Genomic Investigation of Carbapenem-Resistant Klebsiella pneumonia Colonization in an Intensive Care Unit in South Africa
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Population
2.2. Sample Collection and Screening for CPEs
2.3. Antimicrobial Susceptibility Testing (AST)
2.4. Genomic Characterization
2.4.1. DNA Extraction of CPKP Isolates
2.4.2. Genomic Fingerprinting
2.4.3. Whole Genome Sequencing (WGS) of CPKP Isolates
2.4.4. Genomic Analyses and Annotation
2.4.5. Phylogenomics and Epidemiological Insights
3. Results
3.1. Population Demographics
3.2. Antimicrobial Resistance Profiles
3.3. Genomic Fingerprinting
3.4. Genome Characteristics of the Isolates
3.5. In Silico ARGs Analysis
3.6. Sequence Types Analysis (MLST), In Silico Mobile Genetic Elements (Mobilome), Virulome and Capsular Serotypes
3.7. Phylogenomic Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Isolate | Demographic Information | Resistome | Plasmid Incompatibility Group | ||||||
---|---|---|---|---|---|---|---|---|---|
Patient | Gender | Date | Study Day | Antibiogram | ERIC Type | Other β-Lactamases | Other ARGs | ||
EC03607709 | P2 | Male | 19 February 2020 | Week 2 | A | 2 | blaCTX-M-15, blaOXA-1, blaSHV-106, blaTEM-1B | aac(6′)-Ib-cr, aph(3″)-Ib, aph(6)-Id, qnrS1, qnrB1, oqxB, oqxA, dfrA14, sul2, fosA, catB3, tet(A) | ColKP3, IncFIB(K), IncFII(K), IncX3 |
EC03605938 | P13 | Male | 18 February 2020 | 48 h | B | 2 | blaCTX-M-15, blaOXA-1, blaSHV-106, blaTEM-1B | aac(6′)-Ib-cr, aph(3′)-VIa, armA, qnrS1, oqxB, oqxA, dfrA14, fosA, msr(E), mph(E), catB3, tet(A), cmlA1, ARR-2 | ColKP3, IncFIB(K), IncFII(K), IncX3 |
EC03607707 | P13 | Male | 19 February 2020 | 72 h | A | 1 | blaCTX-M-15, blaOXA-1, blaSHV-106, blaTEM-1B | aac(6′)-Ib-cr, aph(3′)-VIa, armA, qnrS1, oqxB, oqxA, dfrA14, fosA, msr(E), mph(E), catB3, tet(A), cmlA1 | ColKP3, IncFIB(K), IncFII(K), IncX3 |
EC03612985 | P22 | Female | 24 February 2020 | Discharge | C | 5 | blaCTX-M-15, blaOXA-1, blaSHV-106, blaTEM-1C | aac(6′)-Ib-cr, aph(3″)-Ib, aph(6)-Id, qnrS1, qnrB1, oqxB, oqxA, dfrA14, sul2, fosA, catB3, tet(A) | ColKP3, IncFIB(pNDM-Mar), IncX3 |
EC03623002 | P30 | Male | 3 March 2020 | 48 h | A | 1 | blaCTX-M-15, blaOXA-1, blaSHV-106, blaTEM-1B | aac(6′)-Ib-cr, aph(3″)-Ib, aph(6)- Id, qnrS1, qnrB1, oqxB, oqxA, dfrA14, sul2, fosA, catB3, tet(A) | ColKP3, IncFIB(K), IncFII(K), IncX3 |
EC03629993 | P30 | Male | 8 March 2020 | Mero D4 | A | 2 | blaCTX-M-15, blaOXA-1, blaSHV-106, blaTEM-1B | aac(6′)-Ib-cr, aph(3″)-Ib, aph(6)-Id, qnrS1, qnrB1, oqxB, oqxA, dfrA14, sul2, fosA, catB3, tet(A) | ColKP3, IncFIB(K), IncFII(K), IncX3 |
