Heterogeneity of Molecular Characteristics among Staphylococcus argenteus Clinical Isolates (ST2250, ST2793, ST1223, and ST2198) in Northern Taiwan
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolates and Identification of S. argenteus by Detection of MALDI-TOF MS, MLST Typing, and Detection of CrtM
2.2. Pulsed-Field Gel Electrophoresis and Spa Typing
2.3. Coa, DnaJ, GroEL Gene and Spacer Sequencing, and AgrD Type
2.4. Detection of Virulence Factors
2.5. Sequencing of CRISPR/cas Loci of S. argenteus ST2250
2.6. Phylogenetic Analysis
2.7. Nucleotide Sequence Accession Numbers
3. Results
3.1. Identification of S. argenteus by MALDI-TOF MS, MLST Typing and Lack of CrtM
3.2. Antimicrobial Susceptibility and Biochemical Characteristics
3.3. Genotyping by Pulsed-Field Gel Electrophoresis (PFGE) and Spa Types
3.4. Phylogenetic Trees of Coa, DnaJ and GroESL and Agr Type
3.5. Examination of Virulence Factors
3.6. Polymorphism of CRISPR/Cas System in ST2250 Isolates
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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ST | No. of Isolates Each Year | |||||
---|---|---|---|---|---|---|
Spa Type | 2000 | 2005 | 2010 | 2011 | 2012 | Total (%) |
ST2250 | 0 | 0 | 19 | 25 | 28 | 72 (75.0) |
t5078 a | 0 | 0 | 15 | 18 | 22 | 55 (57.3) |
t5787 | 0 | 0 | 0 | 1 | 0 | 1 (1.0) |
t6675 | 0 | 0 | 0 | 2 | 3 | 5 (5.2) |
t7960 | 0 | 0 | 1 | 1 | 1 | 3 (3.1) |
t10900 | 0 | 0 | 0 | 0 | 1 | 1 (1.0) |
t17928 | 0 | 0 | 0 | 2 | 0 | 2 (2.1) |
Unknown b | 0 | 0 | 3 | 1 | 1 | 5 (5.3) |
ST2793 | 1 | 2 | 4 | 4 | 1 | 12 (12.5) |
Unknown c | 1 | 2 | 4 | 4 | 1 | 12 (12.5) |
ST1223 | 0 | 3 | 5 | 1 | 1 | 10 (10.4) |
t5142 | 0 | 2 | 2 | 0 | 0 | 4 (4.2) |
t7463 | 0 | 1 | 0 | 0 | 0 | 1 (1.0) |
t9791 | 0 | 0 | 3 | 0 | 1 | 4 (4.2) |
t18323 | 0 | 0 | 0 | 1 | 0 | 1 (1.0) |
ST2198 | 0 | 0 | 1 | 1 | 0 | 2 (2.1) |
t9505 | 0 | 0 | 0 | 1 | 0 | 1 (1.0) |
Unknown d | 0 | 0 | 1 | 0 | 0 | 1 (1.0) |
Total (%) | 1 (1.0) | 5 (5.2) | 29 (30.2) | 31 (32.3) | 30 (31.3) | 96 (100) |
ST Type | Spa Repeat Profile | No. of Isolates |
---|---|---|
ST2250 | 299-31-25-17-16-16-16-16 | 1 |
ST2250 | 299-31-25-16-16-16-16-16 | 1 |
ST2250 | 299-31-25-17-119-16-16-16-16 | 1 |
ST2250 | 299-31-17-17-16-16-16-16-16-16-16 | 1 |
ST2250 | 299-31-31-31-25-17-17-16-16-16-16 | 1 |
ST2793 | 259-31-16-16-16-23-17-360-360-25 (t19483) | 8 |
ST2793 | 259-31-16-16-23-307-360-360-25 | 1 |
ST2793 | 259-31-307-16-23-17-360-360-25 | 1 |
ST2793 | 259-25-25 | 1 |
ST2793 | 259-25 | 1 |
ST2198 | 259-23-23-17-17-17-23-23-23-17-17-16 | 1 |
Strain | Spacer Length (bp) | Spacer Sequence (5′-3′) |
---|---|---|
S.ag. MSHR1132 (ST1850) (NC016941) | 71 | TACAGAACTTAATTCATAAATAAATTATTAAGAACAATAATCAAACA....TTAAAAAATGGAGGTTTATTATAT |
