Genetic variation of Echinococcus spp. in yaks and sheep in the Tibet Autonomous Region of China based on mitochondrial DNA

Whole-genomic comparison reveals complex population dynamics and parasitic adaptation of Echinococcus granulosus sensu stricto

Cystic echinococcosis (CE), caused by Echinococcus granulosus sensu stricto (s.s.), poses a substantial risk to both humans and domestic animals globally. Here, we compared the whole genomes of 111 E. granulosus s.s. samples from China. Genomic variation data revealed frequent cross-fertilization in the hermaphroditic E. granulosus. The G1 and G3 genotypes represent distinct mitochondrial lineages, while showing no differentiation in the nuclear genome, suggesting mito-nuclear discordance caused by historical geographic separation and subsequent fusion. Population structure, demographic history, and gene flow among populations reflected the transmission route of E. granulosus s.s. from the Middle East to Qinghai-Xizang Plateau through the migration of nomadic people, followed by introgression during secondary contact. Genomic variations highlighted selection signatures within the genome prone to balancing selection, particularly impacting genes encoding membrane-related proteins, representing a potential evolutionary strategy for adaptation to parasitic life. Balancing selection pressure on the gene-coding sodium/bile acid cotransporter led to its high level of genetic stability, which may play a crucial role in the survival and development of E. granulosus during the parasitic stage, making it a potential drug target for the treatment of CE. Meanwhile, other genomic regions under strong balancing selection may provide potential targets for protective immunity. These findings offer valuable insights into the complex dynamics and adaptive evolution of E. granulosus s.s. in China.IMPORTANCEEchinococcus granulosus sensu stricto (s.s.) is the primary cause of cystic echinococcosis (CE), a parasitic disease affecting humans and livestock with significant health and economic impacts. Previous studies on this parasite relied on mitochondrial DNA to classify its genotypes and understand its genetic diversity. However, these studies cannot capture the full complexity of its evolutionary dynamics and adaptation strategies. Our research employs comprehensive genome-wide sequencing, offering a more nuanced view of its genetic landscape. We discovered that cross-fertilization appears to be a prevalent reproductive strategy in the hermaphroditic E. granulosus, underpinning the observed deep mitochondrial divergence between genotypes G1 and G3, as well as gene flow among populations. The transmission history of E. granulosus s.s. in China and its widespread genetic mixing were likely facilitated by the migrations of nomadic peoples. Furthermore, we identified genes under balancing selection, including the gene involved in the uptake of host bile acids, which play a crucial role in the parasite's survival and development, potentially offering new targets for intervention. Our research advances the understanding of the genetic diversity and evolutionary strategies of E. granulosus, laying the foundation for improved control measures of CE.

Zoonotic Echinococcus granulosus sensu lato genotypes G6 and G7: new insights from the global mitogenome analysis

Cystic echinococcosis is a severe zoonotic disease caused by different species and genotypes belonging to the Echinococcus granulosus sensu lato (s.l.) complex. Among these, genotypes G6 and G7 are the second most common cause of human cystic echinococcosis. One of the very first steps towards understanding the epidemiology of G6 and G7 is to study their genetic and host diversity, population structure and phylogenetic relationships. For this, we sequenced near-complete mitochondrial genomes (12,850-12,856 bp) of 72 new G6 and G7 samples from eight countries and six host species, including humans. By adding 103 sequences from previous studies, the total dataset for further analyses comprised of 175 sequences from 20 countries and seven host species. This is the most comprehensive global mitogenome study of Echinococcus granulosus s.l. G6 and G7 to date. The results of this work revealed: (i) a new divergent haplogroup G6b from Mongolia; (ii) the subdivision of genotype G6 into two major haplogroups: G6a (the nominal haplogroup) and G6b (the Mongolian haplogroup); (iii) highly divergent haplotypes of G6 and G7; (iv) the first molecularly confirmed findings of genotype G7 in camel; (v) genotype G7 in sheep - a rare species for G7; (vi) the importance of using long DNA sequences in phylogenetic analysis.

