scholarly journals Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34melT

2015 ◽  
Vol 81 (15) ◽  
pp. 5235-5248 ◽  
Author(s):  
María Elisa Pavan ◽  
Esteban E. Pavan ◽  
Nancy I. López ◽  
Laura Levin ◽  
M. Julia Pettinari
Keyword(s):  
Genome Analysis ◽  
Aeromonas Salmonicida ◽  
Genomic Islands ◽  
Polluted Environment ◽  
Pectin Degradation ◽  
Fish Pathogens ◽  
Melanin Production ◽  
Melanin Biosynthesis ◽  
Content Type ◽  
Metabolic Versatility

ABSTRACTAeromonas salmonicidasubsp.pectinolytica34melTcan be considered an extremophile due to the characteristics of the heavily polluted river from which it was isolated. While four subspecies ofA. salmonicidaare known fish pathogens, 34melTbelongs to the only subspecies isolated solely from the environment. Genome analysis revealed a high metabolic versatility, the capability to cope with diverse stress agents, and the lack of several virulence factors found in pathogenicAeromonas. The most relevant phenotypic characteristics of 34melTare pectin degradation, a distinctive trait ofA. salmonicidasubsp.pectinolytica, and melanin production. Genes coding for three pectate lyases were detected in a cluster, unique to this microorganism, that contains all genes needed for pectin degradation. Melanin synthesis in 34melTis hypothesized to occur through the homogentisate pathway, as no tyrosinases or laccases were detected and the homogentisate 1,2-dioxygenase gene is inactivated by a transposon insertion, leading to the accumulation of the melanin precursor homogentisate. Comparative genome analysis of other melanogenicAeromonasstrains revealed that this gene was inactivated by transposon insertions or point mutations, indicating that melanin biosynthesis inAeromonasoccurs through the homogentisate pathway. Horizontal gene transfer could have contributed to the adaptation of 34melTto a highly polluted environment, as 13 genomic islands were identified in its genome, some of them containing genes coding for fitness-related traits. Heavy metal resistance genes were also found, along with others associated with oxidative and nitrosative stresses. These characteristics, together with melanin production and the ability to use different substrates, may explain the ability of this microorganism to live in an extremely polluted environment.

scholarly journals Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Lin Zhao ◽  
Hongyou Chen ◽  
Xavier Didelot ◽  
Zhenpeng Li ◽  
Yinghui Li ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Vibrio Parahaemolyticus ◽  
Type Species ◽  
Genomic Islands ◽  
Content Type ◽  
Pan Genome ◽  
Link Type ◽  
Gene Segregation ◽  
Strain Collection ◽  
The Usa

Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has been observed in V. parahaemolyticus , including in the genomic regions encoding the O and K antigens. V. parahaemolyticus serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of V. parahaemolyticus have been reported in China. However, the relationships among this serotype of V. parahaemolyticus strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the V. parahaemolyticus serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of V. parahaemolyticus isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of V. parahaemolyticus were acquired from within the genus Vibrio . Hence, we have shown that multiple distinct lineages exist in V. parahaemolyticus serotype O4:K12 and have provided more evidence about the gene segregation found in V. parahaemolyticus isolated in different continents.

scholarly journals Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species

2013 ◽  
Vol 79 (20) ◽  
pp. 6351-6361 ◽  
Author(s):  
Jaejoon Jung ◽  
Woojun Park
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Pectin Degradation ◽  
Transcriptional Responses ◽  
Natural Habitats ◽  
Content Type ◽  
Habitat Differentiation

ABSTRACTAlishewanellaspecies are expected to have high adaptability to diverse environments because they are isolated from different natural habitats. To investigate how the evolutionary history ofAlishewanellaspecies is reflected in their genomes, we performed comparative genomic and transcriptomic analyses ofA. jeotgali,A. aestuarii, andA. agri, which were isolated from fermented seafood, tidal flat sediment, and soil, respectively. Genomic islands with variable GC contents indicated that invasion of prophage and transposition events occurred inA. jeotgaliandA. agribut not inA. aestuarii. Habitat differentiation ofA. agrifrom a marine environment to a terrestrial environment was proposed because the species-specific genes ofA. agriwere similar to those of soil bacteria, whereas those ofA. jeotgaliandA. aestuariiwere more closely related to marine bacteria. Comparative transcriptomic analysis with pectin as a sole carbon source revealed different transcriptional responses inAlishewanellaspecies, especially in oxidative stress-, methylglyoxal detoxification-, membrane maintenance-, and protease/chaperone activity-related genes. Transcriptomic and experimental data demonstrated thatA. agrihad a higher pectin degradation rate and more resistance to oxidative stress under pectin-amended conditions than the other 2Alishewanellaspecies. However, expression patterns of genes in the pectin metabolic pathway and of glyoxylate bypass genes were similar among all 3Alishewanellaspecies. Our comparative genomic and transcriptomic data revealed thatAlishewanellaspecies have evolved through horizontal gene transfer and habitat differentiation and that pectin degradation pathways inAlishewanellaspecies are highly conserved, although stress responses of eachAlishewanellaspecies differed under pectin culture conditions.

