TABLE 3

Chromosome and plasmids of FAM21845

Genetic locationSize (bp)% G+CNo. of CDSAMR gene(s)aOther resistance gene(s)Biofilm-relevant operon(s)bPlasmid replicon(s)cPlasmid maintenanceAccession no.
FAM21845 chromosome4,901,98951.04,812β-Lactam resistance: ampC (ampH)Arsenic resistance: arsRBC, arsRDABCCellulose synthesis: bcsABZC, bcsEFGCP017220
Other: RND efflux pumpsSilver resistance: silRSE, silCFBAPCurli synthesis: csgDEFG, csgBAC
Copper resistance: cusCFBA, cusRS, pcoABCDRSEPGA synthesis: pgaABCD
Other: see Table S3 in the supplemental materialColanic acid synthesis: wza to wcaL
pFAM21845_1147,22551.7174Tetracycline resistance: tet(B)Mercury resistance: merR, merTPCADEIncFIApemIK, ccdAB, vapBC, hok/sok, srnB/CCP017221
Aminoglycoside resistance: strA (2×), strB (2×), aph(3′)-Ic, aph(4)-Ia, aac(3)-IVa, aadA1Disinfectant resistance: qacEΔ1IncFIB (AP001918)
Trimethoprim resistance: dfrA1IncFII (pCoo)
Sulfonamide resistance: sul1
β-Lactam resistance: blaTEM-1
pFAM21845_254,15944.957β-Lactam resistance: blaTEM-1Type III fimbriae: mrkABCDFIncX1stbDECP017222
pFAM21845_35,82846.68CP017223
pFAM21845_42,45448.84CP017224
pFAM21845_51,93451.42CP017225
  • a Antimicrobial resistance (AMR) genes were detected by use of the NCBI annotation pipeline, using BLAST searches against β-lactamase sequences (http://www.lahey.org/studies/; accessed October 2016), the ARG-ANNOT database (http://www.mediterranee-infection.com/article.php?laref=282&titer=arg-annot) (94), and ResFinder 2.1 with default settings (%ID threshold of 90.00% and minimum length of 60%) (https://cge.cbs.dtu.dk/services/ResFinder/; accessed October 2016) (91). ampC encodes a class C β-lactamase; ampH encodes a d-alanyl-d-alanine-carboxypeptidase/endopeptidase closely related to AmpC β-lactamases, with very-low-level β-lactamase activity (98). RND efflux pumps, resistance-nodulation-cell division efflux pumps (AcrAB, AcrAD, AcrEF, MdtABC, and MdtEF, each with TolC and CusCFBA) with broad substrate ranges including antimicrobials (43).

  • b PGA, poly-beta-1,6-N-acetyl-d-glucosamine (poly-β-1,6-GlcNAc). The bcs operon lacks bcsQ and bcsR.

  • c Detected using PlasmidFinder 1.3 with default settings (95% ID threshold) (https://cge.cbs.dtu.dk/services/PlasmidFinder/; accessed October 2016) (92).