Whole-Genome Sequencing of a Colistin-Resistant <i>Acinetobacter baumannii</i> Strain Isolated at a Tertiary Health Facility in Pretoria, South Africa
Background: <i>Acinetobacter baumannii</i>'s (<i>A. baumannii</i>) growing resistance to all available antibiotics is of concern. The study describes a colistin-resistant <i>A. baumannii</i> isolated at a clinical facility from a tracheal aspirate sample. Fur...
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| Main Authors: | , , , , , |
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| Format: | Book |
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MDPI AG,
2022-04-01T00:00:00Z.
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| Summary: | Background: <i>Acinetobacter baumannii</i>'s (<i>A. baumannii</i>) growing resistance to all available antibiotics is of concern. The study describes a colistin-resistant <i>A. baumannii</i> isolated at a clinical facility from a tracheal aspirate sample. Furthermore, it determines the isolates' niche establishment ability within the tertiary health facility. Methods: An antimicrobial susceptibility test, conventional PCR, quantitative real-time PCR, phenotypic evaluation of the efflux pump, and whole-genome sequencing and analysis were performed on the isolate. Results: The antimicrobial susceptibility pattern revealed a resistance to piperacillin/tazobactam, ceftazidime, cefepime, cefotaxime/ceftriaxone, imipenem, meropenem, gentamycin, ciprofloxacin, trimethoprim/sulfamethoxazole, tigecycline, and colistin. A broth microdilution test confirmed the colistin resistance. Conventional PCR and quantitative real-time PCR investigations revealed the presence of <i>adeB</i>, <i>adeR</i>, and <i>adeS</i>, while <i>mcr-1</i> was not detected. A MIC of 0.38 µg/mL and 0.25 µg/mL was recorded before and after exposure to an AdeABC efflux pump inhibitor. The whole-genome sequence analysis of antimicrobial resistance-associated genes detected beta-lactam: <i>bla<sub>OXA-66</sub></i>; <i><sub>blaOXA-23</sub></i>; <i>bla<sub>ADC-25</sub></i>; <i>bla<sub>ADC-73</sub></i>; <i>bla<sub>A1</sub></i>; <i>bla<sub>A2</sub></i>, and <i>bla<sub>MBL</sub></i>; aminoglycoside: <i>aph(6)-Id</i>; <i>aph(3")-Ib</i>; <i>ant(3")-IIa</i> and <i>armA)</i> and a colistin resistance-associated gene <i>lpsB</i>. The whole-genome sequence virulence analysis revealed a biofilm formation system and cell-cell adhesion-associated genes: <i>bap</i>, <i>bfmR</i>, <i>bfmS</i>, <i>csuA</i>, <i>csuA/B</i>, <i>csuB</i>, <i>csuC</i>, <i>csuD</i>, <i>csuE</i>, <i>pgaA</i>, <i>pgaB</i>, <i>pgaC</i>, and <i>pgaD</i>; and quorum sensing-associated genes: <i>abaI</i> and <i>abaR</i> and iron acquisition system associated genes: <i>barA</i>, <i>barB</i>, <i>basA</i>, <i>basB</i>, <i>basC</i>, <i>basD</i>, <i>basF</i>, <i>basG</i>, <i>basH</i>, <i>basI</i>, <i>basJ</i>, <i>bauA</i>, <i>bauB</i>, <i>bauC</i>, <i>bauD</i>, <i>bauE</i>, <i>bauF</i>, and <i>entE</i>. A sequence type classification based on the Pasteur scheme revealed that the isolate belongs to sequence type ST2. Conclusions: The mosaic of the virulence factors coupled with the resistance-associated genes and the phenotypic resistance profile highlights the risk that this strain is at this South African tertiary health facility. |
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| Item Description: | 10.3390/antibiotics11050594 2079-6382 |