scholarly journals Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Austin Wesevich ◽  
Granger Sutton ◽  
Felicia Ruffin ◽  
Lawrence P. Park ◽  
Derrick E. Fouts ◽  
...  
Keyword(s):  
Clinical Outcome ◽  
Hospital Mortality ◽  
Clinical Outcomes ◽  
Genome Analysis ◽  
Enterobacter Aerogenes ◽  
Genomic Islands ◽  
Klebsiella Aerogenes ◽  
Poor Clinical Outcome ◽  
Content Type ◽  
Pan Genome

ABSTRACT Enterobacter aerogenes was recently renamed Klebsiella aerogenes. This study aimed to identify differences in clinical characteristics, outcomes, and bacterial genetics among patients with K. aerogenes versus Enterobacter species bloodstream infections (BSI). We prospectively enrolled patients with K. aerogenes or Enterobacter cloacae complex (Ecc) BSI from 2002 to 2015. We performed whole-genome sequencing (WGS) and pan-genome analysis on all bacteria. Overall, 150 patients with K. aerogenes (46/150 [31%]) or Ecc (104/150 [69%]) BSI were enrolled. The two groups had similar baseline characteristics. Neither total in-hospital mortality (13/46 [28%] versus 22/104 [21%]; P = 0.3) nor attributable in-hospital mortality (9/46 [20%] versus 13/104 [12%]; P = 0.3) differed between patients with K. aerogenes versus Ecc BSI, respectively. However, poor clinical outcome (death before discharge, recurrent BSI, and/or BSI complication) was higher for K. aerogenes than Ecc BSI (32/46 [70%] versus 42/104 [40%]; P = 0.001). In a multivariable regression model, K. aerogenes BSI, relative to Ecc BSI, was predictive of poor clinical outcome (odds ratio 3.3; 95% confidence interval 1.4 to 8.1; P = 0.008). Pan-genome analysis revealed 983 genes in 323 genomic islands unique to K. aerogenes isolates, including putative virulence genes involved in iron acquisition (n = 67), fimbriae/pili/flagella production (n = 117), and metal homeostasis (n = 34). Antibiotic resistance was largely found in Ecc lineage 1, which had a higher rate of multidrug resistant phenotype (23/54 [43%]) relative to all other bacterial isolates (23/96 [24%]; P = 0.03). K. aerogenes BSI was associated with poor clinical outcomes relative to Ecc BSI. Putative virulence factors in K. aerogenes may account for these differences.

AsaGEI2d: a new variant of a genomic island identified in a group of Aeromonas salmonicida subsp. salmonicida isolated from France, which bears the pAsa7 plasmid

2021 ◽  
Author(s):  
Antony T Vincent ◽  
Laurent Intertaglia ◽  
Victor Loyer ◽  
Valérie E Paquet ◽  
Émilie Adouane ◽  
...  
Keyword(s):  
Genomic Island ◽  
Insertion Site ◽  
Aeromonas Salmonicida ◽  
Genomic Islands ◽  
The Other ◽  
Fish Pathogen ◽  
Integrase Gene ◽  
New Variant ◽  
Cat Gene ◽  
Unique Genes

Abstract Genomic islands (Aeromonas salmonicida genomic islands, AsaGEIs) are found worldwide in many isolates of Aeromonas salmonicida subsp. salmonicida, a fish pathogen. To date, five variants of AsaGEI (1a, 1b, 2a, 2b and 2c) have been described. Here, we investigate a sixth AsaGEI, which was identified in France between 2016 and 2019 in 20 A. salmonicida subsp. salmonicida isolates recovered from sick salmon all at the same location. This new AsaGEI shares the same insertion site in the chromosome as the other AsaGEI2s as they all have a homologous integrase gene. This new AsaGEI was thus named AsaGEI2d, and has 5 unique genes compared to the other AsaGEIs. The isolates carrying AsaGEI2d also bear the plasmid pAsa7, which was initially found in an isolate from Switzerland. This plasmid provides resistance to chloramphenicol thanks to a cat gene. This study reveals more about the diversity of the AsaGEIs.