Assembly, Annotation, and Comparative Analysis of Mitochondrial Genomes in Trichoderma

Trichoderma is a widely studied ascomycete fungal genus, including more than 400 species. However, genetic information on Trichoderma is limited, with most species reporting only DNA barcodes. Mitochondria possess their own distinct DNA that plays a pivotal role in molecular function and evolution. Here, we report 42 novel mitochondrial genomes (mitogenomes) combined with 18 published mitogenomes of Trichoderma. These circular mitogenomes exhibit sizes of 26,276-94,608 bp, typically comprising 15 core protein-coding genes (PCGs), 2 rRNAs, and 16-30 tRNAs; however, the number of endonucleases and hypothetical proteins encoded in the introns of PCGs increases with genome size enlargement. According to the result of phylogenetic analysis of the whole mitogenome, these strains diverged into six distinct evolutionary branches, supported by the phylogeny based on 2830 single-copy nuclear genes. Comparative analysis revealed that dynamic Trichoderma mitogenomes exhibited variations in genome size, gene number, GC content, tRNA copy, and intron across different branches. We identified three mutation hotspots near the regions encoding nad3, cox2, and nad5 that caused major changes in the mitogenomes. Evolutionary analysis revealed that atp9, cob, nad4L, nad5, and rps3 have been influenced by positive selection during evolution. This study provides a valuable resource for exploring the important roles of the genetic and evolutionary dynamics of Trichoderma mitogenome in the adaptive evolution of biocontrol fungi.

First report of Echinococcus granulosus genotype 1 in a wild boar (Sus scrofa) from China

Echinococcosis is a worldwide disease endemic to the western region of China. In 2023, echinococcosis was detected in one of 27 wild boars (Sus scrofa) in Yili Prefecture, Xinjiang, northwestern China. Histopathological staining and full sequence mitochondrial (mt) analysis were used to determine the infection genotype. Echinococcus granulosus was detected in the wild boar liver, and the cystic lesion characteristics indicated the E. granulosus genotype (G1). This case is the first confirmation of wild boar serving as a transmitter for the G1 genotype of E. granulosus within China. These findings suggest that surveillance is needed to assess the risk of E. granulosus sensu lato transmission to humans and wild animals.

First Case Report of Cystic Echinococcosis Caused by G7 Genotype Echinococcus intermedius Confirmed by Genetic Sequencing - Southern China, December 2023

WHAT IS ALREADY KNOWN ABOUT THIS TOPIC?

Echinococcosis exhibits a global distribution. In China, the primary endemic area is the northwest region. In December 2023, we documented a case of echinococcosis in an individual lacking any travel or residential history in endemic regions.

WHAT IS ADDED BY THIS REPORT?

This is the first laboratory-confirmed case of hepatic echinococcosis reported in Guangdong Province, associated with the G7 genotype of Echinococcus granulosus (E. granulosus). The most probable mode of transmission is a local infection resulting from E. granulosus introduced from endemic regions.

WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE?

As the circulation of agricultural products increases, it is essential to enhance the quarantine and management of livestock from epidemic areas to prevent and control the spread of echinococcosis to non-epidemic regions.

Molecular phylogenetic analysis of Echinococcus granulosus sensu lato infecting sheep in Italy

Cystic Echinococcosis (CE), caused by the larval form of Echinococcus granulosus sensu lato, is a neglected zoonosis still threatening public health worldwide. In Italy different epidemiological scenarios were reported depending on the geographical area and associated socio-economic activities. Although in northern Italy the occurrence of E. granulosus is considered sporadic, in the southern regions and, particularly in Sardinia, CE prevalence reaches high levels. We analysed CE cysts collected from infected sheep from various areas of mainland Italy and the Sardinia island, with the main objective to investigate intergenotypic and intragenotypic variations at national level. CE cysts were collected from slaughtered sheep following post mortem inspection at local abattoirs. Total genomic DNA was extracted and amplification and sequencing of the partial mitochondrial genes nad5 and cox1 were performed. A Bayesian phylogenetic tree was estimated on a nad5 dataset (n = 260) composed of E. granulosus samples from this study (n = 126) and all the nad5 haplotypes available in GenBank (n = 134). In addition, haplotype network, diversity and neutrality analysis were performed on nad5 and cox1 sequences of Italian origin obtained in this study. E. granulosus sensu stricto (s.s.) was found to be the only Echinococcus species infecting sheep in Italy, mainly represented by G1 genotype (76 %) and, to a lower extent, by G3 genotype (24 %). Phylogenetic analyses revealed 40 nad5 and 33 cox 1 haplotypes, and the presence of two founder haplotypes, belonging to G1 and G3 genotype, showing 100 % similarity with DNA sequences from different geographic regions. The lack of geographical segregation, high haplotype and low nucleotide diversity coupled with significant negative values of Tajima's D and Fu's Fs observed in this study indicated high genetic variation and demographic expansion of E. granulosus s.s. in Italy.

