Genomic miscellany and allelic frequencies of Plasmodium falciparum msp-1, msp-2 and glurp in parasite isolates

Plasmodium falciparum, the main causative agent of malaria is an important public health vector in Khyber Pakhtunkhwa, Pakistan. Identification of the genetic diversity of malaria parasites can inform the intensity of transmission and identify potential deficiencies in malaria control programs. The aim of this study was to investigate the genetic diversity, allele frequencies and multiplicity of infection (MOI) of P. falciparum in Khyber Pakhtunkhwa, Pakistan. Methods: A total of 85 isolates from patients presenting to the local health centers with P. falciparum species were collected from 2017 to 2019. Parasite DNA was extracted from a total of 200 micro litter whole blood per patient using the Qiagen DNA extraction kit according to manufactures instructions. The polymorphic region of msp-1, msp-2 and glurp loci were genotyped by using nested polymerase chain reactions followed by gel electrophoresis for fragment analysis. Results: Genetic diversity and allelic frequencies of msp-1, msp-2 and glurp were identified in 85 blood samples. A total of 62 msp alleles were detected in which 30 for msp-1 and 32 for msp-2. For msp-1 the successful amplification occurred in (75/85) 88.23% isolates for msp-1, 78.9% (67/85) for msp-2 and 70% (60/85) for glurp. For msp-1, the K1 allelic family was predominant at 66.66% (50/75), followed by RO33 and MAD20. The frequency of samples having only K1, MAD20 and RO33 were 21.34% (16/75), 8% (6/75) and 10.67% (8/75) respectively. In msp-2, the FC27 allelic family was the most abundant with 70.14% (47/67) compared to 3D7 with 67.16% (45/67). Nine glurp RII region genotypes were identified. The overall mean multiplicity of infection was 2.6 with1.8 and 1.4 for msp-1 and msp-2 respectively while for glurp RII genes (MOI=1.03). There was no significant association between multiplicity of infection and age group (Spearman rank coefficient = 0.050; P = 0.6). There was significant correlation between MOI and parasite density for msp-2 allelic family. Conclusion: Our study showed high genetic diversity and allelic frequency with multiple clones of msp-1, msp-2 and glurp in P. falciparum isolates from malaria patients in Khyber Pakhtunkhwa Pakistan. In the present study the genotype data provided the valuable information which is essential for monitoring the impact of malaria eradication efforts in this region.

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Genetic diversity and genotype multiplicity of Plasmodium falciparum infection in patients with uncomplicated malaria in Chewaka district, Ethiopia

10.21203/rs.2.24526/v2 ◽

2020 ◽

Author(s):

Abdulhakim Abamecha ◽

Hassan El-Abid ◽

Daniel Yilma ◽

Wondimagegn Addisu ◽

Achim Ibenthal ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Malaria Control ◽

