Shigella sonnei
is a major cause of bacillary dysentery, and of increasing concern due to the spread of multi-drug resistance.
S. sonnei
harbours pINV, a ∼ 210 kb plasmid that encodes a Type III secretion system (T3SS), which is essential for virulence. During growth in the laboratory, avirulence arises spontaneously in
S. sonnei
at high frequency, hampering studies on and vaccine development against this important pathogen. Here we investigated the molecular basis for the emergence of avirulence in
S. sonnei
, and show that avirulence mainly results from pINV loss, consistent with previous findings. Ancestral deletions have led to the loss from
S. sonnei
pINV of two toxin:antitoxin (TA) systems involved in plasmid maintenance, CcdAB and GmvAT, which are found on pINV in
Shigella flexneri
. We show that introduction of these TA systems into
S. sonnei
pINV reduced but did not eliminate pINV loss, while single amino acid polymorphisms found in the
S. sonnei
VapBC TA system compared with
S. flexneri
VapBC also contribute to pINV loss. Avirulence also results from deletions of T3SS-associated genes on pINV through recombination between insertion sequences (ISs) on the plasmid; these events differ from those observed in
S. flexneri
due to the different distribution and repertoire of ISs. Our findings demonstrate that TA systems and ISs influence plasmid dynamics and loss in
S. sonnei
, and could be exploited for the design and evaluation of vaccines.
IMPORTANCE
Shigella sonnei
is the major cause of shigellosis in high-income and industrialising countries, and an emerging multi-drug resistant pathogen. A significant challenge when studying this bacterium is that it spontaneously becomes avirulent during growth in the laboratory, through loss of its virulence plasmid (pINV). Here we decipher the mechanisms leading to avirulence in
S. sonnei
and how the limited repertoire and amino acid sequences of plasmid-encoded toxin:antitoxin (TA) systems make the maintenance of pINV in this bacterium less efficient compared with
Shigella flexneri
. Our findings highlight how subtle differences in plasmids in closely-related species have marked effects and could be exploited to reduce plasmid loss in
S. sonnei
. This should facilitate research on this bacterium and vaccine development.