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staphopia / staphopia-sccmec

A standalone version of Staphopia's SCCmec typing method.
MIT License
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Update to include latest SCCmec types #4

Open rpetit3 opened 2 years ago

rpetit3 commented 2 years ago

https://www.mdpi.com/2079-6382/11/1/86

SCCmec Types

image

  1. Katayama, Y.; Ito, T.; Hiramatsu, K. A new class of genetic element, staphylococcus cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 2000, 44, 1549–1555. [CrossRef]

  2. Ito, T.; Katayama, Y.; Asada, K.; Mori, N.; Tsutsumimoto, K.; Tiensasitorn, C.; Hiramatsu, K. Structural comparison of three types of staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 2001, 45, 1323–1336. [CrossRef]

  3. García-Álvarez, L.; Holden, M.T.G.; Lindsay, H.; Webb, C.R.; Brown, D.F.J.; Curran, M.D.; Walpole, E.; Brooks, K.; Pickard, D.J.; Teale, C.; et al. Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: A descriptive study. Lancet Infect. Dis. 2011, 11, 595–603. [CrossRef]

  4. Ma, X.X.; Ito, T.; Tiensasitorn, C.; Jamklang, M.; Chongtrakool, P.; Boyle-Vavra, S.; Daum, R.S.; Hiramatsu, K. Novel type of staphylococcal cassette chromosome mec identified in community-acquired methicillin-resistant Staphylococcus aureus strains. Antimicrob. Agents Chemother. 2002, 46, 1147–1152. [CrossRef] [PubMed]

  5. Ito, T.; Ma, X.X.; Takeuchi, F.; Okuma, K.; Yuzawa, H.; Hiramatsu, K. Novel type V staphylococcal cassette chromosome mec driven by a novel cassette chromosome recombinase, ccrC. Antimicrob. Agents Chemother. 2004, 48, 2637–2651. [CrossRef] [PubMed]

  6. Oliveira, D.C.; Milheirico, C.; de Lencastre, H. Redefining a structural variant of staphylococcal cassette chromosome mec, SCCmec type VI. Antimicrob. Agents Chemother. 2006, 50, 3457–3459. [CrossRef] [PubMed]

  7. Berglund, C.; Ito, T.; Ikeda, M.; Ma, X.X.; Soderquist, B.; Hiramatsu, K. Novel type of staphylococcal cassette chromosome mec in a methicillin-resistant Staphylococcus aureus strain isolated in Sweden. Antimicrob. Agents Chemother. 2008, 52, 3512–3516. [CrossRef]

  8. Zhang, K.; McClure, J.A.; Elsayed, S.; Conly, J.M. Novel staphylococcal cassette chromosome mec type, tentatively designated type VIII, harboring class A mec and type 4 ccr gene complexes in a Canadian epidemic strain of methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 2009, 53, 531–540. [CrossRef] [PubMed]

  9. Li, S.; Skov, R.L.; Han, X.; Larsen, A.R.; Larsen, J.; Sorum, M.; Wulf, M.; Voss, A.; Hiramatsu, K.; Ito, T. Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains. Antimicrob. Agents Chemother. 2011, 55, 3046–3050. [CrossRef]

  10. Wu, Z.; Li, F.; Liu, D.; Xue, H.; Zhao, X. Novel type XII staphylococcal cassette chromosome mec harboring a new cassette chromosome recombinase, CcrC2. Antimicrob. Agents Chemother. 2015, 59, 7597–7601. [CrossRef]

  11. Baig, S.; Johannesen, T.B.; Overballe-Petersen, S.; Larsen, J.; Larsen, A.R.; Stegger, M. Novel SCCmec type XIII (9A) identified in an ST152 methicillin-resistant Staphylococcus aureus. Infect. Genet. Evol. 2018, 61, 74–76. [CrossRef] [PubMed]

  12. Urushibara, N.; Aung, M.S.; Kawaguchiya, M.; Kobayashi, N. Novel staphylococcal cassette chromosome mec (SCCmec) type XIV (5A) and a truncated SCCmec element in SCC composite islands carrying speG in ST5 MRSA in Japan. J. Antimicrob. Chemother. 2020, 75, 46–50. [CrossRef]