Study on the genotypes of Echinococcus granulosus in yaks and sheep from Langkazi County in Tibet Autonomous Region of China based on mitochondrial cox1 and nad1

To determine the genotypes of the epidemic strains of Echinococcus granulosus in livestock in Tibet, samples of E. granulosus cysts were collected from 11 yaks and 62 sheep. Genomic DNA was extracted from these samples, and gene fragments of mitochondrial cytochrome c oxidase subunit I (cox1) and NADH dehydrogenase subunit I (nad1) were amplified by PCR and sequenced. DNASTAR and MAGA7.0 were employed for homology analysis and phylogenetic tree construction. Echinococcus granulosus cysts were detected in 56.2% (41/73) of the samples screened. Of these, 63.4% (26/41) were identified as E. granulosus G1 genotype (common sheep strain), 24.4% (10 /41) as G3 genotype (buffalo strain), and 12.2% (5/41) were G6 genotype (camel strain). The study concludes that yaks and sheep in Langkazi county, Tibet, carry three E. granulosus genotypes (G1, G3, and G6), with the G1 genotype the predominant genotype in the region. This study clarifies the distribution of E. granulosus genotypes, providing genetic data and insight for the surveillance and prevention of echinococcosis.

First report of Echinococcus ortleppi and E. canadensis (genotype G6) from southern Punjab, Pakistan and a global overview on genetic structure and host adaptation of E. ortleppi

Cystic echinococcosis (CE), caused by Echinococcus granulosus sensu lato, is a neglected tropical disease known mainly for its zoonotic nature. CE is endemic to Pakistan, however, the disease is not given due consideration and millions of people remain at health risk. This study was undertaken to assess the species and genotypes of E. granulosus sensu lato in sheep, buffaloes and cattle, brought to slaughterhouses of two major cities (Multan and Bahawalpur) of south Punjab, Pakistan. A total of 26 hydatid cyst specimens were characterized through complete cox1 mitochondrial gene (1609 bp) sequencing. Species and genotypes of E. granulosus sensu lato discovered in the southern Punjab consisted of E. granulosus sensu stricto (n =21), E. ortleppi (n=4) and E. canadensis G6 genotype (n=1). Of E. granulosus s.s. isolates, the genotype G3 was predominantly involved in causing infections to the livestock of this region. Since all of these species are zoonotic, wide and effective surveillance studies are required to ascertain the risks to human population in Pakistan. Additionally, a global overview on cox1 phylogenetic structure of E. ortleppi was carried out. Despite the widespread occurrence, the species is mostly limited to the southern hemisphere. The highest burden has been reported in the South America (62.15%) and Africa (28.44%) and by far the most common host is cattle, accounting for >90% of cases.

