TABLE 1.
Properties of Mycobacterium abscessus clinical isolates
| Straina | Originb | CFc | Sspd | R/Se | Seqf | Prophagesg | Plasmidsh |
|---|---|---|---|---|---|---|---|
| GD01 | London, UK | Y | m | R | Com | None | None |
| GD02 | London, UK | Y | m | R | WGS | prophiGD02-1 (MabN), prophiGD02-2 (MabA2) | pGD02 (pF) |
| GD03 | Seattle, WA | N | m | S | WGS | prophiGD03-1 (MabG) | None |
| GD04 | Los Angeles, CA | Y | m | S | WGS | prophiGD04-1 (MabE1) | None |
| GD05 | Winston-Salem, NC | N | a | R | Com | prophiGD05-1 (MabD), prophiGD05-2 (MabH), prophiGD05-3 (MabM) | None |
| GD08 | Indianapolis, IN | Y | a | R | WGS | prophiGD08-1 (MabA1), prophiGD08-2 (MabB), prophiGD08-3 (MabF) | pGD08 (pA) |
| GD09 | Netherlands | Y | a | S | WGS | prophiGD09-1 (MabE1) | None |
| GD10 | Pittsburgh, PA | N | m | R | WGS | prophiGD10-1 (MabA1) | pGD10 (pSin) |
| GD11 | Pittsburgh, PA | Y | a | R | WGS | prophiGD11-1 (MabA1), prophiGD11-2 (MabB), phophiGD11-3 (MabF) | None |
| GD12 | Pittsburgh, PA | NA | a | R | WGS | prophiGD12-1 (MabA1), prophiGD12-2 (MabD) | None |
| GD13 | Pittsburgh, PA | NA | a | R | WGS | prophiGD13-1 (MabA1), prophiGD13-2 (MabC) | pGD13 (Sin) |
| GD14 | Pittsburgh, PA | NA | a | R | WGS | prophiGD14-1 (MabA1), prophiGD14-2 (MabD) | None |
| GD15 | Pittsburgh, PA | NA | a | R | WGS | prophiGD15-1 (MabA1) | None |
| GD16 | St Louis, MO | Y | m | S | WGS | prophiGD16-1 (MabB), prophiGD16-2 (MabA2) | pGD16 (pH) |
| GD17 | Durham, NC | Y | a | R | Com | prophiGD17-1 (MabD), prophiGD17-2 (MabA1) | None |
| GD18 | San Diego, CA | N | a | S | WGS | None | pGD18 (pB) |
| GD19 | San Diego, CA | Y | a | R | Com | None | pGD19 (pD) |
| GD20 | Durham, NC | Y | a | R | Com | prophiGD20-1 (MabA1) | None |
| GD21 | Baton Rouge, LA | N | a | S | Com | prophiGD21-1 (MabB), prophiGD21-2 (MabA1), prophiGD21-3 (MabG), prophiGD21-4 (MabJ) | pGD21-1 (pSin), pGD21-2 (pSin) |
| GD22 | Pittsburgh, PA | Y | a | R | Com | prophiGD22-1 (MabA1) | pGD22-1 (pSin), pGD22-2 (pC) |
| GD23 | St. Louis, MO | NA | a | R | WGS | prophiGD23-1 (MabA1) | pGD23 (pB) |
| GD24 | Genoa, Italy | Y | a | R | WGS | prophiGD24-1 (MabA1), prophiGD24-2 (MabG), prophiGD24-3 (MabJ) | pGD24 (pC) |
| GD25 | Anchorage, AL | Y | a | R | Com | prophiGD25-1 (MabE1) | pGD25-1 (pF), pGD25-2 (pG), pGD25-3 (pSin) |
| GD26 | Pittsburgh, PA | Y | a | R | Com | prophiGD26-1 (MabA1) | None |
| GD27 | Boston, MA | Y | a | R | WGS | prophiGD27-1 (MabA1) | None |
| GD28 | Durham, NC | NA | a | S | WGS | None | None |
| GD30 | Durham, NC | NA | m | R | WGS | prophiGD30-1 (MabA1) | None |
| GD33 | Illes Balears, Spain | Y | a | S | WGS | prophiGD33-1 (MabC) | pGD33 (pE) |
| GD34 | Boston, MA | N | a | S | WGS | prophiGD34-1 (MabA1), prophiGD34-2 (MabB) | pGD34 (pC) |
| GD35 | New York, NY | Y | a | R | WGS | prophiGD35-1 (MabA1) | None |