Allelic Variation ◽

Multiplicity Of Infection ◽

Chain Reactions ◽

Allelic Family ◽

Polymerase Chain Reactions ◽

Control Programmes ◽

Study Participants

Abstract Background: Genetic diversity in Plasmodium falciparum poses a major threat to malaria control and elimination interventions. Characterization of the genetic diversity of Plasmodium falciparum strains can be used to assess intensity of parasite transmission and identify potential deficiencies in malaria control programmes, which provides vital information to evaluating malaria elimination efforts. In this study, we investigated the P. falciparum genetic diversity and genotype multiplicity of infection in parasite isolates from cases with uncomplicated P. falciparum malaria in Southwest Ethiopia.Methods: A total of 80 P. falciparum microscopy and qPCR positive blood samples were collected from study participants aged six months to sixty years, who visited the health facilities during study evaluating the efficacy of arthemeter-lumefantrine from September-December, 2017. Polymorphic regions of the msp-1 and msp-2 were genotyped by nested polymerase chain reactions (nPCR) followed by gel electrophoresis for fragment analysis.Results: Of 80 qPCR-positive samples analyzed for polymorphisms on msp-1 and msp-2 genes, the efficiency of msp-1 and msp-2 gene amplification reactions with family-specific primers were 95 % and 98.8%, respectively. Allelic variation of 90% (72/80) for msp-1 and 86.2% (69/80) for msp-2 were observed. K1 was the predominant msp-1 allelic family detected in 20.8% (15/72) of the samples followed by MAD20 and RO33. Within msp-2, allelic family FC27 showed a higher frequency (26.1%) compared to IC/3D7 (15.9%). Ten different alleles were observed in msp-1 with 6 alleles for K1, 3 alleles for MAD20 and 1 allele for RO33. In msp-2, 19 individual alleles were detected with 10 alleles for FC27 and 9 alleles for 3D7. Eighty percent (80%) of isolates had multiple genotypes and the overall mean multiplicity of infection was 3.2 (95% CI: 2.87- 3.46). The heterozygosity indices were 0.43 and 0.85 for msp-1 and msp-2, respectively. There was no significant association between multiplicity of infection and age or parasite density.Conclusions: The study revealed high levels of genetic diversity and mixed-strain infections of P. falciparum populations in Chewaka district, Ethiopia, suggesting that both, endemicity level and malaria transmission remain high and that strengthened control efforts are needed in Ethiopia.

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Genetic diversity and genotype multiplicity of Plasmodium falciparum infection in patients with uncomplicated malaria in Chewaka district, Ethiopia

10.21203/rs.2.24526/v3 ◽

2020 ◽

Author(s):

Abdulhakim Abamecha ◽

Hassan El-Abid ◽

Daniel Yilma ◽

Wondimagegn Addisu ◽

Achim Ibenthal ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Malaria Control ◽

Allelic Variation ◽

Multiplicity Of Infection ◽

Chain Reactions ◽

Allelic Family ◽

Polymerase Chain Reactions ◽

Control Programmes ◽

Study Participants

Abstract Background Genetic diversity in Plasmodium falciparum poses a major threat to malaria control and elimination interventions. Characterization of the genetic diversity of P. falciparum strains can be used to assess intensity of parasite transmission and identify potential deficiencies in malaria control programmes, which provides vital information to evaluating malaria elimination efforts. This study investigated the P. falciparum genetic diversity and genotype multiplicity of infection in parasite isolates from cases with uncomplicated P. falciparum malaria in Southwest Ethiopia.Methods A total of 80 P. falciparum microscopy and qPCR positive blood samples were collected from study participants aged six months to sixty years, who visited the health facilities during study evaluating the efficacy of artemether-lumefantrine from September-December, 2017. Polymorphic regions of the msp-1 and msp-2 were genotyped by nested polymerase chain reactions (nPCR) followed by gel electrophoresis for fragment analysis.Results Of 80 qPCR-positive samples analysed for polymorphisms on msp-1 and msp-2 genes, the efficiency of msp-1 and msp-2 gene amplification reactions with family-specific primers were 95 % and 98.8%, respectively. Allelic variation of 90% (72/80) for msp-1 and 86.2% (69/80) for msp-2 were observed. K1 was the predominant msp-1 allelic family detected in 20.8% (15/72) of the samples followed by MAD20 and RO33. Within msp-2, allelic family FC27 showed a higher frequency (26.1%) compared to IC/3D7 (15.9%). Ten different alleles were observed in msp-1 with 6 alleles for K1, 3 alleles for MAD20 and 1 allele for RO33. In msp-2, 19 individual alleles were detected with 10 alleles for FC27 and 9 alleles for 3D7. Eighty percent (80%) of isolates had multiple genotypes and the overall mean multiplicity of infection was 3.2 (95% CI: 2.87- 3.46). The heterozygosity indices were 0.43 and 0.85 for msp-1 and msp-2, respectively. There was no significant association between multiplicity of infection and age or parasite density.Conclusions The study revealed high levels of genetic diversity and mixed-strain infections of P. falciparum populations in Chewaka district, Ethiopia, suggesting that both endemicity level and malaria transmission remain high and that strengthened control efforts are needed in Ethiopia.

