Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. Isolation and Identification of K. pneumoniae
2.3. Antimicrobial Susceptibility Testing
2.4. Efflux Pump Inhibition Assays
2.5. Genomic DNA Isolation and Whole-Genome Sequencing
2.6. Bioinformatic and Statistical Analyses
2.7. Data Availability
2.8. Ethics Approval
3. Results
3.1. A Total of 147 K. pneumoniae Complex Isolates Were Identified
3.2. K. pneumoniae Complex Resistant to Ceftazidime, Ciprofloxacin and Trimethoprim-Sulfamethoxazole was Isolated
3.3. Multidrug Resistance (MDR) Was Prevalent within RACFs, Especially within Facility 1
3.4. Resistome Analysis of a Subset of K. pneumoniae Complex Could Not Identify the Genomic Basis for the Cephalosporin or Colistin Resistance
3.5. Mutations in Genes Known to Confer Resistance to Antimicrobials
3.6. The Majority of the K. pneumoniae Complex Isolates were the MDR-Outbreak-Causing Sequence Type 323
3.7. Clonal Spread of K. pneumoniae within RACFs was Observed within Facility 1
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Accession: | Isolate: | Accession: | Isolate: |
---|---|---|---|
SAMN33942927 | A031 | SAMN33942935 | 2401 |
SAMN33942928 | A026 | SAMN33942936 | 2404 |
SAMN33942929 | A095 | SAMN33942937 | 2410 |
SAMN33942930 | A529 | SAMN33942938 | 2418 |
SAMN33942931 | A629 | SAMN33942939 | A922 |
SAMN33942932 | A413 | SAMN33942940 | 2362 |
SAMN33942933 | A409 |
Sample Type | |||||
---|---|---|---|---|---|
K. pneumoniae Complex Isolates n (%) | Faecal n (%) | Urine n (%) | Facility Swab n (%) | Wastewater n (%) | |
Facility 1 | 97 (66) | 46 (47) | 0 (0) | 4 (4) | 47 (48) |
Facility 2 | 25 (17) | 16 (64) | 0 (0) | 0 (0) | 9 (36) |
Facility 3 | 7 (5) | 5 (71) | 2 (29) | 0 (0) | 0 (0) |
Retirement | 18 (12) | 15 (83) | 0 (0) | 0 (0) | 3 (17) |
Total: | 147 (100) | 82 (56) | 2 (1) | 4 (2) | 59 (40) |
MIC (mg/L) | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Antimicrobial | <0.125 | 0.125 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | 16 | 32 | 64 | >64 | % Resistant |
Ceftazidime | 3 | 1 | 5 | 19 | 23 | 18 | 11 | 4 | 0 | 4 | 2 | 57 | 46 |
Cefepime | 32 | 3 | 12 | 33 | 21 | 15 | 8 | 3 | 1 | 3 | 1 | 15 | 16 |
Ciprofloxacin | 13 | 5 | 8 | 19 | 9 | 17 | 26 | 24 | 7 | 4 | 7 | 8 | 69 |
Tobramycin | 0 | 0 | 6 | 43 | 62 | 21 | 3 | 1 | 3 | 4 | 3 | 1 | 10 |
Amikacin | 0 | 0 | 3 | 4 | 15 | 72 | 36 | 9 | 6 | 1 | 0 | 1 | 5 |
Meropenem | 31 | 0 | 6 | 13 | 35 | 46 | 14 | 2 | 0 | 0 | 0 | 0 | 0 |
Colistin | 0 | 0 | 3 | 11 | 41 | 90 | 1 | 0 | 0 | 1 | 0 | 0 | 1 |
<0.125 | 0.125 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | >8 | |||||
Trimethoprim sulfamethoxazole | 2 | 8 | 16 | 14 | 13 | 16 | 9 | 7 | 62 | 47 |
MIC (mg/L) | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Antimicrobial | ≤0.125 | 0.125 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | 16 | 32 | 64 | >64 | % Tolerant | |
Biocide | CHG | 2 | 0 | 1 | 0 | 5 | 8 | 33 | 41 | 32 | 21 | 2 | 2 | 1 |
TRI | 5 | 1 | 7 | 14 | 20 | 33 | 27 | 26 | 5 | 0 | 1 | 8 | 46 | |
BZK | 0 | 0 | 0 | 0 | 4 | 2 | 0 | 1 | 21 | 88 | 27 | 4 | 21 |
MIC (mg/L) | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
CTZ | FEP | CIP | TOB | AMI | MER | COL | SXT | |||
EUCAST Breakpoint | >4 | >4 | >0.5 | >2 | >8 | >8 | >2 | >4 | ||
Isolate | ST | Source | ||||||||
A031 | 4726 | Faecal | 2 | 0.125 | 0.25 | 0.25 | 0.25 | <0.125 | 1 | 4 |
A922 | 661 | Wastewater | 32 | 8 | 2 | 1 | 1 | 1 | 2 | >8 |
A026 | 323 | Faecal | 64 | 1 | 2 | 1 | 1 | 4 | 2 | >8 |
A095 | 661 | Faecal | >64 | 32 | 4 | 2 | 2 | 1 | 2 | >8 |
A409 | 323 | Facility | >64 | 1 | 2 | 0.25 | 0.25 | 2 | 1 | >8 |
A413 | 323 | Facility | 64 | 1 | 4 | 1 | 1 | 2 | 2 | >8 |
A529 | 661 | Facility | 32 | 0.5 | 1 | 1 | 1 | 1 | 2 | >8 |
A629 | 323 | Faecal | 64 | 1 | 4 | 0.5 | 0.5 | 1 | 2 | >8 |
2362 | 323 | Wastewater | >64 | 0.5 | 4 | 0.5 | 0.5 | 2 | 2 | >8 |
2401 | 323 | Faecal | 64 | 1 | 4 | 0.5 | 0.5 | 2 | 2 | >8 |
2404 | 323 | Faecal | 64 | 1 | 4 | 1 | 1 | 4 | 2 | >8 |
2410 | 661 | Faecal | >64 | 64 | 8 | 0.25 | 0.25 | <0.125 | 32 | >8 |
2418 | 661 | Faecal | >64 | 64 | 8 | 1 | 1 | 1 | 2 | >8 |
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Blaikie, J.M.; Sapula, S.A.; Siderius, N.L.; Hart, B.J.; Amsalu, A.; Leong, L.E.X.; Warner, M.S.; Venter, H. Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates. Microorganisms 2024, 12, 751. https://doi.org/10.3390/microorganisms12040751
Blaikie JM, Sapula SA, Siderius NL, Hart BJ, Amsalu A, Leong LEX, Warner MS, Venter H. Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates. Microorganisms. 2024; 12(4):751. https://doi.org/10.3390/microorganisms12040751
Chicago/Turabian StyleBlaikie, Jack M., Sylvia A. Sapula, Naomi L. Siderius, Bradley J. Hart, Anteneh Amsalu, Lex E.X. Leong, Morgyn S. Warner, and Henrietta Venter. 2024. "Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates" Microorganisms 12, no. 4: 751. https://doi.org/10.3390/microorganisms12040751