Genomics of Staphylococcus aureus Strains Isolated from Infectious and Non-Infectious Ocular Conditions
Abstract
:1. Introduction
2. Results
2.1. General Features of the Genomes
2.2. Acquired Antimicrobial Resistance Genes
2.3. S. aureus Virulence Determinants
2.4. Sequence Types and Clonal Complexes of S. aureus Isolates
3. Discussion
4. Material and Methods
4.1. Bacterial Isolates
4.2. Whole Genome Sequencing
4.3. Statistical Analysis
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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Ocular Condition | S. aureus Isolates | Region | GC Content (%) | No. of Contigs | Total Sequence Length (bp) | CDSs (Total) | tRNAs |
---|---|---|---|---|---|---|---|
Microbial keratitis | SA107 | USA | 32.8 | 1173 | 3,599,003 | 3302 | 71 |
SA111 | 33 | 655 | 3,113,006 | 2858 | 85 | ||
SA112 | 32.9 | 614 | 3,170,760 | 2930 | 74 | ||
SA113 | 32.8 | 530 | 3,014,859 | 2771 | 72 | ||
SA114 | 32.9 | 1332 | 3,175,242 | 2877 | 60 | ||
SA34 | AUS | 32.9 | 349 | 2,914,342 | 2694 | 60 | |
SA129 | 32.9 | 694 | 3,105,791 | 2897 | 66 | ||
M5-01 | 32.9 | 624 | 2,975,620 | 2701 | 85 | ||
M19-01 | 33 | 429 | 2,893,905 | 2614 | 77 | ||
M28-01 | 32.8 | 475 | 2,960,866 | 2715 | 62 | ||
M43-01 | 33.1 | 985 | 3,029,867 | 2741 | 89 | ||
M71-01 | 32.9 | 536 | 2,918,758 | 2665 | 74 | ||
Conjunctivitis | SA86 | USA | 32.9 | 3916 | 4,579,417 | 3873 | 76 |
SA90 | 32.8 | 404 | 3,015,554 | 2755 | 62 | ||
SA101 | 32.6 | 998 | 3,602,977 | 3296 | 63 | ||
SA102 | 32.8 | 1067 | 3,406,253 | 3085 | 65 | ||
SA103 | 32.9 | 479 | 3,069,147 | 2857 | 72 | ||
SA46 | AUS | 32.9 | 388 | 2,903,724 | 2646 | 62 | |
SA136 | 32.8 | 735 | 3,035,909 | 2803 | 76 | ||
niCIE | SA20 | AUS | 32.8 | 385 | 2,909,603 | 2660 | 61 |
SA25 | 32.8 | 366 | 2,907,754 | 2622 | 61 | ||
SA27 | 32.8 | 345 | 2,919,830 | 2686 | 67 | ||
SA31 | 32.8 | 328 | 2,976,006 | 2782 | 60 | ||
SA32 | 32.7 | 649 | 2,990,036 | 2665 | 65 | ||
SA48 | 32.8 | 338 | 2,922,947 | 2665 | 64 |
Gene | USA Infectious Isolates (MK+ Conjunctivitis) | Australian Infectious Isolates (MK+ Conjunctivitis) | niCIE | ||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
107 | 111 | 112 | 113 | 114 | 86 | 90 | 101 | 102 | 103 | 34 | 129 | M5-01 | M19-01 | M28-01 | M43-01 | M71-01 | 46 | 136 | 20 | 25 | 27 | 31 | 32 | 48 | |
Beta lactamase resistance gene | |||||||||||||||||||||||||
blaZ | |||||||||||||||||||||||||
mecA | |||||||||||||||||||||||||
Aminoglycoside resistance gene | |||||||||||||||||||||||||
aac(6′) | |||||||||||||||||||||||||
aph(2′) | |||||||||||||||||||||||||
ant(6)-la | |||||||||||||||||||||||||
aph(3′)-III | |||||||||||||||||||||||||
ant(9)-la | |||||||||||||||||||||||||
aadD | |||||||||||||||||||||||||
Macrolide, Lincosamide, Streptogramin B | |||||||||||||||||||||||||
erm(A) | |||||||||||||||||||||||||