Subtypes

image

  1. Katayama, Y.; Ito, T.; Hiramatsu, K. A new class of genetic element, staphylococcus cassette chromosome mec, encodes methicillin resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 2000, 44, 1549–1555. [CrossRef]

  2. Ito, T.; Katayama, Y.; Asada, K.; Mori, N.; Tsutsumimoto, K.; Tiensasitorn, C.; Hiramatsu, K. Structural comparison of three types of staphylococcal cassette chromosome mec integrated in the chromosome in methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 2001, 45, 1323–1336. [CrossRef]

  3. Ma, X.X.; Ito, T.; Tiensasitorn, C.; Jamklang, M.; Chongtrakool, P.; Boyle-Vavra, S.; Daum, R.S.; Hiramatsu, K. Novel type of staphylococcal cassette chromosome mec identified in community-acquired methicillin-resistant Staphylococcus aureus strains. Antimicrob. Agents Chemother. 2002, 46, 1147–1152. [CrossRef] [PubMed]

  4. Ito, T.; Ma, X.X.; Takeuchi, F.; Okuma, K.; Yuzawa, H.; Hiramatsu, K. Novel type V staphylococcal cassette chromosome mec driven by a novel cassette chromosome recombinase, ccrC. Antimicrob. Agents Chemother. 2004, 48, 2637–2651. [CrossRef] [PubMed]

  5. Li, S.; Skov, R.L.; Han, X.; Larsen, A.R.; Larsen, J.; Sorum, M.; Wulf, M.; Voss, A.; Hiramatsu, K.; Ito, T. Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains. Antimicrob. Agents Chemother. 2011, 55, 3046–3050. [CrossRef]

  6. Shore, A.; Rossney, A.S.; Keane, C.T.; Enright, M.C.; Coleman, D.C. Seven novel variants of the staphylococcal chromosomal cassette mec in methicillin-resistant Staphylococcus aureus isolates from Ireland. Antimicrob. Agents Chemother. 2005, 49, 2070–2083. [CrossRef]

  7. Han, X.; Ito, T.; Takeuchi, F.; Ma, X.X.; Takasu, M.; Uehara, Y.; Oliveira, D.C.; de Lencastre, H.; Hiramatsu, K. Identification of a novel variant of staphylococcal cassette chromosome mec, type II.5, and its truncated form by insertion of putative conjugative transposon Tn6012. Antimicrob. Agents Chemother. 2009, 53, 2616–2619. [CrossRef]

  8. Oliveira, D.C.; Milheirico, C.; Vinga, S.; de Lencastre, H. Assessment of allelic variation in the ccrAB locus in methicillin-resistant Staphylococcus aureus clones. J. Antimicrob. Chemother. 2006, 58, 23–30. [CrossRef]

  9. Hisata, K.; Kuwahara-Arai, K.; Yamanoto, M.; Ito, T.; Nakatomi, Y.; Cui, L.; Baba, T.; Terasawa, M.; Sotozono, C.; Kinoshita, S.; et al. Dissemination of methicillin-resistant Staphylococci among healthy Japanese children. J. Clin. Microbiol. 2005, 43, 3364–3372. [CrossRef]

  10. Kondo, Y.; Ito, T.; Ma, X.X.; Watanabe, S.; Kreiswirth, B.N.; Etienne, J.; Hiramatsu, K. Combination of multiplex PCRs for staphylococcal cassette chromosome mec type assignment: Rapid identification system for mec, ccr, and major differences in junkyard regions. Antimicrob. Agents Chemother. 2007, 51, 264–274. [CrossRef] [PubMed]

  11. Ma, X.X.; Ito, T.; Chongtrakool, P.; Hiramatsu, K. Predominance of clones carrying Panton-Valentine leukocidin genes among methicillin-resistant Staphylococcus aureus strains isolated in Japanese hospitals from 1979 to 1985. J. Clin. Microbiol. 2006, 44, 4515–4527. [CrossRef] [PubMed]

  12. Kwon, N.H.; Park, K.T.; Moon, J.S.; Jung, W.K.; Kim, S.H.; Kim, J.M.; Hong, S.K.; Koo, H.C.; Joo, Y.S.; Park, Y.H. Staphylococcal cassette chromosome mec (SCCmec) characterization and molecular analysis for methicillin-resistant Staphylococcus aureus and novel SCCmec subtype IVg isolated from bovine milk in Korea. J. Antimicrob. Chemother. 2005, 56, 624–632. [CrossRef] [PubMed]

