Genomic Study of Chromosomally and Plasmid-Mediated Multidrug Resistance and Virulence Determinants in Klebsiella Pneumoniae Isolates Obtained from a Tertiary Hospital in Al-Kharj, KSA
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Characterization of the Isolate
2.2. Genome Characterization and Typing
2.3. Plasmids and Chromosomally Mediated Mobilome
2.4. Phylogenetic Analysis
3. Discussion
4. Methods
4.1. Bacterial Isolate and Identification
4.2. Antibiotic Susceptibility Testing and Minimum Inhibitory Concentration (MIC)
4.3. Genomic Analysis
4.4. Phylogenetic Tree Construction
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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MIC = µg/mL | |||||
---|---|---|---|---|---|
Strains | K6 (Vaginal Swab) | K7 (Blood) | K16 (Urine) | K8 (Urine) | |
Drugs | |||||
Amikacin | ≤16 (S) | ≤16 (S) | ≤16 (S) | ≤16 (S) | |
Amox/Clav | ≤8/4 (S) | ≤8/4 (S) | ≤8/4 (S) | ≤8/4 (S) | |
Amp/Sulbactam | >16/8 (R) | >16/8 (R) | 16/8 (I) | ≤8/4 (S) | |
Ampicillin | >16 (R*) | >16 (R*) | >16 (R*) | >16 (R) | |
Aztreonam | >16 | >16 | >16 | ≤4 (S) | |
Cefazolin | >4 (R*) | >4 (R*) | >4 (R*) | ≤2 (S) | |
Cefepime | >16 (R*) | >16 (R*) | >16 (R*) | ≤8 (S) | |
Cefotaxime | >16 | >16 | >16 | ≤1 (S) | |
Cefoxitin | ≤8 (S) | ≤8 (S) | ≤8 (S) | ≤8 (S) | |
Ceftazidime | 8 | 8 | >16 | ≤1 (S) | |
Cefuroxime | >16 (R*) | >16 (R*) | >16 (R*) | ≤4 (S) | |
Ciprofloxacin | ≤1 (S) | ≤1 (S) | ≤1 (S) | ≤1 (S) | |
Colistin | ≤2 | ≤2 | ≤2 | ≤2 (S) | |
Ertapenem | ≤0.5 (S) | ≤0.5 (S) | ≤0.5 (S) | ≤0.5 (S) | |
Gentamycin | ≤4 (S) | ≤4 (S) | ≤4 (S) | ≤4 (S) | |
Imipenem | ≤1 (S) | ≤1 (S) | ≤1 (S) | ≤1 (S) | |
Levofloxacin | ≤2 (S) | ≤2 (S) | ≤2 (S) | ≤2 (S) | |
Meropenem | ≤1 (S) | ≤1 (S) | ≤1 (S) | ≤1 (S) | |
Moxifloxacin | ≤0.5 (S) | ≤0.5 (S) | 1 | ≤0.5 (S) | |
Nitrofurantion | ≤32 (S) | ≤32 (S) | ≤32 (S) | ≤32 (S) | |
Norfloxacin | ≤4 (S) | ≤4 (S) | ≤4 (S) | ≤4 (S) | |
Pip/Tazo | ≤16 (S) | ≤16 (S) | ≤16 (S) | ≤16 (S) | |
Tigecycline | ≤1(S) | ≤1 (S) | ≤1 (S) | ≤1 (S) | |
Tobramycin | ≤4 (S) | ≤4 (S) | ≤4 (S) | ≤4 (S) | |
Trimeth/Sulfa | >2/38 (R) | >2/38 (R) | ≤2/38 (S) | ≤2/38 (S) |
ID | Genome Length | No. of Contigs | Average Contig Length | N50 | L50 | GC Content | CDS | tRNA | rRNA | STs | K Locus Type | O Locus Type |
---|---|---|---|---|---|---|---|---|---|---|---|---|
K6 | 5,397,408 | 56 | 96,382 | 44,7087 | 4 | 57.4% | 5215 | 68 | 3 | 23 | K1 | O1 |
K7 | 5,446,096 | 62 | 87,840 | 44,7087 | 4 | 57.4% | 5284 | 68 | 3 | 23 | K1 | O1 |
K8 | 5,388,197 | 126 | 42,763 | 203,642 | 8 | 57.2% | 5374 | 76 | 4 | 592 | K57 | O3b |
K16 | 5,483,033 | 69 | 79,464 | 357,616 | 6 | 57.1% | 5417 | 74 | 4 | 353 | K110 | O3b |
