Molecular methods for the diagnosis and characterization ofCryptococcus: a review

2010 ◽  
Vol 56 (6) ◽  
pp. 445-458 ◽  
Author(s):  
José Júlio Costa Sidrim ◽  
Ana Karoline Freire Costa ◽  
Rossana Aguiar Cordeiro ◽  
Raimunda Sâmia Nogueira Brilhante ◽  
Fernanda Edna Araújo Moura ◽  
...  
Keyword(s):  
Pathogen Detection ◽  
Positive Impact ◽  
Final Diagnosis ◽  
Molecular Methods ◽  
Specific Gene ◽  
Healthy Individuals ◽  
Pcr Rflp ◽  
Resistant Strains ◽  
Genomic Regions ◽  
Identification Techniques

Cryptococcosis is a fungal infection caused by yeasts of the genus Cryptococcus , with Cryptococcus neoformans and Cryptococcus gattii as the primary pathogenic species. This disease is a threat to immunocompromised patients, especially those who have AIDS. However, the disease has also been described in healthy individuals. The tests used to identify these microorganisms have limitations that make final diagnosis difficult. However, currently there are specific gene sequences that can be used to detect C. neoformans and C. gattii from clinical specimens and cultures. These sequences can be used for identification, typing, and the study of population genetics. Among the main identification techniques are hybridization, which was the pioneer in molecular identification and development of specific probes for pathogen detection; PCR and other PCR-based methods, particularly nested PCR and multiplex PCR; and sequencing of specific genomic regions that are amplified through PCR, which is especially useful for diagnosis of cryptococcosis caused by unconventional Cryptococcus sp. Concerning microorganism typing, the following techniques have shown the best ability to differentiate between fungal serotypes and molecular types: PCR fingerprinting, PCR–RFLP, AFLP, and MLST. Thus, the accumulation of data generated by molecular methods can have a positive impact on monitoring resistant strains and treating diseases.

PCR-RFLP for detection of Fusarium graminearum genotypes with resistance to phenamacril

Plant Disease ◽  
2020 ◽  
Author(s):  
Jiao-Sheng Li ◽  
Luo-Yu Wu ◽  
Hui Zhang ◽  
Xiu-Shi Song ◽  
Jian-Xin Wang ◽  
...  
Keyword(s):  
Fusarium Graminearum ◽  
Conventional Method ◽  
Resistance Mutations ◽  
Head Blight ◽  
Fusarium Asiaticum ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Resistant Strains ◽  
Codon Mutation

Phenamacril is a cyanoacrylate fungicide that provides excellent control of Fusarium head blight (FHB) or wheat scab, which is caused predominantly by Fusarium graminearum and Fusarium asiaticum. Previous studies revealed that codon mutations of the myosin-5 gene of Fusarium spp. conferred resistance to phenamacril in vitro lab experiments. In this study, PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) was developed to detect three common mutations (A135T, GCC to ACC at codon 135; S217L, TCA to TTA at codon 217, and E420K, GAA to AAA at codon 420) in F. graminearum induced by fungicide domestication in vitro. PCR products of 841 bp (for mutation of A135T), 802 bp (for mutation of S217L) or 1649 bp (for mutation of E420K) in myosin-5 gene were amplified respectively by appropriate primer pairs. Restriction enzyme KpnⅠ, TasⅠ or DraⅠ was used to distinguish phenamacril-sensitive and -resistant strains with mutation genotypes of A135T, S217L and E420K, respectively. KpnⅠ digested the 841 bp PCR products of phenamacri-resistant strains with codon mutation A135T into two fragments of 256 bp and 585 bp. In contrast, KpnⅠ did not digest the PCR products of sensitive strains. TasⅠ digested the 802 bp PCR products of phenamacril-strains with codon mutation S217L into three fragments of 461 bp, 287bp and 54 bp. In contrast, TasⅠ digestion of the 802 bp PCR products of phenamacril-sensitive strains resulted in only two fragments of 515bp and 287bp. DraⅠ digested the 1649 bp PCR products of phenamacril-resistant strains with codon mutation E420K into two fragments of 932 bp and 717 bp, while the PCR products of phenamacril-sensitive strains was not digested. The three genotypes of resistance mutations were determined by analyzing electrophoresis patterns of the digestion fragments of PCR products. The PCR-RFLP method was evaluated on 48 phenamacril-resistant strains induced by fungicide domestication in vitro and compared with the conventional method (mycelial growth on fungicide-amended agar). The accuracy of the PCR-RFLP method for detecting the three resistant mutation genotypes of F. graminearum to phenamacril was 95.12% compared with conventional method. Bioinformatics analysis revealed that the PCR-RFLP method could also be used to detect the codon mutations of A135T and E420K in F. asiaticum.

