A Stenotrophomonas maltophilia multilocus sequence typing scheme for inferring population structure

Abstract

Stenotrophomonas maltophilia is an opportunistic, highly resistant, and ubiquitous pathogen. Strains have been assigned to genogroups using amplified fragment length polymorphism. Hence, isolates of environmental and clinical origin predominate in different groups. A multilocus sequence typing (MLST) scheme was developed using a highly diverse selection of 70 strains of various ecological origins from seven countries on all continents including strains of the 10 previously defined genogroups. Sequence data were assigned to 54 sequence types (ST) based on seven loci. Indices of association for all isolates and clinical isolates of 2.498 and 2.562 indicated a significant linkage disequilibrium, as well as high congruence of tree topologies from different loci. Potential recombination events were detected in one-sixth of all ST. Calculation of the mean divergence between and within predicted clusters confirmed previously defined groups and revealed five additional groups. Consideration of the different ecological origins showed that 18 out of 31 respiratory tract isolates, including 12 out of 19 isolates from cystic fibrosis (CF) patients, belonged to genogroup 6. In contrast, 16 invasive strains isolated from blood cultures were distributed among nine different genogroups. Three genogroups contained isolates of strictly environmental origin that also featured high sequence distances to other genogroups, including the S. maltophilia type strain. On the basis of this MLST scheme, isolates can be assigned to the genogroups of this species in order to further scrutinize the population structure of this species and to unravel the uneven distribution of environmental and clinical isolates obtained from infected, colonized, or CF patients.

FIG. 1.

NJ tree based on the concatenated data for all seven loci of the 70 S. maltophilia strains. The isolates originated from blood culture, CF patients, tracheal secretions from outbreaks, sputum, pus, conjunctivitis, environmental specimens, hospital environment, patient, and one CSF isolate of S. africana (strain abbreviations are identified in Table 1). Previously defined genogroups were numbered (#1 to #9) according to previously investigated strains (35) included here and shown in small rectangular boxes. An uppercase letter indicates groups newly detected in this work. Bootstrap values (200 random seeds) are given as percentages for the main branches. The tree was rooted with the corresponding concatenate of X. campestris (53).