| GD36 | Vancouver, BC, Canada | N | a | S | WGS | prophiGD36-1 (MabA1), prophiGD36-2 (MabH) | pGD36-1 (pB), pGD36-2 (pE) |
| GD37 | Vancouver, BC, Canada | N | b | S | WGS | None | None |
| GD38 | Hamilton, ON, Canada | NA | a | R | Com | None | None |
| GD39 | Hartford, CT | Y | a | S | WGS | prophiGD39-1 (MabA1), prophiGD39-2 (MabC) | pGD39 (pC) |
| GD40 | NSW, Australia | Y | a | R | WGS | prophiGD40-1 (MabA1) | None |
| GD41 | Pittsburgh, PA | Y | a | R | Com | prophiGD41-1 (MabA1) | None |
| GD42 | Pittsburgh, PA | Y | a | S | Com | prophiGD42-1 (MabA1), prophiGD42-2 (MabB), prophiGD42-3 (MabC) | pGD42-1 (pB), pGD42-2 (pA) |
| GD43A | NSW, Australia | Y | a | S | Com | prophiGD43A-1 (MabA1), prophiGD43A-2 (MabB), prophiGD43A-3 (MabC), prophiGD43A-4 (MabJ), prophiGD43A-5 (MabK), prophiGD43A-6 (MabL) | None |
| GD43B | NSW, Australia | Y | a | R | Com | prophiGD43B-1 (MabL), prophiGD43B-2 (MabK), prophiGD43B-3 (MabA1), prophiGD43B-4 (MabJ) | None |
| GD44 | Winnipeg, Canada | N | m | S | WGS | prophiGD44-1 (MabC) | None |
| GD45 | Miami, FL | Y | a | R | WGS | prophiGD45-1 (MabE1) | pGD45-1 (pG), pGD45-2 (pD) |
| GD47 | Dallas, TX | N | a | S | WGS | prophiGD47-1 (MabA1) | pGD47 (pB) |
| GD51 | Portland, OR | Y | a | R | WGS | prophiGD51-1 (MabC), prophiGD51-2 (MabP) | pGD51 (pSin) |
| GD52 | Sheffield, UK | Y | a | R | WGS | prophiGD52-1 (MabC), prophiGD52-2 (MabE1) | pGD52 (pSin) |
| GD53 | Lebanon, NH | Y | m | S | WGS | prophiGD53-1 (MabE1), prophiGD53-2 (MabK), prophiGD53-3 (MabN) | None |
| GD54 | NSW, Australia | Y | a | R | Com | prophiGD54-1 (MabE1), prophiGD54-2 MabI) | pGD54 (pF) |
| GD55 | Cincinnati, OH | Y | a | S | WGS | prophiGD55-1 (MabL) | pGD55 (pSin) |
| GD56 | San Jose, CA | NA | a | R | WGS | prophiGD56-1 (MabC), prophiGD56-2 (MabH) | None |
| GD57 | Barcelona, Spain | Y | a | R | Com | prophiGD57-1 (MabC), prophiGD57-2 (MabA1) | None |
| GD58 | Chapel Hill, NC | NA | m | S | WGS | prophiGD58-1 (MabG), prophiGD58-2 (MabA1) | pGD58 (pH) |
| GD59 | Chapel Hill, NC | NA | a | R | Com | prophiGD59-1 (MabA1) | None |
| GD60 | San Diego, CA | N | m | R | WGS | prophiGD60-1 (MabL) | None |
| GD61 | San Jose, CA | NA | a | S | WGS | prophiGD61-1 (MabC), prophiGD61-2 (MabH) | None |
| GD62 | Baton Rouge, LA | N | a | R | WGS | prophiGD62-1 (MabB), prophiGD62-2 (MabF), prophiGD62-3 (MabN) | pGD62-1 (pB), pGD62-2 (pC) |
| GD63 | Memphis, TN | Y | a | S | WGS | None | None |
| GD64 | Cambridge, UK | N | a | S | WGS | None | None |
| GD68A | Long Beach, CA | Y | m | R | Com | prophiGD68-1 (MabE1) | None |
| GD68B | Long Beach, CA | Y | m | S | Com | prophiGD68-1 (MabE1) | None |
| GD69A | Long Beach, CA | N | a | R | Com | prophiGD69-1 (MabN) | pGD69-1 (pB), pGD69-2 (pC) |
