Whole-Genome Sequencing of a Colistin-Resistant <i>Acinetobacter baumannii</i> Strain Isolated at a Tertiary Health Facility in Pretoria, South Africa

• Main Authors: Noel-David Nogbou (Author), Mbudzeni Ramashia (Author), Granny Marumo Nkawane (Author), Mushal Allam (Author), Chikwelu Lawrence Obi (Author), Andrew Munyalo Musyoki (Author)
• Format: Book
• Published: MDPI AG, 2022-04-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.
• Notes: 10.3390/antibiotics11050594; 2079-6382
• Keywords: <i>Acinetobacter baumannii</i>; colistin resistance; resistance mechanism; virulence factors; South Africa; Therapeutics. Pharmacology; RM1-950
• Source: Antibiotics, Vol 11, Iss 5, p 594 (2022)

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_OXA-66</i>; <i>_blaOXA-23</i>; <i>bla_ADC-25</i>; <i>bla_ADC-73</i>; <i>bla_A1</i>; <i>bla_A2</i>, and <i>bla_MBL</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.