A Comprehensive Genomic Analysis of the Emergent <i>Klebsiella pneumoniae</i> ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain
<i>Klebsiella pneumoniae</i> is considered an opportunistic pathogen frequently involved with healthcare-associated infections. The genome of <i>K. pneumoniae</i> is versatile, harbors diverse virulence factors and easily acquires and exchanges resistance plasmids, facilitati...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/11/12/1394 |
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| author | Romário Oliveira de Sales Laura Leaden Letícia Busato Migliorini Patricia Severino |
| author_facet | Romário Oliveira de Sales Laura Leaden Letícia Busato Migliorini Patricia Severino |
| author_sort | Romário Oliveira de Sales |
| collection | DOAJ |
| description | <i>Klebsiella pneumoniae</i> is considered an opportunistic pathogen frequently involved with healthcare-associated infections. The genome of <i>K. pneumoniae</i> is versatile, harbors diverse virulence factors and easily acquires and exchanges resistance plasmids, facilitating the emergence of new threatening clones. In the last years, ST16 has been described as an emergent, clinically relevant strain, increasingly associated with outbreaks, and carrying virulence factors (such as ICE<i>Kp</i>, <i>iuc</i>, <i>rmpADC/2</i>) and a diversity of resistance genes. However, a far-reaching phylogenetic study of ST16, including geographically, clinically and temporally distributed isolates is not available. In this work, we analyzed all publicly available ST16 <i>K. pneumoniae</i> genomes in terms of virulence factors, including capsular lipopolysaccharide and polysaccharide diversity, plasmids and antimicrobial resistance genes. A core genome SNP analysis shows that less than 1% of studied sites were variant sites, with a median pairwise single nucleotide polymorphism difference of 87 SNPs. The number and diversity of antimicrobial resistance genes, but not of virulence-related genes, increased consistently in ST16 strains during the studied period. A genomic comparison between ST16 and the high-risk clone ST11 <i>K. pneumoniae</i>, showed great similarities in their capacity to acquire resistance and virulence markers, differing mostly in the great diversity of capsular lipopolysaccharide and polysaccharide types in ST11, in comparison with ST16. While virulence and antimicrobial resistance scores indicated that ST11 might still constitute a more difficult-to-manage strain, results presented here demonstrate the great potential of the ST16 clone becoming critical in public health. |
| first_indexed | 2024-03-09T16:00:51Z |
| format | Article |
| id | doaj.art-f8e2dd6adc394387b963a6b3f12bb35f |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-09T16:00:51Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-f8e2dd6adc394387b963a6b3f12bb35f2023-11-24T17:11:56ZengMDPI AGPathogens2076-08172022-11-011112139410.3390/pathogens11121394A Comprehensive Genomic Analysis of the Emergent <i>Klebsiella pneumoniae</i> ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 StrainRomário Oliveira de Sales0Laura Leaden1Letícia Busato Migliorini2Patricia Severino3Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, BrazilAlbert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, BrazilAlbert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, BrazilAlbert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Sao Paulo 05652-900, Brazil<i>Klebsiella pneumoniae</i> is considered an opportunistic pathogen frequently involved with healthcare-associated infections. The genome of <i>K. pneumoniae</i> is versatile, harbors diverse virulence factors and easily acquires and exchanges resistance plasmids, facilitating the emergence of new threatening clones. In the last years, ST16 has been described as an emergent, clinically relevant strain, increasingly associated with outbreaks, and carrying virulence factors (such as ICE<i>Kp</i>, <i>iuc</i>, <i>rmpADC/2</i>) and a diversity of resistance genes. However, a far-reaching phylogenetic study of ST16, including geographically, clinically and temporally distributed isolates is not available. In this work, we analyzed all publicly available ST16 <i>K. pneumoniae</i> genomes in terms of virulence factors, including capsular lipopolysaccharide and polysaccharide diversity, plasmids and antimicrobial resistance genes. A core genome SNP analysis shows that less than 1% of studied sites were variant sites, with a median pairwise single nucleotide polymorphism difference of 87 SNPs. The number and diversity of antimicrobial resistance genes, but not of virulence-related genes, increased consistently in ST16 strains during the studied period. A genomic comparison between ST16 and the high-risk clone ST11 <i>K. pneumoniae</i>, showed great similarities in their capacity to acquire resistance and virulence markers, differing mostly in the great diversity of capsular lipopolysaccharide and polysaccharide types in ST11, in comparison with ST16. While virulence and antimicrobial resistance scores indicated that ST11 might still constitute a more difficult-to-manage strain, results presented here demonstrate the great potential of the ST16 clone becoming critical in public health.https://www.mdpi.com/2076-0817/11/12/1394<i>Klebsiella pneumoniae</i>ST16ST11antimicrobial resistancevirulence factorshigh-risk clone |
| spellingShingle | Romário Oliveira de Sales Laura Leaden Letícia Busato Migliorini Patricia Severino A Comprehensive Genomic Analysis of the Emergent <i>Klebsiella pneumoniae</i> ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain Pathogens <i>Klebsiella pneumoniae</i> ST16 ST11 antimicrobial resistance virulence factors high-risk clone |
| title | A Comprehensive Genomic Analysis of the Emergent <i>Klebsiella pneumoniae</i> ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain |
| title_full | A Comprehensive Genomic Analysis of the Emergent <i>Klebsiella pneumoniae</i> ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain |
| title_fullStr | A Comprehensive Genomic Analysis of the Emergent <i>Klebsiella pneumoniae</i> ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain |
| title_full_unstemmed | A Comprehensive Genomic Analysis of the Emergent <i>Klebsiella pneumoniae</i> ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain |
| title_short | A Comprehensive Genomic Analysis of the Emergent <i>Klebsiella pneumoniae</i> ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain |
| title_sort | comprehensive genomic analysis of the emergent i klebsiella pneumoniae i st16 lineage virulence antimicrobial resistance and a comparison with the clinically relevant st11 strain |
| topic | <i>Klebsiella pneumoniae</i> ST16 ST11 antimicrobial resistance virulence factors high-risk clone |
| url | https://www.mdpi.com/2076-0817/11/12/1394 |
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