Molecular characterization of acute hepatopancreatic necrosis disease causing Vibrio parahaemolyticus strains in cultured shrimp Penaeus monodon in south‐west farming region of Bangladesh

Acute hepatopancreatic necrosis disease (AHPND) is an emerging shrimp disease caused by strains of Vibrio parahaemolyticus containing a unique virulent plasmid, responsible for substantial economic losses since 2009; caused up to 100% mortality in farmed shrimp Penaeus monodon. The purpose of this study was to isolate and identify the pathogenic strain of V. parahaemolyticus causing AHPND in cultured shrimp (Penaeus monodon) using classical and molecular techniques. Samples were collected from three different locations of south-west shrimp farming regions of Bangladesh viz. Sadar Upazilla of Satkhira; Mongla and Morrelganj under Bagerhat district. In this study, three selective media were used for primary isolation of V. parahaemolyticus. Among 46 primary isolates, 18 representative isolates were checked for the species-specific detection of V. parahaemolyticus using ldh primers and all of them were found to be positive. 16S rRNA gene sequencing were used to further confirm the isolates as V. parahaemolyticus. tdh primer was used to check human pathogenicity but all 18 isolates showed negative result. The isolates were further characterized to check their AHPND positivity using AP3 and AP4 primers. Ten isolates showed positive results for AP3 (55.56%) and 9 showed positive results for AP4 (50%) which indicated that the isolates were AHPND positive. This study also reported that all AHPND positive strains were resistant to the antibiotic gentamycin but sensitive to chloramphenicol, nalidixic acid, nitrofurantoin and tetracycline. The findings of this study will help the shrimp farmers and policy makers to take proper biosecurity measures to protect shrimps from AHPND and thereby sustain the shrimp production in Bangladesh. Dhaka Univ. J. Biol. Sci. 27(1): 57-68, 2018 (January)

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Molecular Identification of AHPND Positive Vibrio Parahaemolyticus causing an outbreak in South-West Shrimp Farming Regions of Bangladesh

Journal of Bangladesh Academy of Sciences ◽

10.3329/jbas.v41i2.35492 ◽

2018 ◽

Vol 41 (2) ◽

pp. 127-135 ◽

Cited By ~ 7

Author(s):

Md Mostavi Enan Eshik ◽

Md Minhazul Abedin ◽

Nusrat Jahan Punom ◽

Mst Khadiza Begum ◽

Mohammad Shamsur Rahman

Keyword(s):

Penaeus Monodon ◽

Molecular Techniques ◽

Shrimp Farming ◽

Bacterial Disease ◽

Policy Makers ◽

Primary Isolation ◽

South West ◽

Species Specific ◽

Acute Hepatopancreatic Necrosis Disease ◽

Academy Of Sciences

Acute hepatopancreatic necrosis disease (AHPND) of shrimps is a bacterial disease, first appeared in China in 2009 and causes mortality up to 100 % which usually occurs early (within approximately first 35 days) after stocking shrimp fry of black tiger shrimp, Penaeus monodon (Fabricius) and white leg shrimp, Litopenaeus vannamei (Boone). The purpose of this study was to isolate and identify the pathogenic strain of V. parahaemolyticus causing AHPND in cultured shrimps (P. monodon) using molecular techniques. After a disease outbreak in April 2017, shrimp samples were collected from three different locations of south-west shrimp farming region of Bangladesh viz. Satkhira, Khulna and Bagerhat districts. In this study, three selective media were used for primary isolation of V. parahaemolyticus. Among 28 primary isolates, representative14 isolates were checked for the species-specific detection of V. parahaemolyticus using ldh primers and all of them were found to be positive. The isolates were further characterized to check their AHPND positivity using AP3 and AP4 primers. Four isolates showed positive results for both AP3 and AP4 which indicated that the isolates were AHPND positive. This study also report that all AHPND positive strains showed sensitivity to the antibiotics Tetracycline and Nalidixic Acid. The results of this study will help the farmers and policy makers to make plan to protect shrimps from AHPND and thereby sustain the shrimp farming in Bangladesh.Journal of Bangladesh Academy of Sciences, Vol. 41, No. 2, 127-135, 2017

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Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh

10.21203/rs.2.14490/v2 ◽

2019 ◽

Author(s):

Shawon Ahmmed ◽

Md. Abdullah-Al-Kamran Khan ◽

Md. Mostavi Enan Eshik ◽

Nusrat Jahan Punom ◽

Abul B.M.M.K. Islam ◽

...