scholarly journals The efficacy of diuretics in complex treatment of patients with hypertension according to the Gly460Trp polymorphism of the α-adducin gene

2021 ◽  
Vol 23 (4) ◽  
pp. 503-508
Author(s):  
S. A. Yermolenko ◽  
V. F. Orlovskyi ◽  
O. V. Orlovskyi ◽  
A. V. Zharkova ◽  
I. O. Moiseienko ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Gene Polymorphism ◽  
Polymorphic Locus ◽  
Polymorphic Marker ◽  
Individual Treatment ◽  
Healthy Individuals ◽  
Group I ◽  
Allelic Distribution ◽  
Pcr Rflp ◽  
Polymerase Chain

The aim of the study was to investigate the effect of thiazide diuretics on blood pressure (BP) depending on Gly460Trp ADD1 gene polymorphism in arterial hypertension (AH) patients of the Ukrainian population in order to predict their individual treatment efficacy. Material and methods. The study included 232 persons: 120 patients with verified stage II AH and 112 healthy individuals. Restriction fragment length polymerase chain reaction (PCR-RFLP) was used to detect genotype (the Gly460Trp-polymorphic locus of the ADD1 gene). The patients received standard therapy, which included ACE inhibitor – ramipril 5 mg, calcium channel antagonist – amlodipine 5 mg, statin – atorvastatin 20 mg, acetylsalicylic acid 75 mg. The patients were randomized into two groups: group I (60 persons) additionally taking treatment with 1.5 mg of indapamide retard and group II (60 persons) – with 25 mg of hydrochlorothiazide. The dynamic reduction of blood pressure has been assessed every 4 weeks for 2 months. Results. Among 120 patients with AH, 91 persons (75.8 %) were homozygous for the G allele (GG), 26 persons (21.7 %) – heterozygous (GT) and 3 persons (2.5 %) – homozygous for the T allele (TT), while the G allele frequency in patients with hypertension was 0.87, and the T allele – 0.13. 98 healthy individuals (87.5 %) were homozygous for the G allele, 13 individuals (11.6 %) were heterozygous, and 1 person (0.9 %) was homozygous for the T allele. The carrier frequency of the G and T alleles was 0.93 and 0.07, respectively. Allelic distribution indicated the predominance of the G allele carriers by Gly460Trp polymorphism of the ADD1 gene among the Ukrainian population, regardless of whether AH symptoms were present. It is noteworthy that the number of the T allele carriers was 2 times large among symptomatic patients than that among healthy individuals. In patients with the T allele, the hypotensive efficacy of indapamide was almost 3 times higher than that in patients with the G allele. The antihypertensive effect of hydrochlorothiazide in patients with the GT and TT genotypes was 2 times greater than that in the GG genotype carriers depending on the presence of the T allele G460T polymorphism of ADD1 gene in the genotype. Conclusions. Allelic distribution indicates the predominance of the G allele carriers by Gly460Trp ADD1 gene polymorphism among the Ukrainian population, regardless of whether AH symptoms are present. Among patients with AH, the accumulation of the T allele G460T polymorphic marker of the α-adducin gene is 2 times more than that in healthy individuals. Patients carrying the T allele demonstrate 2 times higher hypotensive efficacy of indapamide compared with hydrochlorothiazide.

