scholarly journals Genetic Diversity of Clinical Bordetella Pertussis ST2 Strains in comparison with Vaccine Reference Strains of India

2021 ◽  
Vol 9 ◽  
pp. 38-42
Author(s):  
Naresh Chand Sharma ◽  
Shalini Anandan ◽  
Naveen Kumar Devanga Ragupathi ◽  
Dhiviya Prabaa Muthuirulandi Sethuvel ◽  
Karthick Vasudevan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bordetella Pertussis ◽  
Reference Strains

scholarly journals Draft Genome Resources Sequences of Six Pseudomonas syringae pv. actinidiae Strains Isolated from Actinidia chinensis var. deliciosa Leaves in Portugal

2020 ◽  
pp. PHYTO-05-20-018
Author(s):  
Aitana Ares ◽  
Marta Tacão ◽  
Daniela Figueira ◽  
Eva Garcia ◽  
Joana Costa
Keyword(s):  
Genetic Diversity ◽  
Pseudomonas Syringae ◽  
Draft Genome ◽  
Clonal Expansion ◽  
Average Nucleotide Identity ◽  
Actinidia Chinensis ◽  
Valuable Resource ◽  
Genetic Population ◽  
Evolutionary Studies ◽  
Reference Strains

Pseudomonas syringae pv. actinidiae is a quarantine bacterium affecting all the Portuguese main areas of kiwifruit production. We report the draft genome of six P. syringae pv. actinidiae strains isolated from symptomatic leaves of Actinidia chinensis var. deliciosa in a study that determined the genetic population structure of the endophytic and epiphytic populations in two consecutive seasons. Average nucleotide identity values were above 99% similarity with reference strains from P. syringae pv. actinidiae biovar 3. The genomic differences found between these strains confirm the genetic diversity described for P. syringae pv. actinidiae population in Portugal. Furthermore, data provide evidence that the initial clonal expansion of P. syringae pv. actinidiae in Europe was followed by a genomic diversification constituting a valuable resource for epidemiological and evolutionary studies, namely when adopting strategies for epidemics management.

An Ecological Study of Lactococci Isolated from Raw Milk in the Camembert Cheese Registered Designation of Origin Area

1998 ◽  
Vol 64 (12) ◽  
pp. 4729-4735 ◽  
Author(s):  
D. Corroler ◽  
I. Mangin ◽  
N. Desmasures ◽  
M. Gueguen
Keyword(s):  
Genetic Diversity ◽  
Geographic Distribution ◽  
Ecological Study ◽  
Raw Milk ◽  
Randomly Amplified Polymorphic Dna ◽  
Histidine Biosynthesis ◽  
Subspecies Level ◽  
Camembert Cheese ◽  
Reference Strains ◽  
Origin Area

ABSTRACT The genetic diversity of lactococci isolated from raw milk in the Camembert cheese Registered Designation of Origin area was studied. Two seasonal samples (winter and summer) of raw milk were obtained from six farms in two areas (Bessin and Bocage Falaisien) of Normandy. All of the strains analyzed had a Lactococcus lactis subsp.lactis phenotype, whereas the randomly amplified polymorphic DNA (RAPD) technique genotypically identified the strains as members of L. lactis subsp. lactis orL. lactis subsp. cremoris. The genotypes were confirmed by performing standard PCR with primers corresponding to a region of the histidine biosynthesis operon. The geographic distribution of each subspecies of L. lactis was determined; 80% of the Bocage Falaisien strains were members ofL. lactis subsp. lactis, and 30.5% of the Bessin strains were members of L. lactis subsp.lactis. A dendrogram was produced from a computer analysis of the RAPD profiles in order to evaluate the diversity of the lactococci below the subspecies level. The coefficient of similarity for 117 of the 139 strains identified as members of L. lactis subsp.cremoris was as high as 66%. The L. lactis subsp. lactis strains were more heterogeneous and formed 10 separate clusters (the level of similarity among the clusters was 18%). Reference strains of L. lactissubsp. lactis fell into 2 of these 10 clusters, demonstrating that lactococcal isolates are clearly different. As determined by the RAPD profiles, some L. lactis subsp.lactis strains were specific to the farms from which they originated and were recovered throughout the year (in both summer and winter). Therefore, the typicality of L. lactissubsp. lactis strains was linked to the farm of origin rather than the area. These findings emphasize the significance of designation of origin and the specificity of “Camembert de Normandie” cheese.