Keyword(s):

Vibrio Parahaemolyticus ◽

Early Stage ◽

Penaeus Monodon ◽

Antibiotic Resistance Genes ◽

Secretion System ◽

Economic Losses ◽

Emergence Pattern ◽

Toxin Genes ◽

South West ◽

Evolutionary Features

Abstract Background Due to its rapid lethal effect in the early stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) causing great economic losses, since its first outbreak in southeast China in 2009. Vibrio parahaemolyticus , carrying the pir A and pir B toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence the whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp ( Peneaus monodon ) of south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen. Results Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh , AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of a total of 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type III secretion system-1 (T3SS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pir A and pir B. Antibiotic resistance genes were predicted against β-lactam, fluoroquinolone, tetracycline and macrolide groups in both MSR16 and MSR17 strains. Conclusions The findings of this research may facilitate the tracking of pathogenic and/or antibiotic-resistant V. parahaemolyticus isolates between production sites, and the identification of candidate strains for the production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.

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Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh

BMC Microbiology ◽

10.1186/s12866-019-1655-8 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Shawon Ahmmed ◽

Md. Abdullah-Al-Kamran Khan ◽

Md. Mostavi Enan Eshik ◽

Nusrat Jahan Punom ◽

Abul Bashar Mir Md. Khademul Islam ◽

...

Keyword(s):

Vibrio Parahaemolyticus ◽

Penaeus Monodon ◽

Antibiotic Resistance Genes ◽

Development Stage ◽

Secretion System ◽

Economic Losses ◽

Emergence Pattern ◽

Toxin Genes ◽

South West ◽

Evolutionary Features

Abstract Background Due to its rapid lethal effect in the early development stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) has been causing great economic losses, since its first outbreak in southeast China in 2009. Vibrio parahaemolyticus, carrying the pirA and pirB toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence the whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp (Peneaus monodon) of the south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen. Results Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh, AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of a total of 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type III secretion system-1 (T3SS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~ 69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pirA and pirB. Antibiotic resistance genes were predicted against β-lactam, fluoroquinolone, tetracycline and macrolide groups in both MSR16 and MSR17 strains. Conclusions The findings of this research may facilitate the tracking of pathogenic and/or antibiotic-resistant V. parahaemolyticus isolates between production sites, and the identification of candidate strains for the production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.

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The infection of Vibrio parahaemolyticus in shrimp and human

Oceana Biomedicina Journal ◽

10.30649/obj.v1i1.6 ◽

2018 ◽

Vol 1 (1) ◽

pp. 44 ◽

Cited By ~ 1

Author(s):

Rian Ka Praja

Keyword(s):

Vibrio Parahaemolyticus ◽

Animal Health ◽

Alternative Therapy ◽

Penaeus Monodon ◽

Early Mortality ◽

Economic Losses ◽

Early Mortality Syndrome ◽

Thermostable Direct Hemolysin ◽

Acute Hepatopancreatic Necrosis Disease ◽

Very High

Vibrio parahaemolyticus is an aquatic zoonotic agent that can threaten human and aquaculture animal health. Humans can be infected by consuming contaminated raw seafood or wound-related infections. Generally infection of V. parahemolyticus is orally transmitted and causes gastroenteritis in humans while in aquaculture animals especially shrimp can cause Acute Hepatopancreatic Necrosis Disease (AHPND) or Early Mortality Syndrome (EMS) with a very high mortality rate and cause economic losses. Shrimp species susceptible to infection are Litopenaeus vannamei, Penaeus monodon, and P. chinensis. V. parahaemolyticus produces several toxins in human disease such as thermostable direct hemolysin (TDH), TDH-related haemolysin (TRH), and thermolabile hemolysin (TLH). Meanwhile, Photorabdus insect-related (Pir) toxins consisting of PirAvp and PirBvp are the toxins associated with AHPND in shrimp. The genes that encode the toxin are used as targets to diagnose V. parahaemolyticus pathogens molecularly. Until now the treatment of V. parahaemolyticus infection is using antibiotics and fluid therapy, but there were V. parahaemolyticus isolates from aquaculture that have been resistant to antibiotics so that the use of antibiotics in aquaculture must be controlled and the use of alternative therapy are very important to be developed to control V. parahaemolyticus infection. Keywords: V. parahaemolyticus, zoonotic, gastroenteritis, Acute Hepatopancreatic Necrosis Disease (AHPND), Early Mortality Syndrome (EMS).

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Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh

10.21203/rs.2.14490/v3 ◽

2019 ◽

Author(s):

Shawon Ahmmed ◽

Md. Abdullah-Al-Kamran Khan ◽

Md. Mostavi Enan Eshik ◽

Nusrat Jahan Punom ◽

Abul B.M.M.K. Islam ◽

...