Update on the genetic diversity and population structure of Echinococcus granulosus in Gansu Province, Tibet Autonomous Region, and Xinjiang Uygur Autonomous Region, Western China, inferred from mitochondrial cox1, nad1, and nad5 sequences

The identification of additional Echinococcus granulosus sensu lato (s.l.) complex species/genotypes in recent years raises the possibility that there might be more variation among this species in China than is currently understood. The aim of this study was to explore intra- and inter-species variation and population structure of Echinococcus species isolated from sheep in three areas of Western China. Of the isolates, 317, 322, and 326 were successfully amplified and sequenced for cox1, nad1, and nad5 genes, respectively. BLAST analysis revealed that the majority of the isolates were E. granulosus s.s., and using the cox1, nad1, and nad5 genes, respectively, 17, 14, and 11 isolates corresponded to Elodea canadensis (genotype G6/G7). In the three study areas, G1 genotypes were the most prevalent. There were 233 mutation sites along with 129 parsimony informative sites. A transition/transversion ratio of 7.5, 8, and 3.25, respectively, for cox1, nad1, and nad5 genes was obtained. Every mitochondrial gene had intraspecific variations, which were represented in a star-like network with a major haplotype with observable mutations from other distant and minor haplotypes. The Tajima's D value was significantly negative in all populations, indicating a substantial divergence from neutrality and supporting the demographic expansion of E. granulosus s.s. in the study areas. The phylogeny inferred by the maximum likelihood (ML) method using nucleotide sequences of cox1-nad1-nad5 further confirmed their identity. The nodes assigned to the G1, G3, and G6 clades as well as the reference sequences utilized had maximal posterior probability values (1.00). In conclusion, our study confirms the existence of a significant major haplotype of E. granulosus s.s. where G1 is the predominant genotype causing of CE in both livestock and humans in China.

The polymorphic analysis of cox1 and cob genes of Echinococcus granulosus in the Ngari region of Tibet in China

Cystic echinococcosis (CE) is an important zoonotic parasitic disease caused by Echinococcus granulosus (E. granulosus). CE seriously threatens human health and the development of animal husbandry. The Ngari region is one of the world's highest endemic regions for CE, while genetic polymorphisms of E. granulosus were unclear. Paraffin slices of liver Cyst were collected from seventy-nine surgical patients with echinococcosis in the Ngari region. DNA was extracted from samples. The cox1 and cob genes of mitochondrial DNA of E. granulosus were simultaneously amplified and sequenced. The sequencing results were compared with the standard sequence (KU925397.1and HF947574.1). Phylogenetic trees and the haplotype network of cob and cox1 genes were constructed and analyzed genotypes of E. granulosus isolated from humans in the Ngari Region of Tibet. Out of 79 hydatid cyst samples collected from surgery patients, 60 isolates were identified as G1/ G3, and two isolates were identified as G6/ G7. Analysis of the cob/ cox1 genes revealed 9/7 mutations resulting in 8/6 haplotypes, respectively. The cob and cox1 neutrality indices computed by Tajima's D and Fu's Fs tests showed high negative values in Echinococcus granulosus sensu stricto (E. granulosus s. s.). The result suggested that E. granulosus in the Ngari region experienced population expansion or a negative selection. We found that G1/ G3 was still the main genotype, and G6/ G7 was found occasionally in humans of the Ngari region. Therefore, we recommend future surveys and control efforts to investigate G1/ G3 and G6/ G7 transmission in the Ngari region.

Cystic echinococcosis in donkeys in eastern Africa

Cystic echinococcosis (CE) is endemic in humans and domestic animals in eastern Africa. All the species of the Echinococcus granulosus sensu lato complex have been reported in this region except for E. equinus, possibly due to the small number of studies involving equids. This study reports the frequency of different Echinococcus species in donkeys from eastern Africa. A total of 5961 donkeys were examined during meat inspection in 3 slaughterhouses in Kenya. Identification of Echinococcus spp. was achieved through polymerase chain reaction-restriction fragment-length polymorphism and sequencing of the mitochondrial nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 1 gene. The prevalence of CE was 5.7% (337/5961). The 263 genotyped cysts belonged to E. equinus (n = 163), E. granulosus sensu stricto (n = 70), E. canadensis (G6/7) (n = 26) and E. ortleppi (n = 4). One donkey harboured a metacestode of Spirometra theileri. All E. equinus cases, except 2, originated from southern Ethiopia, whereas the other species were more evenly distributed across the study area. Most of the cysts belonging to E. equinus were fertile (111/163), while those of the other species were non-fertile. This is the first report of Echinococcus spp. in donkeys from sub-Saharan Africa and the first confirmation of E. equinus in East Africa. The frequent fertility of E. equinus cysts in donkeys affirms their suitability as intermediate hosts of this species, while low frequency and cyst fertility suggest a marginal role of donkeys in the transmission of E. granulosus s. s., E. canadensis (G6/7) and E. ortleppi.

