Bacteriocin-mediated competition in cystic fibrosis lung infections

Bacteriocins are toxins produced by bacteria to kill competitors of the same species. Theory and laboratory experiments suggest that bacteriocin production and immunity play a key role in the competitive dynamics of bacterial strains. The extent to which this is the case in natural populations, especially human pathogens, remains to be tested. We examined the role of bacteriocins in competition using Pseudomonas aeruginosa strains infecting lungs of humans with cystic fibrosis (CF). We assessed the ability of different strains to kill each other using phenotypic assays, and sequenced their genomes to determine what bacteriocins (pyocins) they carry. We found that (i) isolates from later infection stages inhibited earlier infecting strains less, but were more inhibited by pyocins produced by earlier infecting strains and carried fewer pyocin types; (ii) this difference between early and late infections appears to be caused by a difference in pyocin diversity between competing genotypes and not by loss of pyocin genes within a lineage over time; (iii) pyocin inhibition does not explain why certain strains outcompete others within lung infections; (iv) strains frequently carry the pyocin-killing gene, but not the immunity gene, suggesting resistance occurs via other unknown mechanisms. Our results show that, in contrast to patterns observed in experimental studies, pyocin production does not appear to have a major influence on strain competition during CF lung infections.

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Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen

Microorganisms ◽

10.3390/microorganisms8121919 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1919

Author(s):

Elina Laanto ◽

Janne J. Ravantti ◽

Lotta-Riina Sundberg

Keyword(s):

Flavobacterium Columnare ◽

Strain Atcc ◽

Human Pathogens ◽

Fish Pathogen ◽

Bacterial Strains ◽

Host Interactions ◽

Different Strains ◽

Gene Orthologs ◽

Similar Genome Organization

The role of prophages in the evolution, diversification, or virulence of the fish pathogen Flavobacterium columnare has not been studied thus far. Here, we describe a functional spontaneously inducing prophage fF4 from the F. columnare type strain ATCC 23463, which is not detectable with commonly used prophage search methods. We show that this prophage type has a global distribution and is present in strains isolated from Finland, Thailand, Japan, and North America. The virions of fF4 are myoviruses with contractile tails and infect only bacterial strains originating from Northern Finland. The fF4 resembles transposable phages by similar genome organization and several gene orthologs. Additional bioinformatic analyses reveal several species in the phylum Bacteroidetes that host a similar type of putative prophage, including bacteria that are important animal and human pathogens. Furthermore, a survey of F. columnare Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers indicate a shared evolutionary history between F. columnare strains and the fF4 phage, and another putative prophage in the F. columnare strain ATCC 49512, named p49512. First, CRISPR spacer content from the two CRISPR loci (types II-C and VI-B) of the fF4 lysogen F. columnare ATCC 23463 revealed a phage terminase protein-matching spacer in the VI-B locus. This spacer is also present in two Chinese F. columnare strains. Second, CRISPR analysis revealed four F. columnare strains that contain unique spacers targeting different regions of the putative prophage p49512 in the F. columnare strain ATCC 49512, despite the geographical distance or genomovar of the different strains. This suggests a common ancestry for the F. columnare prophages and different host strains.

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Characterization by pyocine typing and serotyping of oral and sputum strains of Pseudomonas aeruginosa isolated from cystic fibrosis patients

Canadian Journal of Microbiology ◽

10.1139/m87-038 ◽

1987 ◽

Vol 33 (3) ◽

pp. 221-225 ◽

Cited By ~ 5

Author(s):

Kunio Komiyama ◽

Brian F. Habbick ◽

Tom Martin ◽

Satwant K. Tumber

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Oral Cavity ◽

Buccal Mucosa ◽

Single Strain ◽

Ecological Sites ◽

Dental Plaques ◽

Different Strains

Oral and sputum isolates of Pseudomonas aeruginosa in patients with cystic fibrosis were investigated. Of the 17 patients studied, 12 patients (71%) yielded both mucoid and nonmucoid variants of Pseudomonas aeruginosa from sputum and (or) various oral ecological sites, such as buccal mucosa, tongue dorsum, dental plaques, and saliva. A total of 51 strains of mucoid and nonmucoid Pseudomonas aeruginosa were isolated from these patients and were phenotypically characterized by both pyocine typing and serotyping. Five patients (42%) were colonized or infected by a single strain of Pseudomonas aeruginosa, whereas 7 patients (58%) were cocolonized or coinfected by two or more phenotypically different strains of Pseudomonas aeruginosa. To understand the mechanisms involved in Pseudomonas aeruginosa colonization, it may be necessary to identify multiple isolates of Pseudomonas aeruginosa not only from the sputum but also from the various oral ecological sites and to further explore the role of the oral cavity in this colonization.

