Table 2 Support for infection transmission between patient pairs with potentially transmitted isolates.

From: The natural history and genetic diversity of Haemophilus influenzae infecting the airways of adults with cystic fibrosis

Patient pair

ST

Isolate pairsa

Distance threshold support

Phylogenetic support

Pangenome support

Carriage overlapb

Epidemiological support

A077, A319

12

A077-H36, A319-H65

Yes

No

No

No

No

A077-H201, A319-H65

A077, A366

12

A077-H36, A366-H58

Yes

No

Yes

No

No

A077-H36, A366-H201

A077-H138, A366-H58

A077-H138, A366-H201

A077-H201, A366-H58

A077-H201, A366-H201

A077-H202, A366-H58

A077-H202, A366-H201

A319, A366

12

A319-H65, A366-H58

Yes

No

No

Yes

Yes

A319-H65, A366-H210

A034, A132

103

A034-H64, A132-H67

Yes

Yes

Yes

Yes

No

A406, A407

145

A406-H162, A407-H184

Yes

No

Partialc

No

No

A406-H224, A407-H184

A090, A321

321

A090-H183, A319-H179

Yes

Yes

Yes

Yes

No

A037, A337

393

A037-H11, A337-H38

Yes

Yes

Yes

No

No

A037-H25, A337-H38

A037-H140, A337-H38

A058, A335

1034

A058-H09, A335-H158

Yes

No

No

No

No

A058-H09, A335-H223

A058-H216, A335-H158

A058-H216, A335-H223

  1. All isolate pairs that had pairwise p-distances below a threshold of 1.68 × 10−5 SNPs per site are included.
  2. aIsolate pairs are presented in the format “Patient Number-Isolate Number”.
  3. bCarriage overlap refers to detection of the associated H. influenzae isolates in both patients within 6 months of each other. It is a sub-category of Epidemiological Support.
  4. cPatient A407’s isolate clustered with one of patient A406’s isolates; the second isolate from patient A406 clustered separately from their first.
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