Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study
Abstract
:1. Introduction
2. Results
2.1. Patient Demographics and Characteristics
2.2. Antibiotic Susceptibility Test Results
2.3. Phenotypic and Genotypic Identification of MRSA Isolates
2.4. Genomic Features
2.5. In Silico ARGs Analysis
2.5.1. MLST, spa Typing, and Clonal Complex
2.5.2. Mobilome (Plasmids, Insertion Sequences, Intact Prophages, and SCCmec Elements)
2.5.3. Virulome and Pathogenicity of S. aureus Strains
2.6. Genetic Environment of the ARGs and Virulence Genes
Regulatory Genes
2.7. Phylogenomics
Strain (MLST) | Strain | Contig | Synteny of Virulence Genes and MGEs | Plasmid/Chromosomal Sequence with Closest Nucleotide Homology (Accession Number) |
---|---|---|---|---|
S11 (ST8) | MRSA | 4 | pmtC:pmtB:pmtA:eap::scn::sak:::sph::lukG::lukH::intergrase:::agrB | S. aureus strain Laus385 chromosome (CP071350.1) |
6 | icaR::icaD:icaB:icaC:vraD:vraE:vraH::IS30:vraH::recombinase:IS6 | S. aureus strain TF3198 chromosome, complete genome (CP023561.1) | ||
10 | lukE:lukD::splA::epiE::splA:splB:splC:splD:splE:splF::pepA1:transposase | S. aureus strain 82 chromosome, complete genome (CP031661.1) | ||
S29 (ST5) | MRSA | 53 | type I toxin–antitoxin system:IS6:cadD | S. aureus strain MIN-175 chromosome (CP086121.1) |
40 | clfA:vwb:emp | S. aureus strain ER02693.3 chromosome, complete genome (CP030605.1) | ||
S31 (ST612) | MRSA | 11 | pmtD:pmtC:pmtB:pmtA::eap:scn::sak | S. aureus strain 2395 USA500, complete genome (CP007499.1) |
15 | lukE:lukD::::splA:splB:splC:splF::type I restriction-modification system | S. aureus strain NRL 02/947 chromosome, complete genome (CP103850.1) | ||
19 | lukG:lukH:pathogenicity island:intergrase::phenol-soluble modulin:agrB | S. aureus strain 2395 USA500, complete genome (CP007499.1) | ||
22 | seq:sek:integrase::::emp:clfA | S. aureus strain 2395 USA500, complete genome (CP007499.1) | ||
33 | recombinase::universal stress protein:::cadD::seq:sek:integrase:::emp:clfA | S. aureus plasmid SAP017A, complete sequence (GQ900382.1) | ||
64 | sea:putative holin-like toxin | S. aureus strain R50 chromosome, complete genome (CP039167.1) | ||
S13 (ST5) | MSSA | 4 | sbi:hlgA:hlgC:hlgB | S. aureus strain AR462 chromosome, complete genome (CP029086.1) |
5 | scpA:::eap::scn:sak::::::intergrase:sph:lukH:sbi:hlgA:hlgC:hlgB | S. aureus strain pt239 chromosome, complete genome (CP049467.1) | ||
15 | IS6::cadD:::sed:sej:ser::recombinases:cpA::eap::scn:sak::integrase:sph:lukH | S. aureus strain ER10678.3 plasmid pER10678.3A.1 (CP051928.1) | ||
S24 (ST152) | MSSA | 8 | arsB::crcB::scn:sak:::recombinase::type II toxin–antitoxin system toxin:intergrase | S. aureus strain UMCG579 chromosome, complete genome (CP091066.1) |
21 | cadD:type toxin–antitoxin::integrase | S. aureus strain GHA13 chromosome (CP043911.1) | ||
11 | BrxA/BrxB:::msrA:msrB:::norD::cspA:cvfB | S. aureus strain NGA84b chromosome, complete genome (CP051165.2) | ||
