Corrigendum: Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters.

[This corrects the article on p. 2200 in vol. 8, PMID: 29201017.].

Draft Genome Sequence of Singapore Klebsiella pneumoniae subsp. pneumoniae Isolate DS32358_14, Which Contains the Carbapenemase Gene blaVIM-1.

We sequenced the first blaVIM-1-positive Klebsiella pneumoniae strain isolated in Singapore. The isolate belongs to multilocus sequence type 2542 (ST2542), and blaVIM-1 was the first gene in an integron that also contained aacA4, aphA15, aadA1, catB2, qacEdelta1, and sul1.

Putative Integrative Mobile Elements That Exploit the Xer Recombination Machinery Carrying blaIMI-Type Carbapenemase Genes in Enterobacter cloacae Complex Isolates in Singapore.

Whole-genome sequencing was performed on 16 isolates of the carbapenemase-producing Enterobacter cloacae complex to determine the flanking regions of blaIMI-type genes. Phylogenetic analysis of multilocus sequence typing (MLST) targets separated the isolates into 4 clusters. The blaIMI-type genes were all found on Xer-dependent integrative mobile elements (IMEX). The IMEX elements of 5 isolates were similar to those described in Canada, while the remainder were novel. Five isolates had IMEX elements lacking a resolvase and recombinase.

Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters.

The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb). A cluster analysis showed that the taxonomic composition of wastewaters was highly similar and had a bacterial community composition enriched in gut bacteria (Bacteroides, Faecalibacterium, Bifidobacterium, Blautia, Roseburia, Ruminococcus), the Enterobacteriaceae group (Klebsiella, Aeromonas, Enterobacter) and opportunistic pathogens (Prevotella, Comamonas, Neisseria). Wastewater, treated effluents and surface waters had a shared resistome of 21 ARGs encoding multidrug resistant efflux pumps or resistance to aminoglycoside, macrolide-lincosamide-streptogramins (MLS), quinolones, sulfonamide, and tetracycline resistance which suggests that these genes are wide spread across different environments. Wastewater had a distinctively higher average abundance of clinically relevant, class A beta-lactamase resistant genes (i.e., blaKPC, blaCTX-M, blaSHV, blaTEM). The wastewaters from clinical isolation wards, in particular, had a exceedingly high levels of blaKPC-2 genes (142,200 x/Gb), encoding for carbapenem resistance. Assembled scaffolds (16 and 30 kbp) from isolation ward wastewater samples indicated this gene was located on a Tn3-based transposon (Tn4401), a mobilization element found in Klebsiella pneumonia plasmids. In the longer scaffold, transposable elements were flanked by a toxin-antitoxin (TA) system and other metal resistant genes that likely increase the persistence, fitness and propagation of the plasmid in the bacterial host under conditions of stress. A few bacterial species (Enterobacter cloacae, Klebsiella pneumoniae, Citrobacter freundii, Pseudomonas aeruginosa) that were cultured from the isolation ward wastewaters on CHROMagar media harbored the blaKPC-2 gene. This suggests that hospital wastewaters derived from clinical specialty wards are hotspots for the spread of AMR. Assembled scaffolds of other mobile genetic elements such as IncQ and IncF plasmids bearing quinolone resistance genes (qnrS1, qnrS2) and the class A beta-lactamase gene (blaTEM-1) were recovered in wastewater samples which may aid the transfer of AMR.

Molecular epidemiology of vancomycin-resistant enterococci in Singapore.

AIMS: To characterise the mechanism of glycopeptide resistance, genetic relatedness, and pathogenicity factors in isolates of vancomycin-resistant enterococci (VRE) in Singapore. METHODS: A total of 292 Enterococcus faecium and 17 Enterococcus faecalis were isolated from humans, and five E. faecium, two Enterococcus durans, two Enterococcus flavescens, one Enterococcus casseliflavus, and one Enterococcus gallinarum from chickens. The mechanism of glycopeptide resistance and pathogenicity factors were studied by PCR and the genetic relatedness determined by pulsed-field gel electrophoresis (PFGE), multi-locus variable number tandem repeat analysis (MLVA), and Tn1546 analysis. RESULTS: There were five outbreak clones among the vancomycin-resistant E. faecium with one clone predominant. Four of the clones were vanB positive, and only one clone carried vanA. All outbreak clones were esp gene positive. Sporadic human isolates and chicken isolates were vanA positive and did not contain any pathogenicity genes. The situation was reversed in vancomycin-resistant E. faecalis where almost all isolates were vanA positive. CONCLUSIONS: Most VRE in Singapore is hospital associated with a small number of clones of esp-positive vanB E. faecium responsible for the majority of isolates.

Use of multiple methods for genotyping Fusarium during an outbreak of contact lens associated fungal keratitis in Singapore.

BACKGROUND: In Singapore, an outbreak of fungal keratitis caused by members of the Fusarium solani species complex (FSSC) was identified in March 2005 to May 2006 involving 66 patients. Epidemiological investigations have indicated that improper contact lens wear and the use of specific contact lens solutions were risk factors. METHODS: We assessed the genetic diversity of the isolates using AFLP, Rep-PCR, and ERIC-PCR and compared the usefulness of these typing schemes to characterize the isolates. RESULTS: AFLP was the most discriminative typing scheme and appears to group FSSC from eye infections and from other infections differently. CONCLUSION: There was a high genomic heterogeneity among the isolates confirming that this was not a point source outbreak.