Antimicrobial resistance and molecular characteristics of Neisseria gonorrhoea isolates in Ghana.

Introduction: Gonorrhoea is a disease associated with humans and caused by Neisseria gonorrhoea. N. gonorrhoea's ability to evolve and evade various treatment regimens can lead to untreatable gonorrhoea. In the absence of a viable vaccine and a national database on the antimicrobial resistance (AMR) and molecular characteristics of N. gonorrhoea, and with reliance on a syndromic management regime, continuous national antimicrobial resistance surveillance and molecular characterization of N. gonorrhoea remain imperative. Only two gonococcal studies have described N. gonorrhoea's molecular characteristics linked to AMR in Ghana. Methods: Secondary N. gonorrhoea isolates (n=4) were collected from two metropolises in Ghana: Tamale in the northern sector (n=1) and Accra in the southern sector (n=3). The isolates were confirmed and characterized using polymerase chain reaction (PCR) targeting the porB and tbpB genes, and the disc diffusion method was used to evaluate AMR. N. gonorrhoea multi-antigen sequence typing (NG-MAST) and porin B (porB) gene sequence analyses were employed to reveal the molecular epidemiology and evolutionary trajectory, respectively. Results: All four isolates showed resistance to at least four of the tested antibiotics. One isolate showed resistance to all seven antibiotics, i.e. ceftriaxone, azithromycin, ciprofloxacin, tetracycline, erythromycin, togamycin and penicillin. NG-MAST typing revealed isolate S3 (MZ313864) as ST211. The locus of S2 (MZ313863) (transferrin-binding protein B; tbpB) was identified as tbpB1844, and its porB locus, as porB6412, with only 4 closely related variants but with 15 nucleotide differences. However, its sequence type does not exist. The porB analysis identified isolate S3 (MZ313864) to be found globally, while S2 (MZ313863) is unique to this study. Discussion: Despite the small number of isolates tested, this study recorded multidrug resistance and previously unknown gonococcal variants based on porB gene. Additionally, the molecular typing schemes revealed a disparity between NG-MAST and the National Center for Biotechnology Information (NCBI) platforms. There is a need for continuous gonococcal AMR and molecular surveillance in Ghana to contribute to the global efforts to describe circulating strains and support proper application of the syndromic management regime to gonorrhoea.

High genetic diversity of Echinococcus canadensis G10 in northeastern Asia: is it the region of origin?

Echinococcus canadensis consists of 4 genotypes: G6, G7, G8 and G10. While the first 2 predominantly infect domestic animals, the latter are sylvatic in nature involving mainly wolves and cervids as hosts and can be found in the northern temperate to Arctic latitudes. This circumstance makes the acquisition of sample material difficult, and little information is known about their genetic structure. The majority of specimens analysed to date have been from the European region, comparatively few from northeast Asia and Alaska. In the current study, Echinococcus spp. from wolves and intermediate hosts from the Republic of Sakha in eastern Russia were examined. Echinococcus canadensis G10 was identified in 15 wolves and 4 cervid intermediate hosts. Complete mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences were obtained from 42 worm and cyst specimens from Sakha and, for comparison, from an additional 13 G10 cysts from Finland. For comparative analyses of the genetic diversity of G10 of European and Asian origin, all available cox1 sequences from GenBank were included, increasing the number of sequences to 99. The diversity found in northeast Asia was by far higher than in Europe, suggesting that the geographic origin of E. canadensis (at least of G10) might be northeast Asia.

Prevalence of Gastrointestinal Parasites in Pigs: A Preliminary Study in Tolon and Kumbungu Districts, Ghana.

Pigs are important livestock that contribute to the economy and food security of Ghana, but the productivity of the sector is hindered by factors such as parasitic disease infections. Here, we detected the prevalence and polyparasitism of gastrointestinal parasites in pigs from selected farms in the Tolon and Kumbungu districts. Faeces of the animals were screened for parasite eggs using the sedimentation and flotation methods. From 56 pigs screened, 91.1% (CI = 95%; χ2 = 0.212) of them had parasitic infections, and affected pigs harboured 1-5 distinct parasites with the most occurring being Strongyloides ransomi (46.43%). Other parasites identified included Hyostrongylusrubidus, Ascaris suum, Trichuris suis, Physocephalus sexalatus, and Coccidia, among others. Parasitism was more frequent in pigs under 2 years (94%) than older ones (66.67%). The high prevalence of GI parasites was attributed to poor husbandry practices and inadequate of veterinary care for the animals. The situation can be improved by farmer education on good husbandry practices and regular deworming of pigs.

