Why the discovery of adherent-invasive Escherichia coli molecular markers is so challenging?

Table 3 Summary of the comparative genomics studies conducted in adherent-invasive Escherichia coli to date

Ref.	AIEC	Non-AIEC	Phylogroup	AIEC origin of isolation
Miquel et al[27], 2010	1	211	AIEC: B2; Commensals: 4A, 2B1, 1B2; ExPEC: 2B1, 6B2, 3D, 3E	From an I-CD patient
Nash et al[28], 2010	2	101	AIEC: B2; Commensals: 2A; ExPEC: 7B2, 1E	From I-CD patients
Dogan et al[31], 2014	24	25	14 strains from A phylogroup, 16 B1, 10 B2 and 9 D2	From I-CD patients and controls
Desilets et al[32], 2015	143	6	AIEC: A: 1; B1: 1; B2: 10; D: 1; F: 1. non-AIEC: A: 2; B1: 2; B2: 2	From CD and UC patients[47]
Zhang et al[35], 2015	13	11	AIEC: 1A, 1B1, 4B2, 1D, 5 Unknown. non-AIEC: 3A, 8 Unknown	From CD and UC patients and non-CD subjects
Deshpande et al[33], 2015	4	13071	All B2	From CD patients
O’Brien et al[34], 2015	11	30	All B2, ST95	From IBD patients and controls
Camprubí-Font et al[36], 2018	3	3	AIEC: 1 B1, 1 B2 and 1 D. Non-AIEC: 1 B1, 1 B2 and 1 D	From CD patients and controls

The strain collection examined according to pathotype and phylogroup is depicted. Adherent-invasive Escherichia coli origin of isolation and study observations are also presented.

¹Include commensals and ExPEC.

²Human AIEC: 1A, 1B1, 1B2 and 1D; Murine AIEC: 1B1 and 1 B2; Dog AIEC: 2 B2; Human non-AIEC A phylogroup.

³Apart from LF82, UM146 and NRG857c the other strains were only assessed for intramacrophage replication in J774 cells. AIEC: Adherent-invasive Escherichia coli; CD: Crohn’s disease; UC: Ulcerative colitis.