EC03632007 | P30 | Male | 10 March 2020 | Mero D6 | A | 4b | blaCTX-M-15, blaOXA-1, blaSHV-106, blaTEM-1B | aac(6′)-Ib-cr, aph(3″)-Ib, aph(6)-Id, qnrS1, qnrB1, oqxB, oqxA, dfrA14, sul2, fosA, catB3, tet(A) | ColKP3, IncFIB(K), IncFII(K) |
EC03638959 | P30 | Male | 14 March 2020 | Week 2 | A | 4a | blaCTX-M-15, blaOXA-1, blaSHV-106, blaTEM-1B | aac(6′)-Ib-cr, aph(3″)-Ib, aph(6)-Id, qnrS1, qnrB1, oqxB, oqxA, dfrA14, sul2, fosA, catB3, tet(A) | ColKP3, IncFII(K) |
Isolate | Plasmids Replicons | pMLST | Integron Class | Integron | Cassette Arrays | |||||
---|---|---|---|---|---|---|---|---|---|---|
GC1 a | GC2 | GC3 | GC4 | GC5 | GC6 | |||||
EC03607709 | ColKP3, IncFIB(K), IncFII(K), IncX3 | [K7:A-:B-] | Integron integrase IntI1 | In191 | dfrA14 | — b | — | — | — | — |
EC03638959 | ColKP3, IncFII(K) | [K7:A-:B-] | Integron integrase IntI1 | In191 | dfrA14 | — | — | — | — | — |
EC03632007 | ColKP3, IncFIB(K), IncFII(K) | [K7:A-:B-] | ND | ND | dfrA14 | — | — | — | — | — |
EC03629993 | ColKP3, IncFIB(K), IncFII(K), IncX3 | [K7:A-:B-] | Integron integrase IntI1 | In191 | dfrA14 | — | — | — | — | — |
EC03607707 | ColKP3, IncFIB(K), IncFII(K), IncX3 | [K7:A-:B-] | Integron integrase IntI1 | In191 | dfrA14 | — | — | — | — | — |
EC03623002 | ColKP3, IncFIB(K), IncFII(K), IncX3 | [K7:A-:B-] | Integron integrase IntI1 | In191 | dfrA14 | — | — | — | — | — |
EC03605938 | ColKP3, IncFIB(K), IncFII(K), IncX3 | [K7:A-:B-] | Integron integrase IntI1 | In191 | dfrA14 | — | — | — | — | — |
EC03612985 | ColKP3, IncFIB(pNDM-Mar), IncX3 | [F-:A-:B-] | Integron integrase IntI1 | In27 | dfrA12 | gcuF | aadA2 | — | — | — |
Isolate | Contig | Synteny of Resistance Genes and MGEs | Plasmid/Chromosomal Sequence with the Closest Nucleotide Homology (Accession Number) |
---|---|---|---|
EC03607709 | 49 | blaOXA-181:EreA::ISKra4 (ISKpn19):recombinase::::recombinase:QnrS1:transposase | E. coli p010_B-OXA181 (99.98%), accession (CP048332.1) (plasmid) |
34 | IS5:IS5075 (IS110)::Sul2:aph(3″)-Ib:aph(6)-Id:IS91:TEM-1B:recombinase::IS1380 (ISEc9):blaCTX-M-15::Tn3 family:IS6 (IS6100) | p72_FIBkpn (100%), accession (CP034282.1) (plasmid) | |
54 | CatB3:blaOXA-1:aac(6′)-Ib-cr5 | E. coli pYJ3-a DNA (100%), accession (AP023228.1) (plasmid) | |
15 | ::::blaSHV-106:::: | K.p F16KP0053 chromosome (100%), accession (CP052727.1) | |
50 | IS6 (IS6100)::dfrA14:IntI1 | K.p pB16KP0177-1 (100%), accession (CP052525.1) (plasmid) | |
EC03638959 | 95 | transposase:QnrS1:recombinase::::recombinase:ISKra4 (ISKpn19)::EreA:blaOXA-181 | E. coli p010_B-OXA181 (99.98%), accession (CP048332.1) (plasmid) |
98 | blaTEM-1B:recombinase::IS1380 (ISEc9):blaCTX-M-15::Tn3 family:IS6 (IS6100) | p72_FIBkpn (100%), accession (CP034282.1) (plasmid) | |