S.ag. NTUH_9546-1 (ST2250) (MT542642) | 71 | -----------------------------------------------....------------------------ |
S.ag. NTUH_8694 (ST2793) (MT542656) | 71 | --g---g----------------------------------------....------------------------ |
S.ag. NTUH_2423 (ST1223) (MT542648) | 75 | ---------------------------aa------g-a---g-----caat-a--c------------------- |
S.ag. NTUH_4882 (ST2198) (MT542652) | 71 | -----------------------------------------------....------------------------ |
S.a. N315 (ST5) (NC002745) | 75 | --t-a--t-a--------g-------g-a------g-a---g---t-tgac-a--c--------------c--t- |
S.a. DSM20231 (ST8) (CP011526) | 75 | ---------------------------aat-----g-a---g-----caac-a--c--------------c--t- |
ST Type (No. of Isolates) | ST2250 (72) | ST2793 (12) | ST1223 (10) | ST2198 (2) |
---|---|---|---|---|
agr type b | I | III | III | IV |
coa genotype b | XId | XVI | XV (serotype VI) | XIV |
CRISPR | + (72) | NT | NT | NT |
IEC type C | sak+, scn+ (60) (Type E) sak+ (1) scn+ (1) NT (10) | scn+ (11) NT(1) | scn+ (9) NT(1) | sak+, scn+, chp+ (1) scn+ (1) |
hla & hld | + (72) | + (12) | + (10) | + (2) |
cna | NT | + (12, type III) | NT | NT |
bbp | NT | NT | NT | + (2) |
seb | NT | NT | + (3) | + (1) |
sec | NT | + (8) | NT | NT |
egc cluster | NT | NT | + (10) | NT |
Type | Sequence | Size(bp) | Note |
---|---|---|---|
DR1 | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACX | 37 | upstream |
DR2 | XATTCGATAACTACCCCGAAGAAGAGGGGACGAGAAC | 37 | downstream |
DR3 | TATTCGATAACTACCCCGAAGAAAAGGGGACGAGAAC | 37 | downstream |
DR4 | TATTCGATAACTACCCCGAAGAAGAGGAGACGAGAAC | 37 | downstream |
DDR | TGATCGATAACTACCCCGAAGAATAGGGGACAGAGTG | 37 | Degenerated DR |
DDR | TATTCGATAAATACCCCGGAGAACAGGGGGCGAAAAC | 37 | Degenerated DR |
S1 | CTACTAAAAAGTTATATGTTTCAACAATTTCGTCA | 35 | upstream |
S2 | GGTTTAAGTTTGTCATTATAATCAATCCTTTTTCTT | 36 | upstream |
S3 | GATTAAAACGGTTTGCTTTATTTGCATTTAAAATAG | 36 | upstream |
S4 | TTTTTCATAGTTAATCAATCCCTTTTCTTTTTT | 33 | upstream |
S5 | TAAATCTTTGATTGCTCTTAGCTCTAGTTATGTAT | 35 | upstream |
S6 | ACGCTGTAGTGAAGTATAGAAACGGCATGAGTACAAT | 37 | upstream |
S7 | TTTTACTGTGTTTTTCATAATTAATCAATCCTTT | 34 | downstream |
S8 | TGCCCACTTAATTAATTCATCTAGTCTCATTTCTT | 35 | downstream |
S9 | CATCAACTGACTTTTTAACTGTTTTAGTGAATTCGTC | 37 | downstream |
S10 | TTAAAGATCTCAACAATAGCGTCCCATATTTTCTG | 35 | downstream |
S11 | TAATTGCATTATCAAATGTATATGCTGGATTCCAT | 35 | upstream |
S12 | GTACTTAAGATTTCATCAACTTTCTTTTGTACT | 33 | upstream |
S13 | CGAATTTTGATTCTTTGTTTGTAAATAATGCTCT | 34 | upstream |
S14 | CTATAATAGTTACTGCTTTTGTAACCGTCCATAT | 34 | downstream |
S15 | AAATGCTTATCCATTCTAATCATATTTTCAATTTGTTTA | 39 | downstream |
