Genome-wide analysis of DNA uptake across the outer membrane of naturally competent Haemophilus influenzae

Mora, Marcelo; Ehrlich, Garth D.; Ehrlich, Rachel; Redfield, Rosemary J.

doi:10.1016/j.isci.2020.102007

Cited by 4 publications

(7 citation statements)

References 55 publications

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“…1 ). To explore further the hypothesis of a mosaicism caused by recombination events in this region involved in cell wall synthesis, USSs (GCGG) described as hotspots of recombination for Haemophilus species [ 29 ] were sought in the sequences of each gene . Five ( ftsI and murE ) or six ( murF ) USSs were found, respectively, and the in-between sequences of these USSs were blast ed to evaluate the closest match for each (Table S1).…”

Section: Resultsmentioning

confidence: 99%

“…They incriminated an association of mutations occurring in sequences framed by USSs within the transpeptidase domain of ftsI and these MGEs [ 3 ]. It has been also proven that non-related isolates were evolving to the same mutations set in the ftsI gene and that the MGE intake and USS mechanism could be the key to that evolution [ 29, 31 ]. In our isolates, none of these MGEs were found and the aligment suggests that the sequences framed by USSs within the transpeptidase domain seem to be inherited from Hpara .…”

Section: Discussionmentioning

confidence: 99%

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Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates

Michel,

Argudín,

Wautier

et al. 2024

Access Microbiology

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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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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates

Michel,

Argudín,

Wautier

et al. 2024

Access Microbiology

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“…Natural competence allows bacteria to respond to environmental and nutritional cues by taking up free DNA from their surroundings, gaining both nutrients and genetic information [37] . H. influenzae intrinsic transformable nature, self-preferences caused by the uptake machinery bias for uptake signal sequences (USS), and the high rate of homologous recombination events they can undergo, have a great impact on the evolution of the genomes of this pathogen, which seems to be higher in NTHi compared to capsulated strains [38] , [39] .…”

Section: Constantly Evolving Information From H Influenzae Whole Genome Sequencingmentioning

confidence: 99%

“…Such observations were independently supported by transformation of the same laboratory strain with donor DNA from a heterologous Hib strain [14] . Detailed genome-wide analyses of not only H. influenzae bacteria experimentally transformed with donor DNA from diverged clinical isolates, but also DNA uptake across the outer membrane of naturally competent H. influenzae bacteria, turned out to be extremely informative to understand the relevance and evolution of uptake sequences in the genome, and even to predict the outcome of competition between self- and non-self DNA in the respiratory tract environment [39] , [45] . Moreover, transformation-based experimental evolution studies showed that transformation of single competent cells is extensive, suggesting that it could be used as a tool to map traits that vary between clinical isolates.…”

Section: Constantly Evolving Information From H Influenzae Whole Genome Sequencingmentioning

confidence: 99%

“…Within-host pathoadaptive traits on longitudinally collected strain sets from chronic respiratory samples – genome evolution in natural settings [32] , [33] , [34] , [36] A3. Natural transformation and recombination-driven genetic variation [9] , [14] , [32] , [38] , [39] , [45] , [46] A4. Methylome profiling [35] , [52] A5.…”

Section: Introductionmentioning

confidence: 99%

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Learning from –omics strategies applied to uncover Haemophilus influenzae host-pathogen interactions: Current status and perspectives

López-López

Gil-Campillo

Díez-Martínez³

et al. 2021

Computational and Structural Biotechnology Journal

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Haemophilus influenzae has contributed to key bacterial genome sequencing hallmarks, as being not only the first bacterium to be genome-sequenced, but also starring the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, and pioneering Tn-seq methodologies. Over the years, the phenomenal and constantly evolving development of –omic technologies applied to a whole range of biological questions of clinical relevance in the H. influenzae -host interplay, has greatly moved forward our understanding of this human-adapted pathogen, responsible for multiple acute and chronic infections of the respiratory tract. In this way, essential genes, virulence factors, pathoadaptive traits, and multi-layer gene expression regulatory networks with both genomic and epigenomic complexity levels are being elucidated. Likewise, the unstoppable increasing whole genome sequencing information underpinning H. influenzae great genomic plasticity, mainly when referring to non-capsulated strains, poses major challenges to understand the genomic basis of clinically relevant phenotypes and even more, to clearly highlight potential targets of clinical interest for diagnostic, therapeutic or vaccine development. We review here how genomic, transcriptomic, proteomic and metabolomic-based approaches are great contributors to our current understanding of the interactions between H. influenzae and the human airways, and point possible strategies to maximize their usefulness in the context of biomedical research and clinical needs on this human-adapted bacterial pathogen.

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Comparative Genomic Analysis Reveals Genetic Diversity and Pathogenic Potential of Haemophilus seminalis and Emended Description of Haemophilus seminalis

et al. 2023

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As a versatile opportunistic pathogen, the accurate identification of Haemophilus species is a challenge in clinical practice. In this study, we characterized the phenotypic and genotypic features of four H. seminalis strains that were isolated from human sputum specimens and propose the “ H . intermedius ” and hemin (X-factor)-independent H. haemolyticus isolates as belonging to H. seminalis .

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Genome-wide analysis of DNA uptake across the outer membrane of naturally competent Haemophilus influenzae

Cited by 4 publications

References 55 publications

Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates

Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates

Learning from –omics strategies applied to uncover Haemophilus influenzae host-pathogen interactions: Current status and perspectives

Comparative Genomic Analysis Reveals Genetic Diversity and Pathogenic Potential of Haemophilus seminalis and Emended Description of Haemophilus seminalis

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