Keyword(s):

Vibrio Parahaemolyticus ◽

Early Stage ◽

Penaeus Monodon ◽

Antibiotic Resistance Genes ◽

Secretion System ◽

Economic Losses ◽

Emergence Pattern ◽

Toxin Genes ◽

South West ◽

Evolutionary Features

Abstract Background Due to its rapid lethal effect in the early stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) causing great economic losses, since its first outbreak in southeast China in 2009. Vibrio parahaemolyticus, carrying the pirA and pirB toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence the whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp (Peneaus monodon) of south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen. Results Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh, AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of a total of 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type III secretion system-1 (T3SS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pirA and pirB. Antibiotic resistance genes were predicted against β-lactam, fluoroquinolone, tetracycline and macrolide groups in both MSR16 and MSR17 strains. Conclusions The findings of this research may facilitate the tracking of pathogenic and/or antibiotic-resistant V. parahaemolyticus isolates between production sites, and the identification of candidate strains for the production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.

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Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh

10.21203/rs.2.14490/v4 ◽

2019 ◽

Author(s):

Shawon Ahmmed ◽

Md. Abdullah-Al-Kamran Khan ◽

Md. Mostavi Enan Eshik ◽

Nusrat Jahan Punom ◽

Abul B.M.M.K. Islam ◽

...

Keyword(s):

Vibrio Parahaemolyticus ◽

Penaeus Monodon ◽

Antibiotic Resistance Genes ◽

Development Stage ◽

Secretion System ◽

Economic Losses ◽

Emergence Pattern ◽

Toxin Genes ◽

South West ◽

Evolutionary Features

Abstract Background Due to its rapid lethal effect in the early development stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) has been causing great economic losses, since its first outbreak in southeast China in 2009. Vibrio parahaemolyticus, carrying the pirA and pirB toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence the whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp (Peneaus monodon) of the south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen. Results Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh, AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of a total of 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type III secretion system-1 (T3SS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pirA and pirB. Antibiotic resistance genes were predicted against β-lactam, fluoroquinolone, tetracycline and macrolide groups in both MSR16 and MSR17 strains. Conclusions The findings of this research may facilitate the tracking of pathogenic and/or antibiotic-resistant V. parahaemolyticus isolates between production sites, and the identification of candidate strains for the production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.

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Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs

Pathogens ◽

10.3390/pathogens9080638 ◽

2020 ◽

Vol 9 (8) ◽

pp. 638

Author(s):

Caitlin E. Older ◽

Aline Rodrigues Hoffmann ◽

Kathleen Hoover ◽

Frane Banovic

Keyword(s):

Quantitative Polymerase Chain Reaction ◽

16S Rrna Gene Sequencing ◽

Molecular Techniques ◽

Rrna Gene ◽

Bacterial Microbiota ◽

Starting Point ◽

Rrna Gene Sequencing ◽

Antimicrobial Treatments ◽

Staphylococcus Spp

Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.

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Hierarchical Microbial Functions Prediction by Graph Aggregated Embedding

Frontiers in Genetics ◽

10.3389/fgene.2020.608512 ◽

2021 ◽

Vol 11 ◽

Author(s):

Yujie Hou ◽

Xiong Zhang ◽

Qinyan Zhou ◽

Wenxing Hong ◽

Ying Wang

Keyword(s):

16S Rrna ◽

Penaeus Monodon ◽

Poor Performance ◽

16S Rrna Gene Sequencing ◽

Reference Database ◽

Rrna Gene ◽

Sequencing Data ◽

Significant Generalization ◽

Rrna Gene Sequencing ◽

Almost All

Matching 16S rRNA gene sequencing data to a metabolic reference database is a meaningful way to predict the metabolic function of bacteria and archaea, bringing greater insight to the working of the microbial community. However, some operational taxonomy units (OTUs) cannot be functionally profiled, especially for microbial communities from non-human samples cultured in defective media. Therefore, we herein report the development of Hierarchical micrObial functions Prediction by graph aggregated Embedding (HOPE), which utilizes co-occurring patterns and nucleotide sequences to predict microbial functions. HOPE integrates topological structures of microbial co-occurrence networks with k-mer compositions of OTU sequences and embeds them into a lower-dimensional continuous latent space, while maximally preserving topological relationships among OTUs. The high imbalance among KEGG Orthology (KO) functions of microbes is recognized in our framework that usually yields poor performance. A hierarchical multitask learning module is used in HOPE to alleviate the challenge brought by the long-tailed distribution among classes. To test the performance of HOPE, we compare it with HOPE-one, HOPE-seq, and GraphSAGE, respectively, in three microbial metagenomic 16s rRNA sequencing datasets, including abalone gut, human gut, and gut of Penaeus monodon. Experiments demonstrate that HOPE outperforms baselines on almost all indexes in all experiments. Furthermore, HOPE reveals significant generalization ability. HOPE's basic idea is suitable for other related scenarios, such as the prediction of gene function based on gene co-expression networks. The source code of HOPE is freely available at https://github.com/adrift00/HOPE.

