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de Palma TH, Powers C, McPartland MJ, Welch JM, Ramsey M. Essential genes for Haemophilus parainfluenzae survival and biofilm growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.31.587483. [PMID: 38585970 PMCID: PMC10996682 DOI: 10.1101/2024.03.31.587483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Haemophilus parainfluenzae ( Hp ) is a Gram-negative, pleomorphic rod, highly prevalent and abundant as a commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the tongue dorsum, keratinized gingiva, and the supragingival plaque biofilm. As a member of the HACEK group, Hp is also known to cause infective endocarditis. Additionally, case reports have identified Hp as the causative agent of meningitis, septic arthritis, chronic osteomyelitis, septicemia, and a variety of other infectious diseases. Little is known about how Hp interacts with its neighbors in the healthy biofilm nor about its mechanisms of pathogenesis as an extraoral opportunistic pathogen. To address these unknowns, we identified the essential genomes of two Hp strains and the conditionally essential genes for their growth in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain ( Hp 392) and a commensal oral isolate EL1 ( Hp EL1), we show that the essential genome of Hp 392 and Hp EL1 is composed of 395 and 384 genes, respectively. The core essential genome, consisting of 341 essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains of Hp . Additionally, RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic biofilm survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo oral habitat. Further, the creation of this library presents a valuable tool for further investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.
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Michel C, Argudín MDLA, Wautier M, Echahidi F, Prevost B, Vandenberg O, Martiny D, Hallin M. Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates. Access Microbiol 2024; 6:000649.v3. [PMID: 38482359 PMCID: PMC10928409 DOI: 10.1099/acmi.0.000649.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/22/2023] [Indexed: 04/12/2024] Open
Abstract
Introduction Haemophilus influenzae (Hi) was long known as an easy-to-treat bacterium, but increasing resistance against beta-lactams and other critically important antibiotics is now a growing concern. We describe here the whole-genome sequencing (WGS) analysis of three non-typeable Hi isolates received in 2018-2019 by the Belgian National Reference Centre (NRC) for Haemophilus influenzae, as they presented an unusual multi-resistant profile. Methods All three isolates were sequenced by WGS and mapped to the reference isolate Hi Rd KW20. Shorten uptake signal sequences (USSs) known to be associated with homologous recombination were sought in ftsI, murE and murF genes, and inner partial sequences were compared against the blast nucleotide database to look for similarity with other Haemophilus species. Their antimicrobial resistance (AMR) genotype was studied. Core-genome multilocus sequence typing (MLST) was performed on the NTHi database pubMLST to place our isolates in the actual worldwide epidemiology. Results The isolates also harboured interspecies recombination patterns in the murF-murE-ftsI region involved in cell wall synthesis. The three isolates were multidrug resistant and two of them were also resistant to amoxicillin-clavulanic acid and showed a reduced susceptibility to meropenem. All three isolates belonged to the MLST clonal complex (CC) 422, and WGS revealed that the three were very similar. They harboured mobile genetic elements (carrying blaTEM-1B, mefA and msrD genes associated with resistance), mutations in gyrA and parC linked to fluoroquinolone resistance as well as remodelling events in ompP2 that might be related to lower carbapenem susceptibility. Conclusion The Hi evolution towards antimicrobial multiresistance (AMR) is a complex and poorly understood phenomenon, although probably linked to a large degree to the presence of USSs and exchange within the family Pasteurellaceae. To better understand the respective roles of clonal expansion, horizontal gene transfers, spontaneous mutations and interspecies genetic rearrangements in shaping Hi AMR, both analysis of Hi communities over time within individuals and worldwide monitoring of non-typeable Hi causing infections should be conducted.
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Affiliation(s)
- Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Maria De Los Angeles Argudín
- Department of Molecular Biology, Cliniques Universitaires Saint Luc (CUSL), Avenue Hippocrate 10, 1200, Brussels, Belgium
| | - Magali Wautier
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Fedoua Echahidi
- Department of Microbiology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Pleinlaan 2, 1050 Brussels, Belgium
| | - Benoit Prevost
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Olivier Vandenberg
- Innovation and Business Development Unit, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Avenue Roosevelt 50, 1050 Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Faculty of Medicine and Pharmacy, Mons University, Chemin du Champ de Mars 37, 7000 Mons, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
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The natural history and genetic diversity of Haemophilus influenzae infecting the airways of adults with cystic fibrosis. Sci Rep 2022; 12:15765. [PMID: 36131075 PMCID: PMC9492733 DOI: 10.1038/s41598-022-19240-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 08/26/2022] [Indexed: 12/04/2022] Open
Abstract
Haemophilus influenzae is a Gram-negative pathobiont, frequently recovered from the airways of persons with cystic fibrosis (pwCF). Previous studies of H. influenzae infection dynamics and transmission in CF predominantly used molecular methods, lacking resolution. In this retrospective cohort study, representative yearly H. influenzae isolates from all pwCF attending the Calgary Adult CF Clinic with H. influenzae positive sputum cultures between 2002 and 2016 were typed by pulsed-field gel electrophoresis. Isolates with shared pulsotypes common to ≥ 2 pwCF were sequenced by Illumina MiSeq. Phylogenetic and pangenomic analyses were used to assess genetic relatedness within shared pulsotypes, and epidemiological investigations were performed to assess potential for healthcare associated transmission. H. influenzae infection was observed to be common (33% of patients followed) and dynamic in pwCF. Most infected pwCF exhibited serial infections with new pulsotypes (75% of pwCF with ≥ 2 positive cultures), with up to four distinct pulsotypes identified from individual patients. Prolonged infection by a single pulsotype was only rarely observed. Intra-patient genetic diversity was observed at the single-nucleotide polymorphism and gene content levels. Seven shared pulsotypes encompassing 39% of pwCF with H. influenzae infection were identified, but there was no evidence, within our sampling scheme, of direct patient-to-patient infection transmission.
