2):36Google Scholar
  184. 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):1107–1121Google Scholar
  185. 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):3984–3991Google Scholar
  186. 186.
  187. 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 9:2928Google Scholar
  188. 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):403–412Google Scholar
  189. 189.
  190. 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):e112626Google Scholar
  191. 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):e39223Google Scholar
  192. 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):55–59Google Scholar
  193. 193.
  194. 194.
  195. 195.
  196. 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 56:5061–5069Google Scholar
  197. 197.
  198. 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):1658–1664Google Scholar
  199. 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):1820–1826Google Scholar
  200. 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):1836–1839Google Scholar
  201. 201.
    Feßler AT, Schwarz S (2017) Antimicrobial resistance in Corynebacterium spp., Arcanobacterium spp., and Trueperella pyogenes. Microbiol Spectr 5(6)Google Scholar
  202. 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):2441–2453Google Scholar
  203. 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–e00114Google Scholar
  204. 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):3580–3587Google Scholar
  205. 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):3519–3524Google Scholar
  206. 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):274–277Google Scholar
  207. 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 bacteriaGoogle Scholar
  208. 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:e4989Google Scholar
  209. 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 14:35Google Scholar
  210. 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):34–42Google Scholar
  211. 211.
  212. 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):3141–3146Google Scholar
  213. 213.
  214. 214.
  215. 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):237–240Google Scholar
  216. 216.
  217. 217.
  218. 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):2078–2080Google Scholar
  219. 219.
  220. 220.
  221. 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):504–511Google Scholar
  222. 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):112–116Google Scholar
  223. 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):117–129Google Scholar
  224. 224.
  225. 225.
  226. 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)Google Scholar
  227. 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):11–21Google Scholar
  228. 228.
  229. 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):632–643Google Scholar
  230. 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):9704Google Scholar
  231. 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. 232.
    Li W, Zhang Z (2013) Implication of ermCX gene of Corynebacterium striatum in macrolide resistance in Beijing, China. Bangladesh J Pharmacol 8(1):54–57Google Scholar
  233. 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.e13Google Scholar
  234. 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):126–139Google Scholar
  235. 235.
    Rosato AE, Lee BS, Nash KA (2001) Inducible Macrolide Resistance inCorynebacterium jeikeium. Antimicrob Agents Chemother 45(7):1982–1989Google Scholar
  236. 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):545–582Google Scholar
  237. 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):1559–1563Google Scholar
  238. 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):919–923Google Scholar
  239. 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):149–161Google Scholar
  240. 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):691–696Google Scholar
  241. 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 105:96–107Google Scholar
  242. 242.
    Campus S (2010) jefA (Rv2459), a drug efflux gene in Mycobacterium tuberculosis confers resistance to isoniazid & ethambutol. Indian J Med Res 132:176–188Google Scholar
  243. 243.
    Rossi ED, Aínsa JA, Riccardi G (2006) Role of mycobacterial efflux transporters in drug resistance: an unresolved question. FEMS Microbiol Rev 30(1):36–52Google Scholar
  244. 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):479Google Scholar
  245. 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):1138–1151Google Scholar
  246. 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):621–630Google Scholar
  247. 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. 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):1417Google Scholar
  249. 249.
    Maus CE, Plikaytis BB, Shinnick T (2005) Mutation of tlyA confers capreomycin resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 49(2):571–577Google Scholar
  250. 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):87Google Scholar
  251. 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):537–544Google Scholar
  252. 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):1182–1185Google Scholar
  253. 253.
    Nash KA (2003) Intrinsic macrolide resistance in Mycobacterium smegmatis is conferred by a novel erm gene, erm (38). Antimicrob Agents Chemother 47(10):3053–3060Google Scholar
  254. 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):3387–3392Google Scholar
  255. 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):19–23Google Scholar
  256. 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):1931–1937Google Scholar
  257. 257.