  13. Milheirico, C.; Oliveira, D.C.; de Lencastre, H. Multiplex PCR strategy for subtyping the staphylococcal cassette chromosome mec type IV in methicillin-resistant Staphylococcus aureus: ‘SCCmec IV multiplex’. J. Antimicrob. Chemother. 2007, 60, 42–48. [CrossRef]

  14. Berglund, C.; Ito, T.; Ma, X.X.; Ikeda, M.; Watanabe, S.; Soderquist, B.; Hiramatsu, K. Genetic diversity of methicillin-resistant Staphylococcus aureus carrying type IV SCCmec in Orebro County and the western region of Sweden. J. Antimicrob. Chemother. 2009, 63, 32–41. [CrossRef] [PubMed]

  15. Iwao, Y.; Ishii, R.; Tomita, Y.; Shibuya, Y.; Takano, T.; Hung, W.C.; Higuchi, W.; Isobe, H.; Nishiyama, A.; Yano, M.; et al. The emerging ST8 methicillin-resistant Staphylococcus aureus clone in the community in Japan: Associated infections, genetic diversity, and comparative genomics. J. Infect. Chemother. 2012, 18, 228–240. [CrossRef]

  16. Hosoya, S.; Ito, T.; Misawa, S.; Yoshiike, T.; Oguri, T.; Hiramatsu, T. MRSA clones identified in outpatients dermatology clinic. J. Jpn. Assoc. Intectious Dis. 2014, 88, 840–848. (In Japanese)

  17. Harris, T.M.; Bowen, A.C.; Holt, D.C.; Sarovich, D.S.; Stevens, K.; Currie, B.J.; Howden, B.P.; Carapetis, J.R.; Giffard, P.M.; Tong, S.Y.C. Investigation of trimethoprim/sulfamethoxazole resistance in an emerging sequence type 5 methicillin-resistant Staphylococcus aureus clone reveals discrepant resistance reporting. Clin. Microbiol. Infect. 2018, 24, 1027–1029. [CrossRef]

  18. Hisata, K.; Ito, T.; Matsunaga, N.; Komatsu, M.; Jin, J.; Li, S.; Watanabe, S.; Shimizu, T.; Hiramatsu, K. Dissemination of multiple MRSA clones among community-associated methicillin-resistant Staphylococcus aureus infections from Japanese children with impetigo. J. Infect. Chemother. 2011, 17, 609–621. [CrossRef]

rpetit3 commented 2 years ago

SCCmec Types

SCCmec Type Ccr Complex Type mec Complex Type Link Notes
Type Ia 1 (A1B1) B https://www.ncbi.nlm.nih.gov/nuccore/AB033763.2/
Type Ib 1 (A1B1) B https://www.ncbi.nlm.nih.gov/nuccore/AB433542
Type IIa 2 (A2B2) A https://www.ncbi.nlm.nih.gov/nuccore/D86934
Type IIb 2 (A2B2) A https://www.ncbi.nlm.nih.gov/nuccore/AB127982
Type IIc 2 (A2B2) A https://www.ncbi.nlm.nih.gov/nuccore/AJ810120
Type IId 2 (A2B2) A https://www.ncbi.nlm.nih.gov/nuccore/AB261975
Type IIe 2 (A2B2) A https://www.ncbi.nlm.nih.gov/nuccore/AB127982
Type III 3 (A3B3) A https://www.ncbi.nlm.nih.gov/nuccore/AB037671
Type IVa 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/AB063172
Type IVb 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/AB063173
Type IVc 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/AB096217
Type IVd 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/AB097677
Type IVg 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/DQ106887
Type IVh 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/HE681097 integrated into chromosome?
Type IVi 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/AB425823
Type IVj 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/AB425824
Type IVk 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/GU122149
Type IVl 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/AB633329
Type IVm 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/AB872254
Type IVn 2 (A2B2) B https://www.ncbi.nlm.nih.gov/nuccore/KX385846
Type IVo 2 (A2B2) B no sequence available?
Type Va 5 (C1) C2 https://www.ncbi.nlm.nih.gov/nuccore/AB121219
Type Vb 5 (C1) C2 https://www.ncbi.nlm.nih.gov/nuccore/AB512767 (5C2&5)
Type Vc 5 (C1) C2 https://www.ncbi.nlm.nih.gov/nuccore/AB505629 (5C2&5)
Type VI 4 (A4B4) B https://www.ncbi.nlm.nih.gov/nuccore/AF411935
Type VII 5 (C1) C1 https://www.ncbi.nlm.nih.gov/nuccore/AB373032
Type VIII 4 (A4B4) A https://www.ncbi.nlm.nih.gov/nuccore/FJ390057
Type IX 1 (A1B1) C2 https://www.ncbi.nlm.nih.gov/nuccore/AB505628
Type X 7 (A1B6) C1 https://www.ncbi.nlm.nih.gov/nuccore/AB505630
Type XI 8 (A1B3) E https://www.ncbi.nlm.nih.gov/nuccore/FR821779 integrated into chromosome?
Type XII 9 (C2) C2 https://www.ncbi.nlm.nih.gov/nuccore/KR187111
Type XIII 9 (22) A https://www.ncbi.nlm.nih.gov/nuccore/MG674089
Type XIV 5 (C1) A https://www.ncbi.nlm.nih.gov/nuccore/LC440647
rpetit3 commented 2 years ago

