In vivo gene expression profile of Haemophilus influenzae during human pneumonia.
Polland, Linnea LU ; Rydén, Hanna LU ; Su, Yi and Paulsson, Magnus LU
(2023)
In Microbiology spectrum
11(5).
- Abstract
Haemophilus influenzae is a major cause of community-acquired pneumonia. While studied extensively in various laboratory models, less is known about the cell function while inside the human lung. We present the first analysis of the global gene expression of
H. influenzae while the bacteria are in the lung during pneumonia (
in vivo conditions) and contrast it with bacterial isolates that have been cultured under standard laboratory conditions (
in vitro conditions). Patients with pneumonia were recruited from emergency departments and intensive care units during 2018-2020 (
n = 102). Lower respiratory samples were collected for bacterial culture and RNA extraction. Patient samples with
H. influenzae... (More)
(Less)
Haemophilus influenzae is a major cause of community-acquired pneumonia. While studied extensively in various laboratory models, less is known about the cell function while inside the human lung. We present the first analysis of the global gene expression of
H. influenzae while the bacteria are in the lung during pneumonia (
in vivo conditions) and contrast it with bacterial isolates that have been cultured under standard laboratory conditions (
in vitro conditions). Patients with pneumonia were recruited from emergency departments and intensive care units during 2018-2020 (
n = 102). Lower respiratory samples were collected for bacterial culture and RNA extraction. Patient samples with
H. influenzae (
n = 8) and colonies from bacterial cultures (
n = 6) underwent RNA sequencing. The reads were then pseudo-aligned to core and pan genomes created from 15 reference strains. While bacteria cultured
in vitro clustered tightly by principal component analysis of core genome (
n = 1067) gene expression, bacteria in the patient samples had more diverse transcriptomic signatures and did not group with their lab-cultured counterparts. In total, 328 core genes were significantly differentially expressed between
in vitro and
in vivo conditions. The most highly upregulated genes
in vivo included
tbpA and
fbpA, which are involved in the acquisition of iron from transferrin, and the stress response gene
msrAB. The biosynthesis of nucleotides/purines and molybdopterin-scavenging processes were also significantly enriched
in vivo. In contrast, major metabolic pathways and iron-sequestering genes were downregulated under this condition. In conclusion, extensive transcriptomic differences were found between bacteria while in the human lung and bacteria that were cultured
in vitro. IMPORTANCE The human-specific pathogen
Haemophilus influenzae is generally not well suited for studying in animal models, and most laboratory models are unlikely to approximate the diverse environments encountered by bacteria in the human airways accurately. Thus, we have examined the global gene expression of
H. influenzae during pneumonia. Extensive differences in the global gene expression profiles were found in
H. influenzae while in the human lung compared to bacteria that were grown in the laboratory. In contrast, the gene expression profiles of isolates collected from different patients were found to cluster together when grown under the same laboratory conditions. Interesting observations were made of how
H. influenzae acquires and uses iron and molybdate, endures oxidative stress, and regulates central metabolism while in the lung. Our results indicate important processes during infection and can guide future research on genes and pathways that are relevant in the pathogenesis of
H. influenzae pneumonia.
- author
- Polland, Linnea
LU
; Rydén, Hanna
LU
; Su, Yi
and Paulsson, Magnus
LU
- organization
- publishing date
- 2023-09-14
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Microbiology spectrum
- volume
- 11
- issue
- 5
- article number
- e0163923
- publisher
- American Society for Microbiology
- external identifiers
-
- pmid:37707456
- scopus:85175539674
- ISSN
- 2165-0497
- DOI
- 10.1128/spectrum.01639-23
- project
- Gene expression profiling of respiratory pathogens: development during infection and the effect of antibiotic treatment
- CLInical TRAnscriptomics, microbial persistence and antibiotics
- language
- English
- LU publication?
- yes
- id
- beb7527c-d6d2-44d1-964c-f1eabb96d14a
- date added to LUP
- 2023-10-06 11:02:00
- date last changed
- 2024-06-15 19:51:15
@article{beb7527c-d6d2-44d1-964c-f1eabb96d14a,
abstract = {{<p><br>
Haemophilus influenzae is a major cause of community-acquired pneumonia. While studied extensively in various laboratory models, less is known about the cell function while inside the human lung. We present the first analysis of the global gene expression of<br>
H. influenzae while the bacteria are in the lung during pneumonia (<br>
in vivo conditions) and contrast it with bacterial isolates that have been cultured under standard laboratory conditions (<br>
in vitro conditions). Patients with pneumonia were recruited from emergency departments and intensive care units during 2018-2020 (<br>
n = 102). Lower respiratory samples were collected for bacterial culture and RNA extraction. Patient samples with <br>
H. influenzae (<br>
n = 8) and colonies from bacterial cultures (<br>
n = 6) underwent RNA sequencing. The reads were then pseudo-aligned to core and pan genomes created from 15 reference strains. While bacteria cultured <br>
in vitro clustered tightly by principal component analysis of core genome (<br>
n = 1067) gene expression, bacteria in the patient samples had more diverse transcriptomic signatures and did not group with their lab-cultured counterparts. In total, 328 core genes were significantly differentially expressed between<br>
in vitro and <br>
in vivo conditions. The most highly upregulated genes <br>
in vivo included <br>
tbpA and <br>
fbpA, which are involved in the acquisition of iron from transferrin, and the stress response gene <br>
msrAB. The biosynthesis of nucleotides/purines and molybdopterin-scavenging processes were also significantly enriched <br>
in vivo. In contrast, major metabolic pathways and iron-sequestering genes were downregulated under this condition. In conclusion, extensive transcriptomic differences were found between bacteria while in the human lung and bacteria that were cultured <br>
in vitro. IMPORTANCE The human-specific pathogen <br>
Haemophilus influenzae is generally not well suited for studying in animal models, and most laboratory models are unlikely to approximate the diverse environments encountered by bacteria in the human airways accurately. Thus, we have examined the global gene expression of <br>
H. influenzae during pneumonia. Extensive differences in the global gene expression profiles were found in <br>
H. influenzae while in the human lung compared to bacteria that were grown in the laboratory. In contrast, the gene expression profiles of isolates collected from different patients were found to cluster together when grown under the same laboratory conditions. Interesting observations were made of how <br>
H. influenzae acquires and uses iron and molybdate, endures oxidative stress, and regulates central metabolism while in the lung. Our results indicate important processes during infection and can guide future research on genes and pathways that are relevant in the pathogenesis of<br>
H. influenzae pneumonia.<br>
</p>}},
author = {{Polland, Linnea and Rydén, Hanna and Su, Yi and Paulsson, Magnus}},
issn = {{2165-0497}},
language = {{eng}},
month = {{09}},
number = {{5}},
publisher = {{American Society for Microbiology}},
series = {{Microbiology spectrum}},
title = {{In vivo gene expression profile of Haemophilus influenzae during human pneumonia.}},
url = {{http://dx.doi.org/10.1128/spectrum.01639-23}},
doi = {{10.1128/spectrum.01639-23}},
volume = {{11}},
year = {{2023}},
}