Differentially methylated regions (DMRs)-dependent cfDNA fragmentation profile for diagnosis of breast cancer

2021 ◽  
Author(s):  
Jun Wang ◽  
Ming Yang ◽  
Mingyang Su ◽  
Lirong Shu ◽  
Hongxian Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Diagnosis ◽  
Validation Cohort ◽  
Breast Cancer Diagnosis ◽  
Fragmentation Pattern ◽  
Healthy Individuals ◽  
Differentially Methylated Regions ◽  
Nuclease Digestion ◽  
Mean Size ◽  
Genomic Regions

Abstract Background Breast cancer, the most common malignancy in women, has been proved to have both altered plasma cell-free DNA (cfDNA) methylation and fragmentation profile, nevertheless, simultaneously detecting both of them for breast cancer diagnosis has never been reported. Moreover, although it is known that fragmentation pattern of cfDNA is determined by nuclease digestion of chromatin, structure of which may be affected by DNA methylation, whether cfDNA methylation and fragmentation are biologically related or not still remains unclear.Methods A total of 25 plasm samples from both healthy individuals and patients with breast cancer were divided into discovery cohort and validation cohort. Improved cfMeDIP-seq were utilized to simultaneously profile both cfDNA methylation and fragments size, short fragments ratio were investigated in differentially methylated regions (DMRs). The feasibility of using cfDNA fragmentation profile in hypo- and hyper- methylated regions as a diagnostic marker for breast cancer was evaluated.Results Mean cfDNA fragments size ranging from 100 to 220 base pairs (bp) was found to increase from 170.06 (Input libraries) to 173.04 (IP libraries) bp in healthy individuals, which was not observed in patients with breast cancer (170.51 to 170.71 bp). Furthermore, mean size of cfDNA fragments mapped to hypomethylated regions decreased more in patients with breast cancer (4.60 bp, 172.33 bp in hypermethylated regions to 167.73 bp in hypomethylated regions) than healthy individuals (2.87 bp, 174.54 bp in hypermethylated regions to 171.67 bp in hypomethylated regions). An approach called ‘correlation assessment of DMRs-dependent cfDNA fragmentation profile’ was developed to evaluate the feasibility of using abnormality of short cfDNA fragments ratio in hypomethylated genomic windows for diagnosis of breast cancer in validation cohort. 7 out of 11 patients were detected as having breast cancer (63.6% sensitivity), whereas no healthy individuals were mis-detected (100% specificity).Conclusion We identified enriched short cfDNA fragments after 5mC-immunoprecipitation (IP) in patients with breast cancer, and demonstrated the enriched short cfDNA fragments might originated from hypomethylated genomic regions. Furthermore, we proved the feasibility of using differentially methylated regions (DMRs)-dependent cfDNA fragmentation profile for breast cancer diagnosis.

scholarly journals A Redox Basis for Metronidazole Resistance in Helicobacter pylori

2009 ◽  
Vol 53 (5) ◽  
pp. 1884-1891 ◽  
Author(s):  
N. O. Kaakoush ◽  
C. Asencio ◽  
F. Mégraud ◽  
G. L. Mendz
Keyword(s):  
Helicobacter Pylori ◽  
Resistant Strain ◽  
Gene Mutations ◽  
Thioredoxin Reductase ◽  
Matched Pair ◽  
Specific Gene ◽  
Two Dimensional Gel Electrophoresis ◽  
Development Of Resistance ◽  
Metronidazole Resistance ◽  
Resistant Strains

ABSTRACT Metronidazole resistance in Helicobacter pylori has been attributed to mutations in rdxA or frxA. Insufficient data correlating RdxA and/or FrxA with the resistant phenotype, and the emergence of resistant strains with no mutations in either rdxA or frxA, indicated that the molecular basis of H. pylori resistance to metronidazole required further characterization. The rdxA and frxA genes of four matched pairs of metronidazole-susceptible and -resistant strains were sequenced. The resistant strains had mutations in either rdxA, frxA, neither gene, or both genes. The reduction rates of five substrates suggested that metabolic differences between susceptible and resistant strains cannot be explained only by mutations in rdxA and/or frxA. A more global approach to understanding the resistance phenotype was taken by employing two-dimensional gel electrophoresis combined with tandem mass spectrometry analyses to identify proteins differentially expressed by the matched pair of strains with no mutations in rdxA or frxA. Proteins involved in the oxireduction of ferredoxin were downregulated in the resistant strain. Other redox enzymes, such as thioredoxin reductase, alkyl hydroperoxide reductase, and superoxide dismutase, showed a pI change in the resistant strain. The data suggested that metronidazole resistance involved more complex metabolic changes than specific gene mutations, and they provided evidence of a role for the intracellular redox potential in the development of resistance.

scholarly journals Analysis of the Expression and Polymorphism ofAPOE, HSP, BDNF,andGRIN2BGenes Associated with the Neurodegeneration Process in the Pathogenesis of Primary Open Angle Glaucoma