mec Classes

*mec Classes Genes Source
A IS431-mecA-mecR1-mecI https://www.mdpi.com/2079-6382/11/1/86/htm
B IS1272-ΔmecR1-mecA-IS431 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC90469/
C1 IS431-mecA-deltamecR1-IS431 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC90585/
C2 IS431-mecA-deltamecR1-IS431 https://www.mdpi.com/2079-6382/11/1/86/htm
E mecI–mecR1–mecA–blaZ https://www.sciencedirect.com/science/article/pii/S1473309911701268

C1 & C2 is431 have different orientations

image

rpetit3 commented 2 years ago

For subtypes 

J regions: regions other than mec and ccr gene complexes.
Besides the mec and ccr gene complexes, the SCCmec element also contains three so-called J regions, 
which constitute nonessential components of the cassette. These regions may carry additional antimicrobial 
resistance determinants. They were first designated as the L-C, C-M, and I-R regions but were later changed 
to J regions. We propose that the term J region refers to “joining region,” rather than the previously 
used “junkyard region.”

J1 (formerly L-C) is the region between the right chromosomal junction and the ccr complex, J2 (C-M) is 
between the ccr gene complex and the mec gene complex, and J3 (I-R) is between the mec complex and 
the left chromosomal junction. Variations in the J regions within the same mec-ccr complex are used for 
defining SCCmec subtypes.

source https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786320/

incoherentian commented 6 months ago

Hi Robert! I think this would be the place you'd mention it if this tool's blastn db gets preliminary updates, so I'm posting here to be among the first to know as much as anything else :)

P.S. FYI I ran a mini-workshop to get some graduate & project students up on bactopia for gram pos work last month - two of the participants were very excited about merlin giving them SCCmec results via this, yet another of your apparently infinite awesome tools :p IIRC one of the students had a potentially questionable negative result I didn't really consider again until seeing your ruminations in https://github.com/bactopia/bactopia/issues/467 referenced just above. I'm not too worried about that (probably from too low coverage honestly, training folks with their project isolates on old flow cells can be hit or miss), but it would be nice to have confidence that causation ≠ missing any types from the blastdb staphopia-sccmec.py points to.

P.P.S. rumination revenge: With the incredible breadth amrfinder+ includes, I'm a little surprised it doesn't include all the SCCmec determinants. Perfect fit for the "+" expanded scope right? If it did you could probably skip the extra BLAST and "just" have a staphopia-sccmec script parse their %coverage and %ID from that preexisting output? A future amrfinder+ inclusion, hopefully, so db maintenance/hosting wouldn't fall to you :)

rpetit3 commented 2 months ago

@incoherentian by chance are interested in testing https://github.com/rpetit3/sccmec ?

JFsanchezherrero commented 2 months ago

Looking forward for new updates and new sccmecs identified!