scholarly journals Broad Diversity of Ralstonia solanacearum Strains in Cameroon

Plant Disease ◽  
2009 ◽  
Vol 93 (11) ◽  
pp. 1123-1130 ◽  
Author(s):  
Gabriel Mahbou Somo Toukam ◽  
Gilles Cellier ◽  
Emmanuel Wicker ◽  
Caroline Guilbaud ◽  
Rémi Kahane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ralstonia Solanacearum ◽  
Central Africa ◽  
Sequence Analyses ◽  
Chain Reaction ◽  
Specific Pcr ◽  
Economic Threat ◽  
The Indian Ocean ◽  
Polymerase Chain ◽  
Reference Strains

In 2005, an extensive survey of bacterial wilt in Cameroon collected 110 strains of Ralstonia solanacearum from wilting tomato, potato, pepper, huckleberry (Solanum scabrum), sesame, and amaranth. The genetic diversity and phylogeny of selected strains from Cameroon were assessed by multiplex–polymerase chain reaction (PCR), race 3/biovar 2–specific PCR, and sequence analyses of the mutS and egl genes. These data were compared with those from 33 reference strains covering the known diversity within the R. solanacearum species complex. Strains isolated in Cameroon clustered into three of the four known phylotypes: I (Asian), II (American), and III (African). Lowland tomato strains belonged to phylotype I and were quite homogeneous. The strains belonging to phylotype II were genetically diverse, and partitioned into subclusters IIA and IIB (sequevar 1, race 3/biovar 2). Cameroon strains in the African phylotype III were distinct from reference strains from Zimbabwe or the Indian Ocean, highlighting the genetic diversity present within this phylotype. Strains from potatoes growing in the highlands of West Cameroon fell into both phylotypes II (race 3/biovar 2) and III. These phylotype II and III highland strains attacked both potato and tomato and could therefore pose an economic threat to potato and tomato crops throughout Central Africa. This is the first comprehensive report on the genetic diversity of R. solanacearum strains in Cameroon.

scholarly journals At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions

2020 ◽  
Author(s):  
Ceren Simsek ◽  
Victor Max Corman ◽  
Hermann Ulrich Everling ◽  
Alexander N. Lukashev ◽  
Andrea Rasche ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Reverse Genetics ◽  
Diarrheal Disease ◽  
Rapid Identification ◽  
Viral Metagenomics ◽  
Current Effort ◽  
Viral Pathogens ◽  
Rotavirus A ◽  
Reference Strains ◽  
Shed Light

ABSTRACTBats host many viruses pathogenic to humans, and increasing evidence suggests that Rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America and Africa were PCR-positive for RVA and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, including evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite varying levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses.ImportanceThe increased research on bat coronaviruses after SARS-CoV and MERS-CoVallowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general and bats in particular, for global preparedness against emerging viral pathogens. The current effort to characterize bat rotavirus strains from 3 continents shed light on the vast genetic diversity of rotaviruses and also hinted at a bat origin for several atypical rotaviruses in humans and animals, implying that zoonoses of bat rotaviruses might occur more frequently than currently realized.

Genome diversity and evolutionary characteristics of clinical isolates of Bordetella pertussis circulating in Iran

2020 ◽  
Author(s):  
Samaneh Saedi ◽  
Azadeh Safarchi ◽  
Mojtaba Noofeli ◽  
Keyvan Tadayon ◽  
Alfred Chin Yen Tay ◽  
...  
Keyword(s):  
Bordetella Pertussis ◽  
Genome Structure ◽  
Genomic Analysis ◽  
Clinical Isolates ◽  
Comparative Genomic ◽  
Waning Immunity ◽  
Promoter Allele ◽  
Structural Adaptations ◽  
Reference Strains ◽  
Unique Snps

