Recovery of Non-tuberculous Mycobacteria from Water is Influenced by Phenotypic Characteristics and Decontamination Methods.

Infections related to non-tuberculous mycobacteria (NTM) have recently increased worldwide. The transmission of these microorganisms from the environment has been suggested as the main source for human infections. To elucidate the epidemiological aspects and distribution of these pathogens, many studies have evaluated several decontamination methods and protocols to properly isolate NTM from environmental samples, mainly from water. However, no satisfactory strategy has been found for isolation of most of the NTM species harboring different phenotypic characteristics. Here, we evaluated the susceptibility of 23 NTM strains presenting variable growth rate and pigmentation patterns to eight different methods: oxalic acid (2.5% and 5%), cetylpyridinium chloride (CPC) (0.0025% and 0.005%), sodium hydroxide (NaOH) (2% and 4%), and sodium dodecyl sulfate (SDS) plus NaOH (SDS 1.5%-NaOH 0.5% and SDS 3%-NaOH 1%). It was found that the viability of NTM exposed to different decontamination methods varies according to their phenotypic characteristics and two methods (SDS 1.5% plus NaOH 0.5% and CPC 0.0025%) were necessary for effective isolation of all of the species tested. These findings supply important insights for future studies on the environmental occurrence of mycobacteria and improving the sensibility of traditional strategies.

Use of fimH single-nucleotide polymorphisms for strain typing of clinical isolates of Escherichia coli for epidemiologic investigation.

Strain typing methods that compare electrophoresis banding patterns are commonly used but are difficult to standardize and poorly portable. Multilocus sequence typing (MLST) is a sequence-based alternative, but it is not practical for large-scale epidemiological studies. In the present study, the usefulness of fimH single-nucleotide polymorphisms (SNPs) for Escherichia coli typing was explored. fimH SNPs were determined for 345 E. coli clinical isolates (including 3 reference strains) and compared to PCR-based ECOR (E. coli reference collection) phylogrouping. The fimH gene could be amplified for 316 (92%) of the 345 isolates. fimH SNP analysis found 46 distinct terminal groups in the nucleotide sequence-based phylogenetic tree (fimH types). A subset of the E. coli isolates (162 clinical isolates and the 3 reference strains) were compared by fimH type, PCR phylogroup, and MLST. These isolates fell into 27 fimH types and 18 MLST clonal complexes (CCs) that contained 2 to 28 isolates per complex. The combination of PCR phylogroup and fimH type corresponded to a single CC for 113 (68%) isolates and 2 or 3 CCs for the other 52 (32%) isolates. We propose that the combination of PCR phylogrouping and fimH SNP analysis may be a useful method to type a large collection of clinical E. coli isolates for epidemiologic studies.

Identification of uropathogenic Escherichia coli clonal group A (CgA) in hospitalised patients.

This study provides the first description of healthcare-associated infections with Escherichia coli clonal group A (CgA) isolates in Latin America. Isolates were typed by enterobacterial repetitive intergenic consensus-PCR, pulsed-field gel electrophoresis, E. coli phylogenetic grouping, multilocus sequence typing and fimH single nucleotide polymorphism analysis. Out of 42 E. coli hospital isolates studied, three belonged to E. coli phylogenetic group D and ST69 and had fimH sequences identical to that of the CgA reference strain ATCC BAA-457. E. coli CgA is another potential source of resistant infections in hospitals.

Clonal composition of Escherichia coli causing community-acquired urinary tract infections in the State of Rio de Janeiro, Brazil.

Recent studies from North America and Europe have demonstrated community-wide clonal spread of uropathogenic Escherichia coli (UPEC). To investigate if a similar pattern of spread occurs in Brazil, we characterized UPEC from women with community-acquired urinary tract infection (UTI) in Rio de Janeiro. E. coli isolates from women with UTI in one public outpatient clinic were evaluated for antibiotic susceptibility, E. coli phylogenetic grouping, enterobacterial repetitive intergenic consensus (ERIC) 2 PCR and pulsed-field gel electrophoresis fingerprinting, and multilocus sequence typing. From March 2005 to November 2006, 344 patients were studied. Of these, 186 (54%) had confirmed UTI, 118 (63.4%) of which were caused by E. coli. More than 50% of these isolates were resistant to ampicillin and trimethoprim/sulfamethoxazole. Of these, 96 (81%) belonged to 19 ERIC2 clonal groups. The largest group included 15 isolates, all belonging to multilocus sequence typing group ST69 and phylogenetic group D; they had pulsed-field gel electrophoresis patterns sharing at least 89% similarity compared with the CgA reference strain ATCC BAA-457. CgA strains have been found to be widespread in the United States in the early 2000s. Clonal group E. coli strains accounted for a large proportion (52%) of all UTIs and 82% of the trimethoprim/sulfamethoxazole-resistant E. coli UTIs. Thus, as in North America and Europe, UPECs that cause UTI in Rio de Janeiro also show clonal distribution, and a substantial proportion of drug-resistant UTI is caused by a small set of genetically related E. coli strains.