Pathogen that turns up regularly in gill pouches (1,4)
I believe the answer is:
'pathogen' is the definition.
(E coli is a pathogenic bacterium)
'turns up regularly in gill pouches' is the wordplay.
'turns up' is a reversal indicator.
'regularly in' indicates alternate letters.
The alternating letters of 'gillpouches' are 'iloce'.
'iloce' back-to-front is 'E COLI'.
'that' is the link.
(Other definitions for e coli that I've seen before include "Cause of internal problem" , "cause of illness" , "cause of serious complaint" , "cause of ill-feeling" , "An infection found in food and water" .)