| GD69B | Long Beach, CA | N | a | S | Com | prophiGD69-1 (MabN) | pGD69-1 (pB), pGD69-2 (pC) |
| GD72 | San Jose, CA | N | a | S | WGS | prophiGD72-1 (MabC) | pGD72 (pB) |
| GD75 | Charleston, SC | N | a | S | WGS | prophiGD75-1 (MabJ), prophiGD75-2 (MabA1) | pGD75 (pC) |
| GD79 | Bethesda, MD | N | m | R | WGS | prophiGD79-1 (MabQ) | None |
| GD81 | Hartford, CT | Y | a | S | WGS | prophiGD81-1 (MabA1) | None |
| GD82 | Baltimore, MD | N | m | R | WGS | prophiGD82-1 (MabC) | None |
| GD84 | Dallas, TX | N | a | S | WGS | prophiGD84-1 (MabA1), prophiGD84-2 (MabD) | None |
| GD85 | Ankara, Turkey | Y | a | S | WGS | None | pGD85 (pD) |
| GD86 | Jerusalem, Israel | Y | a | R | WGS | prophiGD86-1 (MabI), prophiGD86-2 (MabE1) | pGD86-1 (pF), pGD86-2 (pG) |
| GD87 | Jerusalem, Israel | Y | a | R | WGS | None | pGD87 (pB) |
| GD88 | Jerusalem, Israel | Y | a | R | WGS | prophiGD88-1 (MabL) | None |
| GD89 | Jerusalem, Israel | Y | a | R | WGS | prophiGD89-1 (MabB) | None |
| GD90 | Jerusalem, Israel | Y | m | S | WGS | prophiGD90-1 (MabA2) | None |
| GD91 | Bordeaux, France | N | b | S | Com | prophiGD91-1 (MabC), prophiGD91-2 (MabA3), prophiGD91-3 (MabO), prophiGD91-4 (MabE2) | None |
| GD92 | Jacksonville, FL | N | a | R | WGS | None | None |
| GD95 | Dallas, TX | N | a | R | WGS | prophiGD95-1 (MabG), prophiGD95-2 (MabN) | pGD95-1 (pB), pGD95-2 (pC) |
| GD97 | Bizkaia, Spain | Y | a | S | WGS | None | None |
| GD100A | Philadelphia, PA | NA | a | S | Com | prophiGD100A-1 (MabA1), prophiGD100A-2 (MabC) | pGD100 (pC) |
| GD100B | Philadelphia, PA | NA | a | R | Com | prophiGD100A-1 (MabA1), prophiGD100A-2 (MabC) | pGD100 (pC) |
| GD102 | Finland | Y | a | R | WGS | prophiGD102-1 (MabA1), prophiGD102 (MabE1) | pGD102-1 (pF), pGD102-2 (pG) |
| GD104 | Knoxville, TN | N | m | R | WGS | prophiGD104-1 (MabA1), phiGD104-2 (MabC) | pGD104 (pSin) |
| GD108 | Dallas, TX | NA | a | S | WGS | prophiGD108-1 (MabN) | pGD108 (pB) |
| GD111 | Morton Grove, IL | N | m | R | WGS | prophiGD111-1 (MabE1) | None |
a
Strains are given a GDXX designation; multiple isolates from the same patient are designated GDXXA, GDXXB, etc.
b
Strain origin indicates the location of the hospital or laboratory from which the strain was sent.
c
Indication of whether strain was from a cystic fibrosis patient; Y, yes; N, no; NA, data not available.
d
Subspecies derived from genome sequencing; a, abscessus; b, bolletii; m, massiliense.
e
Colony morphotype is shown as R, rough or S, smooth.
f
Genome sequencing with Illumina whole-genome sequencing (WGS) or Illumina and Nanopore to completion (Com).
g
Prophages are designated prophiGDXX, with -1, -2-, etc. extensions denoting different prophages in the same strain.
h
Plasmids are designated pGDXX, with -1, -2-, etc. extensions if there is more than one plasmid in the same strain.