Food-borne zoonotic echinococcosis: A review with special focus on epidemiology

Echinococcosis is a neglected, WHO-listed cyclozoonotic parasitic disease that is caused by a number of species belonging to the genus Echinococcus. This disease is widespread across the globe, resulting in heavy economic losses for farmers and cystic disease in aberrant human hosts. This review paper briefly discussed taxonomy, a brief history, the magnitude of economic losses, host spectrum and life cycle, risk factors, and clinical manifestations. Furthermore, the copro- and sero-ELISA-based prevalence of echinococcosis on different continents was summarized. Finally, the authors analyzed the frequency and use of molecular epidemiology in the taxonomy of Echinococcus species based on molecular markers. This review will serve as a quick reference to Echinococcus.

Genetic diversity and haplotype analysis of yak and sheep echinococcal cysts isolates from the mitochondrial cox1 gene in parts of Tibet, China

Echinococcosis, also known as hydatid disease, is caused by the metacestode stage of the species cluster Echinococcus granulosus sensu lato (E. granulosus s.l.). It is almost widespread worldwide, especially in countries and regions dominated by animal husbandry. It is a major parasitic disease that seriously endangers human health, public health safety, environmental safety, and the development of animal husbandry production in western China. In this study, the mitochondrial cox1 gene was used to analyze the genetic diversity and haplotype of bovine and sheep echinococcal cysts isolated in Tibet. Echinococcus granulosus sensu stricto (E. granulosus s.s., G1, G3) was still the dominant species in the infected samples of yak and sheep in some parts of Tibet. Through haplotype analysis, Hap_1 was deemed the dominant haplotype, 14 of the 20 haplotypes were similar to the reference sequence previously published in Genbank, and the rest of the 6 haplotypes were found for the first time. Through Tajima's D value, neutral test Fu's Fs analysis, and haplotype network map, it can be concluded that Echinococcus population expansion has occurred in Xigaze, Tibet. This study provides basic data for understanding the genetic characteristics, epidemiology, and control of echinococcosis in this area.

Echinococcus spp. and genotypes infecting humans in Tibet Autonomous Region of China: a molecular investigation with near-complete/complete mitochondrial sequences

Background

Molecular markers are essential to identify Echinococcus species and genotypes in areas with multiple Echinococcus species to understand their epidemiology and pathology. Tibet Autonomous Region (TAR) is one of the areas worst hit by echinococcosis. However, molecular epidemiology is still missing among echinococcosis patients in TAR. This research explored the Echinococcus species and genotypes infecting humans in TAR and the population diversity and the possible origin of G1 in TAR.

Methods

Cyst samples were collected in one echinococcosis-designated hospital in TAR. Echinococcus species and genotypes were identified through a maximum-likelihood approach with near-complete/complete mtDNA using IQ-TREE. Phylogenetic networks were built with PopART, and the phylogeographical diffusion pattern was identified using a Bayesian discrete phylogeographic method.

Results

Using phylogenetic trees made with near-complete/complete mtDNA obtained from 92 cysts from TAR patients, the Echinococcus species and genotypes infecting humans in TAR were identified as Echinococcus granulosus (s.s.) G1 (81, 88.04%), accounting for the majority, followed by G6 of the E. canadensis cluster (6, 6.52%), E. granulosus (s.s.) G3 (3, 3.26%), and E. multilocularis (2, 2.17%). An expansion trend and a possible recent bottleneck event were confirmed among the G1 samples in TAR. Adding the other near-complete mtDNA of G1 samples globally from the literature, we identified the possible phylogeographic origin of the G1 samples in TAR as Turkey.

