Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling
Abstract
:1. Introduction
2. Results and Discussion
2.1. Antibiotic Resistance Phenotypes of Aci46
2.2. Whole Genome Sequencing Data
2.3. Antibiotic Resistance Gene, Efflux Pump, and Virulence Gene Predictions
2.4. Comparative Pangenomic Analysis against Other A. baumannii Strains
2.5. Pairwise SNP Analysis
3. Materials and Methods
3.1. Bacterial Strains
3.2. Antibiotic Susceptibility Testing by Disk Diffusion and Microdilution
3.3. Genomic DNA Extraction and Whole Genome Sequencing
3.4. Genome Assembly, Annotation, and Pathogenicity Island Prediction
3.5. MLST and Phylogenetic Analysis
3.6. Comparative Pangenome and Pairwise SNP Analysis
4. 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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Class of Antibiotic | Drug | ID | Dose | Zone of Inhibition (mm) * | Interpretation |
---|---|---|---|---|---|
Aminoglycosides | Gentamicin | CN10 | 10 µg | 0 | R |
Kanamycin | K30 | 30 µg | 0 | R | |
Streptomycin | S10 | 10 µg | 0 | R | |
Beta-lactams | Ampicillin | AMP10 | 10 µg | 0 | R |
Cephalothin | KF30 | 30 µg | 0 | R | |
Cefoxitin | FOX30 | 30 µg | 0 | R | |
Cefotaxime | CTX30 | 30 µg | 0 | R | |
Ceftazidime | CAZ30 | 30 µg | 0 | R | |
Ceftriaxone | CRO30 | 30 µg | 0 | R | |
Beta-lactam combined | Amoxycillin/clavulanic acid | AMC30 | 30 µg | 0 | R |
Carbapenems | Imipenem | IPM10 | 10 µg | 7–8 | R |
Meropenem | MEM10 | 10 µg | 0 | R | |
Quinolones | Ciprofloxacin | CIP5 | 5 µg | 0 | R |
Nalidixic acid | NA30 | 30 µg | 0 | R | |
Norfloxacin | NOR10 | 10 µg | 0 | R | |
Folate pathway blocks | Trimethoprim | W5 | 5 µg | 0 | R |
Trimethoprim-sulfamethoxazole | SXT25 | 25 µg | 0 | R | |
Phenical | Chloramphenicol | C30 | 30 µg | 10–11 | R |
Tetracycline | Tetracycline | TE30 | 30 µg | 0 | R |
Feature | Chromosome | |
Total number of bases (bp) | 3,887,827 | |
G + C content (%) | 38.87 | |
number of contigs | 80 | |
genome coverage (x) | 686.7 | |
number of coding sequences | 3754 | |
rRNA | 3 | |
tRNA | 63 | |
N50 | 135,425 | |
L50 | 11 | |
Feature | pAci46a | pAci46b |
Total number of bases (bp) | 70,873 | 8808 |
G + C content (%) | 33.39 | 34.31 |
number of contigs | 1 | 1 |
genome coverage (x) | 1189.0 | 7787.5 |
number of coding sequences | 102 | 11 |
rRNA | 0 | 0 |
tRNA | 0 | 0 |
Target | Location | Product | ||||
---|---|---|---|---|---|---|
Gene | Contig | Start | Stop | Length (bp) | ||
Antibiotics | ||||||
Aminoglycosides | aph(3″)-Ib | Aci46-0022 | 7765 | 8568 | 804 | Aminoglycoside 3″-phosphotransferase |
aph(6)-Id | Aci46-0022 | 6929 | 7765 | 837 | Aminoglycoside 6-phosphotransferase | |
armA | Aci46-0031 | 687 | 1460 | 774 | hypothetical protein | |
Beta-lactams/ carbapenems | blaOXA-23 | Aci46-0058 | 1667 | 2488 | 882 | Class D beta-lactamase OXA-23 |
blaOXA-66 | Aci46-0018 | 65,582 | 66,406 | 825 | Class D beta-lactamase OXA-66 or OXA-51-like | |
OprD family | Aci46-0035 | 24,815 | 26,131 | 1317 | Outer membrane low permeability porin, OprD family | |
Beta-lactams/ cephalosporins | blaADC-25 | Aci46-0017 | 86 | 1237 | 1152 | Class C beta-lactamase ADC-25 |
Colistin | lpxA | Aci46-0001 | 58,724 | 59,512 | 789 | Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase |
lpxC | Aci46-0006 | 139,160 | 140,062 | 903 | UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase | |