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Risk factors for respiratory Aspergillus fumigatus in German Cystic Fibrosis patients and impact on lung function

Scientific Reports ◽

10.1038/s41598-020-75886-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Uta Düesberg ◽

Julia Wosniok ◽

Lutz Naehrlich ◽

Patience Eschenhagen ◽

Carsten Schwarz

Keyword(s):

Risk Factors ◽

Cystic Fibrosis ◽

Lung Function ◽

Aspergillus Fumigatus ◽

Age Groups ◽

Antibiotic Use ◽

Lower Lung ◽

Lung Infections ◽

The Impact

Abstract Airway inflammation and chronic lung infections in cystic fibrosis (CF) patients are mostly caused by bacteria, e.g. Pseudomonas aeruginosa (PA). The role of fungi in the CF lung is still not well elucidated, but evidence for a harmful and complex role is getting stronger. The most common filamentous fungus in CF is Aspergillus fumigatus (AF). Age and continuous antibiotic treatment have been discussed as risk factors for AF colonisation but did not differentiate between transient and persistent AF colonisation. Also, the impact of co-colonisation of PA and AF on lung function is still under investigation. Data from patients with CF registered in the German Cystic Fibrosis Registry database in 2016 and 2017 were retrospectively analysed, involving descriptive and multivariate analysis to assess risk factors for transient or persistent AF colonisation. Age represented an independent risk factor for persistent AF colonisation. Prevalence was low in children less than ten years, highest in the middle age and getting lower in higher age (≥ 50 years). Continuous antibiotic lung treatment was significantly associated with AF prevalence in all age groups. CF patients with chronic PA infection had a lower lung function (FEV1%predicted), which was not influenced by an additional AF colonisation. AF colonisation without chronic PA infection, however, was significantly associated with a lower function, too. Older age up to 49 years and continuous antibiotic use were found to be the main risk factors for AF permanent colonisation. AF might be associated with decrease of lung function if not disguised by chronic PA infection.

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Potential of preventing Pseudomonas aeruginosa lung infections in cystic fibrosis patients: Experimental studies in animals

Apmis ◽

10.1111/j.1600-0463.1996.tb05581.x ◽

1996 ◽

Vol 104 (S63) ◽

pp. 5-42 ◽

Cited By ~ 13

Author(s):

HELLE KROGH JOHANSEN

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Experimental Studies ◽

Lung Infections

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Pathogenic Escherichia coli – virulence mechanisms

Medycyna Weterynaryjna ◽

10.21521/mw.5522 ◽

2016 ◽

Vol 72 (6) ◽

pp. 352-357

Author(s):

Katarzyna Półtorak ◽

Kinga Wieczorek ◽

Jacek Osek

Keyword(s):

Bloodstream Infections ◽

Epidemiological Data ◽

Intestinal Epithelial ◽

Bacterial Strains ◽

Internal Organs ◽

E Coli ◽

Cellular Processes ◽

Pathogenic Escherichia Coli ◽

Different Strains

E. coli are the predominant microorganisms in the human gastrointestinal tract. In most cases, they exist as harmless comensals, and some of them are beneficial to their host in balancing gut flora and absorption of nutrients. However, there are pathogenic strains that cause a broad range of diseases in humans and animals, from diarrhea to bloodstream infections. Among bacterial strains causing these symptoms, seven pathotypes are now recognized: enteropathogenic E. coli (EPEC), shiga toxin-producing E. coli (STEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), and adherent-invasive E. coli (AIEC). Several different strains cause diverse diseases by means of virulence factors that facilitate their interactions with the host, including colonization of the intestinal epithelial surfaces, crossing of the mucosal barriers, invasion of the bloodstream and internal organs or producing toxins that affect various cellular processes. Pathogenic E. coli are commonly studied in humans, animals, food and the environment, in developed and developing countries. The presented paper reviews recent information concerning the pathogenic mechanisms of E. coli, the role of animals and food in the transmission chain and a short overview of epidemiological data.

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Microbiome data enhances predictive models of lung function in people with cystic fibrosis

The Journal of Infectious Diseases ◽

10.1093/infdis/jiaa655 ◽

2020 ◽

Author(s):

Conan Y Zhao ◽

Yiqi Hao ◽

Yifei Wang ◽

John J Varga ◽

Arlene A Stecenko ◽

...

Keyword(s):

Cystic Fibrosis ◽

Lung Function ◽

Clinical Microbiology ◽

Linear Models ◽

Human Pathogens ◽

Chronic Infections ◽

Airway Microbiome ◽

Lung Infections ◽

Lung Health ◽

Microbiome Data

Abstract Background Microbiome sequencing has brought increasing attention to the polymicrobial context of chronic infections. However, clinical microbiology continues to focus on canonical human pathogens, which may overlook informative, but non-pathogenic, biomarkers. We address this disconnect in lung infections in people with cystic fibrosis (CF). Methods We collected health information (lung function, age, BMI) and sputum samples from a cohort of 77 children and adults with CF. Samples were collected during a period of clinical stability and 16S rDNA sequenced for airway microbiome compositions. We use Elastic Net regularization to train linear models predicting lung function and extract the most informative features. Results Models trained on whole microbiome quantitation outperform models trained on pathogen quantitation alone, with or without the inclusion of patient metadata. Our most accurate models retain key pathogens as negative predictors (Pseudomonas, Achromobacter) along with established correlates of CF disease state (age, BMI, CF related diabetes). In addition, our models select non-pathogen taxa (Fusobacterium, Rothia) as positive predictors of lung health. Conclusions These results support a reconsideration of clinical microbiology pipelines to ensure the provision of informative data to guide clinical practice.