Ultraviolet Treatment of Water for Destruction of Five Gram-Negative Bacteria Pathogenic to Fishes

1977 ◽  
Vol 34 (8) ◽  
pp. 1244-1249 ◽  
Author(s):  
G. L. Bullock ◽  
H. M. Stuckey
Keyword(s):  
Particulate Matter ◽  
Ultraviolet Irradiation ◽  
Vibrio Anguillarum ◽  
Spring Water ◽  
Aeromonas Salmonicida ◽  
Water Disinfection ◽  
Gram Negative Bacteria ◽  
Fish Pathogens ◽  
Gram Negative ◽  
Ultraviolet Treatment

Filtration (25 nm) and ultraviolet irradiation dosages of 13,100–29,400 microwatt seconds per square centimetre (μW∙s∙cm−2) effected a 99.98–100% reduction of five gram-negative fish pathogens — Aeromonas salmonicida, A. hydrophila, Vibrio anguillarum, Pseudomonas fluorescens, and the enteric redmouth organism in 12.5 °C clear spring water or spring water containing particulate matter. Filtration and a dosage of 4500 μW∙s∙cm−2 killed 99.83–100% of test strains in spring water and 4000–4750 μW∙s∙cm−2 killed 99.33–99.99% in water with particulate matter. Irradiation of unfiltered water containing particulate matter was less effective, especially at dosages of 5000 μW∙s∙cm−2 or less, which killed 97–99.94% of strains. Filtration and 13,100 μW∙s∙cm−2 irradiation of water containing A. salmonicida prevented transmission of furunculosis. Key words: ultraviolet irradiation, bacterial fish pathogens, water disinfection

scholarly journals Interplay of Nitric Oxide Synthase (NOS) and SrrAB in Modulation ofStaphylococcus aureusMetabolism and Virulence

2018 ◽  
Vol 87 (2) ◽  
Author(s):  
Kimberly L. James ◽  
Austin B. Mogen ◽  
Jessica N. Brandwein ◽  
Silvia S. Orsini ◽  
Miranda J. Ridder ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Nitric Oxide Synthase ◽  
Double Mutant ◽  
Nitrate Assimilation ◽  
Arginine Deiminase ◽  
Growth Defect ◽  
Content Type ◽  
Metabolic Versatility ◽  
Oxide Synthase

ABSTRACTStaphylococcus aureusnitric oxide synthase (saNOS) is a major contributor to virulence, stress resistance, and physiology, yet the specific mechanism(s) by which saNOS intersects with other known regulatory circuits is largely unknown. The SrrAB two-component system, which modulates gene expression in response to the reduced state of respiratory menaquinones, is a positive regulator ofnosexpression. Several SrrAB-regulated genes were also previously shown to be induced in an aerobically respiringnosmutant, suggesting a potential interplay between saNOS and SrrAB. Therefore, a combination of genetic, molecular, and physiological approaches was employed to characterize anos srrABmutant, which had significant reductions in the maximum specific growth rate and oxygen consumption when cultured under conditions promoting aerobic respiration. Thenos srrABmutant secreted elevated lactate levels, correlating with the increased transcription of lactate dehydrogenases. Expression of nitrate and nitrite reductase genes was also significantly enhanced in thenos srrABdouble mutant, and its aerobic growth defect could be partially rescued with supplementation with nitrate, nitrite, or ammonia. Furthermore, elevated ornithine and citrulline levels and highly upregulated expression of arginine deiminase genes were observed in the double mutant. These data suggest that a dual deficiency in saNOS and SrrAB limitsS. aureusto fermentative metabolism, with a reliance on nitrate assimilation and the urea cycle to help fuel energy production. Thenos,srrAB, andnos srrABmutants showed comparable defects in endothelial intracellular survival, whereas thesrrABandnos srrABmutants were highly attenuated during murine sepsis, suggesting that SrrAB-mediated metabolic versatility is dominantin vivo.

scholarly journals Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

2014 ◽  
Vol 80 (17) ◽  
pp. 5503-5514 ◽  
Author(s):  
Christophe Habib ◽  
Armel Houel ◽  
Aurélie Lunazzi ◽  
Jean-François Bernardet ◽  
Anne Berit Olsen ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Multilocus Sequence Analysis ◽  
Fish Pathogens ◽  
Long Distance ◽  
Marine Aquaculture ◽  
Content Type ◽  
The Family ◽  
Cohesive Group

ABSTRACTThe genusTenacibaculum, a member of the familyFlavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogenTenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the speciesT. maritimumconstitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoringTenacibaculuminfections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related toT. dicentrarchi, a recently described species.

scholarly journals 4-hydroxyphenylpyruvate dioxygenase thermolability is responsible for temperature-dependent melanogenesis inAeromonas salmonicidasubsp.salmonicida