  Background and Objectives: The re-emergence of pertussis still is being reported all over the world. Pathogen adaptation and antigenic divergence of circulating isolates from vaccine strains are the main reasons of infection resurgence. Waning immunity is also an important factor contributing to resurgence of pertussis. Materials and Methods: The genetic diversity and evolutionary characteristics of circulating Iranian isolates of Bordetella pertussis during February 2015 to October 2018 was investigated by pulsed-field gel electrophoresis (PFGE) and subse- quently ptxA, ptxP and fim3 alleles were characterized. The next generation genome sequencing was then used to compare the genomics of ptxP1 and ptxP3 of selected isolates from PFGE dendrogram. Results: PFGE differentiated 62 clinical isolates and vaccine and reference strains into 19 PFGE profiles, indicating the higher level of heterogeneity in the population during 2015-2018. The predominant B. pertussis genotype harbored pertussis toxin promoter allele, ptxP3 and the expansion of ptxA1 isolates, were also observed in our population. Conclusion: No changes in allelic profile of predominant clone in recent years was observed but antigenic divergence between recently circulating isolates and the vaccine strain has been progressed and significantly was higher than previous studies. The comparative genomic analysis of the ptxP3 and ptxP1 isolates indicate that changes in ptxP3 genome structure including 32 unique SNPs and three unique indels may have contributed to the expansion of the ptxP3 clone. We compared ptxP3 and ptxP1 isolates in pathogenicity-associated genes and found five of them were specific for the ptxP3 isolates. The polymorphisms in pathogenicity-associated genes suggest structural adaptations for these virulence factors.  

scholarly journals A Highly Conserved Residue in HIV-1 Nef Alpha Helix 2 Modulates Protein Expression

mSphere ◽  
2016 ◽  
Vol 1 (6) ◽  
Author(s):  
Aaron L. Johnson ◽  
Brennan S. Dirk ◽  
Mathieu Coutu ◽  
S. M. Mansour Haeryfar ◽  
Eric J. Arts ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Protein Expression ◽  
Protein Turnover ◽  
Reference Strain ◽  
Alpha Helix ◽  
Major Determinant ◽  
Specific Reference ◽  
Subtype C ◽  
Reference Strains ◽  
Hiv 1

ABSTRACT The HIV-1 Nef protein has been established as a key pathogenic determinant of HIV/AIDS, but there is little knowledge of how the extensive genetic diversity of HIV-1 affects Nef function. Upon compiling a set of subtype-specific reference strains, we identified a subtype C reference strain, C.BR92025, that contained natural polymorphisms at otherwise highly conserved residues 13, 84, and 92. Interestingly, strain C.BR92025 Nef displayed impaired Nef function and had decreased protein expression. We have demonstrated that strain C.BR92025 Nef has a higher rate of protein turnover than highly expressed Nef proteins and that this higher rate of protein turnover is due to an alanine-to-valine substitution at Nef residue 84. These findings highlight residue A84 as a major determinant of HIV-1 Nef expression. Extensive genetic diversity is a defining characteristic of human immunodeficiency virus type 1 (HIV-1) and poses a significant barrier to the development of an effective vaccine. To better understand the impact of this genetic diversity on the HIV-1 pathogenic factor Nef, we compiled a panel of reference strains from the NIH Los Alamos HIV Database. Initial sequence analysis identified point mutations at Nef residues 13, 84, and 92 in subtype C reference strain C.BR92025 from Brazil. Functional analysis revealed impaired major histocompatibility complex class I and CD4 downregulation of strain C.BR92025 Nef, which corresponded to decreased protein expression. Metabolic labeling demonstrated that strain C.BR92025 Nef has a greater rate of protein turnover than subtype B reference strain B.JRFL that, on the basis of mutational analysis, is related to Nef residue A84. An alanine-to-valine substitution at position 84, located in alpha helix 2 of Nef, was sufficient to alter the rate of turnover of an otherwise highly expressed Nef protein. In conclusion, these findings highlight HIV-1 Nef residue A84 as a major determinant of protein expression that may offer an additional avenue to disrupt or mediate the effects of this key HIV-1 pathogenic factor. IMPORTANCE The HIV-1 Nef protein has been established as a key pathogenic determinant of HIV/AIDS, but there is little knowledge of how the extensive genetic diversity of HIV-1 affects Nef function. Upon compiling a set of subtype-specific reference strains, we identified a subtype C reference strain, C.BR92025, that contained natural polymorphisms at otherwise highly conserved residues 13, 84, and 92. Interestingly, strain C.BR92025 Nef displayed impaired Nef function and had decreased protein expression. We have demonstrated that strain C.BR92025 Nef has a higher rate of protein turnover than highly expressed Nef proteins and that this higher rate of protein turnover is due to an alanine-to-valine substitution at Nef residue 84. These findings highlight residue A84 as a major determinant of HIV-1 Nef expression.

scholarly journals Duplications drive diversity in Bordetella pertussis on an underestimated scale

