Table 1

Strains used for comparative genomic analysis

Strain designation^a

Source, geographic origin, lineage^b

Genome size (Mbp)^C

Hemolytic activity

Pathogen^d

Genbank acc. number or Genome project ID^e

L. monocytogenes

F2365^†

food, listeriosis outbreak, CA, USA, 1985, lineage I

2.91

+

+

AE017262

EGD-e^†

lab strain derived from isolate of rabbit, England, 1924, lineage II

2.94

+

+

AL591824

FSL F2-208*

blood, human listeriosis case, USA, 1999, lineage IIIC

3.20

+

+

ADXE00000000*

HCC23^†

naturally avirulent serotype 4a strain from catfish, USA, lineage IIIA

2.98

+

-

CP001175

CLIP80459^†

human epidemic, France, 1999, lineage I

2.91

+

+

FM242711

L. marthii

FSL S4-120*

soil, forest, NY, USA, 2001

2.87

-

-

ADXF00000000*

L. innocua

CLIP11262^†

food, Morocco

3.01

-

-

AL592102

FSL S4-378*

puddle of water, NY, USA, 2002

3.09

-

-

ADXG00000000*

FSL J1-023*

obtained from Qualicon, exact origin unknown

2.91

+

-

ADXH00000000*

L welshimeri

SLCC5334^†

decaying vegetation, USA

2.81

-

-

AM263198

L. ivanovii

FSL F6-596*

food, France

3.10

+

+

ADXI00000000*

L. seeligeri

FSL N1-067*

food processing plant, NY, USA

3.09

+

-

ADXJ00000000*

FSL S4-171*

urban environment, NY, USA, 2001

2.89

-

-

ADXK00000000*

^a A † indicates strains for which the complete genome sequence is publicly available, an * indicates strains that were sequenced as part of the study reported here. The L. ivanovii strain sequenced here is the type strain of L. ivanovii subsp londoniensis (ATCC 49954). L. monocytogenes FSL R2-574, a duplicate of L. monocytogenes F2365, was sequenced to assess the performance of the sequence and genome assembly methods.

^b For L. monocytogenes the intraspecific phylogenetic lineage to which the isolates belong is indicated.

^c Sizes of newly sequenced genomes were derived from the sum of the length of all contigs from the de novo assembly.

^d All L. monocytogenes strains were classified as pathogens based on their involvement in clinical cases and/or their virulence in mouse studies (i.e., EGD-e [86], F2365 [87]) except for L. monocytogenes HCC23, which has been shown to be non-pathogenic [78]. The hemolytic L. innocua FSL J1-023 was considered non-pathogenic based on its avirulence in a mouse infection experiment [22]. All non-hemolytic strains were considered avirulent as they lack the prfA virulence cluster. Avirulence for some strains was also supported by animal experiments (i.e., L. welshimeri [77]; L. innocua CLIP11262 [21]) or tissue culture data (i.e., L. marthii [1]). The hemolytic L. seeligeri strain was considered avirulent as it shows low invasion efficiencies for Caco-2 cells (comparable to avirulent L. innocua; see Figure 5) and as other hemolytic L. seeligeri strains have been shown to be avirulent in mouse infection experiments [77].

^e Accession numbers marked with an asterisk have been deposited as Whole Genome Shotgun projects at DDBJ/EMBL/GenBank under the accession xxxx00000000. The version described in this paper is the first version, xxxx01000000.

den Bakker et al. BMC Genomics 2010 11:688   doi:10.1186/1471-2164-11-688