Complete genome sequence analysis of the fish pathogen Flavobacterium columnare provides insights into antibiotic resistance and pathogenicity related genes

Zhang, Yulei; Zhao, Lijuan; Chen, Wenjie; Huang, Yunmao; Yang, Ling; Sarathbabu, V.; Wu, Zaohe; Li, Jun; Nie, Pin; Lin, Li

doi:10.1016/j.micpath.2017.08.035

Cited by 21 publications

(8 citation statements)

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“…The vaccine is not commercially available for salmonids. Disease management therefore relies on antibiotics ( Laanto et al 2015 ), the routine use and need of which is less than ideal, due to environmental impact concerns, and due to the risk of selection of antibiotic resistance ( Declercq, Haesebrouck, et al 2013 ; Laanto et al 2015 ; Zhang et al 2017 ). There is therefore a strong interest in selecting for improved resistance in breeding programs of aquaculture species, an approach that may adapt farmed fish also to climate change ( Sae-Lim et al 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Conserved QTL and chromosomal inversion affect resistance to columnaris disease in 2 rainbow trout (Oncorhyncus mykiss) populations

Calboli

Koskinen

Nousianen

et al. 2022

G3 Genes|Genomes|Genetics

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We present a comparative genetic analysis of the quantitative trait loci (QTL) underlying resistance to warm water columnaris disease in two farmed rainbow trout (Oncorhynchus mykiss) populations. We provide evidence for the conservation of a major QTL on Omy03, and the putative role played by a chromosomal rearrangement on Omy05. A total of 3,962 individuals from the two populations experienced a natural Flavobacterium columnare outbreak. Data for 25,823 genome-wide SNPs were generated for both cases (fatalities) and controls (survivors). FST and pairwise additive genetic relationships suggest that, despite being currently kept as separate broodstocks, the two populations are closely related. Association analyses identified a major QTL on chromosome Omy03 and a second smaller QTL on Omy05. QTL on Omy03 consistently explained 3%-11% of genetic variation in both populations, whereas QTL on Omy05 showed different degree of association across populations and sexes. The QTL on Omy05 was found within a naturally occurring, 54.84 cM long inversion which is easy to tag due to a strong linkage disequilibrium between the 375 tagging SNPs. The ancestral haplotype on Omy05 was associated with decreased mortality. Genetic correlation between mortality in the two populations was estimated at 0.64, implying that the genetic basis of resistance is partly similar in the two populations. Our QTL validation identifies markers that can be potentially used to complement breeding value evaluations to increase resistance against columnaris disease, and help to mitigate effects of climate change on aquaculture.

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Section: Introductionmentioning

confidence: 99%

Conserved QTL and chromosomal inversion affect resistance to columnaris disease in 2 rainbow trout (Oncorhyncus mykiss) populations

Calboli

Koskinen

Nousianen

et al. 2022

G3 Genes|Genomes|Genetics

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“…Iron acquisition systems have been identified in F . columnare ( Guan et al, 2013 ; Zhang et al, 2017 ), F . psychrophilum ( Møller et al, 2005 ), F .…”

Section: Bacteroidetesmentioning

confidence: 99%

“…Secretion of exopolysaccharides by pathogenic bacteria provides a beneficial environment for survival in the host. F. columnare secretes large quantities of exopolysaccharides during infection using polysaccharide exporters that transport polysaccharides from the cytoplasm to the periplasm ( Zhang et al, 2017 ).…”

Section: Bacteroidetesmentioning

confidence: 99%

“…Bacteroidetes harbor genes encoding superoxide dismutase, catalase-peroxidase, and thiol peroxidase to resist ROS-mediated killing (Duchaud et al, 2007;Levipan et al, 2018). Iron acquisition systems have been identified in F. columnare (Guan et al, 2013;Zhang et al, 2017), F. psychrophilum (Møller et al, 2005), F. spartansii , F. branchiophilum, and T. maritimum (Avendaño-Herrera et al, 2005), whose function is to compete for the limited iron stock in host cells. The uptake of iron-siderophore complexes by bacteroidetes are not fully explored, however, several TonB-dependent outer membrane receptors such as, OmpA related proteins, ferrichrome-iron receptor precursor (FhuA) and ferric uptake receptor (Fur) protein are identified in the genomes of F. columnare (Dumpala et al, 2010;Guan et al, 2013), F. psychrophilum (Alvarez et al, 2008) T. maritimum (Avendaño-Herrera et al, 2005) that may function as iron importer across the outer membrane as is shown for several Gram-negative bacteria (Letain and Postle, 1997;Braun et al, 1998).…”

Section: Survival Mechanisms In the Hostmentioning

confidence: 99%

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Secretion Systems in Gram-Negative Bacterial Fish Pathogens

Mekasha

Linke

2021

Front. Microbiol.

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Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.

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“…Several studies explored iron acquisition by F. columnare and related fish pathogens ( Avendano-Herrera et al., 2005 ; Moller et al., 2005 ; Guan et al., 2013 ; Bruce et al., 2021 ). Genes predicted to be involved in iron uptake have been identified by analyses of F. columnare genomes ( Tekedar et al., 2017 ; Zhang et al., 2017 ). Iron deprivation is known to alter expression of some of these genes and to alter virulence ( Beck et al., 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Flavobacterium columnare ferric iron uptake systems are required for virulence

Conrad

Evenhuis

Lipscomb

et al. 2022

Front. Cell. Infect. Microbiol.

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Flavobacterium columnare, which causes columnaris disease, is one of the costliest pathogens in the freshwater fish-farming industry. The virulence mechanisms of F. columnare are not well understood and current methods to control columnaris outbreaks are inadequate. Iron is an essential nutrient needed for metabolic processes and is often required for bacterial virulence. F. columnare produces siderophores that bind ferric iron for transport into the cell. The genes needed for siderophore production have been identified, but other components involved in F. columnare iron uptake have not been studied in detail. We identified the genes encoding the predicted secreted heme-binding protein HmuY, the outer membrane iron receptors FhuA, FhuE, and FecA, and components of an ATP binding cassette (ABC) transporter predicted to transport ferric iron across the cytoplasmic membrane. Deletion mutants were constructed and examined for growth defects under iron-limited conditions and for virulence against zebrafish and rainbow trout. Mutants with deletions in genes encoding outer membrane receptors, and ABC transporter components exhibited growth defects under iron-limited conditions. Mutants lacking multiple outer membrane receptors, the ABC transporter, or HmuY retained virulence against zebrafish and rainbow trout mirroring that exhibited by the wild type. Some mutants predicted to be deficient in multiple steps of iron uptake exhibited decreased virulence. Survivors of exposure to such mutants were partially protected against later infection by wild-type F. columnare.

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Complete genome sequence analysis of the fish pathogen Flavobacterium columnare provides insights into antibiotic resistance and pathogenicity related genes

Cited by 21 publications

References 64 publications

Conserved QTL and chromosomal inversion affect resistance to columnaris disease in 2 rainbow trout (Oncorhyncus mykiss) populations

Conserved QTL and chromosomal inversion affect resistance to columnaris disease in 2 rainbow trout (Oncorhyncus mykiss) populations

Secretion Systems in Gram-Negative Bacterial Fish Pathogens

Flavobacterium columnare ferric iron uptake systems are required for virulence

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