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Genomic and evolutionary features of two AHPND positive Vibrio parahaemolyticus strains isolated from shrimp (Penaeus monodon) of south-west Bangladesh

10.21203/rs.2.14490/v1 ◽

2019 ◽

Author(s):

Shawon Ahmmed ◽

Md. Abdullah-Al-Kamran Khan ◽

Md. Mostavi Enan Eshik ◽

Nusrat Jahan Punom ◽

Abul B.M.M.K. Islam ◽

...

Keyword(s):

Antibiotic Resistance ◽

Vibrio Parahaemolyticus ◽

Early Stage ◽

Antibiotic Resistance Genes ◽

Secretion System ◽

Economic Losses ◽

Emergence Pattern ◽

Toxin Genes ◽

South West ◽

Evolutionary Features

Abstract Background Due to its rapid lethal effect in the early stage of shrimp, acute hepatopancreatic necrosis disease (AHPND) causing great economic losses, since it first outbreak in southeast China in 2009. Vibrio parahaemolyticus , carrying the pir A and pir B toxin genes is known to cause AHPND in shrimp. The overall objective of this study was to sequence whole genome of AHPND positive V. parahaemolyticus strains isolated from shrimp ( Peneaus monodon ) of south-west region of Bangladesh in 2016 and 2017 and characterize the genomic features and emergence pattern of this marine pathogen. Results Two targeted AHPND positive V. parahaemolyticus strains were confirmed using PCR with 16S rRNA, ldh , AP3 and AP4 primers. The assembled genomes of strain MSR16 and MSR17 were comprised of total 5,393,740 bp and 5,241,592 bp, respectively. From annotation, several virulence genes involved in chemotaxis and motility, EPS type II secretion system, Type three secretion system-1 (TTSS-1) and its secreted effectors, thermolabile hemolysin were found in both strains. Importantly, the ~69 kb plasmid was identified in both MSR16 and MSR17 strains containing the two toxin genes pir A and pir B. Antibiotic resistance genes were predicted against β-lactam, fluoroquinolone, tetracycline, macrolide and cephalosporin groups in both MSR16 and MSR17 strains. Conclusions The findings of this research may facilitate the tracking of pathogenic and/or antibiotic resistance V. parahaemolyticus isolates between production sites, and the identification of candidate strains for production of vaccines as an aid to control of this devastating disease. Also, the emergence pattern of this pathogen can be highlighted to determine the characteristic differences of other strains found all over the world.

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Genetic and Biochemical Diversity ofPaenibacillus larvaeIsolated from Tunisian Infected Honey Bee Broods

BioMed Research International ◽

10.1155/2013/479893 ◽

2013 ◽

Vol 2013 ◽

pp. 1-9 ◽

Cited By ~ 6

Author(s):

Chadlia Hamdi ◽

Jihène Essanaa ◽

Luigi Sansonno ◽

Elena Crotti ◽

Khaoula Abdi ◽

...

Keyword(s):

Phenotypic Diversity ◽

16S Rrna Gene Sequencing ◽

Intraspecific Diversity ◽

Economic Losses ◽

Rrna Gene ◽

Biochemical Tests ◽

Phenotypic Differences ◽

Ecological Aspects ◽

Rrna Gene Sequencing

Paenibacillus larvaeis the causative agent of American foulbrood (AFB), a virulent disease of honeybee (Apis mellifera) larvae. In Tunisia, AFB has been detected in many beekeeping areas, where it causes important economic losses, but nothing is known about the diversity of the causing agent. Seventy-five isolates ofP. larvae, identified by biochemical tests and 16S rRNA gene sequencing, were obtained from fifteen contaminated broods showing typical AFB symptoms, collected in different locations in the northern part of the country. Using BOX-PCR, a distinct profile ofP. larvaewith respect to relatedPaenibacillusspecies was detected which may be useful for its identification. SomeP. larvae-specific bands represented novel potential molecular markers for the species. BOX-PCR fingerprints indicated a relatively high intraspecific diversity among the isolates not described previously with several molecular polymorphisms identifying six genotypes on polyacrylamide gel. Polymorphisms were also detected in several biochemical characters (indol production, nitrate reduction, and methyl red and oxidase tests). Contrary to the relatively high intraspecies molecular and phenotypic diversity, thein vivovirulence of three selectedP. larvaegenotypes did not differ significantly, suggesting that the genotypic/phenotypic differences are neutral or related to ecological aspects other than virulence.

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