    Li X-Z, Zhang L, Nikaido H (2004) Efflux pump-mediated intrinsic drug resistance in Mycobacterium smegmatis. Antimicrob Agents Chemother 48(7):2415–2423Google Scholar
  258. 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 7:43232Google Scholar
  259. 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):3635–3639Google Scholar
  260. 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):1408–1412Google Scholar
  261. 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):170–177Google Scholar
  262. 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):3920–3922Google Scholar
  263. 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):347–353Google Scholar
  264. 264.
  265. 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):2625–2630Google Scholar
  266. 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 6:376Google Scholar
  267. 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):1644–1650Google Scholar
  268. 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):1342–1346Google Scholar
  269. 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):14925–14930Google Scholar
  270. 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):e0162578Google Scholar
  271. 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):e0173198Google Scholar
  272. 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):1313–1317Google Scholar
  273. 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):727–738Google Scholar
  274. 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):218–221Google Scholar
  275. 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):3520–3523Google Scholar
  276. 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):703Google Scholar
  277. 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):3184–3190Google Scholar
  278. 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):661–665Google Scholar
  279. 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):2377–2385Google Scholar
  280. 280.
  281. 281.
  282. 282.
    McCormick MH (1956) Vancomycin, a new antibiotic. I. Chemical and biologic properties. Antibiot Annu 3:606–611Google Scholar
  283. 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 PressGoogle Scholar
  284. 284.
    Yao RC, Crandall LSW (1994) Glycopeptides: classification, occurrence and discovery,” in Glycopeptide Atibiotics, ed. R. Nagarajan (New York: Taylor & Francis Group), 1–28.Google Scholar
  285. 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):2436–2447Google Scholar
  286. 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):e7Google Scholar
  287. 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):595–606Google Scholar
  288. 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):e0156182Google Scholar
  289. 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–e00216Google Scholar
  290. 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):244–248Google Scholar
  291. 291.
    Davies J, Wright GD (1997) Bacterial resistance to aminoglycoside antibiotics. Trends Microbiol 5(6):234–240Google Scholar
  292. 292.
    Umezawa H (1957) Production and isolation of a new antibiotic, kanamycin. J Antibiot 10(5):181–188Google Scholar
  293. 293.
    Waksman SA, Lechevalier HA, Harris DA (1949) Neomycin—production and antibiotic properties. J Clin Invest 28(5):934–939Google Scholar
  294. 294.
    Vakulenko SB, Mobashery S (2003) Versatility of aminoglycosides and prospects for their future. Clin Microbiol Rev 16(3):430–450Google Scholar
  295. 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):466–471Google Scholar
  296. 296.
    Waglechner N, Wright GD (2017) Antibiotic resistance: it’s bad, but why isn’t it worse? BMC Biol 15(1):84Google Scholar
  297. 297.
  298. 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):277–288Google Scholar
  299. 299.
  300. 300.
    Kelemen GH, Cundliffe E, Financsek I (1991) Cloning and characterization of gentamicin-resistance genes from Micromonospora purpurea and Micromonospora rosea. Gene 98(1):53–60Google Scholar
  301. 301.
    Goldberg SL, Romero JG, DEO YM (1990) Cloning and characterization of the sisomicin-resistance gene from Micromonospora inyoensis. J Antibiot 43(8):992–999Google Scholar
  302. 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):2336–3341Google Scholar
  303. 303.
  304. 304.
    Schwarz S, Kehrenberg C, Doublet B, Cloeckaert A (2004) Molecular basis of bacterial resistance to chloramphenicol and florfenicol. FEMS Microbiol Rev 28(5):519–542Google Scholar
  305. 305.
  306. 306.
    Weisblum B (1995) Erythromycin resistance by ribosome modification. Antimicrob Agents Chemother 39(3):577–585Google Scholar
  307. 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):2823–2830Google Scholar
  308. 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 10:116–121Google Scholar
  309. 309.
  310. 310.