S34 (ST5) | MSSA | 7 | eap/map::scn:sak::::sea:::type II toxin–antitoxin:integrase:sph:lukG:lukH | S. aureus strain HPV107 chromosome, complete genome (CP026074.1) |
8 | clfA:vwb:emp::thermonuclease protein:::sek:seq::pathogenicity island | S. aureus strain B4-59C chromosome, complete genome (CP042153.1) | ||
12 | sem:sei:seu:sen:seg:::lukE:lukD::splA:splB:splC:splD:splF | S. aureus strain ER03588.3 chromosome, complete genome (CP030595.1) | ||
14 | isdB:isdA:isdC:isdD:isdE:isdF::isdG::ecb::efb:scb | S. aureus strain B3-17D chromosome, complete genome (CP042157.1) | ||
20 | SSL13:SSL12:hyl | S. aureus strain NAS_AN_239 chromosome, complete genome (CP062409.1) |
Isolate ID (MLST) | Strain | Contig | Synteny of Resistance Genes and MGEs | Plasmid/Chromosomal Sequence with Closest Nucleotide Homology (Accession Number) |
---|---|---|---|---|
S11 (ST8) | MRSA | 4 | blaI:blaR1:blaZ::recombinase/integrase | S. aureus strain ER02826.3 chromosome (CP030661.1) |
7 | recombinase::dfrG:insertionelement:::ISL3:::recombinase: | S. aureus strain UP_403 chromosome (CP047849.1) | ||
59 | IS6::mecA:MecR1:IS6:: | S. aureus strain ER03868.3 chromosome (CP030403.1) | ||
123 | Plasmid recombination:tet(K) | S. epidermidis isolate BPH0662 genome assembly, plasmid: 1 (LT614820.1) | ||
S29 (ST5) | MRSA | 8 | erm(A):ant(9)-Ia:transposase:recombinase:integrase | S. aureus strain 628 chromosome (CP022905.1) |
11 | gyrB:gyrA:::ligase | S. aureus strain MIN-175 chromosome (CP086121.1) | ||
38 | recombinase:IS1182::mecR1:mecA:::IS6 | S. aureus subsp. aureus strain FDAARGOS_5 chromosome (CP007539.3) | ||
51 * | recombinase:blaI:blaR1:blaZ:cadC:cadA | S. aureus plasmid pSK57, partial sequence (GQ900493.1) | ||
56 | ant(6)-Ia:sat4:aph(3′)-IIIa | S. pseudintermedius strain MAD627 chromosome (CP039743.1) | ||
64 | qacA/B:qacR | S. aureus strain MIN-175 chromosome (CP086121.1) | ||
67 | ermCL:erm(C) | S. epidermidis strain TMDU-137 plasmid p5, complete sequence (CP093178.1) | ||
S31 (ST612) | MRSA | 23 | mecA:mecR1::IS1182::recombinase | S. aureus strain 2395 USA500 (CP007499.1) |
17 | integrase::::::tet(M):::IS256 | S. aureus strain NRS120 chromosome, complete genome (CP026072.1) | ||
S13 (ST5) | MSSA | 15 * | IS6 IS6::cadD:::type I toxin–antitoxin::recombinase::blaI:blaR1:blaZ | S. aureus strain ER10678.3 plasmid pER10678.3A.1 (CP051928.1) |
S24 (ST152) | MSSA | 21 | cadD:typetoxinantitoxin::recombinase:blaI:blaR1:blaZ:recombinase | S. aureus strain GHA13 chromosome (CP043911.1) |
S34 (ST5) | MSSA | 19 | recombinase:blaZ:blaR1:blaI:recombinase:integrase | S. aureus strain UP_678 plasmid unnamed (CP047840.1) |
3. Discussion
4. Materials and Methods
4.1. Ethical Consideration
4.2. Sample Collection and Bacterial Identification
4.3. Antimicrobial Susceptibility and MRSA Detection
4.4. Whole-Genome Sequencing (WGS) and Bioinformatic Analysis
4.5. Genomic Analysis
4.6. Phylogenomic Analysis
4.7. Nucleotide Sequence Accession Number
