Genome comparison of Listeria monocytogenes serotype 4a strain HCC23 with selected lineage I and lineage II L. monocytogenes strains and other Listeria strains

Abstract

More than 98% of reported human listeriosis cases are caused by specific serotypes within genetic lineages I and II. The genome sequence of Listeria monocytogenes lineage III strain HCC23 (serotype 4a) enables whole genomic comparisons across all three L. monocytogenes lineages. Protein cluster analysis indicated that strain HCC23 has the most unique protein pairs with nonpathogenic species Listeria innocua. Orthology analysis of the genome sequences of representative strains from the three L. monocytogenes genetic lineages and L. innocua (CLIP11262) identified 319 proteins unique to nonpathogenic strains HCC23 and CLIP11262 and 58 proteins unique to pathogenic strains F2365 and EGD-e. BLAST comparison of these proteins with all the sequenced L. monocytogenes and L. innocua revealed 126 proteins unique to serotype 4a and/or L. innocua; 14 proteins were only found in pathogenic serotypes. Some of the 58 proteins unique to pathogenic strains F2365 and EGD-e were previously published and are already known to contribute to listerial virulence.

Keywords: Comparative genomics; Genetic lineage; Listeria monocytogenes; Virulence.

Fig. 1

Circular map of the Listeria monocytogenes serotype 4a strain HCC23 genome. From outside to inside, the circles represent: 1) COG group classification of proteins encoded on the positive strand, 2) CDS, tRNA, and rRNA on the positive strand, 3) CDS, tRNA and rRNA on the negative strand, 4) COG group classifications of proteins encoded on the negative strand, 5) BLAST results with L. monocytogenes serotype 1/2a strain EGD-e, 6) BLAST results with L. monocytogenes serotype 4b strain F2365, 7) G + C content, and 8) GC skew. BLAST results identified 11 clusters of strain HCC23-specific genes (labeled 1–11). COG group classifications:C

Energy production and conversion

D

Cell cycle control mitosis and meiosis

E

Amino acid transport and metabolism

F

Nucleotide transport and metabolism

G

Carbohydrate metabolism and transport

H

Coenzyme transport and metabolism

I

Lipid transport and metabolism

J

Translation

K

Transcription

L

DNA replication, recombination, and repair

M

Cell wall/membrane biogenesis

N

Cell motility

O

Posttranslational modification, protein turnover

P

Inorganic ion transport and metabolism

Q

Secondary metabolism biosynthesis, transport and catabolism

S

Function unknown

T

Signal transduction mechanisms

U

Intracellular trafficking and secretion

V

Defense mechanisms

.

Fig. 2

Visualization of synteny analysis of six Listeria strains. Parallel axes with lengths corresponding to the genome sizes are used to represent each genome, and a ribbon corresponding to the width of each gene is drawn to connect corresponding genes on the parallel axes. The use of a color spectrum across the genome is used to facilitate visualization of inversions, deletions, and insertions.

Fig. 3

Protein cluster analysis of six Listeria strains. Shared clusters are the number of protein clusters shared by both strains. Different clusters are the number of protein clusters present in only one of the strains. Pair unique clusters are the number of protein clusters present in these two strains and no other strains.