Conclusions

Using near-complete/complete mtDNA sequences of Echinococcus spp. obtained from echinococcosis patients, a variety of Echinococcus species and genotypes infecting humans throughout TAR were identified. As far as we know, this is the first comprehensive molecular investigation of Echinococcus species and genotypes infecting humans throughout TAR. We identified, for the first time to our knowledge, the possible origin of the G1 in TAR. We also enriched the long mtDNA database of Echinococcus spp. and added two complete E. multilocularis mtDNA sequences from human patients. These findings will improve our knowledge of echinococcosis, help to refine the targeted echinococcosis control measures, and serve as a valuable baseline for monitoring the Echinococcus species and genotypes mutations and trends of the Echinococcus spp. population in TAR.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05199-6.

Genetic structure and phylogeography of Echinococcus granulosus sensu stricto genotypes G1 and G3 in Pakistan and other regions of the world based on nad5 gene

Pakistan is a neglected endemic focus for Echinococcus granulosus sensu lato, a zoonotic parasite species complex with the ability to infect wide spectrum of hosts. Wide gaps exist in literature for etiological agents of cystic echinococcosis (CE) in Pakistan due to a very low number of studies on identifying the exact genotypes involved in epidemiological manifestation of this disease. Focusing on transmission patterns and epidemiological dynamics, this study aimed at investigating infective genotypes among the cattle population of south Punjab, Pakistan, employing a mitochondrial marker nad5 (680 bp). Nucleotide sequences retrieved from 28 hydatid cyst isolates displayed considerable intraspecific variation revealing the existence of G3 and G1 strains of Echinococcus granulosus sensu stricto. The G3 genotype emerged as the predominant cause (78.57%) of hydatidosis in cattle. Apart from this, to understand phylogeographical relations, homologous nucleotide sequences of the partial nad5 gene from six major regions of the world were employed in the population genetics analysis to have an insight into genetic variability and demographics of G3 genotype in particular. Diversification of G3 and its haplotypes in Pakistan (n = 11) and other regions of the world (India, Iran, Turkey, Italy and France) was demonstrated. It was further demonstrated that the South Asian population (Pakistan and India) was highly differentiated from the other regions. It could, therefore, be speculated that G3 is diverging and expanding its population with South Asia as the main focal point.

DEVELOPMENT OF A TRIPLEX REAL-TIME PCR ASSAY TO DETECT ECHINOCOCCUS SPECIES IN CANID FECAL SAMPLES

Echinococcosis is a zoonotic disease with great significance to public health, and appropriate detection and control strategies should be adopted to mitigate its impact. Most cases of echinococcosis are believed to be transmitted by the consumption of food and/or water contaminated with canid stool containing Echinococcus spp. eggs. Studies assessing Echinococcus multilocularis, Echinococcus granulosus sensu stricto, and Echinococcus shiquicus coinfection from contaminated water-derived, soil-derived, and food-borne samples are scarce, which may be due to the lack of optimized laboratory detection methods. The present study aimed to develop and evaluate a novel triplex TaqMan-minor groove binder probe for real-time polymerase chain reaction (rtPCR) to simultaneously detect the 3 Echinococcus spp. mentioned above from canid fecal samples in the Qinghai-Tibetan Plateau area (QTPA). The efficiency and linearity of each signal channel in the triplex rtPCR assay were within acceptable limits for the range of concentrations tested. Furthermore, the method was shown to have good repeatability (standard deviation ≤0.32 cycle threshold), and the limit of detection was estimated to be 10 copies plasmid/μl reaction. In summary, the evaluation of the present method shows that the newly developed triplex rtPCR assay is a highly specific, precise, consistent, and stable method that could be used in epidemiological investigations of echinococcosis.

Advances in research on echinococcoses epidemiology in China

Echinococcoses are serious zoonotic diseases in China's vast, western and north-western pastoral areas that has one of the highest prevalence in the world. The two most common forms, cystic echinococcosis (CE) and alveolar echinococcosis (AE), are co-epidemic in some areas causing a grave threat to people's health and economic development. Echinococcus spp. are transmitted through domestic, sylvatic and mixed cycles involving many kinds of host. Successful transmission requires a favourable environment for the growth of the parasites and survival of their eggs, while the unique customs and religious beliefs in the endemic areas pose a challenge to the prevention and control of these parasites. Based on previous epidemiological studies, this paper reviews the particular factors affecting the transmission of Echinococcus parasites in China, with a focus on biological (parasite genotype and the species, age, sex and density of hosts), environmental (landscape and climate) and social (age, gender, ethnicity, education, occupation, life style, cultural customs, living conditions and hygiene practices of humans in the endemic areas). These three factors interact with each other and jointly determine the parasites' transmission intensity, the study of which supports the formulation of the strategies and measures that are significant for control of these infections.