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Alicja Nowak ◽  
Ireneusz Majsterek ◽  
Karolina Przybyłowska-Sygut ◽  
Dariusz Pytel ◽  
Katarzyna Szymanek ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Nerve Fiber ◽  
Primary Open Angle Glaucoma ◽  
Open Angle Glaucoma ◽  
Blood Analysis ◽  
Specific Gene ◽  
Qrt Pcr ◽  
Pcr Rflp ◽  
Allele Specific ◽  
Peripheral Blood Analysis

Glaucoma is characterized by optic neuropathy of the RGC or retinal nerve fiber. The aim of this study was to evaluate a relationship between the neurodegenerative genes’ polymorphisms of theAPOE(rs449647),BDNF(rs2030324),GRIN2B(rs3764028), andHSP70-1(rs1043618) and the occurrence risk of POAG and to investigate its effect on allele-specific gene expression. Genomic DNA was extracted from peripheral blood. Analysis of the genes’ polymorphisms was performed using PCR-RFLP. The level of mRNA expression was determined by QRT-PCR. We showed a statistically significant association ofBDNFandAPOEgenes’ polymorphisms with a risk of POAG occurrence. There was a statistically significant association of the rs2030324 polymorphism with progression of POAG based on cup disc ratio value and rs1043618 polymorphism based on nerve fiber index and rim area. Furthermore, we found that meanHSP70-1mRNA expression was significantly lower in the case of individuals with the G/G genotype than in the case of minor allele carriers, that is, G/C and C/C. We also found thatBDNFandHSP70-1expression level are associated with the progression of POAG based on rim area value. In conclusion, our results suggest thatBDNF,APOE, andHSP70-1genes might be associated with a risk of POAG occurrence in the Polish population.

Wireless Video-Capsule Endoscopy Is a More Sensitive Investigative Method Than Gastro-Intestinal Endoscopy and Biopsies for the Diagnosis of Acute GI-Gvhd.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1123-1123
Author(s):  
Jean-Baptiste Micol ◽  
Valerie Coiteux ◽  
Laurent Pascal ◽  
Louis Terriou ◽  
Christophe Willekens ◽  
...  
Keyword(s):  
Capsule Endoscopy ◽  
Positive Impact ◽  
Specific Treatment ◽  
Final Diagnosis ◽  
Response To Therapy ◽  
Video Capsule Endoscopy ◽  
High Morbidity ◽  
Gi Tract ◽  
Wireless Video ◽  
Post Transplant

Abstract Acute gastro-intestinal graft-versus-host disease (GI-GVHD) is a major complication following allogeneic stem cell transplantation (allo-SCT) and results in high morbidity and mortality. Diagnosis of GI-GVHD is problematic due a lack of specific symptoms and confounding variables in allo-SCT patients. Although diarrhea is the most common (but non-specific) presenting symptom in acute GI-GVHD, diagnosis is especially difficult when the diarrheal disorder is atypical (i.e. when there is no or limited skin involvement). In a previous study, we reported the positive impact of wireless video-capsule endoscopy (VCE) in the diagnosis of post-transplant diarrhea. Here, we report our experience over the last 5 years with an overall diagnostic approach (including VCE) to the management of allo-SCT patients with suspected acute GI-GVHD. In addition to wireless VCE, patients with atypical post-transplant diarrhea underwent bacterial and viral investigations and upper and/or lower GI-tract endoscopy (plus biopsies, as appropriate). VCE images were scored according to standard endoscopic classification. The final diagnosis took account of the results of the investigation as a whole and the response to therapy. Between August 2002 and October 2007, 240 patients underwent allo-SCT. Thirty patients underwent 37 extensive investigations, with VCE being performed in the following situations: febrile and/or hemorrhagic diarrhea (n=17), isolated diarrhea (n=15), persistent diarrhea or relapse despite appropriate adjustment of immunosuppressive (IS) treatment (n=5). Median time between allo-SCT and VCE was 50 days (range: 19–197). The final diagnosis was acute GVHD (n=19), viral infection (n=6, with 5 CMVs and 1 HHV6s) and a combination of both in 3 cases. The result of our approach was negative in 9 cases (with a normal GI tract by VCE in 8 of them) who were ultimately diagnosed as having functional diarrhea and recovered without any specific treatment. We observed 5 (14%) VCE failures, either due to an absence of intestinal passage (n=3) or major GI hemorrhage (n=2). In the other cases, VCE results were concordant with the final diagnosis. It was noteworthy that VCE was superior to biopsies in some cases. Thus, while VCE demonstrated typical GI-GVHD lesions in 8 patients with histological proven GI-GVHD, VCE showed a normal GI tract (n=4) or GI-GVHD features in 8 other cases where the biopsies were uncertain (n=7) or non-contributive (n=1). The response to appropriate treatment was favorable in 20 cases but was unfavorable and required further therapeutic adjustment in 8 cases (7 GVHDs, 1 CMV). Five patients died of GVHD (n=3), HHV6 infection (n=1) or both (n=1). This study confirms that VCE is a more sensitive investigative method than GI-endoscopy and biopsies. This approach enhanced our ability to modulate IS treatments in patients suffering from atypical post-transplant diarrhea. With its apparently high predictive value, routine use of VCE could be of great interest, particularly with a view to avoiding unnecessary digestive biopsies.