109 | aac(6′)-Ib-cr5:blaOXA-1:CatB3 | E. coli pYJ3-a DNA (100%), accession (AP023228.1) (plasmid) | |
24 | ::::blaSHV-106:::: | K.p F16KP0053 chromosome (100%), accession (CP052727.1) | |
102 | dfrA14::IS6 (IS6100) | K.p pB16KP0177-1 (100%), accession (CP052525.1) (plasmid) | |
EC03632007 | 93 | blaOXA-181:EreA::ISKra4 (ISKpn19):recombinase::::recombinase:QnrS1:transposase | E. coli p010_B-OXA181 (99.98%), accession (CP048332.1) (plasmid) |
96 | Tn3 family::blaCTX-M-15:IS1380 (ISEc9)::recombinase:TEM-1B | p72_FIBkpn (100%), accession (CP034282.1) (plasmid) | |
112 | CatB3:blaOXA-1:aac(6′)-Ib-cr5 | E. coli pYJ3-a DNA (100%), accession (AP023228.1) (plasmid) | |
23 | ::::blaSHV-106:::: | K.p F16KP0053 chromosome (100%), accession (CP052727.1) | |
101 | dfrA14::IS6 (IS6100) | K.p pB16KP0177-1 (100%), accession (CP052525.1) (plasmid) | |
EC03629993 | 47 | blaOXA-181:EreA::ISKra4 (ISKpn19):recombinase::::recombinase:QnrS1:transposase | E. coli p010_B-OXA181 (99.98%), accession (CP048332.1) (plasmid) |
35 | IS5:IS5075 (IS110)::Sul2:aph(3″)-Ib:aph(6)-Id:IS91:TEM-1B:recombinase::IS1380 (ISEc9):blaCTX-M-15::Tn3 family:IS6 (IS6100) | p72_FIBkpn (100%), accession (CP034282.1) (plasmid) | |
55 | aac(6′)-Ib-cr5:blaOXA-1:CatB3 | E. coli pYJ3-a DNA (100%), accession (AP023228.1) (plasmid) | |
16 | ::::blaSHV-106:::: | K.p F16KP0053 chromosome (100%), accession (CP052727.1) | |
49 | IntI1:dfrA14::IS6 (IS6100) | K.p pB16KP0177-1 (100%), accession (CP052525.1) (plasmid) | |
EC03607707 | 50 | blaOXA-181:EreA::ISKra4 (ISKpn19):recombinase::::recombinase:QnrS1:transposase | E. coli p010_B-OXA181 (99.98%), accession (CP048332.1) (plasmid) |
36 | IS6 (IS6100):Tn3 family::blaCTX-M-15:IS1380 (ISEc9)::recombinase:TEM-1B:IS91:aph(6)-Id:aph(3″)-Ib:Sul2::IS5075 (IS110):IS5 | p72_FIBkpn (100%), accession (CP034282.1) (plasmid) | |
56 | CatB3:blaOXA-1:aac(6′)-Ib-cr5 | E. coli pYJ3-a DNA (100%), accession (AP023228.1) (plasmid) | |
13 | ::::blaSHV-106:::: | K.p F16KP0053 chromosome (100%), accession (CP052727.1) | |
52 | IS6(IS6100)::dfrA14:IntI1 | K.p pB16KP0177-1 (100%), accession (CP052525.1) (plasmid) | |
EC03623002 | 45 | blaOXA-181:EreA::ISKra4 (ISKpn19):recombinase::::recombinase:QnrS1:transposase | E. coli p010_B-OXA181 (99.98%), accession (CP048332.1) (plasmid) |
32 | IS5:IS5075 (IS110)::Sul2:aph(3″)-Ib:aph(6)-Id:IS91:TEM-1B:recombinase::IS1380 (ISEc9):blaCTX-M-15::Tn3 family:IS6 (IS6100) | p72_FIBkpn (100%), accession (CP034282.1) (plasmid) | |
54 | aac(6′)-Ib-cr5:blaOXA-1:CatB3 | E. coli pYJ3-a DNA (100%), accession (AP023228.1) (plasmid) | |