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Ciuca IM, Dediu M, Popin D, Pop LL, Tamas LA, Pilut CN, Almajan Guta B, Popa ZL. Antibiotherapy in Children with Cystic Fibrosis—An Extensive Review. CHILDREN 2022; 9:children9081258. [PMID: 36010149 PMCID: PMC9406924 DOI: 10.3390/children9081258] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
In cystic fibrosis (CF), the respiratory disease is the main factor that influences the outcome and the prognosis of patients, bacterial infections being responsible for severe exacerbations. The etiology is often multi-microbial and with resistant strains. The aim of this paper is to present current existing antibiotherapy solutions for CF-associated infections in order to offer a reliable support for individual, targeted, and specific treatment. The inclusion criteria were studies about antibiotherapy in CF pediatric patients. Studies involving adult patients or those with only in vitro results were excluded. The information sources were all articles published until December 2021, in PubMed and ScienceDirect. A total of 74 studies were included, with a total number of 26,979 patients aged between 0–18 years. We approached each pathogen individual, with their specific treatment, comparing treatment solutions proposed by different studies. Preservation of lung function is the main goal of therapy in CF, because once parenchyma is lost, it cannot be recovered. Early personalized intervention and prevention of infection with reputable germs is of paramount importance, even if is an asymmetrical challenge. This research received no external funding.
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Affiliation(s)
- Ioana Mihaiela Ciuca
- Pediatric Department, University of Medicine and Pharmacy “Victor Babes” Timisoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
- Pediatric Pulmonology Unit, Clinical County Hospital Timisoara, Evlia Celebi 1-3, 300226 Timisoara, Romania
| | - Mihaela Dediu
- Pediatric Department, University of Medicine and Pharmacy “Victor Babes” Timisoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Diana Popin
- Pediatric Pulmonology Unit, Clinical County Hospital Timisoara, Evlia Celebi 1-3, 300226 Timisoara, Romania
| | - Liviu Laurentiu Pop
- Pediatric Department, University of Medicine and Pharmacy “Victor Babes” Timisoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Liviu Athos Tamas
- Biochemistry Department, University of Medicine and Pharmacy “Victor Babes” Timisoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
- Correspondence: ; Tel.: +40-744-764737
| | - Ciprian Nicolae Pilut
- Microbiology Department, University of Medicine and Pharmacy “Victor Babes” Timisoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Bogdan Almajan Guta
- Kinesiotherapy and Special Motricity Department, West University of Timisoara, 4 Vasile Parvan bld., 300223 Timisoara, Romania
| | - Zoran Laurentiu Popa
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy “Victor Babes” Timisoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
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Wick RR, Judd LM, Wyres KL, Holt KE. Recovery of small plasmid sequences via Oxford Nanopore sequencing. Microb Genom 2021; 7:000631. [PMID: 34431763 PMCID: PMC8549360 DOI: 10.1099/mgen.0.000631] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/11/2021] [Indexed: 12/13/2022] Open
Abstract
Oxford Nanopore Technologies (ONT) sequencing platforms currently offer two approaches to whole-genome native-DNA library preparation: ligation and rapid. In this study, we compared these two approaches for bacterial whole-genome sequencing, with a specific aim of assessing their ability to recover small plasmid sequences. To do so, we sequenced DNA from seven plasmid-rich bacterial isolates in three different ways: ONT ligation, ONT rapid and Illumina. Using the Illumina read depths to approximate true plasmid abundance, we found that small plasmids (<20 kbp) were underrepresented in ONT ligation read sets (by a mean factor of ~4) but were not underrepresented in ONT rapid read sets. This effect correlated with plasmid size, with the smallest plasmids being the most underrepresented in ONT ligation read sets. We also found lower rates of chimaeric reads in the rapid read sets relative to ligation read sets. These results show that when small plasmid recovery is important, ONT rapid library preparations are preferable to ligation-based protocols.
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Affiliation(s)
- Ryan R. Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Louise M. Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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