  311. 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–e01217Google Scholar
  312. 312.
    Watanabe T (1963) Infective heredity of multiple drug resistance in bacteria. Bacteriol Rev 27(1):87–115Google Scholar
  313. 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):551–559Google Scholar
  314. 314.
    Roberts MC, Moncla B, Hillier S (1991) Characterization of unusual tetracycline-resistant gram-positive bacteria. Antimicrob Agents Chemother 35(12):2655–2657Google Scholar
  315. 315.
  316. 316.
  317. 317.
    Hooper DC (1995) Quinolone mode of action. Drugs 49(2):10–15Google Scholar
  318. 318.
    Domagk G (1935) Ein beitrag zur chemotherapie der bakteriellen infektionen. DMW- Dtsch Med Wochenschr 61(07):250–253Google Scholar
  319. 319.
    Sköld O (2001) Resistance to trimethoprim and sulfonamides. Vet Res 32(3–4):261–273Google Scholar
  320. 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):3409–3412Google Scholar
  321. 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 7:11343Google Scholar
  322. 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):e0122076Google Scholar
  323. 323.
    Tribuddharat C, Fennewald M (1999) Integron-mediated rifampin resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 43(4):960–962Google Scholar
  324. 324.
    Yazawa K, Mikami Y, Maeda A, Morisaki N, Iwasaki S (1994) Phosphorylative inactivation of rifampicin by Nocardia otitidiscaviarum. J Antimicrob Chemother 33(6):1127–1135Google Scholar
  325. 325.
    Dabbs ER (1987) Rifampicin inactivation by Rhodococcus and Mycobacterium species. FEMS Microbiol Lett 44(3):395–399Google Scholar
  326. 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):1007–1009Google Scholar
  327. 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):1–4Google Scholar
  328. 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):2456–2460Google Scholar
  329. 329.
    Barr J (2010) A short history of dapsone, or an alternative model of drug development. J Hist Med Allied Sci 66(4):425–467Google Scholar
  330. 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):1584–1585Google Scholar
  331. 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):238–241Google Scholar
  332. 332.
    Aminov R (2017) History of antimicrobial drug discovery: major classes and health impact. Biochem Pharmacol 133:4–19Google Scholar
  333. 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):1150–1166Google Scholar
  334. 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):46143–46152Google Scholar
  335. 335.
    WHO GotPMoD-R (n.d.) Tuberculosis Aahwwip, 2006/9241546956_eng.pdfGoogle Scholar
  336. 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):3272–3276Google Scholar
  337. 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):175–188Google Scholar
  338. 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):3799–3805Google Scholar
  339. 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):73–78Google Scholar
  340. 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):227–230Google Scholar
  341. 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):1009–1015Google Scholar
  342. 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):11919–11924Google Scholar
  343. 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):567–570Google Scholar
  344. 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):2629–2633Google Scholar
  345. 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):2270–2273Google Scholar
  346. 346.
    Arbiser JL, Moschella SL (1995) Clofazimine: a review of its medical uses and mechanisms of action. J Am Acad Dermatol 32(2):241–247Google Scholar
  347. 347.
    Cholo MC, Steel HC, Fourie PB, Germishuizen WA, Anderson R (2011) Clofazimine: current status and future prospects. J Antimicrob Chemother 67(2):290–298Google Scholar
  348. 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):4590–4599Google Scholar
  349. 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–e00518Google Scholar
  350. 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):164Google Scholar
  351. 351.
    Timmins GS, Deretic V (2006) Mechanisms of action of isoniazid. Mol Microbiol 62(5):1220–1227Google Scholar
  352. 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):1Google Scholar
  353. 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):e0119628Google Scholar
  354. 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):4775–4777Google Scholar
  355. 355.