Plasmid | Identity | Accession | ARG | VG | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
K6 | pB-8922_OXA-48 | 100% | CP094368.2 | catB3 | blaOXA-1 | aac(6′)-Ib-cr | ||||||
pCEX23 | 100% | LC556222.1 | qacE | sul1 | dfrA12 | aadA2 | ||||||
pColKP3 | 99 | CP036331.1 | blaCTX-M-3 | blaOXA-232 | ||||||||
pC16KP0122-2 | 99.99% | CP052433.1 | dfrA14 | |||||||||
pF16KP0037-1 | 100% | CP052182.1 | iroB | iroC | iroD | iroN | ||||||
K7 | p1527854_3 | 100% | CP102116.1 | blaCTX-M-3 | ||||||||
pC16KP0122-2 | 99.99 | CP052433.1 | dfrA14 | |||||||||
pEC422_4 | 99.65% | CP018958.1 | iucA | iucB | iucC | iucD | iutA | |||||
pF16KP0037-1 | 100% | CP052182.1 | iroB | iroC | iroD | iroN | ||||||
K8 | pMBRCAV1205 | 100% | ON911500.1 | qnrB4 | qnrB55 | |||||||
p19-Pyelo_1 | 93% | CP048854.1 | afaD | senB | ||||||||
pYJ6-NDM5 | 100% | AP023236.1 | traT | |||||||||
K16 | pIPCEC48_1 | 100% | AP026795.1 | blaCTX-M-15 | ||||||||
pK92-qnrS | 100% | OL828743.1 | qnrS1 | aph(3″)-Ib | sul2 | aph(6)-Id |
ID_Integron | Element | Pos_Beg | Pos_End | Strand | E Value | Type_Elt | Annotation | Model |
---|---|---|---|---|---|---|---|---|
Integron 1 | NODE_13_ | 1902 | 2249 | −1 | NA | protein | protein | NA |
attc_001 | 2352 | 2411 | −1 | 2.70 × 10−10 | attC | attC | attc_4 | |
NODE_13_ | 2413 | 3192 | −1 | NA | protein | protein | NA | |
attc_002 | 3208 | 3267 | −1 | 1.90 × 10−7 | attC | attC | attc_4 | |
attc_003 | 3528 | 3617 | −1 | 5.20 × 10−6 | attC | attC | attc_4 | |
NODE_13 | 3612 | 4109 | −1 | NA | protein | protein | NA | |
NODE_23 | 140 | 1153 | 1 | 9.10 × 10−27 | protein | intI | Inter section_tyr_intI |
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Moglad, E.; Alanazi, N.; Altayb, H.N. Genomic Study of Chromosomally and Plasmid-Mediated Multidrug Resistance and Virulence Determinants in Klebsiella Pneumoniae Isolates Obtained from a Tertiary Hospital in Al-Kharj, KSA. Antibiotics 2022, 11, 1564. https://doi.org/10.3390/antibiotics11111564
Moglad E, Alanazi N, Altayb HN. Genomic Study of Chromosomally and Plasmid-Mediated Multidrug Resistance and Virulence Determinants in Klebsiella Pneumoniae Isolates Obtained from a Tertiary Hospital in Al-Kharj, KSA. Antibiotics. 2022; 11(11):1564. https://doi.org/10.3390/antibiotics11111564
Chicago/Turabian StyleMoglad, Ehssan, Nuor Alanazi, and Hisham N. Altayb. 2022. "Genomic Study of Chromosomally and Plasmid-Mediated Multidrug Resistance and Virulence Determinants in Klebsiella Pneumoniae Isolates Obtained from a Tertiary Hospital in Al-Kharj, KSA" Antibiotics 11, no. 11: 1564. https://doi.org/10.3390/antibiotics11111564