Table 1 A non-exhaustive list of broadly used A. baumannii strains and some of their variants including sequencing platform and assembly software, if available
From: Inter- and intra-bacterial strain diversity remains the “elephant in the (living) room”
GIVEN NAME | REFERENCE | GENBANK ACCESSION NUMBERS | SEQUENCING PLATFORM* | ASSEMBLER* |
|---|---|---|---|---|
AB5075-UW | BioSample: SAMN36911450, JAVSCP000000000.1, SAMN02894434 | MiSeq (Illumina), PacBio | Unicycler, HGAP v. 2.0 | |
AB5075-VUB | BioSample: SAMN17898087, CP070362.2 (chromosome), CP070363.1 (pAB5075-VUB_1), CP070364.1 (pAB5075-VUB_2), CP070365.1 (pAB5075-VUB_3) | Oxford Nanopore MinION; Illumina | Flye v. 2.8.2 | |
AB5075_WT | BioSample: SAMN10580593, SRA: SRS4138705 | MiSeq (Illumina) | N/A | |
AB5075 | BioSample: SAMN20368080, SRA: SRS9575594 | MiSeq (Illumina) | N/A | |
AB5075-BLOKESCHLAB | BioSample: SAMN31681936, SRA: SRS15726398 | PacBio RSII | HGAP v. 3.0 | |
ATCC 17978 | BioSample: SAMN02604331, CP000521.1 (chromosome), CP000522.1 (pAB1), CP000523.1 (ATCC 17978 pAB2) | 454 | Sequencher assembly program (Gene Codes) | |
17978-MFF | BioSample: SAMN03817043, CP012004.1 (chromosome), CP012005.1 (pAB3) | Illumina; PacBio | SPAdes v. 2.5.0; HGAP v. 2.2.0.133377-patch-3 | |
17978 VU | BioSample: SAMN04273153, CP018664.1 (chromosome) | MiSeq (Illumina) | Geneious v. 9.1.5 | |
17978 UN | BioSample: SAMN20326334, CP079931.1 (chromosome), CP079932.1 (pAB3), CP079933.1 (pAB1), CP079934.1 (pAB2) | Oxford Nanopore | Unicycler v. 0.4.8 | |
ATCC17978-VUB | BioSample: SAMN25131675, CP091335.1 (chromosome) | Oxford Nanopore MinION; Illumina | Flye v. 2.9 | |
ATCC17978-BLOKESCHLAB | BioSample: SAMN15507625, CP059041.1 (chromosome), CP059042.1 (plasmid unnamed) | PacBio RSII | HGAP v. 3.0 | |
ATCC 17978 | BioSample: SAMN14217790, CP049363.1 (chromosome), CP049364.1 (pAB1), CP049365.1 (pAB2) | PacBio | Pacbio v. 20 K | |
ATCC 17978 SUBSTR. LAB-WT | BioSample: SAMN11304548, CP039028.2 (chromosome), CP039027.1 (plasmid unnamed1), CP039029.1 (plasmid unnamed2), CP039030.1 (plasmid unnamed3) | PacBio | PacBio SMRT Analysis v. 2.3.0 | |
ATCC17978 | BioSample: SAMN35788762, SRA: SRS18007186 | NovaSeq 6000 (Illumina) | N/A | |
ATCC17978 M_AB_NON_SELECTIVE | BioSample: SAMN37365860, SRA: SRS18868469 | HiSeq X Ten (Illumina) | N/A | |
ATCC17978 | Leyn A,S.; Sanford Burnham Prebys Medical Discovery Institute (Unpublished) | BioSample: SAMEA6463085, CACVBA000000000.1 (4 contigs) | Nanopore + Illumina | N/A |
AB_ATCC17978 | Monk,J.M.; UC San Diego (Unpublished) | BioSample: SAMN14779651, CP053098.1 (chromosome), CP053099.1 (plasmid unnamed1), CP053100.1 (plasmid unnamed2) | Oxford Nanopore MinION; HiSeq (Illumina) | Unicycler v. 0.4.2 |
ATCC17978 | Third Military Medical University, China (Unpublished) | BioSample: SAMN06169813, SRA: SRS1874154 | HiSeq 2500 (Illumina) | N/A |
ATCC19606 | BioSample: SAMD00206871, AP022836.1 (chromosome), AP022837.1 (pATCC19606-1), AP0228338.1 (pATCC19606-2) | Illumina MiniSeq; ONT MinION | Unicycler v. 0.4.6. | |
ATCC 19606 | BioSample: SAMN12389466, CP045110.1 (chromosome), CP045108.1 (p1ATCC19606), CP045109.1 (p2ATCC19606) | Illumina MiSeq; Oxford Nanopore MiniION | “Hybrid assembly v. July-31” | |
ATCC19606-VUB | BioSample: SAMN25131676, CP091334.1 (chromosome) | MiSeq (Illumina) | Geneious v. 9.1.5 | |
ATCC19606-BLOKESCHLAB | BioSample: SAMN15507635, CP059040.1 (chromosome) | PacBio RSII | HGAP v. 3.0 | |
ATCC 19606 | BioSample: SAMN13045090, CP046654.1 (chromosome), CP046655.1 (pMAC) | PacBio RSII | HGAP v. 3.0 | |
ATCC19606 | BioSample: SAMN35788763, SRA: SRS18007187 | NovaSeq 6000 (Illumina) | N/A |