16 | ::::blaSHV-106:::: | K.p F16KP0053 chromosome (100%), accession (CP052727.1) | |
47 | IntI1:dfrA14::IS6 (IS6100) | K.p pB16KP0177-1 (100%), accession (CP052525.1) (plasmid) | |
EC03605938 | 48 | transposase:QnrS1:recombinase::::recombinase:ISKra4 (ISKpn19)::EreA:blaOXA-181 | E. coli p010_B-OXA181 (99.98%), accession (CP048332.1) (plasmid) |
34 | IS6 (IS6100):Tn3 family::blaCTX-M-15:IS1380 (ISEc9)::recombinase:TEM-1B:IS91:aph(6)-Id:aph(3″)-Ib:Sul2::IS5075 (IS110):IS5 | p72_FIBkpn (100%), accession (CP034282.1) (plasmid) | |
53 | aac(6′)-Ib-cr5:blaOXA-1:CatB3 | E. coli pYJ3-a DNA (100%), accession (AP023228.1) (plasmid) | |
14 | ::::blaSHV-106:::: | K.p F16KP0053 chromosome (100%), accession (CP052727.1) | |
50 | IntI1:dfrA14::IS6 (IS6100) | K.p pB16KP0177-1 (100%), accession (CP052525.1) (plasmid) | |
EC03612985 | 48 | Tn3-like IS3000:blaOXA-181:EreA::ISKra4 (ISKpn19):recombinase::::recombinase:QnrS1:transposase | E. coli p010_B-OXA181 (99.98%), accession (CP048332.1) (plasmid) |
54 | ::blaCTX-M-15:IS1380 (ISEc9)::recombinase:blaTEM-1C:: | E. coli str. 473 pRCS52 (99.9%), accession (LO017736.1) (plasmid) | |
61 | aac(6′)-Ib-cr5:blaOXA-1:CatB3 | E. coli pYJ3-a DNA (100%), accession (AP023228.1) (plasmid) | |
2 | ::::blaSHV-106:::: | K.p F16KP0053 chromosome (100%), accession (CP052727.1) | |
49 | recombinase::IntI1:dfrA12:gcuF:aadA2::Sul1::::::::IS6 (IS6100)::::Mph(A) | K.p plasmid unnamed1 (99.99%), accession (CP060050.1) (plasmid) | |
59 | IS3:aac(3)-IIa | K.p pMS14393B (100%), accession (CP054305.1) (plasmid) |
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Madni, O.; Amoako, D.G.; Abia, A.L.K.; Rout, J.; Essack, S.Y. Genomic Investigation of Carbapenem-Resistant Klebsiella pneumonia Colonization in an Intensive Care Unit in South Africa. Genes 2021, 12, 951. https://doi.org/10.3390/genes12070951
Madni O, Amoako DG, Abia ALK, Rout J, Essack SY. Genomic Investigation of Carbapenem-Resistant Klebsiella pneumonia Colonization in an Intensive Care Unit in South Africa. Genes. 2021; 12(7):951. https://doi.org/10.3390/genes12070951
Chicago/Turabian StyleMadni, Osama, Daniel G. Amoako, Akebe Luther King Abia, Joan Rout, and Sabiha Yusuf Essack. 2021. "Genomic Investigation of Carbapenem-Resistant Klebsiella pneumonia Colonization in an Intensive Care Unit in South Africa" Genes 12, no. 7: 951. https://doi.org/10.3390/genes12070951
APA StyleMadni, O., Amoako, D. G., Abia, A. L. K., Rout, J., & Essack, S. Y. (2021). Genomic Investigation of Carbapenem-Resistant Klebsiella pneumonia Colonization in an Intensive Care Unit in South Africa. Genes, 12(7), 951. https://doi.org/10.3390/genes12070951