pmrA | Aci46-0016 | 34,812 | 35,486 | 675 | Polymyxin resistant component PmrA | |
pmrB | Aci46-0016 | 35,512 | 36,846 | 1335 | Polymyxin resistant component PmrB | |
Fluoroquinolones | gyrA | Aci46-0003 | 54,354 | 57,068 | 2715 | DNA gyrase subunit A |
gyrB | Aci46-0028 | 32,254 | 34,722 | 2469 | DNA gyrase subunit B | |
Macrolide | mph(E) | Aci46-0054 | 2308 | 3192 | 885 | Mph(E) family macrolide 2′-phosphotransferase |
msr(E) | Aci46-0054 | 3248 | 4723 | 1476 | ABC-F type ribosomal protection protein Msr(E) | |
Tetracycline | tetA | Aci46-0022 | 2357 | 3556 | 1200 | Tetracycline resistance protein |
tetR | Aci46-0022 | 3638 | 4261 | 624 | Tetracycline resistance regulatory protein TetR | |
Sulfonamide | sul2 | Aci46-0064 | 97 | 912 | 816 | Dihydropteroate synthase type-2 |
Drug transporters | ||||||
RND efflux system | adeA | Aci46-0019 | 60,468 | 61,658 | 1191 | RND efflux system, membrane fusion protein |
adeB | Aci46-0019 | 61,655 | 64,765 | 3111 | RND efflux system, inner membrane transporter | |
adeF | Aci46-0011 | 61,731 | 62,951 | 1221 | RND efflux system, membrane fusion protein | |
adeG | Aci46-0011 | 62,958 | 66,137 | 3180 | RND efflux system, inner membrane transporter | |
adeH | Aci46-0011 | 6389 | 6835 | 447 | Efflux transport system, outer membrane factor (OMF) lipoprotein | |
adeI | Aci46-0016 | 53,597 | 54,847 | 1251 | RND efflux system, membrane fusion protein | |
adeJ | Aci46-0016 | 50,408 | 53,584 | 3177 | RND efflux system, inner membrane transporter | |
adeK | Aci46-0016 | 48,954 | 50,408 | 1455 | Efflux transport system, outer membrane factor (OMF) lipoprotein | |
adeN | Aci46-0001 | 43,293 | 43,946 | 654 | Transcriptional regulator, AcrR family | |
adeR | Aci46-0019 | 59,579 | 60,322 | 744 | Two-component transcriptional response regulator, LuxR family | |
adeS | Aci46-0019 | 58,474 | 59,547 | 1074 | Osmosensitive K+ channel histidine kinase KdpD | |
mexT | Aci46-0029 | 34,598 | 35,587 | 990 | Transcriptional regulator, LysR family | |
opmH | Aci46-0022 | 48,920 | 50,266 | 1347 | Outer membrane channel TolC (OpmH) | |
MFS family transporter | emrA | Aci46-0024 | 20,758 | 21,909 | 1152 | Multidrug efflux system EmrAB-OMF, membrane fusion component EmrA |
emrB | Aci46-0024 | 19,228 | 20,751 | 1524 | Multidrug efflux system EmrAB-OMF, inner-membrane proton/drug antiporter EmrB | |
mdfA | Aci46-0002 | 123,994 | 125,223 | 1230 | Multidrug efflux pump MdfA/Cmr (of MFS type), broad spectrum | |
ABC transporter | macA | Aci46-0012 | 77,649 | 78,989 | 1341 | Macrolide-specific efflux protein MacA |
macB | Aci46-0012 | 78,992 | 80,986 | 1995 | Macrolide export ATP-binding/permease protein MacB | |
MATE family transporter | abeM | Aci46-0007 | 67,926 | 69,272 | 1347 | Multidrug efflux transporter MdtK/NorM (MATE family) |
SMR | abeS | Aci46-0011 | 56,864 | 57,193 | 330 | small multidrug resistance family (SMR) protein |
Pathogenicity Island | Contig | Start | Stop | Length (bp) | GC Content (%) | Number of CDS |
---|---|---|---|---|---|---|
Prophage-1 | Aci46-0033 | 9107 | 23,948 | 14,842 | 40.09 | 14 |
Prophage-2 | Aci46-0033 | 27,330 | 37,053 | 9724 | 40.71 | 11 |
Prophage-3 | Aci46-0036 | 785 | 30,936 | 30,152 | 38.52 | 46 |
Prophage-4 | Aci46-0041 | 806 | 17,770 | 16,965 | 40.29 | 29 |
Type 4 secretion system, T4SS | pAci46a | 20,944 | 48,690 | 27,747 | 34.60 | 32 |