scholarly journals Quinolone-Containing Therapies in the Eradication ofHelicobacter pylori

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Seng-Kee Chuah ◽  
Wei-Chen Tai ◽  
Chen-Hsiang Lee ◽  
Chih-Ming Liang ◽  
Tsung-Hui Hu
Keyword(s):  
Bacterial Resistance ◽  
Rescue Therapy ◽  
Molecular Methods ◽  
Health Issues ◽  
Consensus Guidelines ◽  
Duration Of Treatment ◽  
Resistant Strains ◽  
Polymerase Chain ◽  
H Pylori ◽  
The Impact

Fluoroquinolones, especially levofloxacin, are used in the eradication ofHelicobacter pyloriworldwide. Many consensus guidelines recommend that the second-line rescue therapy forH. pylorieradication consists of a proton pump inhibitor, a quinolone, and amoxicillin as an option. Unfortunately, quinolone is well associated with a risk of developing bacterial resistance. In this paper, we review quinolone-containingH. pylorieradication regimens and the challenges that influence the efficacy of eradication. It is generally suggested that the use of levofloxacin should be confined to “rescue” therapy only, in order to avoid a further rapid increase in the resistance ofH. pylorito quinolone. The impact of quinolone-containingH. pylorieradication regimens on public health issues such as tuberculosis treatment must always be taken into account. Exposure to quinolone is relevant to delays in diagnosing tuberculosis and the development of drug resistance. Extending the duration of treatment to 14 days improves eradication rates by >90%. Tailored therapy to detect fluoroquinolone-resistant strains can be done by culture-based and molecular methods to provide better eradication rates. Molecular methods are achieved by using a real-time polymerase chain reaction to detect the presence of agyrAmutation, which is predictive of treatment failure with quinolones-containing triple therapy.

scholarly journals CREAM: Clustering of genomic REgions Analysis Method

2017 ◽  
Author(s):  
Seyed Ali Madani Tonekaboni ◽  
Parisa Mazrooei ◽  
Victor Kofia ◽  
Benjamin Haibe-Kains ◽  
Mathieu Lupien
Keyword(s):  
Expression Profiles ◽  
Gene Expression Profiles ◽  
R Package ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Analysis Method ◽  
Chromatin Interactions ◽  
Super Enhancer ◽  
Highly Expressed Genes ◽  
Genomic Regions

ABSTRACTCellular identity relies on cell type-specific gene expression profiles controlled by cis-regulatory elements (CREs), such as promoters, enhancers and anchors of chromatin interactions. CREs are unevenly distributed across the genome, giving rise to distinct subsets such as individual CREs and Clusters Of cis-Regulatory Elements (COREs), also known as super-enhancers. Identifying COREs is a challenge due to technical and biological features that entail variability in the distribution of distances between CREs within a given dataset. To address this issue, we developed a new unsupervised machine learning approach termed Clustering of genomic REgions Analysis Method (CREAM) that outperforms the Ranking Of Super Enhancer (ROSE) approach. Specifically CREAM identified COREs are enriched in CREs strongly bound by master transcription factors according to ChIP-seq signal intensity, are proximal to highly expressed genes, are preferentially found near genes essential for cell growth and are more predictive of cell identity. Moreover, we show that CREAM enables subtyping primary prostate tumor samples according to their CORE distribution across the genome. We further show that COREs are enriched compared to individual CREs at TAD boundaries and these are preferentially bound by CTCF and factors of the cohesin complex (e.g.: RAD21 and SMC3). Finally, using CREAM against transcription factor ChIP-seq reveals CTCF and cohesin-specific COREs preferentially at TAD boundaries compared to intra-TADs. CREAM is available as an open source R package (https://CRAN.R-project.org/package=CREAM) to identify COREs from cis-regulatory annotation datasets from any biological samples.