    Heym B, Cole S (1992) Isolation and characterization of isoniazid-resistant mutants of Mycobacterium smegmatis and M. aurum. Res Microbiol 143(7):721–730Google Scholar
  356. 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):1223–1233Google Scholar
  357. 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):288–298Google Scholar
  358. 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):e8Google Scholar
  359. 359.
    Konno K, Feldmann FM, McDermott W (1967) Pyrazinamide susceptibility and amidase activity of tubercle bacilli. Am Rev Respir Dis 95(3):461–469Google Scholar
  360. 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):5267–5277Google Scholar
  361. 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):537–542Google Scholar
  362. 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):1439–1440Google Scholar
  363. 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):1359–1367Google Scholar
  364. 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):3367–3373Google Scholar
  365. 365.
  366. 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):79–83Google Scholar
  367. 367.
  368. 368.
    Kon K, Rai M (2016) Antibiotic resistance: mechanisms and new antimicrobial approaches. Academic press. 1 editionGoogle Scholar
  369. 369.
  370. 370.
  371. 371.
  372. 372.
  373. 373.
  374. 374.
  375. 375.
  376. 376.
  377. 377.
  378. 378.
  379. 379.
  380. 380.
  381. 381.
  382. 382.
  383. 383.
  384. 384.
  385. 385.
  386. 386.
  387. 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):447Google Scholar
  388. 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 8:501–513Google Scholar
  389. 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 21:42–48Google Scholar
  390. 390.
  391. 391.
  392. 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–e02816Google Scholar
  393. 393.
  394. 394.
  395. 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):15582–15587Google Scholar
  396. 396.
  397. 397.
  398. 398.
  399. 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 5:133Google Scholar
  400. 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):e64285Google Scholar
  401. 401.
  402. 402.
  403. 403.
  404. 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 91:1–10Google Scholar
  405. 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):1669–1683Google Scholar
  406. 406.
    Gillings MR (2014) Integrons: past, present, and future. Microbiol Mol Biol Rev 78(2):257–277Google Scholar
  407. 407.
    Domingues S, da Silva GJ, Nielsen KM (2012) Integrons: vehicles and pathways for horizontal dissemination in bacteria. Mob Genet Elem 2(5):211–223Google Scholar
  408. 408.
    Cambray G, Guerout A-M, Mazel D (2010) Integrons. Annu Rev Genet 44:141–166Google Scholar
  409. 409.
    Boucher Y, Labbate M, Koenig JE, Stokes H (2007) Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol 15(7):301–309Google Scholar
  410. 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):209–215Google Scholar
  411. 411.
    Toleman MA, Walsh TR (2011) Combinatorial events of insertion sequences and ICE in Gram-negative bacteria. FEMS Microbiol Rev 35(5):912–935Google Scholar
  412. 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):739–743Google Scholar
  413. 413.
  414. 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. 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):108–120Google Scholar
  416. 416.
    Harris SR, Okoro CK (2014) Whole-genome sequencing for rapid and accurate identification of bacterial transmission pathways. Methods Microbiol 41:123–152Google Scholar
  417. 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):75Google Scholar
  418. 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):212–220Google Scholar
  419. 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):5–7Google Scholar
  420. 420.
    Liu B, Pop M (2008) ARDB—antibiotic resistance genes database. Nucleic Acids Res 37(suppl_1):D443–D4D7Google Scholar
  421. 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):3348–3357Google Scholar
  422. 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–D3D4Google Scholar
  423. 423.
    Call DR, Bakko MK, Krug MJ, Roberts MC (2003) Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob Agents Chemother 47(10):3290–3295Google Scholar
  424. 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):922Google Scholar
  425. 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):1195–1200Google Scholar
  426. 426.
    Ogawara H (2016) Self-resistance in Streptomyces, with special reference to β-lactam antibiotics. Molecules 21(5):605Google Scholar
  427. 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):6683–6689Google Scholar
  428. 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):2276–2280Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Microbiology, Faculty of MedicineShahid Sadoughi University of Medical SciencesYazdIran

Personalised recommendations