Type 6 secretion system, T6SS | Aci46-0010 | 8673 | 27,581 | 19,412 | 36.92 | 15 |
Integrative and conjugation element, ICE | pAci46a | 1 | 70,873 | 70,873 | 33.39 | 94 |
Target | Gene | Aci46 vs. ATCC17978 | Aci46 vs. ACICU | ||
---|---|---|---|---|---|
Nucleotide Change | Amino Acid Change | Nucleotide Change | Amino Acid Change | ||
Antibiotic Resistance Genes | |||||
Beta-lactams/ cephalosporins | blaADC-25 | 356TG > AA | Val119Glu | 238C > A | Arg80Ser |
448C > A | Gln150Lys | 448C > A | Gln150Lys | ||
499C > T | Pro167Ser | 487C > A | Gln163Lys | ||
739G > A | Gly247Ser | 499C > T | Pro167Ser | ||
843AGGGTT > GGGTCG | GlnGlyPhe281GlnGlyArg | 547A > G | Arg183Gly | ||
1022A > C | Asn341Thr | 739G > A | Gly247Ser | ||
843AGGGTT > GGGTCG | GlnGlyPhe281GlnGlyArg | ||||
932G > A | Ser311Asn | ||||
1020CAA > TAC | ThrAsn340ThrThr | ||||
1135G > A | Asp379Asn | ||||
Beta-lactams/ carbapenems | blaOXA-66 | 107A > T | Glu36Val | ||
315CGGGC > TGGTA | AspGlyGln105AspGlyLys | ||||
673G > A | Asp225Asn | ||||
Colistin | lpxA | 391T > C | Tyr131His | ||
lpxC | 358T > C | Cys120Arg | |||
859A > G | Asn287Asp | ||||
pmrB | 412G > A | Ala138Thr | 412G > A | Ala138Thr | |
599C > T | Pro200Leu | 599C > T | Glu229Asp | ||
687A > C | Glu229Asp | 687A > C | Pro200Leu | ||
1331C > T | Ala444Val | ||||
Fluoroquinolones | gyrA | 173C > T | Ser58Leu | ||
gyrB | 2059A > G | Ile687Val | 1738T > C | Tyr580His | |
Drug Transporters | |||||
RND efflux system | adeA | 70A > G | Lys24Glu | ||
adeB | 917G > T | Gly306Val | |||
1279AAT > TCG | Asn427Ser | ||||
1654G > A | Ala552Thr | ||||
1928C > A | Ala643Asp | ||||
1936A > T | Thr646Ser | ||||
2191C > T | Leu731Phe | ||||
adeF | 1163A > G | Asn388Ser | |||
adeG | 1540G > T | Val514Leu | |||
adeH | 214A > G | Thr72Ala | |||
683T > G | Val228Gly | ||||
adeJ | 2482A > G | Lys828Glu | |||
adeR | 358G > A | Val120Ile | |||
407C > T | Ala136Val | ||||
adeS | 515T > C | Leu172Pro | |||
557G > T | Gly186Val | ||||
802A > C | Asn268His | ||||
908A > T | Tyr303Phe | ||||
1042G > A | Val348Ile | ||||
opmH | 386A > G | Lys129Arg | |||
512A > G | Asn171Ser | ||||
MFS family transporter | emrB | 715A > G | Ile239Val | ||
mdfA | 1157C > T | Ala386Val | |||
ABC transporter | macB | 1462G > A | Val488Ile | ||
SMR | abeS | 121A > G | Ile41Val | ||
165G > C | Met55Ile | ||||
250G > T | Val84Leu | ||||
268CTTA > TTGG | LeuThr90LeuAla | ||||
292ATC > GTG | Ile98Val |
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Thadtapong, N.; Chaturongakul, S.; Soodvilai, S.; Dubbs, P. Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling. Antibiotics 2021, 10, 1054. https://doi.org/10.3390/antibiotics10091054
Thadtapong N, Chaturongakul S, Soodvilai S, Dubbs P. Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling. Antibiotics. 2021; 10(9):1054. https://doi.org/10.3390/antibiotics10091054
Chicago/Turabian StyleThadtapong, Nalumon, Soraya Chaturongakul, Sunhapas Soodvilai, and Padungsri Dubbs. 2021. "Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling" Antibiotics 10, no. 9: 1054. https://doi.org/10.3390/antibiotics10091054
APA StyleThadtapong, N., Chaturongakul, S., Soodvilai, S., & Dubbs, P. (2021). Colistin and Carbapenem-Resistant Acinetobacter baumannii Aci46 in Thailand: Genome Analysis and Antibiotic Resistance Profiling. Antibiotics, 10(9), 1054. https://doi.org/10.3390/antibiotics10091054