Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) <i>Klebsiella pneumoniae</i> Strain Lacking the Hypermucoviscous Regulators (<i>rmpA</i>/<i>rmpA2</i>)
Hypervirulent <i>K. pneumoniae</i> (hvKP) strains possess distinct characteristics such as hypermucoviscosity, unique serotypes, and virulence factors associated with high pathogenicity. To better understand the genomic characteristics and virulence profile of the isolated hvKP strain, g...
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MDPI AG
2022-04-01
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| Series: | Antibiotics |
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| Online Access: | https://www.mdpi.com/2079-6382/11/5/596 |
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| author | Hisham N. Altayb Hana S. Elbadawi Othman Baothman Imran Kazmi Faisal A. Alzahrani Muhammad Shahid Nadeem Salman Hosawi Kamel Chaieb |
| author_facet | Hisham N. Altayb Hana S. Elbadawi Othman Baothman Imran Kazmi Faisal A. Alzahrani Muhammad Shahid Nadeem Salman Hosawi Kamel Chaieb |
| author_sort | Hisham N. Altayb |
| collection | DOAJ |
| description | Hypervirulent <i>K. pneumoniae</i> (hvKP) strains possess distinct characteristics such as hypermucoviscosity, unique serotypes, and virulence factors associated with high pathogenicity. To better understand the genomic characteristics and virulence profile of the isolated hvKP strain, genomic data were compared to the genomes of the hypervirulent and typical <i>K. pneumoniae</i> strains. The <i>K. pneumoniae</i> strain was isolated from a patient with a recurrent urinary tract infection, and then the string test was used for the detection of the hypermucoviscosity phenotype. Whole-genome sequencing was conducted using Illumina, and bioinformatics analysis was performed for the prediction of the isolate resistome, virulome, and phylogenetic analysis. The isolate was identified as hypermucoviscous, type 2 (K2) capsular polysaccharide, ST14, and multidrug-resistant (MDR), showing resistance to ciprofloxacin, ceftazidime, cefotaxime, trimethoprim-sulfamethoxazole, cephalexin, and nitrofurantoin. The isolate possessed four antimicrobial resistance plasmids (<i>p</i>KPN3-307_type B, <i>p</i>ECW602, <i>p</i>MDR, and <i>p</i>3K157) that carried antimicrobial resistance genes (ARGs) (<i>bla</i><sub>OXA-1,</sub><i>bla</i><sub>CTX-M-15</sub>, <i>sul2</i>, <i>APH(3″)-Ib</i>, <i>APH(6)-Id</i>, and <i>AAC(6′)-Ib-cr6</i>). Moreover, two chromosomally mediated ARGs (<i>fosA6</i> and <i>SHV-28)</i> were identified. Virulome prediction revealed the presence of 19 fimbrial proteins, one aerobactin (<i>iutA</i>) and two salmochelin (<i>iroE</i> and <i>iroN</i>). Four secretion systems (T6SS-I (13), T6SS-II (9), T6SS-III (12), and Sci-I T6SS (1)) were identified. Interestingly, the isolate lacked the known hypermucoviscous regulators (<i>rmpA/rmpA2</i>) but showed the presence of other <i>RcsAB</i> capsule regulators (<i>rcsA</i> and <i>rcsB</i>). This study documented the presence of a rare MDR hvKP with hypermucoviscous regulators and lacking the common capsule regulators, which needs more focus to highlight their epidemiological role. |
| first_indexed | 2024-03-10T03:27:51Z |
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| last_indexed | 2024-03-10T03:27:51Z |
| publishDate | 2022-04-01 |
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| spelling | doaj.art-f1759335b17d45c791b356d0d8730f3d2023-11-23T09:48:20ZengMDPI AGAntibiotics2079-63822022-04-0111559610.3390/antibiotics11050596Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) <i>Klebsiella pneumoniae</i> Strain Lacking the Hypermucoviscous Regulators (<i>rmpA</i>/<i>rmpA2</i>)Hisham N. Altayb0Hana S. Elbadawi1Othman Baothman2Imran Kazmi3Faisal A. Alzahrani4Muhammad Shahid Nadeem5Salman Hosawi6Kamel Chaieb7Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaMicrobiology and Parasitology Department, Soba University Hospital, University of Khartoum, Khartoum 11115, SudanDepartment of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaDepartment of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaDepartment of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaDepartment of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaDepartment of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaDepartment of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi ArabiaHypervirulent <i>K. pneumoniae</i> (hvKP) strains possess distinct characteristics such as hypermucoviscosity, unique serotypes, and virulence factors associated with high pathogenicity. To better understand the genomic characteristics and virulence profile of the isolated hvKP strain, genomic data were compared to the genomes of the hypervirulent and typical <i>K. pneumoniae</i> strains. The <i>K. pneumoniae</i> strain was isolated from a patient with a recurrent urinary tract infection, and then the string test was used for the detection of the hypermucoviscosity phenotype. Whole-genome sequencing was conducted using Illumina, and bioinformatics analysis was performed for the prediction of the isolate resistome, virulome, and phylogenetic analysis. The isolate was identified as hypermucoviscous, type 2 (K2) capsular polysaccharide, ST14, and multidrug-resistant (MDR), showing resistance to ciprofloxacin, ceftazidime, cefotaxime, trimethoprim-sulfamethoxazole, cephalexin, and nitrofurantoin. The isolate possessed four antimicrobial resistance plasmids (<i>p</i>KPN3-307_type B, <i>p</i>ECW602, <i>p</i>MDR, and <i>p</i>3K157) that carried antimicrobial resistance genes (ARGs) (<i>bla</i><sub>OXA-1,</sub><i>bla</i><sub>CTX-M-15</sub>, <i>sul2</i>, <i>APH(3″)-Ib</i>, <i>APH(6)-Id</i>, and <i>AAC(6′)-Ib-cr6</i>). Moreover, two chromosomally mediated ARGs (<i>fosA6</i> and <i>SHV-28)</i> were identified. Virulome prediction revealed the presence of 19 fimbrial proteins, one aerobactin (<i>iutA</i>) and two salmochelin (<i>iroE</i> and <i>iroN</i>). Four secretion systems (T6SS-I (13), T6SS-II (9), T6SS-III (12), and Sci-I T6SS (1)) were identified. Interestingly, the isolate lacked the known hypermucoviscous regulators (<i>rmpA/rmpA2</i>) but showed the presence of other <i>RcsAB</i> capsule regulators (<i>rcsA</i> and <i>rcsB</i>). This study documented the presence of a rare MDR hvKP with hypermucoviscous regulators and lacking the common capsule regulators, which needs more focus to highlight their epidemiological role.https://www.mdpi.com/2079-6382/11/5/596antimicrobial resistancehvKPK2 capsuleST14fimbrial proteinsaerobactin |
| spellingShingle | Hisham N. Altayb Hana S. Elbadawi Othman Baothman Imran Kazmi Faisal A. Alzahrani Muhammad Shahid Nadeem Salman Hosawi Kamel Chaieb Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) <i>Klebsiella pneumoniae</i> Strain Lacking the Hypermucoviscous Regulators (<i>rmpA</i>/<i>rmpA2</i>) Antibiotics antimicrobial resistance hvKP K2 capsule ST14 fimbrial proteins aerobactin |
| title | Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) <i>Klebsiella pneumoniae</i> Strain Lacking the Hypermucoviscous Regulators (<i>rmpA</i>/<i>rmpA2</i>) |
| title_full | Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) <i>Klebsiella pneumoniae</i> Strain Lacking the Hypermucoviscous Regulators (<i>rmpA</i>/<i>rmpA2</i>) |
| title_fullStr | Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) <i>Klebsiella pneumoniae</i> Strain Lacking the Hypermucoviscous Regulators (<i>rmpA</i>/<i>rmpA2</i>) |
| title_full_unstemmed | Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) <i>Klebsiella pneumoniae</i> Strain Lacking the Hypermucoviscous Regulators (<i>rmpA</i>/<i>rmpA2</i>) |
| title_short | Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) <i>Klebsiella pneumoniae</i> Strain Lacking the Hypermucoviscous Regulators (<i>rmpA</i>/<i>rmpA2</i>) |
| title_sort | genomic analysis of multidrug resistant hypervirulent hypermucoviscous i klebsiella pneumoniae i strain lacking the hypermucoviscous regulators i rmpa i i rmpa2 i |
| topic | antimicrobial resistance hvKP K2 capsule ST14 fimbrial proteins aerobactin |
| url | https://www.mdpi.com/2079-6382/11/5/596 |
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