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Genetic Polymorphisms of Plasmodium Falciparum Isolates From Melka-werer, North East Ethiopia Based on the Merozoite Surface Protein-2 (msp-2) Gene as a Molecular Marker

10.21203/rs.3.rs-116121/v1 ◽

2020 ◽

Author(s):

Hussein Mohammed Ali ◽

Ashenafi Assefa ◽

Melkie Chernet ◽

Yonas Wulataw ◽

Robert J Commons

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Molecular Marker ◽

Surface Protein ◽

Merozoite Surface Protein ◽

Arid Area ◽

Chain Reactions ◽

Allelic Family ◽

North East ◽

Semi Arid

Abstract Background: The characterization of parasite populations circulating in malaria endemic areas is necessary to evaluate the success of ongoing interventions and malaria control strategies. This study was designed to investigate the genetic diversity of Plasmodium falciparum isolates from the semi-arid area in North East Ethiopia, using the highly polymorphic merozoite surface protein-2 (msp2) gene as a molecular marker. Methods: Dried blood spot isolates were collected from patients with Plasmodium falciparum infection between September 2014 and January 2015 from Melka-Werer, North East Ethiopia. Parasite DNA was extracted and genotyped using allele-specific nested polymerase chain reactions for msp2. Results: 52 isolates were collected with msp2 identified in 41 (78.8%) isolates. Allele typing of the msp2 gene detected the 3D7/IC allelic family in 54% and FC27 allelic family in 46%. A total of 14 different msp2 genotypes were detected including 6 belonging to the 3D7/IC family and 8 to the FC27 family. Forty percent of isolates had multiple genotypes and the overall mean multiplicity of infections (MOI) was 1.2 (95%CI 0.96-1.42). The heterozygosity index was 0.50 for the msp2 locus. There was no difference in MOI between age groups. A negative correlation between parasite density and multiplicity of infection was found (p = 0.02).Conclusion: P. falciparum isolates from the semi-arid area of North East Ethiopia are mainly monoclonal with low MOI and limited genetic diversity in the study population.

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Genetic polymorphisms of Plasmodium falciparum isolates from Melka-Werer, North East Ethiopia based on the merozoite surface protein-2 (msp-2) gene as a molecular marker

10.21203/rs.3.rs-116121/v2 ◽

2021 ◽

Author(s):

Hussein Mohammed Ali ◽

Ashenafi Assefa ◽

Melkie Chernet ◽

Yonas Wulataw ◽

Robert J Commons

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Molecular Marker ◽

Surface Protein ◽

Merozoite Surface Protein ◽

Arid Area ◽

Chain Reactions ◽

Allelic Family ◽

North East ◽

Semi Arid

Abstract Background The characterization of parasite populations circulating in malaria endemic areas is necessary to evaluate the success of ongoing interventions and malaria control strategies. This study was designed to investigate the genetic diversity of Plasmodium falciparum isolates from the semi-arid area in North East Ethiopia, using the highly polymorphic merozoite surface protein-2 (msp2) gene as a molecular marker. Methods Dried blood spot isolates were collected from patients with P. falciparum infection between September 2014 and January 2015 from Melka-Werer, North East Ethiopia. Parasite DNA was extracted and genotyped using allele-specific nested polymerase chain reactions for msp2. Results 52 isolates were collected with msp2 identified in 41 (78.8%) isolates. Allele typing of the msp2 gene detected the 3D7/IC allelic family in 54% and FC27 allelic family in 46%. A total of 14 different msp2 genotypes were detected including 6 belonging to the 3D7/IC family and 8 to the FC27 family. Forty percent of isolates had multiple genotypes and the overall mean multiplicity of infections (MOI) was 1.2 (95%CI 0.96-1.42). The heterozygosity index was 0.50 for the msp2 locus. There was no difference in MOI between age groups. A negative correlation between parasite density and multiplicity of infection was found (p = 0.02).Conclusion Plasmodium falciparum isolates from the semi-arid area of North East Ethiopia are mainly monoclonal with low MOI and limited genetic diversity in the study population.