2020 ◽  
Author(s):  
Jonathan S. Abrahams ◽  
Michael R. Weigand ◽  
Natalie Ring ◽  
Iain MacArthur ◽  
Scott Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Sequence ◽  
Bordetella Pertussis ◽  
Sequence Data ◽  
Read Depth ◽  
Sequence Element ◽  
Genome Sequence Data ◽  
Genome Dynamics ◽  
Tandem Duplications

AbstractBacterial genetic diversity is often described using solely base pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplications of genomic loci are thought to be widespread among bacteria but due to their often intractable size and instability, comprehensive studies of the range and genome dynamics of these mutations are rare. We define a methodology to investigate duplications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for duplications to occur. Analysis of genome sequence data for 2430 B. pertussis isolates identified 272 putative duplications, of which 94% were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of duplications, suggesting unstable and sporadic characteristics. Genome instability was further described in-vitro using long read sequencing via the Nanopore platform. Clonally derived laboratory cultures produced heterogenous populations containing multiple structural variants. Short read data was used to predict 272 duplications, whilst long reads generated on the Nanopore platform enabled the in-depth study of the genome dynamics of tandem duplications in B. pertussis. Our work reveals the unrecognised and dynamic genetic diversity of B. pertussis and, as the complexity of the B. pertussis genome is not unique, highlights the need for a holistic and fundamental understanding of bacterial genetics.

scholarly journals Changes in genetic diversity of the Bordetella pertussis population in Serbia between 1953 and 2011

2014 ◽  
Vol 66 (1) ◽  
pp. 107-116 ◽  
Author(s):  
Tatjana Pljesa ◽  
Qiushui He ◽  
Gordana Dakic ◽  
Mirjana Vignjevic-Krastavcevic ◽  
Nevenka Mikovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pertussis Vaccine ◽  
Vaccination Coverage ◽  
Pertussis Toxin ◽  
Bordetella Pertussis ◽  
Bacterial Population ◽  
Mass Vaccination ◽  
Whole Cell

Mass vaccination has significantly reduced the incidence of pertussis, however, the disease is re-emerging, even in some countries with high vaccination coverage. In Serbia, whole cell pertussis vaccine was introduced in 1957. To monitor changes in bacterial population, 77 isolates collected from 1953 to 2011 were studied. The methods included serotyping of fimbriae (Fim), genotyping of pertactin (prn) and pertussis toxin S1 subunit (ptxA). A shift from ptxA2 to ptxA1 has been observed in isolates since the late of 1960s. In the period 1961-1979, the genotype ptxA1 became as common as genotype ptxA2. After that, during the period 1980-1989, the predominant ptx genotype was ptxA1. The reappearance of the ptxA2 allele followed an addition of the two strains harboring ptxA1 in the vaccine in 1985. The allele prn1 was predominant among the Serbian isolates, though prn3 and prn11 have been detected since 1981. The prn2 allele was only found in one strain isolated in 1984, two of the four strains isolated in 2000 and in three isolated strains from 2011. Serotype Fim2.3 disappeared before 1980 and serotype Fim2 became predominant thereafter. The results of this study indicate that the B. pertussis population in Serbia is different from other vaccinated populations and that this difference may be related to the vaccine used.

scholarly journals Genetic diversity of clinicalBordetella pertussisST2 strains in comparison with vaccine reference strains of India

2019 ◽  
Author(s):  
Naresh Chand Sharma ◽  
Shalini Anandan ◽  
Naveen Kumar Devanga Ragupathi ◽  
Dhiviya Prabaa Muthuirulandi Sethuvel ◽  
Karthick Vasudevan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Respiratory Tract ◽  
Sequence Type ◽  
Effective Vaccine ◽  
Complete Genomes ◽  
First Time ◽  
Genome Information ◽  
Reference Strains ◽  
Nose And Throat ◽  
Genome Degradation

AbstractPertussis is a highly contagious disease of the respiratory tract caused byBordetella pertussis, a bacteria that lives in the mouth, nose, and throat. Current study reports the highly accurate complete genomes of two clinicalB. pertussisstrains from India for the first time. The analysis revealed insertional elements flanked by IS481, which has been previously regarded as the important component for bacterial evolution. The twoB. pertussisclinical strains exhibited diversity through genome degradation when compared to whole-cell pertussis vaccine reference strains of India. These isolates harboured multiple genetic virulence traits and toxin subunits, which belonged to sequence type ST2. The genome information of Indian clinicalB. pertussisstrains will serve as a baseline data to decipher more information on the genome evolution, virulence factors and their role in pathogenesis for effective vaccine strategies.

Sign in / Sign up

Export Citation Format

Share Document