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Cystic Fibrosis Lung Immunity: The Role of the Macrophage

Journal of Innate Immunity ◽

10.1159/000446825 ◽

2016 ◽

Vol 8 (6) ◽

pp. 550-563 ◽

Cited By ~ 54

Author(s):

Emanuela M. Bruscia ◽

Tracey L. Bonfield

Keyword(s):

Cystic Fibrosis ◽

Modifier Genes ◽

Cystic Fibrosis Lung ◽

Environmental Cues ◽

Major Morbidity ◽

Adaptive Immune ◽

Lung Infections ◽

Lung Immunity

Cystic fibrosis (CF) pathophysiology is hallmarked by excessive inflammation and the inability to efficiently resolve lung infections, contributing to major morbidity and eventually the mortality of patients with this disease. Macrophages (MΦs) are major players in lung homeostasis through their diverse contributions to both the innate and adaptive immune networks. The setting of MΦ function and activity in CF is multifaceted, encompassing the response to the unique environmental cues in the CF lung as well as the intrinsic changes resulting from CFTR dysfunction. The complexity is further enhanced with the identification of modifier genes, which modulate the CFTR contribution to disease, resulting in epigenetic and transcriptional shifts in MΦ phenotype. This review focuses on the contribution of MΦ to lung homeostasis, providing an overview of the diverse literature and various perspectives on the role of these immune guardians in CF.

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Inoculation of stigma colonizing microbes to apple stigmas alters microbiome structure and reduces the occurrence of fire blight disease

Phytobiomes Journal ◽

10.1094/pbiomes-04-20-0035-r ◽

2020 ◽

Author(s):

Zhouqi Cui ◽

Regan B. Huntley ◽

Neil Schultes ◽

Blaire Steven ◽

Quan Zeng

Keyword(s):

Fire Blight ◽

Plant Diseases ◽

Disease Suppression ◽

Bacterial Strains ◽

Microbiome Composition ◽

Microbial Inoculation ◽

Short Life Span ◽

Blight Disease ◽

Different Strains

Flowers secrete nutrient rich exudates that support the growth of an assemblage of microorganisms, including both beneficial and pathogenic members, most of which belong to the phylum Proteobacteria. Given the potential role of the microbiome in plant health, manipulating the microbiome to promote growth of beneficial members holds promise in controlling plant diseases. In this study we inoculated four different bacterial strains that were originally isolated from apple stigmas, alone or in mixtures of increasing complexity, onto apple flowers during bloom. We tested if such treatments would influence fire blight occurrence, a disease caused by Erwinia amylovora, and if we could detect a shift in the structure of the microbiome due to the treatments. We show that various inoculations did influence the occurrence of fire blight, although the level of disease suppression was dependent upon specific bacterial strains. Furthermore, treatments using different strains or strain mixtures predominantly resulted in increased representation of the inoculated strains, suggesting that disease suppression was due to an alteration of the stigma microbiome structure. Compared to treatments with single strains, a Pantoea-Pseudomonas strain mixture produced a homogeneous microbiome structure with less inter-flower variability. Findings from this study suggest the microbiome on the flower stigma can be manipulated through microbial inoculation. Due to flowers’ short life span yet important role in plant disease infection, even a shot-term influence on microbiome composition may result in significant decreases in disease susceptibility.

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Microbiome data enhances predictive models of lung function in people with cystic fibrosis

10.1101/656066 ◽

2019 ◽

Author(s):

Conan Y. Zhao ◽

Yiqi Hao ◽

Yifei Wang ◽

John J. Varga ◽

Arlene A. Stecenko ◽

...

Keyword(s):

Cystic Fibrosis ◽

Lung Function ◽

Clinical Microbiology ◽

Linear Models ◽

Human Pathogens ◽

Chronic Infections ◽

Airway Microbiome ◽

Lung Infections ◽

Lung Health ◽

Microbiome Data

AbstractBackgroundMicrobiome sequencing has brought increasing attention to the polymicrobial context of chronic infections. However, clinical microbiology continues to focus on canonical human pathogens, which may overlook informative, but non-pathogenic, biomarkers. We address this disconnect in lung infections in people with cystic fibrosis (CF).MethodsWe collected health information (lung function, age, BMI) and sputum samples from a cohort of 77 children and adults with CF. Samples were collected during a period of clinical stability and 16S rDNA sequenced for airway microbiome compositions. We use Elastic Net regularization to train linear models predicting lung function and extract the most informative features.ResultsModels trained on whole microbiome quantitation outperform models trained on pathogen quantitation alone, with or without the inclusion of patient metadata. Our most accurate models retain key pathogens as negative predictors (Pseudomonas, Achromobacter) along with established correlates of CF disease state (age, BMI, CF related diabetes). In addition, our models select non-pathogen taxa (Fusobacterium, Rothia) as positive predictors of lung health.ConclusionsThese results support a reconsideration of clinical microbiology pipelines to ensure the provision of informative data to guide clinical practice.

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