Echinococcus shiquicus in Qinghai-Tibet plateau: population structure and confirmation of additional endemic areas

Echinococcus shiquicus is currently limited to the Qinghai–Tibet plateau, a large mountainous region in China. Although the zoonotic potential remains unknown, progress is being made on the distribution and intermediate host range. In this study, we report E. shiquicus within Gansu and Qinghai provinces in regions located not only around the central areas but also the southeast edge of the plateau and describe their genetic relationship with previous isolates from the plateau. From 1879 plateau pikas examined, 2.39% (95% CI 1.79–3.18) were infected with E. shiquicus. The highest prevalence of 10.26% (4.06–23.58) was recorded in Makehe town, Qinghai province. Overall the prevalence was marginally higher in Qinghai (2.5%, CI 1.82–3.43) than in Gansu (2%, CI 1.02–3.89). The cox1 and nad1 genes demonstrated high and low haplotype and nucleotide diversities, respectively. The median-joining network constructed by the cox1–nad1 gene sequences demonstrated a star-like configuration with a median vector (unsampled haplotype) occupying the centre of the network. No peculiar distinction or common haplotype was observed in isolates originating from the different provinces. The presence of E. shiquicus in regions of the southeast and northeast edges of the Qinghai–Tibet plateau and high genetic variation warrants more investigation into the haplotype distribution and genetic polymorphism by exploring more informative DNA regions of the mitochondrial genome to provide epidemiologically useful insight into the population structure of E. shiquicus across the plateau and its axis.

The Molecular Epidemiology of Echinococcus Infections

Molecular epidemiology (ME) is the application of molecular tools to determine the causation of disease. With infectious diseases, such as echinococcosis, this applies to identifying and characterising the aetiological agents and elucidating host range. Such an approach has been very successful with the causative agents of echinococcosis, species of Echinococcus, initially by providing a workable and practical taxonomy and subsequently determining transmission patterns in endemic areas. This review summarises the taxonomy and nomenclature of species of Echinococcus and provides an update on ME investigations of the ecology of Echinococcus transmission, particularly in areas where more than one species of Echinococcus is maintained in cycles of transmission that may interact.

Complete mitochondrial genome analysis confirms the presence of Echinococcus granulosus sensu lato genotype G6 in Nigeria

Cystic echinococcosis (CE) is common in Africa especially in northern and eastern countries where it is highly prevalent and mainly caused by Echinococcus granulosus sensu stricto and Echinococcus granulosus sensu lato (G6/7). In a recent epidemiological survey in Nigeria, the G6/7 genotype was reportedly responsible for the majority of CE infection. In this study, considering the taxonomic challenges of the G6/7 genotype and the limitation of the cox1/nad1 genes in resolving the differences, we sequenced the complete mitochondrial (mt) genome of seven larval isolates of E. granulosus s.l. G6/7 haplotypes recently reported in Nigeria to correctly assign them to either (G6/7) genotype and to understand the mt genome variation with isolates from other geographical regions. On analysis, a total of 13,731 bp in a covalently closed circular molecule were realized. The total mt length was ≥10 bp than previously reported G6 and G7 mt genome sequences. Also, the median-joining network and phylogeny based on the 12 protein-coding sequences correctly identified them as G6 genotype. Since longer mt genome sequences have shown some advantage over individual genes in resolving taxonomic challenges, we confirm that the genotype responsible for the majority of CE infection in livestock in Nigeria is the G6 genotype and the availability of the complete mt genome from different Nigerian intermediate hosts will prove useful in future genetic population studies across the country and the West African sub-region.