2018 ◽  
Author(s):  
Yunqian Qiao ◽  
Jiao Wang ◽  
He Wang ◽  
Baozhong Chai ◽  
Chufeng Rao ◽  
...  
Keyword(s):  
Cold Water ◽  
Biological Significance ◽  
Adaptive Strategy ◽  
Aeromonas Salmonicida ◽  
Temperature Dependent ◽  
Ideal Model ◽  
Melanin Production ◽  
Water Fish ◽  
Insight Into

AbstractAeromonas salmonicidasubsp.salmonicida(A.s.s) is a major pathogen affecting fisheries worldwide. It is a well-known member of the pigmentedAeromonasspecies, which produces melanin at ≤ 22 °C. However, melanogenesis decreases as the culture temperature increases and is completely suppressed at 30-35 °C while bacterial growth is not affected. The mechanism and biological significance of this temperature-dependent melanogenesis are not clear. Heterologous expression of anA.s.s.4-hydroxyphenylpyruvate dioxygenase (HppD), the most crucial enzyme in the HGA-melanin synthesis pathway, results in thermosensitive pigmentation inEscherichia coli, suggesting that HppD plays a key role in this process. In the current study, we demonstrated that the extreme thermolability of HppD is responsible for the temperature-dependent melanization ofA.s.s.Substitutions in three residues, Ser18, Pro103, or Leu119 of HppD fromA.s.sincreases the thermolability of this enzyme and results in temperature-independent melanogenesis. Moreover, replacing the corresponding residues of HppD fromAeromonasmedia strain WS, which forms pigment independent of temperature, with those ofA.s.sHppD leads to thermosensitive melanogenesis. Structural analysis suggested that mutations at these sites, especially at position P103, can strengthen the secondary structure of HppD and greatly improve its thermal stability. In addition, we found that HppD sequences of allA.s.sisolates are identical and that two of the three residues are completely conserved withinA.s.sisolates, which clearly distinguishes these from otherAeromonasstrains. We suggest that this property represents an adaptive strategy to the psychrophilic lifestyle ofA.s.s.ImportanceAeromonas salmonicidasubsp.salmonicida(A.s.s) is the causative agent of furunculosis, a bacterial septicemia of cold water fish of theSalmonidaefamily. As it has a well-defined host range,A.s.shas become an ideal model to investigate the co-evolution of host and pathogen. For many pathogens, melanin production is associated with virulence. Although other species ofAeromonascan produce melanin,A.s.sis the only member of this genus that has been reported to exhibit temperature-dependent melanization. Here we demonstrate that thermosensitive melanogenesis inA.s.sstrains is due to the thermolability of 4-hydroxyphenylpyruvate dioxygenase (HppD). The strictly conservedhppDsequences amongA.s.sand the exclusive thermosensitive pigmentation of these strains might provide insight into the role of melanin in the adaptation to a particular host, and offer a novel molecular marker to readily differentiateA.s.sstrains from otherA. salmonicidasubspecies andAeromonasspecies.

scholarly journals Molecular Basis of Sulfonamide and Trimethoprim Resistance in Fish-Pathogenic Aeromonas Isolates

2011 ◽  
Vol 77 (20) ◽  
pp. 7147-7150 ◽  
Author(s):  
Kristina Kadlec ◽  
Ellen von Czapiewski ◽  
Heike Kaspar ◽  
Jürgen Wallmann ◽  
Geovana Brenner Michael ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Molecular Basis ◽  
Aeromonas Salmonicida ◽  
The Novel ◽  
Content Type ◽  
Gene Cassettes ◽  
Class 1 Integrons ◽  
Novel Gene ◽  
Class 1 ◽  
Diseased Fish

ABSTRACTSulfonamide-trimethoprim-resistantAeromonas salmonicidaand motileAeromonasspp. from diseased fish of the GERM-Vet study carried thesul1gene together with mostly cassette-borne trimethoprim resistance genes, including the novel genedfrA28. The sevendfrAanddfrBgenes identified were located mostly in class 1 integrons which commonly harbored other gene cassettes.

scholarly journals Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy

2014 ◽  
Vol 53 (1) ◽  
pp. 323-326 ◽  
Author(s):  
Birgit De Smet ◽  
Derek S. Sarovich ◽  
Erin P. Price ◽  
Mark Mayo ◽  
Vanessa Theobald ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Burkholderia Pseudomallei ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Sequence Types

Burkholderia pseudomalleiisolates with shared multilocus sequence types (STs) have not been isolated from different continents. We identified two STs shared between Australia and Cambodia. Whole-genome analysis revealed substantial diversity within STs, correctly identified the Asian or Australian origin, and confirmed that these shared STs were due to homoplasy.

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