Table 4.
Overview of whole genomea genes with most frequent within-host genetic changes in paired meningococcal carriage isolates. Genes belonging to the core genomeb are highlighted in bold italic
| NEIS no | Gene | Gene product | Function | % of pairsc with genetic difference | Mechanisms and percent of pairsd with genetic difference | ||||
|---|---|---|---|---|---|---|---|---|---|
| (n = 46) | All STs (n = 46) | ST-11 (n = 5) | ST-53 (n = 4) | ST-192 (n = 23) | ST-2880 (n = 7) | ||||
| NEIS0210 | pilE | pilin | Pilin | 85% | GC 85% | no change | GC 75% | GC 96% | GC 100% |
| pilS | pilS | pilin | Pilin | 76% | GC 76% | no change | GC 75% | GC 96% | GC 71% |
| NEIS2649 | - | hypothetical protein | Unknown | 74% | PM 37%, R 37% | PM 80%, R 20% | R 25% | PM 39%, R 39% | R 57%, PM 14% |
| NEIS1310 | modA | type III restriction/modification system methyltransferase | DNA repair | 70% | PV 70% | PV 100% | no change | PV 83% | PV 71% |
| NEIS1403 | opaB | opacity protein B | Outer membrane component | 63% | PV 59%, PM 2%, R 2% | PV 20% | PV 50% | PV 78% | PV 29% |
| NEIS1719 | opa1800 | outer membrane protein | Outer membrane component | 61% | PV 57%, R 9% | PV 20% | PV 50% | PV 78%, R 9% | PV 29% |
| NEIS1655 | relA | GTP pyrophosphokinase | Housekeeping | 47% | PM 43%, R 4% | PM 40% | PM 25% | PM 43%, R 4% | PM 57% |
| NEIS0400 | pglH | glycosyltransferase | Protein glycosylation system | 46% | PV 46% | PV 60% | no change | PV 74% | PV 14% |
| NEIS0401 | pglG | glycosyltransferase | Protein glycosylation system | 44% | PV 37%, R 7% | PV 40%, R 20% | PV 50% | PV 57%, R 9% | no change |
| NEIS0380 | pglI | O-acetyltransferase | Protein glycosylation system | 41% | PV 41% | PV 60% | gene absent | PV 52% | PV 43% |
| NEIS1829 | tspA | neisseria-specific antigen protein | Outer membrane component | 41% | R 33%, D 15%, PM 2%, I 2% | no change | D 25%, R 25% | R 61%, D 22%, PM 4% | no change |
| NEIS1750 | - | hypothetical protein | Unknown | 37% | PV 35%, PM 2% | PV 20% | no change | PV 43%, PM 4% | PV 29% |
| NEIS1946 | hpuA | haemoglobin-haptoglobin utilisation protein | Outer membrane component | 35% | PV 33%, PM 2%, R 2% | PV 40% | no change | PV 52%, PM 4%, R 4% | no change |
| NEIS1288 | - | putative aldehyde dehydrogenase | Putative housekeeping | 35% | R 22%, PM 13% | PM 20%, R 20% | PM 75% | R 26% | PM 29%, R 29% |
| NEIS1902 | lgtA | lacto-N-neotetraose biosynthesis glycosyl transferase | LOS biosynthesis | 34% | PV 30%, D 4% | no change | no change | PV 61%, D 9% | no change |
| NEIS1418 | - | putative membrane peptidase | Putative housekeeping | 33% | D 13%, R 11%, PM 9% | PM 20% | PM 25%, D 25% | D 22%, PM 9%, R 4% | R 57% |
| NEIS1852 | emrB | multidrug resistance translocase | Outer membrane component | 33% | PM 24%, R 9% | PM 60% | PM 50%, R 25% | PM 9% | PM 29%, R 29% |
D Deletion, GC gene conversion, I insertion, PM point mutation, PV phase variation, R recombination
aAll 2701 annotated genes accessible in Genome Comparator on pubMLST.org as of 27 Oct 2016
b1605 genes defined as the core genome (N. meningitidis cgMLST v1.0) in the database pubMLST.org
cPairs with any genetic differences. Pairs from individuals carrying different strains at the two time points were excluded from the analysis
dIn some pairs, more than one mechanism of genetic change were observed