Update included genomes

[erinyoung]

Right now this is what is included

Assembly Accession Assembly Refseq Category Assembly Level Organism Name Assembly Stats Total Ungapped Length GCF_008632635.1 representative genome Complete Genome Acinetobacter baumannii 3980230 GCF_000191145.1 reference genome Complete Genome Acinetobacter pittii PHEA-2 3862530 GCF_001558935.2 representative genome Complete Genome Citrobacter amalonaticus 5084037 GCF_003812345.1 representative genome Complete Genome Citrobacter freundii 5102161 GCF_000018045.1 representative genome Complete Genome Citrobacter koseri ATCC BAA-895 4735357 GCF_900638065.1 Complete Genome Citrobacter youngae 4867355 GCF_002023665.2 representative genome Complete Genome Elizabethkingia anophelis R26 4058311 GCF_007035805.1 representative genome Complete Genome Enterobacter asburiae 4768325 GCF_015137655.1 Complete Genome Enterobacter bugandensis 4635750 GCF_023702375.1 Contig Enterobacter cloacae 5112849 GCF_019048625.1 representative genome Complete Genome Enterobacter hormaechei 4762440 GCF_000534275.1 representative genome Scaffold Enterobacter kobei 4769038 GCA_002741475.1 Complete Genome Escherichia coli O27:H7 4952219 GCF_007632255.1 representative genome Complete Genome Klebsiella aerogenes 5249267 GCF_015139575.1 representative genome Complete Genome Klebsiella michiganensis 6041841 GCF_003812925.1 representative genome Complete Genome Klebsiella oxytoca 5879076 GCF_000240185.1 reference genome Complete Genome Klebsiella pneumoniae subsp. pneumoniae HS11286 5682322 GCF_016415705.1 representative genome Complete Genome Klebsiella quasipneumoniae 5391123 GCF_009648975.1 representative genome Complete Genome Klebsiella variicola 5536651 GCF_902387845.1 representative genome Complete Genome Morganella morganii 3906921 GCF_003019925.1 representative genome Complete Genome Pluralibacter gergoviae 5408082 GCF_000069965.1 representative genome Complete Genome Proteus mirabilis HI4320 4099895 GCF_003204135.1 representative genome Complete Genome Providencia rettgeri 4454136 GCF_023547145.1 Complete Genome Providencia stuartii 4837555 GCF_000006765.1 reference genome Complete Genome Pseudomonas aeruginosa PAO1 6264404 GCF_901421005.1 representative genome Contig Raoultella ornithinolytica 5606861 GCF_003516165.1 representative genome Chromosome Serratia marcescens 5238337 GCF_900475405.1 representative genome Complete Genome Stenotrophomonas maltophilia 4481118

[erinyoung]

From https://www.cdc.gov/hai/organisms/organisms.html:

Acinetobacter baumannii Burkholderia cepacia Clostridioides difficile Clostridium sordellii Staphylococcus aureus Pseudomonas aeruginosa Staphylococcus aureus

[erinyoung]

From Bioproject PRJNA288601 :

$ datasets summary genome accession PRJNA288601 --as-json-lines | dataformat tsv genome --fields organism-name | sort | uniq -c
   6887 Acinetobacter baumannii
      2 Acinetobacter nosocomialis
     24 Acinetobacter pittii
      1 Aeromonas hydrophila
      2 Alcaligenes faecalis
     11 Citrobacter amalonaticus
      1 Citrobacter braakii
      7 Citrobacter farmeri
    195 Citrobacter freundii
      2 Citrobacter freundii complex sp. 2022EL-00793
      2 Citrobacter freundii complex sp. 2022EL-00822
      2 Citrobacter freundii complex sp. 2022EL-00971
      2 Citrobacter freundii complex sp. 2022EL-00972
     11 Citrobacter koseri
      3 Citrobacter portucalensis
      2 Citrobacter sedlakii
     22 Elizabethkingia anophelis
     13 Enterobacter asburiae
      5 Enterobacter bugandensis
     23 Enterobacter cloacae
      2 Enterobacter cloacae complex sp. 2021EL-01169
      2 Enterobacter cloacae complex sp. 2021EL-01261
      2 Enterobacter cloacae complex sp. 2022EL-00747
      2 Enterobacter cloacae complex sp. 2022EL-00759
      2 Enterobacter cloacae complex sp. 2022EL-00787
      2 Enterobacter cloacae complex sp. 2022EL-00788
      2 Enterobacter cloacae complex sp. 2022EL-00981
      2 Enterobacter cloacae complex sp. 2023EL-00493
      2 Enterobacter cloacae complex sp. 2023EL-00494
      2 Enterobacter cloacae complex sp. 2023EL-00495
    240 Enterobacter hormaechei
      2 Enterobacter hormaechei subsp. steigerwaltii
      1 Enterobacter hormaechei subsp. xiangfangensis
      8 Enterobacter kobei
      8 Enterobacter ludwigii
      1 Enterobacter mori
     17 Enterobacter roggenkampii
      2 Enterobacter roggenkampii MGH 34
      2 Enterobacter sichuanensis
      4 Enterobacter soli
   1271 Escherichia coli
      1 Escherichia coli O2:H6
    119 Klebsiella aerogenes
     27 Klebsiella michiganensis
     54 Klebsiella oxytoca
     10 Klebsiella pasteurii
   3639 Klebsiella pneumoniae
     45 Klebsiella quasipneumoniae
     58 Klebsiella variicola
      1 Kluyvera ascorbata
      2 Leclercia adecarboxylata
     45 Morganella morganii
     16 Pluralibacter gergoviae
    256 Proteus mirabilis
      2 Proteus vulgaris
     12 Providencia huaxiensis
    218 Providencia rettgeri
     13 Providencia stuartii
      2 Providencia thailandensis
      2 Pseudocitrobacter sp. 2023EL-00150
   1130 Pseudomonas aeruginosa
      1 Pseudomonas putida
      2 Pseudomonas tohonis
     34 Raoultella ornithinolytica
      5 Raoultella planticola
      2 Salmonella enterica
     39 Serratia marcescens
      2 Serratia nevei
      1 Shigella dysenteriae
     26 Staphylococcus aureus
     12 Stenotrophomonas maltophilia

[erinyoung]

Alright, the new fastani reference is 218M

Let's hope this downloads okay.