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Table 1 Gene-specific PCR and Sanger sequencing validation of differences detected by NGS

From: Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak

 

N. meningitidisserogroup C isolates

CDS ID

A

K1207

B

C

D

E

F

S0108

G

 

Nov 2007

Dec 2007

Dec 2007

Dec 2007

Dec 2007

Dec 2007

Dec 2007

Jan 2008

Apr 2008

K1207-specific CDSs

         

GI:352289428 (SacB, capsular polysaccharide phosphotransferase)

-

+

+

+

+

+

+

-

-

GI:254805876 (putative endonuclease)

-

+

+

+

+

+

+

-

-

GI:388935 (TDP-deoxymannose-dehydratase)

-

+

+

+

+

+

+

-

-

GI:254673887 (lipA5, capsule polysaccharide modification protein)

-

+

+

+

+

+

+

-

-

GI:254671124 (hypothetical protein)

-

+

+

+

+

+

+

-

-

S0108-specific CDSs

         

GI:121635673 (putative pilin)

+

-

-

-

-

-

-

+

+

GI:254673874 (hypothetical protein)

+

-

-

-

-

-

-

+

+

GI:254671515 (LipA, Capsule polysaccharide export protein)

+

-

-

-

-

-

-

+

+

GI:385323246 (hypothetical protein)

+

-

-

-

-

-

-

+

+

MLST

ST-11/ET-37

ST-11/ET-37

ST-11/ET-37

ST-11/ET-37

ST-11/ET-37

ST-11/ET-37

ST-11/ET-37

ST-11/ET-37

ST-11/ET-37

PorA VR1/2

P1.5-1, 10-8

P1.5-1,10-8

P1.5-1,10-8

P1.5-1,10-8

P1.5-1,10-8

P1.5-1,10-8

P1.5-1,10-8

P1.5-1,10-8

P1.5-1,10-8

  1. + present, by PCR; - not present, by PCR.
  2. The target CDSs that were specifically detected in the K1208 and S0108 genomes by 454 pyrosequencing were validated by means of PCR and Sanger sequencing. Then, they were searched also in N. meningitidis isolates A-G, which represent all the N. meningitidis serogroup C isolates classified as ST-11/ET-15 that were collected in Veneto Region in 2007–2008. Isolates B-F show the same pattern of K1207 and are classified as “outbreak cases”; isolates A and G are sporadic cases and are similar to S0108.