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Genetic polymorphisms of Plasmodium falciparum isolates from Melka-Werer, North East Ethiopia based on the merozoite surface protein-2 (msp-2) gene as a molecular marker

Malaria Journal ◽

10.1186/s12936-021-03625-1 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Hussein Mohammed ◽

Ashenafi Assefa ◽

Melkie Chernet ◽

Yonas Wuletaw ◽

Robert J. Commons

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Molecular Marker ◽

Surface Protein ◽

Merozoite Surface Protein ◽

Arid Area ◽

Chain Reactions ◽

Allelic Family ◽

North East ◽

Semi Arid

AbstractBackgroundThe characterization of parasite populations circulating in malaria endemic areas is necessary to evaluate the success of ongoing interventions and malaria control strategies. This study was designed to investigate the genetic diversity ofPlasmodium falciparumisolates from the semi-arid area in North East Ethiopia, using the highly polymorphic merozoite surface protein-2 (msp2) gene as a molecular marker.MethodsDried blood spot isolates were collected from patients withP. falciparuminfection between September 2014 and January 2015 from Melka-Werer, North East Ethiopia. Parasite DNA was extracted and genotyped using allele-specific nested polymerase chain reactions formsp2.Results52 isolates were collected withmsp2identified in 41 (78.8%) isolates. Allele typing of themsp2gene detected the 3D7/IC allelic family in 54% and FC27 allelic family in 46%. A total of 14 differentmsp2genotypes were detected including 6 belonging to the 3D7/IC family and 8 to the FC27 family. Forty percent of isolates had multiple genotypes and the overall mean multiplicity of infections (MOI) was 1.2 (95%CI 0.96–1.42). The heterozygosity index was 0.50 for themsp2locus. There was no difference in MOI between age groups. A negative correlation between parasite density and multiplicity of infection was found (p = 0.02).ConclusionPlasmodium falciparumisolates from the semi-arid area of North East Ethiopia are mainly monoclonal with low MOI and limited genetic diversity in the study population.

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Genetic diversity and genotype multiplicity of Plasmodium falciparum infection in patients with uncomplicated malaria in Chewaka district, Ethiopia

10.21203/rs.2.24526/v1 ◽

2020 ◽

Author(s):

Abdulhakim Abamecha ◽

Hassan El-Abid ◽

Daniel Yilma ◽

Wondimagegn Addisu ◽

Achim Ibenthal ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Malaria Control ◽

Multiplicity Of Infection ◽

Fragment Analysis ◽

Chain Reactions ◽

Polymerase Chain Reactions ◽

Control Programmes ◽

Study Participants

Abstract Background: Genetic diversity in Plasmodium falciparum poses a major threat to malaria control and elimination interventions. Characterization of the genetic diversity of Plasmodium falciparum strains can be used to assess intensity of parasite transmission and identify potential deficiencies in malaria control programmes, which provides vital information to evaluating malaria elimination efforts. In this study, we investigated the P. falciparum genetic diversity and genotype multiplicity of infection in parasite isolates from cases with uncomplicated P. falciparum malaria in Southwest Ethiopia.Methods: A total of 80 P. falciparum microscopy and qPCR positive blood samples were collected from study participants aged six months to sixty years, who visited the health facilities during the evaluation of a therapeutic efficacy study of arthemeter-lumefantrine from September-December, 2017. Polymorphic regions of the msp-1 and msp-2 were genotyped by nested polymerase chain reactions (nPCR) followed by gel electrophoresis for fragment analysis.Results: Of 80 qPCR-positive samples analyzed for polymorphisms on msp-1 and msp-2 genes, the efficiency of msp-1 and msp-2 gene amplification reactions with family-specific primers were 95 % and 98.8%, respectively. A total of 29 msp alleles (10 for msp-1and 19 for msp-2) were detected. In msp-1, K1 was the predominant allelic family detected in 47.7% (42/88) of the samples followed by Mad20 and RO33. For msp-2, the frequency of FC27 and IC/3D7 were 77% (57/74) and 76% (56/74), respectively. Eighty percent (80%) of isolates had multiple genotypes and the overall mean multiplicity of infection was 3.2 (95% CI: 2.87- 3.46). The heterozygosity index was 0.43, and 0.85 for msp-1 and msp-2, respectively. There was no significant association between multiplicity of infection and age or parasite density.Conclusions: The study revealed high levels of genetic diversity and mixed-strain infections of P. falciparum populations in Chewaka district, Ethiopia; reflecting both the endemicity level and malaria transmission remained high and more strengthened control efforts are needed in Ethiopia.