scholarly journals Independent Evolution of Sex Chromosomes in Eublepharid Geckos, a Lineage with Environmental and Genotypic Sex Determination

2020 ◽  
Author(s):  
Eleonora Pensabene ◽  
Lukáš Kratochvíl ◽  
Michail Rovatsos
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Gene Content ◽  
Gene Copy ◽  
Specific Gene ◽  
Evolution Of Sex ◽  
Copy Numbers ◽  
Genotypic Sex Determination ◽  
The Difference ◽  
Genomic Regions

Geckos demonstrate a remarkable variability in sex determination systems, but our limited knowledge prohibits accurate conclusions on the evolution of sex determination in this group. Eyelid geckos (Eublepharidae) are of particular interest, as they encompass species with both environmental and genotypic sex determination. We identified for the first time the X-specific gene content in the Yucatán banded gecko, Coleonyx elegans, possessing X1X1X2X2/X1X2Y multiple sex chromosomes by comparative genome coverage analysis between sexes. The X-specific gene content of Coleonyx elegans was revealed to be partially homologous to genomic regions linked to the chicken autosomes 1, 6 and 11. A qPCR-based test was applied to validate a subset of X-specific genes by comparing the difference in gene copy numbers between sexes, and to explore the homology of sex chromosomes across 11 eublepharid, two phyllodactylid and one sphaerodactylid species. Homologous sex chromosomes are shared between Coleonyx elegans and Coleonyx mitratus, two species diverged approximately 34 million years ago, but not with other tested species. As far as we know, the X-specific gene content of Coleonyx elegans / Coleonyx mitratus was never involved in the sex chromosomes of other gecko lineages, indicating that the sex chromosomes in this clade of eublepharid geckos evolved independently.

scholarly journals Pseudogenization, genome streamlining and specific gene repertoire landmark the genomes ofCarnobacterium maltaromaticumisolated from diseased sharks

2019 ◽  
Author(s):  
Laura Martinez Steele ◽  
Christopher G Lowe ◽  
Mark S Okihiro ◽  
Jesse G. Dillon ◽  
Renaud Berlemont
Keyword(s):  
Specific Gene ◽  
Shark Species ◽  
Gene Repertoire ◽  
Genomic Signatures ◽  
Thresher Shark ◽  
Independent Life ◽  
Conserved Gene ◽  
Genomic Regions ◽  
High Degree

AbstractCarnobacterium maltaromaticumis a well-known pathogen of bony fish. More recently,C. maltaromaticumhave been isolated from the brain and inner ear of disorientated and stranded common thresher (Alopias vulpinus) and salmon shark (Lamna ditropis). While thresher shark strandings are recent, salmon sharks have been stranding for decades, suggesting a long-term association betweenC. maltaromaticumand sharks. Interestingly, some strains ofC. maltaromaticumare used by the food industry for their probiotic and antimicrobial activity. Here, we sequenced the genome of 9C. maltaromaticumstrains (SK-isolates) from diseased common thresher and salmon sharks and compared them to otherC. maltaromaticumstrains in order to identify the genomic signatures that differentiate the disease-associated from the innocuousC. maltaromaticumisolates. SK strains formed a monophyletic clade, with a conserved gene repertoire, and shared a high degree of pseudogenization even though isolates were from different shark species, locations, and across years. In addition, these strains displayed few virulence associated genes and unique genomic regions, some resulting from horizontal gene transfer. The association of diseased sharks and SK strains suggests their role as potential pathogens. Although the high degree of pseudogenization suggests a transition to a host-adapted lifestyle, a set of conserved functional genes highlights the need of essential functions required for a host-independent life style. Globally, this work identifies specific genomic signatures ofC. maltaromaticumstrains isolated from infected sharks, provides the framework to elucidate the role of SK strains in the development of the disease in sharks, and further investigate the dissemination of SK strains in populations of wild fish.

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