Water Treatment Resistance, Antimicrobial Resistance, and Pathogenicity in Klebsiella pneumoniae Isolates from Alberta Sewage
Bibliographic record
Abstract
Water treatment represents a critical barrier to the transmission of infectious diseases. There is evidence that some bacteria may be developing resistance to the disinfection processes commonly applied in water treatment. Previous work revealed that certain strains of Escherichia coli, including pathogenic strains (e.g., extraintestinal pathogenic E. coli [ExPEC]), appear capable of resisting both wastewater treatment and antimicrobial drugs. This thesis investigated whether a similar phenotype of water treatment resistance exists in the Klebsiella pneumoniae species complex (KpSC), and whether it may also co-occur with antimicrobial resistance or pathogenicity. The KpSC is a group of largely opportunistic pathogens known for their environmental ubiquity and their tendency to exhibit high levels of antimicrobial resistance (AMR). Twenty-one KpSC isolates were obtained from sewage samples treated with a chlorine dose sufficient to kill 99.99% of coliform bacteria. These chlorine-resistant KpSC isolates were tested for heat resistance, a phenotype linked to chlorine and advanced oxidant resistance through the transmissible locus of stress tolerance (tLST). Overall, 18 KpSC chlorine-resistant isolates (86%) exhibited an elevated heat resistance phenotype relative to clinical control strains. Whole genome sequencing revealed that that nine of the isolates harbored the transmissible locus of stress tolerance (tLST). Other chlorine-resistance mechanisms were also examined, including biofilm formation and hypermucoviscosity. Substantial biofilm formation was observed in only two isolates, and most isolates produced biofilms at a level equal to, or less than, the biofilm production seen in a positive control strain. However, five isolates were hypermucoviscous based on the string test. Susceptibility to 17 clinical antimicrobials was also evaluated using VITEK®2 ASTGN98 cards. All 21 isolates were phenotypically susceptible to most antimicrobials at clinical/veterinary breakpoints, and although they carried a large complement of antimicrobial resistance genes, they lacked key genes such as those associated with extended-spectrum beta- lactamase and carbapenemase enzymes. Virulence gene screening revealed that several of the isolates might potentially be associated with an opportunistic pathogen lifestyle, but virulence genes associated with community-acquired hypervirulence were absent. Comparative genomics was used to compare these Alberta sewage isolates to the publicly available genomes of clinical, environmental, and wastewater isolates. The species and multi- locus sequence type (MLST) of the sewage isolates were identified using their assembled genomes. The goal of this analysis was to identify phylogenetic relationships to clinical strains and antimicrobial resistance genes (ARGs), along with a comprehensive analysis of virulence gene carriage in the chlorine-resistant sewage isolates. The sewage KpSC isolates in this study included Klebsiella pneumoniae, Klebsiella quasipneumoniae, and Klebsiella variicola belonging to 15 different sequence types. Of the 21 sewage isolates, eight resolved into a clade with one or more exclusively clinical RefSeq genomes. Single-nucleotide polymorphism (SNP) analysis showed that six sewage isolates differed from at least one of those clinical isolates by <80 SNPs. The virulence gene profiles of the sewage and clinical isolates were also remarkably similar. This suggests a close genomic and phylogenetic relationship between some of the chlorine-resistant sewage isolates and clinically relevant pathogenic strains. However, key differences were noted in the resistomes of the sewage isolates, as they lacked many clinically relevant ARGs such as extended-spectrum beta-lactamase and carbapenemase enzymes, and which were frequently detected in the closely related clinical KpSC genomes. The findings of this thesis represented an initial exploration of water treatment resistance, pathogenicity, and AMR in chlorine-resistant sewage isolates of the KpSC. The chlorine and heat resistance found among these isolates may be explained by a combination of the tLST, the hypermucoviscous phenotype, and other alternative mechanisms. Many of the characterized isolates could potentially be pathogenic, although their susceptibility to antimicrobials and the absence of key antimicrobial resistance genes (ARGs) from their genomes suggest that they are unlikely to represent a substantial AMR threat. Future research should include more in-depth bioinformatic analysis of the isolates studied in the present thesis, as well as continued monitoring of sewage bacteria, including KpSC, to evaluate evolutionary trends over time.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".