Pathogenicity island markers, virulence determinants malX and usp, and the capacity of Escherichia coli to persist in infants' commensal microbiotas.

Virulence-associated genes in bacteria are often located on chromosomal regions, termed pathogenicity islands (PAIs). Several PAIs are found in Escherichia coli strains that cause extraintestinal infections, but their role in commensal bowel colonization is unknown. Resident strains are enriched in adhesins (P fimbriae and type 1 fimbriae), capsular antigens (K1 and K5), hemolysin, and aerobactin and mostly belong to phylogenetic group B2. Here, we investigated whether six pathogenicity islands and the virulence determinants malX and usp are associated with fitness of E. coli in the infant bowel microbiota. E. coli strains isolated from stools of 130 Swedish infants during the first year of life were examined for their carriage of PAI markers, malX, and usp by PCR. Carriage was related to strain persistence: long-term colonizers (≥12 months) carried significantly more of PAI II from strain CFT703 (II(CFT703)), IV(536,) and II(J96) and malX and usp than intermediate colonizers (1 to 11 months) and transient strains (<3 weeks). The accumulation of PAI markers in each individual strain correlated positively with its time of persistence in the colon. Phylogenetic group B2 accounted for 69% of long-term colonizers, 46% of intermediate colonizers and 14% of transient strains. These results support the hypothesis that some bacterial traits contributing to extraintestinal infections have in fact evolved primarily because they increase the fitness of E. coli in its natural niche, the colon; accordingly, they may be regarded as fitness islands in the gut.