S16 | TGCCCACTTAATTAATTCATCTAGTCTTATTTCTT | 35 | downstream similar to S8 |
Isolate ID a (Accession No.) | Number of Spacers | Direct Repeat | |
---|---|---|---|
Upstream | Downstream | ||
MSHR 1132 (ST1850) (NC016941) | 6 (S1~6) | 4 (S7~10) | DR1, 2, 3, 4 |
TD13 (ST2854) (MH513583) | 5 (S11~13,5~6) | - | DR1 |
TD162 (ST2250) (MF167423) | 5 (S11~13,5~6) | - a | DR1 |
SH3 (ST2250) (PRJEB8900) | 5 (S11~13,5~6) | 5 (S14~15,8~10) | DR1, 2, 3 |
36 isolates (NTUH_9546-1) (MT542645) | 5 (S11~13,5~6) | 5 (S14~15,8~10) | DR1, 2, 3 |
9 isolates (MT542659~60) | 4 (S11~13,5) | 5 (S14~15,8~10) | DR1, 2, 3 |
6 isolates (MT542661~62) | 4 (S11,13,5~6) | 5 (S14~15,8~10) | DR1, 2, 3 |
5 isolates (MT542663~64) | 3 (S13,5~6) | 5 (S14~15,8~10) | DR1, 2, 3 |
3 isolates (MT542665~66) | 5 (S11~13,5~6) | 4 (S14,8~10) | DR1, 2, 3 |
2 isolates (MT542667~68) | 2 (S11,6) | 5 (S14~15,8~10) | DR1, 2, 3 |
2 isolates (MT542669~70) | 4 (S11~12,5~6) | 4 (S15,8~10) | DR1, 2, 3 |
1 isolate (MT542671~72) | 5 (S11~13,5~6) | 7 (S14~15, 8~9, 8~10) | DR1, 2, 3 |
1 isolate (MT542673~74) | 4 (S11~13,5) | 5 (S14~16, 9~10) | DR1, 2, 3 |
1 isolate (MT542675~76) | 4 (S11~13,6) | 5 (S14~15,8~10) | DR1, 2, 3 |
1 isolate (MT542677~78) | 3 (S12~13,5) | 5 (S14~15,8~10) | DR1, 2, 3 |
1 isolate (NTUH_4415) (MT542646) | 3 (S11,13,5) | 5 (S14~15,8~10) | DR1, 2, 3 |
1 isolate (MT542679~80) | 3 (S11,5~6) | 5 (S14~15,8~10) | DR1, 2, 3 |
1 isolate (MT542681~82) | 2 (S11,5) | 5 (S14~15,8~10) | DR1, 2, 3 |
1 isolate (MT542683~84) | 2 (S5,6) | 5 (S14~15,8~10) | DR1, 2, 3 |
1 isolate (MT542685~86) | 4 (S11~13,6) | 3 (S8~10) | DR1, 2, 3 |
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Hsu, J.-C.; Wan, T.-W.; Lee, H.; Wang, X.-M.; Lin, Y.-T.; Jung, C.-J.; Lee, T.-F.; Hsueh, P.-R.; Teng, L.-J. Heterogeneity of Molecular Characteristics among Staphylococcus argenteus Clinical Isolates (ST2250, ST2793, ST1223, and ST2198) in Northern Taiwan. Microorganisms 2020, 8, 1157. https://doi.org/10.3390/microorganisms8081157
Hsu J-C, Wan T-W, Lee H, Wang X-M, Lin Y-T, Jung C-J, Lee T-F, Hsueh P-R, Teng L-J. Heterogeneity of Molecular Characteristics among Staphylococcus argenteus Clinical Isolates (ST2250, ST2793, ST1223, and ST2198) in Northern Taiwan. Microorganisms. 2020; 8(8):1157. https://doi.org/10.3390/microorganisms8081157
Chicago/Turabian StyleHsu, Jia-Chuan, Tsai-Wen Wan, Hao Lee, Xiao-Mei Wang, Yu-Tzu Lin, Chiau-Jing Jung, Tai-Fen Lee, Po-Ren Hsueh, and Lee-Jene Teng. 2020. "Heterogeneity of Molecular Characteristics among Staphylococcus argenteus Clinical Isolates (ST2250, ST2793, ST1223, and ST2198) in Northern Taiwan" Microorganisms 8, no. 8: 1157. https://doi.org/10.3390/microorganisms8081157