Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential

Figures & data

Characteristics and phenotype data for Campylobacter concisus strains used in the study

Strain	Patient	Patient group	Sample type	Diagnosis	Country of origin	Sequencing platform
2009–118452	2009–118452	Adult	Faecal	Crohn’s disease	Denmark	IM
2009–119100	2009–119100	Adult	Faecal	Collagenous colitis	Denmark	IM
2009–129008	2009–129008	Adult	Faecal	Gastroenteritis	Denmark	IM
2009–130586	2009–130586	Adult	Faecal	Gastroenteritis	Denmark	IM
2009–158448	2009–158448	Adult	Faecal	Collagenous colitis	Denmark	IM
2009–173039	2009–173039	Adult	Faecal	Gastroenteritis	Denmark	IM
2009–42653	2009–42653	Adult	Faecal	Gastroenteritis	Denmark	IM
2009–75710	2009–75710	Adult	Faecal	Gastroenteritis	Denmark	IM
2009–75775	2009–75775	Adult	Faecal	Crohn’s disease	Denmark	IM
2009–86120	2009–86120	Adult	Faecal	Bloody diarrhoea	Denmark	IM
2009–91522	2009–91522	Adult	Faecal	Crohn’s disease	Denmark	IM
2010–112100-F	2010–112100	Adult	Faecal	Crohn’s disease	Denmark	IM
2010–112100-O	2010–112100	Adult	Saliva	Crohn’s disease	Denmark	IM
2010–112708	2010–112708	Adult	Faecal	Bloody diarrhoea	Denmark	IM
2010–112758	2010–112758	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–112825	2010–112825	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–113332-F	2010–113332	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–113332-O	2010–113332	Adult	Saliva	Gastroenteritis	Denmark	IM
2010–113862	2010–113862	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–113862-O	2010–113862	Adult	Saliva	Gastroenteritis	Denmark	IM
2010–115605-F	2010–115605	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–115605-O	2010–115605	Adult	Saliva	Gastroenteritis	Denmark	IM
2010–131105	2010–131105	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–16206	2010–16206	Adult	Faecal	Collagenous colitis	Denmark	IM
2010–164712	2010–164712	Adult	Faecal	Bloody diarrhoea	Denmark	IM
2010–1718	2010–1718	Adult	Faecal	Crohn’s disease	Denmark	IM
2010–25654-F	2010–25654	Adult	Faecal	Bloody diarrhoea	Denmark	IM
2010–25654-O	2010–25654	Adult	Saliva	Bloody diarrhoea	Denmark	IM
2010–30795	2010–30795	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–30800	2010–30800	Adult	Faecal	Lymphocytic colitis	Denmark	IM
2010–31374	2010–31374	Adult	Faecal	Bloody diarrhoea	Denmark	IM
2010–33561	2010–33561	Adult	Faecal	Crohn’s disease	Denmark	IM
2010–34330	2010–34330	Adult	Faecal	Crohn’s disease	Denmark	IM
2010–347972	2010–347972	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–36743	2010–36743	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–378007-F	2010–378007	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–378007-O	2010–378007	Adult	Saliva	Gastroenteritis	Denmark	IM
2010–43100	2010–43100	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–6073	2010–6073	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–8194	2010–8194	Adult	Faecal	Gastroenteritis	Denmark	IM
2010–88823	2010–88823	Adult	Faecal	Gastroenteritis	Denmark	IM
2012–164712	2012–164712	Adult	Faecal	Bloody diarrhoea	Denmark	IM
2012–191940	2012–191940	Adult	Faecal	Gastroenteritis	Denmark	IM
2012–37302	2012–37302	Adult	Faecal	Gastroenteritis	Denmark	IM
2013–101463	2013–101463	Adult	Faecal	Gastroenteritis	Denmark	IM
2013–39845	2013–39845	Adult	Faecal	Gastroenteritis	Denmark	IM
2013–42088	2013–42088	Adult	Faecal	Gastroenteritis	Denmark	IM
2013–87946	2013–87946	Adult	Faecal	Gastroenteritis	Denmark	IM
B124_Slimy-small	B124	Paediatric	Biopsy	Crohn’s disease	UK	IM
B124_Small-clear	B124	Paediatric	Biopsy	Crohn’s disease	UK	IM + PB-RSII
B124_Small-grey	B124	Paediatric	Biopsy	Crohn’s disease	UK	IM
B38_Tiny-mucoid	B38	Paediatric	Biopsy	Crohn’s disease	UK	IM + PB-RSII
B124_Slimy-large	B124	Paediatric	Biopsy	Crohn’s disease	UK	IM