msr(A) | |||||||||||||||||||||||||
erm(C) | |||||||||||||||||||||||||
mph(C) | |||||||||||||||||||||||||
Tetracycline, chloramphenicol resistance genes | |||||||||||||||||||||||||
tetK | |||||||||||||||||||||||||
cat(pC233) | |||||||||||||||||||||||||
tetM | |||||||||||||||||||||||||
Quaternary ammonium compounds | |||||||||||||||||||||||||
qacB | |||||||||||||||||||||||||
qacD | |||||||||||||||||||||||||
Pseudomonic acid (Mupirocin) | |||||||||||||||||||||||||
mupA |
S. aureus Isolates | Sequence Type | Clonal Complex | Number of: | ||
---|---|---|---|---|---|
Core Genes | Shell Genes | Pan/Total Genes | |||
107 | 15 | CC15 | 2392 | 1187 | 3579 |
111 | 105 | CC5 | 2382 | 770 | 3152 |
112 | 5 | CC5 | 2380 | 841 | 3221 |
113 | 105 | CC5 | 2330 | 782 | 3112 |
114 | 30 | CC30 | 2168 | 129 | 3377 |
86 | 840 | CC5 | 1984 | 2577 | 4561 |
90 | 5 | CC5 | 2342 | 739 | 3089 |
101 | 8 | CC8 | 2533 | 898 | 3431 |
102 | 8 | CC8 | 2497 | 760 | 3257 |
103 | 8 | CC8 | 2514 | 498 | 3012 |
34 | 508 | CC45 | 2194 | 974 | 3168 |
129 | 34 | CC30 | 2227 | 1112 | 3339 |
M5-01 | 188 | CC1 | 2267 | 844 | 3111 |
M19-01 | NI | NI | 2302 | 684 | 2986 |
M28-01 | 109 | CC1 | 2304 | 775 | 3079 |
M43-01 | 672 | NI | 2296 | 827 | 3123 |
M71-01 | 97 | CC97 | 2315 | 705 | 3020 |
46 | 5 | CC5 | 2325 | 664 | 2989 |
136 | 188 | CC1 | 2328 | 821 | 3149 |
20 | 121 | NI | 2252 | 824 | 3076 |
25 | 5 | CC5 | 2341 | 608 | 2949 |
27 | 39 | CC30 | 2180 | 996 | 3176 |
31 | 34 | CC30 | 2220 | 1010 | 3230 |
32 | 8 | CC8 | 2416 | 501 | 2917 |
48 | 5 | CC5 | 2300 | 736 | 3036 |
Ocular Condition | Stain Number | Phenotypic Resistance (R) and Susceptibility (S) Profile | Profile of Virulence Genes Known to Be Possessed by the Isolates |
---|---|---|---|
Microbial keratitis USA | SA107 | CIP, CEFT, OXA, AZI, POLYB (R) GN, VAN, CHL (S) | fnbpA, eap, sspB, sspA, coa, hla, hlg, hld. |
SA111 | CIP, CEFT, OXA, GN, AZI, POLYB (R) VAN, CHL (S) | clfA, fnbpA, eap, sspB, sspA, coa, hla, hlg, hld | |
SA112 | CIP, CEFT, OXA, AZI, POLYB (R) GN, VAN, CHL (S) | clfA, fnbpA, eap, sspB, sspA, coa, hla, hlg, hld | |
SA113 | CIP, CEFT, OXA, AZI, POLYB (R) GN, VAN, CHL (S) | clfA, fnbpA, eap, sspB, sspA, coa, hla, hlg, hld | |
SA114 | CIP, CEFT, AZI, POLYB (R) GN, VAN, OXA, CHL (S) | clfA, fnbpA, eap, sspB, sspA, coa, hla, hlg, hld | |
Microbial keratitis Australia | SA34 | CEFT, AZI, POLYB (R) CIP, GN, VAN, OXA, CHL (S) | fnbpA, eap, scpAsspB, sspA, coa, seb, hla, hlg, hld |
SA129 | CEFT, CHL, AZI, POLYB (R) CIP, GN, VAN, OXA (S) | clfA, fnbpA, eap, sspB, sspA, coa, hla, hlg, hld | |
M5-01 | CIP, CEFT, CHL, AZI (R) GN, VAN, OXA, POLYB (S) | clfA, fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld | |
M19-01 | CEFT, AZI, POLYB (R) CIP, GN, VAN, OXA, CHL (S) | fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld | |