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Quantifying the effect of human practices on S. cerevisiae vineyard metapopulation diversity

Scientific Reports ◽

10.1038/s41598-020-73279-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Marine Börlin ◽

Olivier Claisse ◽

Warren Albertin ◽

Franck Salin ◽

Jean-Luc Legras ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Genetic Diversity ◽

Farming System ◽

Conventional Farming ◽

Global Effect ◽

High Genetic Diversity ◽

Tight Connection ◽

Human Practices ◽

The Impact ◽

Very High

Abstract Saccharomyces cerevisiae is the main actor of wine fermentation but at present, still little is known about the factors impacting its distribution in the vineyards. In this study, 23 vineyards and 7 cellars were sampled over 2 consecutive years in the Bordeaux and Bergerac regions. The impact of geography and farming system and the relation between grape and vat populations were evaluated using a collection of 1374 S. cerevisiae merlot grape isolates and 289 vat isolates analyzed at 17 microsatellites loci. A very high genetic diversity of S. cerevisiae strains was obtained from grape samples, higher in conventional farming system than in organic one. The geographic appellation and the wine estate significantly impact the S. cerevisiae population structure, whereas the type of farming system has a weak global effect. When comparing cellar and vineyard populations, we evidenced the tight connection between the two compartments, based on the high proportion of grape isolates (25%) related to the commercial starters used in the cellar and on the estimation of bidirectional geneflows between the vineyard and the cellar compartments.

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SIGNIFICANT LINKAGE DISEQUILIBRIUM AND HIGH GENETIC DIVERSITY IN A POPULATION OF PLASMODIUM FALCIPARUM FROM AN AREA (REPUBLIC OF THE CONGO) HIGHLY ENDEMIC FOR MALARIA

American Journal of Tropical Medicine and Hygiene ◽

10.4269/ajtmh.2003.68.345 ◽

2003 ◽

Vol 68 (3) ◽

pp. 345-349 ◽

Cited By ~ 28

Author(s):

P. DURAND ◽

M. TIBAYRENC ◽

F. RENAUD ◽

M.C. LECLERC ◽

B. OURY ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Linkage Disequilibrium ◽

Significant Linkage Disequilibrium ◽

High Genetic Diversity ◽

Republic Of The Congo ◽

Significant Linkage

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Prevalence and Genetic Diversity of Arcobacter in Food Products in the North of Spain

Journal of Food Protection ◽

10.4315/0362-028x.jfp-13-014 ◽

2013 ◽

Vol 76 (8) ◽

pp. 1447-1450 ◽

Cited By ~ 22

Author(s):

BARBARA NIEVA-ECHEVARRIA ◽

IRATI MARTINEZ-MALAXETXEBARRIA ◽

CECILIA GIRBAU ◽

RODRIGO ALONSO ◽

AURORA FERNÁNDEZ-ASTORGA

Keyword(s):

Public Health ◽

Genetic Diversity ◽

Basque Country ◽

Food Products ◽

High Genetic Diversity ◽

The North ◽

Arcobacter Butzleri ◽

North Of Spain ◽

The Impact ◽

The Relationship

The bacterial contamination of food products can cause serious public health problems. Interest in Arcobacter contamination has increased due to the relationship between these bacteria and human enteritis. We studied the prevalence and genetic diversity of Arcobacter species at the retail level in the province of Alava in Basque Country, Spain. The results showed a high genetic diversity and indicated the regular presence of the main Arcobacter spp. associated with human enteric illness in food products. Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii were detected with an overall prevalence close to 40% and were isolated from 15 (42.8%) fresh cow's milk samples, 12 (73.3%) shellfish samples, 11 (55%) chicken samples, 2 (10%) pork samples, and 1 (5%) beef sample. The results indicate the need to investigate the impact of Arcobacter spp. on public health.

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