IM Illumina MiSeq, PB-RSII PacBio-RSII

Fig. 1 Phylogenetic tree based on whole genome sequences of Campylobacter concisus strains used in this study, incorporating all published genomes.

Columns: Full stars represent Faecal samples, empty stars represent Oral samples. Squares represent presences in genome assemblies and circles presence in plasmid assemblies. Red represents Exo9 whilst blue represents ZOT presence. Full shapes indicate presence, empty shapes indicate absence. For plasmids, there are some samples with no shape, this indicates that plasmidSPAdes software was unable to assemble any plasmids for the sample

Clinical source of strains based on ZOT and Exotoxin 9 positivity as well as the percentage of isolates that belonged to Genomospecies (GS) I and II

Clinical source	Total strains	ZOT positivity	Exotoxin 9 positivity	GSI	GSII
CD	29	72.41	72.41	10.34	89.66
Gastroenteritis	31	70.97	51.61	35.48	64.52
Lymphocytic colitis	1	100	100	0	100
Collagenous colitis	3	33.33	100	33.33	66.67
Bloody diarrhoea	8	100	37.5	50	50
Periodontal disease	1	100	100	100	0
Healthy	11	72.73	63.64	27.27	72.73
UC	4	25	50	50	50
All	88	71.59	60.22	28.41	71.59

GS genomospecies; CD Crohn’s disease, UC ulcerative colitis

Fig. 2 Presence of virulence factors in genomes of isolates sequenced for this study.

Contains VFDB hits from the VFDB all dataset. Virulence factors were detected using the Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB). There are two colour columns representing metadata for the samples. The first represents the disease presentation of the host with a legend available. The second represent the genomospecies (GS) of the isolate with “red” referring to GSI and “blue” to GSII

Fig. 3 T4SS and T6SS presence within the assembled genomes.

There are two colour columns representing metadata for the samples. The first represents the host disease presentation with a legend available. The second represent the GS of the isolate with red referring to GSI and blue to GSII

Fig. 4 a Pangenome summary of all C. concisus used in this study. The figure displays the number of genes found to be shared across a certain percentage of samples in different groupings of isolates. This figure uses a bin size of 5% on the x-axis. GS Genomospecies, and b Pangenome summary of all Campylobacter. This was produced by carrying out pangenome analysis of all the C. concisus isolates and one reference assembly for each non-C. concisus species that was available. The figure displays how many genes were found to be shared across a certain percentage of samples in different groupings of isolates. The figure depicts a bin size of 5% on the x-axis

Fig. 5 Plasmid KEGG Orthology (ko0001) KEGG BRITE hierarchies present within the amino acid sequences present in plasmid sequences of samples.

Hierarchies which were shared by five or fewer isolates were not included. There are two colour columns representing metadata for the samples. The first represents host disease presentation with a legend available. The second represent the GS of the isolate with “red” referring to GSI and “blue” to GSII

Fig. 6 Phylogenetic tree. a

Phylogenetic tree of faecal/oral paired samples based on the whole genome and b Heatmap of genes found to be core only in oral samples and core in only faecal samples from oral/faecal paired samples. Columns: Full stars represent faecal samples, empty stars represent oral samples. Squares represent presence in genome assemblies and circles presence in plasmid assemblies. “Red” represents Exo9 whilst “blue” represents ZOT presence. Full shapes indicate presence, empty shapes indicate absence. For plasmids, there are some samples with no shape. This indicates that plasmids were not assembled for this sample. Heatmap: There are two colour rows representing metadata for the samples. The first represents the host disease presentation with a legend available. The second represent the GS of the isolate with “red” referring to GSI and “blue” to GSII