Vol. 277 no. 5333 pp. 1833-1834
DOI: 10.1126/science.277.5333.1833
Highly Variable Mutation Rates in Commensal and Pathogenic Escherichia coli
- ↵*To whom correspondence should be addressed.
Escherichia coli in humans is a commensal inhabitant of the gastrointestinal tract as well as one of the most frequently isolated bacterial pathogens (1). In studying food- borne E. coli pathogens, as well as the ECOR collection of natural isolates (2), LeClerc et al. found that mutant bacteria—defective in methyl-directed mismatch repair (MMR)—were present in pathogenic strains at an unexpectedly high frequency (over 1%), thus raising the possibility of a link between mutator phenotype and pathogenicity (3).
In an independent study, we have surveyed mutation rates among different E. coli populations isolated from distinct environments. We studied 504 natural isolates, which represented the genetic diversity of the species as a whole, encompassing both human commensal [n = 216 (4)] and pathogenic [n = 288 (5)] strains. Our data (Fig.1) show a frequency of strains bearing defects in MMR genes similar to that reported by LeClerc et al., but such defects were found in all the phylogenetic groups and independently of the commensal or pathogenic nature of the strains. The MMR defective strains were distributed 3/288 in pathogens versus 1/216 in nonpathogens, a difference that is not statistically significant (χ2 = 0.05, P > 0.5). Likewise, taking the data in the study by LeClerc et al. (3) all together, MMR defective strains were distributed 9/268 in pathogens versus 0/81 in nonpathogens, which is also not statistically significant (χ2 = 1.6, P = 0.2), the Yates correction for small numbers has been applied to the chi2\'s). The two data sets do not differ significantly (χ2 = 0.96, P = 0.2 to 0.5). In short, the numbers are too small at this point to support any hypothesis.
Frequency of mutation to rifampicin resistance among mutator strains. Five hundred and four natural E. coli isolates were screened for forward mutagenesis in the lacI gene. A total of 69 strains (14%) has been found to form dark blue papillae on minimum medium containing limited glucose, X-gal, and P-gal (the latter can only be used as a carbon source by lacI − mutants). We monitored the frequency of rifampicin-resistant mutants in three independent cultures of these strains (median value is presented), as well as the frequency of 52 non-papillating strains (data not shown). Non-papillating strains had an average mutation rate to rifampicin resistance of about 1 × 10−8 (a value commonly found for wild-type laboratory strains like E. coli K-12) and a small variance (data not shown). Papillating strains had an average mutation rate of 2.6 × 10−7, ranging from less than 10−8 to more than 10−6, thus validating our initial screen. Strains that do not have increased mutagenesis to rifampicin resistance [which reveals base substitutions (7)] are likely to involve other classes of mutators such as those generating frameshifts, deletions, or insertions. This high polymorphism of mutation rates was observed in all groups [commensal strains isolated from France (□), Mali (○), or Croatia (▵) and in strains involved in diverse pathologies, urinary tract infections (⧫), bacteremia (x), pus (▴), neonatal meningitis (▪), and haemolytic-uremic syndrome or haemorrhagic diarrhea (•)]. Defects in mismatch repair genes were identified by complementation with plasmid-carrying wild-typeMMR genes.
Besides MMR defect, however, there are other pathways leading to a mutator phenotype. Therefore, to detect a wide range of mutator effects, we undertook the screen of all mutational events leading to gene inactivation (6), unlike LeClerc et al. (3), who could detect only a few point mutations in the essential rpoB gene that confer resistance to rifampicin (7). Furthermore, we could also detect clones with small increases in mutation rate because each papillating colony could be an independent assay for mutation rate. With this assay, we found that as much as 14% of bacteria had an enhanced mutation rate, the majority being mild mutators. These mutators were also present in all phylogenetic groups, including pathogenic and commensal strains ofE. coli. When the mutation rate to rifampicin resistance of these mutators was monitored, a high level of polymorphism was observed, ranging continuously from less than 10−8 to more than 10−6 (Fig. 1). In general, the highest values correspond to MMR deficiencies, whereas other mutators are likely to be due to different mechanisms.
A high incidence of mutators was observed not only among emerging pathogens, but also among classical pathogenic and commensal strains, such as those isolated from feces of healthy Dogons for whom there is no record of antibiotic treatment (8). This suggests that all bacterial populations have recently experienced adaptive evolution (9, 10). Even a modest increase in mutation rate has been shown to be advantageous during the adaptive evolution of bacteria (10, 11). Therefore, a higher percentage of such mild mutators observed in some pathogenic isolates might be a consequence of stronger selection in that specific environment (12). A direct link between increased genetic variability and pathogenesis, however (for example, transition between commensalism and parasitism), remains to be demonstrated.
- Received for publication 5 March 1997.
- Accepted for publication 7 July 1997.