M28-01 | CEFT, CHL, AZI, POLYB (R) CIP, GN, VAN, OXA (S) | clfA, fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld | |
M43-01 | CIP, CEFT, OXA, CHL, AZI, POLYB (R) GN, VAN (S) | clfA, eap, scpA, sspB, sspA, coa, hla, hlg, hld | |
M71-01 | CIP, CEFT, CHL, AZI, POLYB (R) GN, VAN, OXA (S) | clfA, fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld | |
Conjunctivitis USA | SA86 | CEFT, CHL, AZI, POLYB (R) CIP, GN, VAN, OXA (S) | clfA, fnbpA, eap, scpA, sspB, coa, seb, hla, hlg, hld, pvl. |
SA90 | CIP, CEFT, AZI, POLYB (R) GN, VAN, OXA, CHL (S) | clfA, fnbpA, eap, scpA, sspB, coa, hla, hlg, hld. | |
SA101 | CIP, CEFT, OXA, AZI, POLYB (R) GN, VAN, CHL (S) | clfA, fnbpA, eap, sspB, sspA, coa, hla, hlg, hld, pvl | |
SA102 | CIP, CEFT, OXA, AZI, POLYB (R) GN, VAN, CHL (S) | clfA, fnbpA, eap, sspB, sspA, coa, seb, hla, hlg, hld. | |
SA103 | CIP, CEFT, OXA, AZI, POLYB (R) GN, VAN, CHL (S) | clfA, fnbpA, eap, sspB, sspA, coa, hla, hlg, hld, pvl | |
Conjunctivitis Australia | SA46 | AZI, POLYB (R) CIP, CEFT, OXA, GN, VAN, CHL (S) | clfA, fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld. |
SA136 | CIP, CEFT, AZI, POLYB (R) GN, VAN, OXA, CHL (S) | fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld. | |
niCIE Australia | SA20 | CEFT, CHL, AZI, POLYB (R) CIP, GN, VAN, OXA (S) | fnbpA, eap, scpA, sspB, sspA, coa, seb, hla, hlg, pvl. |
SA25 | AZI, POLYB (R)CIP, CEFT, GN, VAN, OXA, CHL (S) | clfA, fnbpA, eap, scpA, sspB, sspA, coa, seb, hla, hlg, hld. | |
SA27 | CEFT, OXA, AZI, POLYB (R) CIP, GN, VAN, CHL (S) | clfA, fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld. | |
SA31 | CIP, CEFT, AZI, POLYB (R) GN, VAN, OXA, CHL (S) | clfA, fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld. | |
SA32 | POLYB (R) CIP, CEFT, AZI, GN, VAN, OXA, CHL (S) | clfA, fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg, hld. | |
SA48 | CEFT, CHL, AZI, POLYB (R) CIP, GN, VAN, OXA (S). | clfA, fnbpA, eap, scpA, sspB, sspA, coa, hla, hlg. |
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Afzal, M.; Vijay, A.K.; Stapleton, F.; Willcox, M.D.P. Genomics of Staphylococcus aureus Strains Isolated from Infectious and Non-Infectious Ocular Conditions. Antibiotics 2022, 11, 1011. https://doi.org/10.3390/antibiotics11081011
Afzal M, Vijay AK, Stapleton F, Willcox MDP. Genomics of Staphylococcus aureus Strains Isolated from Infectious and Non-Infectious Ocular Conditions. Antibiotics. 2022; 11(8):1011. https://doi.org/10.3390/antibiotics11081011
Chicago/Turabian StyleAfzal, Madeeha, Ajay Kumar Vijay, Fiona Stapleton, and Mark D. P. Willcox. 2022. "Genomics of Staphylococcus aureus Strains Isolated from Infectious and Non-Infectious Ocular Conditions" Antibiotics 11, no. 8: 1011. https://doi.org/10.3390/antibiotics11081011