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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Isolate ID | Species | Sex | Ward | Age | Antibiotics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PEN | AMP | FOX | CIP | MXF | LEV | GEN | AMK | ERY | CLI | TET | DOX | TGC | CHL | NIT | SXT | VAN | RIF | LZD | TEC | |||||
S11 | MRSA | F | Surgical ward | 17 years | R | R | R | R | R | R | R | R | R | R | R | R | R | I | S | R | S | R | R | R |
S29 | MRSA | M | Pediatric ward | <1 year | R | R | R | R | R | R | R | R | I | R | R | R | S | I | S | R | S | I | R | R |
S31 | MRSA | F | Surgical ward | 3 years | R | R | R | R | R | R | R | R | R | R | R | R | S | R | S | R | S | R | R | R |
S24 | MSSA | M | ICU | 33 years | R | S | S | R | R | R | S | S | R | R | R | I | S | I | R | R | S | R | I | I |
S13 | MSSA | M | ICU | <1 year | R | S | S | R | R | R | I | R | I | R | I | R | S | S | S | I | S | S | I | R |
S34 | MSSA | M | NICU | <1 year | R | S | S | R | R | R | I | R | I | R | R | R | S | I | S | S | S | I | S | S |
Isolate ID | MRSA/MSSA | MLST | spa Type | Resistome | Plasmid Replicon Type | Insertion Sequences | Confirmed CRISPRs (CAS) | Clonal Complex | * SCCmec Type | agr Type | Pathogenicity Score |
---|---|---|---|---|---|---|---|---|---|---|---|
S11 | MRSA | ST8 | t9475 | blaZ, mecA, aac(6′)-aph(2″), parC, dfrG, erm(C), grlA, tetK, mepR, mepA, norA, norC, fosB | rep10, rep7a, rep7c | - | 6 (0) | CC8 | NT | Type I | 0.982 (882) |
S29 | MRSA | ST5 | t045 | blaZ, mecA, aph(3′)-III, aac(6′)-aph(2″), ant(6)-Ia, ant(9)-Ia, aad(6′), erm(C), erm(A), qacA, mepR, fosB, norA, norC, sat-4 | rep10, rep21 | IS6, IS256 | 12 (0) | CC5 | SCCmec type I(1B) | Type II | 0.98 (914) |
S31 | MRSA | ST612 | t1257 | blaZ, mecA, aac(6′)-aph(2″), aph(2″)-Ia, aad(6′), ant(6)-Ia, ant(9)-Ia, tet(M), mepR, mepA, dfrC, parC, erm(C), parE, gyrA, rpoB, fosB, norA, norC, murA | rep7c, rep20 | IS256, IS6 | 7 (0) | CC8 | SCCmec type IVd(2B) | Type I | 0.976 (978) |
S24 | MSSA | ST152 | t355 | blaZ, dfrG, mepR, norC, murA | rep16, rep5a | - | 8 (0) | - | NA | Type IV | 0.975(225) |
S13 | MSSA | ST5 | t1265 | blaZ, norA, norC, fosB | rep20 | - | 9 (0) | CC5 | NA | Type II | 0.985 (844) |
S34 | MSSA | ST5 | t7888 | blaZ, norA, norC, mepR, fosB | rep19, rep16, rep20, rep5a | 1S6 | 7 (0) | CC5 | NA | Type II | 0.983 (871) |
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Hetsa, B.A.; Asante, J.; Mbanga, J.; Ismail, A.; Abia, A.L.K.; Amoako, D.G.; Essack, S.Y. Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study. Antibiotics 2024, 13, 796. https://doi.org/10.3390/antibiotics13090796
Hetsa BA, Asante J, Mbanga J, Ismail A, Abia ALK, Amoako DG, Essack SY. Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study. Antibiotics. 2024; 13(9):796. https://doi.org/10.3390/antibiotics13090796
Chicago/Turabian StyleHetsa, Bakoena A., Jonathan Asante, Joshua Mbanga, Arshad Ismail, Akebe L. K. Abia, Daniel G. Amoako, and Sabiha Y. Essack. 2024. "Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study" Antibiotics 13, no. 9: 796. https://doi.org/10.3390/antibiotics13090796