Whole-Genome Sequencing of ST2 A. baumannii Causing Bloodstream Infections in COVID-19 Patients
Abstract
:1. Introduction
2. Results
2.1. Minimal Inhibitory Concentrations (MICs)
2.2. WGS and Multi-Locus Sequence Typing (MLST)
2.3. Antimicrobial Resistance Genes (ARGs)
2.3.1. β-Lactam Resistance Genes
2.3.2. Aminoglycoside Resistance Genes
2.3.3. Fluoroquinolone Resistance Genes
2.3.4. Other Antimicrobial Resistance Genes
2.4. Mobile Genetic Elements (MGEs)
2.5. Virulence Factors and Other Mechanisms of Resistance
3. Discussion
4. Materials and Methods
4.1. Strains Selection and Identification
4.2. Antimicrobial Susceptibility
4.3. WGS
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Strain | Genome Size (bp) | MGEs | Β-Lactam Resistance | Aminoglycoside Resistance | Macrolide Resistance | Fluoroquinolone Resistance | Others |
---|---|---|---|---|---|---|---|
A. baumannii PE1 (ST2) | 4,023,584 | Tn6207 ISEc29 ISAba26 IS26 ISAba125 | blaADC-25 blaOXA-23 blaOXA-66 | aadA1 aacA4 aph(3′)-VIa aac(6′)Ib-cr strB strA armA | mph(E) msr(E) | aac(6′)Ib-cr | sul1 tet(B) catB8 |
A. baumannii PE2 (ST2) | 4,023,635 | Tn6207 ISAba125 ISAba26 ISVsa3 | blaADC-25 blaOXA-23 blaOXA-66 | aadA1 aacA4 aph(3′)-VIa aac(6′)Ib-cr strB strA armA | mph(E) msr(E) | aac(6′)Ib-cr | sul1 tet(B) catB8 |
A. baumannii PE3 (ST2) | 3,850,309 | ISEc29 ISAba125 ISAba2 ISAba13 IS17 IS6100 | blaADC-25 blaOXA-23 blaOXA-82 | aadA1 aacA2 aacA4 aadB aph(3′)-Ic aac(3)-Ia armA | mph(E) msr(E) | aac(6′)Ib-cr | sul1 catB8 |
A. baumannii PE4 (ST2) | 3,965,839 | Tn6207 ISVsa3 ISEc29 ISAba125 ISAba26 | blaADC-25 blaOXA-23 blaOXA-66 | aadA1 aacA4 strB strA armA | mph(E) msr(E) | aac(6′)Ib-cr | sul1 tet(B) catB8 |
A. baumannii PE5 (ST2) | 3,829,825 | ISEc29 ISAba125 ISAba2 ISAba13 IS17 IS6100 | blaADC-25 blaOXA-23 blaOXA-82 | aadA1 aacA2 aacA4 aadB aph(3′)-VIa aph(3′)-Ic aac(3)-Ia armA | mph(E) msr(E) | aac(6′)Ib-cr | sul1 catB8 |
A. baumannii PE6 (ST2) | 4,041,529 | Tn6207 ISVsa3 ISEc29 ISAba125 ISAba26 | blaADC-25 blaOXA-23 blaOXA-66 | aadA1 aacA4 strB strA armA | mph(E) msr(E) | aac(6′)Ib-cr | sul1 tet(B) catB8 |
A. baumannii PE7 (ST2) | 3,841,128 | ISEc29 ISAba125 ISAba2 ISAba13 IS17 IS6100 | blaADC-25 blaOXA-23 blaOXA-82 | aadA1 aacA2 aacA4 aadB aph(3′)-VIa aph(3′)-Ic aac(3)-Ia armA | mph(E) msr(E) | aac(6′)Ib-cr | sul1 catB8 |
A. baumannii PE8 (ST2) | 3,852,243 | ISEc29 ISAba125 ISAba2 ISAba13 IS17 IS6100 | blaADC-25 blaOXA-23 blaOXA-82 | aadA1 aacA2 aacA4 aadB aph(3′)-Ic aac(3)-Ia armA | mph(E) msr(E) | aac(6′)Ib-cr | sul1 catB8 |
Category | Virulence Factors | Related Genes |
---|---|---|
Adherence | Outer membrane protein | ompA |
Biofilm formation | AdeFGH efflux pump | adeF; adeG; adeH |
Biofilm-associated protein | bap | |
Csu fimbriae | csuA; csuB; csuC; csuD; csuE | |
Polysaccharide poly-N-acetylglucosamine | pgaA; pgaB; pgaC; pgaD | |
Enzyme | Phospholipase C | plc |
Phospholipase D | plcD | |
Immune evasion | LPS | lpsB; lpxA; lpxB; lpxD; lpxL; lpxM |
Iron uptake | Acinetobactin | barA; barB; basA; basB; basC; basD; basF; basG; basH; basI; basJ; bauA; bauB; bauC; bauD; bauE; bauF; entE; |
Heme utilization | hemO | |
Regulation | Quorum sensing | abaI; abaR |
Two-component system (BfmRS) | bfmR; bfmS | |
Serum resistance | PbpG (Penicillin-binding protein) | pbpG |
Stress adaption | Catalase | katA |
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Cherubini, S.; Perilli, M.; Segatore, B.; Fazii, P.; Parruti, G.; Frattari, A.; Amicosante, G.; Piccirilli, A. Whole-Genome Sequencing of ST2 A. baumannii Causing Bloodstream Infections in COVID-19 Patients. Antibiotics 2022, 11, 955. https://doi.org/10.3390/antibiotics11070955
Cherubini S, Perilli M, Segatore B, Fazii P, Parruti G, Frattari A, Amicosante G, Piccirilli A. Whole-Genome Sequencing of ST2 A. baumannii Causing Bloodstream Infections in COVID-19 Patients. Antibiotics. 2022; 11(7):955. https://doi.org/10.3390/antibiotics11070955
Chicago/Turabian StyleCherubini, Sabrina, Mariagrazia Perilli, Bernardetta Segatore, Paolo Fazii, Giustino Parruti, Antonella Frattari, Gianfranco Amicosante, and Alessandra Piccirilli. 2022. "Whole-Genome Sequencing of ST2 A. baumannii Causing Bloodstream Infections in COVID-19 Patients" Antibiotics 11, no. 7: 955. https://doi.org/10.3390/antibiotics11070955
APA StyleCherubini, S., Perilli, M., Segatore, B., Fazii, P., Parruti, G., Frattari, A., Amicosante, G., & Piccirilli, A. (2022). Whole-Genome Sequencing of ST2 A. baumannii Causing Bloodstream Infections in COVID-19 Patients. Antibiotics, 11(7), 955. https://doi.org/10.3390/antibiotics11070955