Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta
Background Haemophilus influenzae is a Gram-negative bacterium that can exist as a commensal organism or cause a range of diseases, from ear infections to invasive conditions like meningitis. While encapsulated H. influenzae strains have historically been linked to severe diseases, non-typeable Haem...
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PeerJ Inc.
2025-03-01
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| author | Brianna J. Bixler Charlotte J. Royer Robert A. Petit III Abraham G. Moller Samantha Sefton Stepy Thomas Amy Tunali Lauren F. Collins Monica M. Farley Sarah W. Satola Timothy D. Read |
| author_facet | Brianna J. Bixler Charlotte J. Royer Robert A. Petit III Abraham G. Moller Samantha Sefton Stepy Thomas Amy Tunali Lauren F. Collins Monica M. Farley Sarah W. Satola Timothy D. Read |
| author_sort | Brianna J. Bixler |
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| description | Background Haemophilus influenzae is a Gram-negative bacterium that can exist as a commensal organism or cause a range of diseases, from ear infections to invasive conditions like meningitis. While encapsulated H. influenzae strains have historically been linked to severe diseases, non-typeable Haemophilus influenzae (NTHi) strains, lacking an intact capsule locus, have emerged as the leading cause of invasive H. influenzae infections, particularly following the widespread use of the H. influenzae serotype b (Hib) vaccine. Methods In response to a significant increase in invasive NTHi infections among persons living with HIV in metropolitan Atlanta during 2017–2018, we conducted a comparative genomic analysis of two predominant NTHi clones, C1 and C2, identified during this period. These clones correspond to multilocus sequence types ST164 and ST1714, respectively. We analyzed the genomic characteristics of C1 and C2 using whole genome sequencing data and compared them to a broader pangenome of H. influenzae strains to identify potential virulence factors and genetic adaptations. Results Both C1 and C2 isolates were highly related within their clusters, with C1 showing a maximum of 132 SNPs and C2 showing 149 SNPs within their respective core genomes. Genomic analysis revealed significant deletions in known virulence genes, surprisingly suggesting possible attenuation of virulence. No unique accessory genes were identified that distinguished C1 and C2 from other H. influenzae strains, although both clusters exhibited a consistent loss of the pxpB gene (encoding 5-oxoprolinase subunit), replaced by a mobile cassette containing genes potentially involved in sugar metabolism. All C1 and C2 isolates showed potential enrichment in accessory genes associated with systemic infections. Conclusions Our study suggests that while C1 and C2 clones possess some genetic markers potentially linked to systemic infections, there are no definitive unique genetic factors that distinguish these clones as more virulent than other H. influenzae strains. The expansion of these clones in a vulnerable population may reflect both chance introduction and potential adaptations to the host environment. Further research is needed to understand the implications of these genetic findings on the clinical management and prevention of invasive NTHi infections. |
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| spelling | doaj-art-0a67605ec50f4d9b94dff4fc81ca7ac32025-08-20T02:41:36ZengPeerJ Inc.PeerJ2167-83592025-03-0113e1908110.7717/peerj.19081Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in AtlantaBrianna J. Bixler0Charlotte J. Royer1Robert A. Petit III2Abraham G. Moller3Samantha Sefton4Stepy Thomas5Amy Tunali6Lauren F. Collins7Monica M. Farley8Sarah W. Satola9Timothy D. Read10Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesDivision of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, United StatesBackground Haemophilus influenzae is a Gram-negative bacterium that can exist as a commensal organism or cause a range of diseases, from ear infections to invasive conditions like meningitis. While encapsulated H. influenzae strains have historically been linked to severe diseases, non-typeable Haemophilus influenzae (NTHi) strains, lacking an intact capsule locus, have emerged as the leading cause of invasive H. influenzae infections, particularly following the widespread use of the H. influenzae serotype b (Hib) vaccine. Methods In response to a significant increase in invasive NTHi infections among persons living with HIV in metropolitan Atlanta during 2017–2018, we conducted a comparative genomic analysis of two predominant NTHi clones, C1 and C2, identified during this period. These clones correspond to multilocus sequence types ST164 and ST1714, respectively. We analyzed the genomic characteristics of C1 and C2 using whole genome sequencing data and compared them to a broader pangenome of H. influenzae strains to identify potential virulence factors and genetic adaptations. Results Both C1 and C2 isolates were highly related within their clusters, with C1 showing a maximum of 132 SNPs and C2 showing 149 SNPs within their respective core genomes. Genomic analysis revealed significant deletions in known virulence genes, surprisingly suggesting possible attenuation of virulence. No unique accessory genes were identified that distinguished C1 and C2 from other H. influenzae strains, although both clusters exhibited a consistent loss of the pxpB gene (encoding 5-oxoprolinase subunit), replaced by a mobile cassette containing genes potentially involved in sugar metabolism. All C1 and C2 isolates showed potential enrichment in accessory genes associated with systemic infections. Conclusions Our study suggests that while C1 and C2 clones possess some genetic markers potentially linked to systemic infections, there are no definitive unique genetic factors that distinguish these clones as more virulent than other H. influenzae strains. The expansion of these clones in a vulnerable population may reflect both chance introduction and potential adaptations to the host environment. Further research is needed to understand the implications of these genetic findings on the clinical management and prevention of invasive NTHi infections.https://peerj.com/articles/19081.pdfHaemophilus influenzaeNTHiSeptic arthritisComparative genomicsNon-typable Haemophilus influenzaeBacterial genomics |
| spellingShingle | Brianna J. Bixler Charlotte J. Royer Robert A. Petit III Abraham G. Moller Samantha Sefton Stepy Thomas Amy Tunali Lauren F. Collins Monica M. Farley Sarah W. Satola Timothy D. Read Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta PeerJ Haemophilus influenzae NTHi Septic arthritis Comparative genomics Non-typable Haemophilus influenzae Bacterial genomics |
| title | Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta |
| title_full | Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta |
| title_fullStr | Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta |
| title_full_unstemmed | Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta |
| title_short | Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta |
| title_sort | comparative genomic analysis of emerging non typeable haemophilus influenzae nthi causing emerging septic arthritis in atlanta |
| topic | Haemophilus influenzae NTHi Septic arthritis Comparative genomics Non-typable Haemophilus influenzae Bacterial genomics |
| url | https://peerj.com/articles/19081.pdf |
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