Antimicrobial Susceptibility and Molecular Characterization of Escherichia coli Recovered from Milk and Related Samples.

There is a rising concern about illnesses resulting from milk consumption due to contamination by pathogenic microorganisms including Escherichia coli. This study examined the occurrence and antimicrobial susceptibility of E. coli isolated from cow milk and related samples. Furthermore, partial sequencing was done to ascertain the genetic relatedness and possible cross contamination among the samples. In all, 250 samples, that is, 50 each of raw milk, cow teat, milkers' hands, milking utensils, and fecal matter of cows, were cultured for the identification of E. coli. E. coli was detected in 101/250 samples (40.4%). Milk and fecal samples recorded the highest percentages of 68.0% and 66.0%, respectively. Forty-two (42) E. coli strains examined for antimicrobial resistance showed an overall 25.5% resistance, 15.0% intermediate resistance, and 59.5% susceptibility. The isolates had a high level of resistance to teicoplanin (100.0%), but were susceptible to chloramphenicol (95.2%) and azithromycin (92.9%). The Multiple Antibiotic Resistance (MAR) index pattern ranged from 0.1 to 0.5, and 40.5% exhibited multiple drug resistance. The E. coli strains formed 11 haplotypes, and a phylogenic tree analysis showed relatedness among the isolates in other African countries. This observation is an indication of cross contamination among the milk and its related samples.

Genetic characterization and antimicrobial susceptibility of Escherichia coli isolated from household water sources in northern Ghana.

The microbial quality of household water is an important issue in developing countries, especially in Ghana, where many people still depend on unimproved sources of water. The present study investigated the prevalence, genetic characteristics, and antimicrobial resistance profile of Escherichia coli from surface water sources. Fifty-two water samples were analyzed by using a spread plate, a biochemical test, and multiplex polymerase chain reactions. E. coli was isolated from each of the 52 water samples. Of these isolates, 75% were noted to possess virulence genes. Approximately 54% of the isolates were characterized as follows: enterotoxigenic E. coli (ETEC, 10.26%), enteropathogenic E. coli (EPEC, 17.95%), verotoxigenic E. coli (VTEC, 23.07%), and enteroinvasive E. coli (EIEC, 2.57%). Eighteen of the fifty-two isolates could not be characterized due to heterogeneity in banding. The disc diffusion method was used to test for antimicrobial susceptibility. The isolates were most resistant to ceftazidime, augmentin, and cefuroxime. Multidrug resistance was recorded in 48.1% of the isolates. In contrast, the isolates were most susceptible to ciprofloxacin (86.5%), nitrofurantoin (84.6%), and ofloxacin (75%). These results revealed a high diversity and widespread of E. coli in northern Ghana. The study provides important data for public health nationwide surveillance of E. coli in surface water across the country.

Cystic echinococcosis of ruminant livestock in Namibia.

Cystic echinococcosis (CE) is widespread and locally frequent in southern Africa where it affects humans, livestock, and wild mammals. However, most data from the region are old and do not provide information on the causative Echinococcus species. For Namibian livestock only anecdotal records were available prior to this preliminary survey. Our retrospective analysis of slaughterhouse records of CE in cattle from the commercial farming area in central and southern Namibia resulted in 1.65% CE prevalence among 35,143 slaughtered cattle in the period 2015-2016. For comparison, carcasses of ruminant livestock were prospectively examined in the communal farming areas of northern Namibia, resulting in three CE cases among only 12 cattle, and no cases among nine goats. To determine the Echinococcus species affecting Namibian livestock, a total of 53 cysts were collected from all parts of the country and analysed for species and genotype by amplification and sequencing of the nad1 gene. All 50 cattle cysts (isolated from 40 cattle), both from the commercial and communal farming areas, were Echinococcus ortleppi (all fertile, and 42/50 from the lungs), while three opportunistically collected cysts from three sheep in southern Namibia were E. canadensis G7. Our data suggest that E. ortleppi is the only CE agent that is relevant for cattle infection in Namibia, and that low prevalence in the commercial farming areas contrasts with high CE burden in the northern traditional husbandry systems. The present data provide baseline information to stimulate epidemiological studies on the transmission pathways of various CE agents in livestock, wildlife, and humans in Namibia and neighbouring countries.

Prevalence and genetic variance of Taenia hydatigena in goats and sheep from northern Ghana: Preliminary data on a globally neglected livestock parasite.

Cysticercosis caused by the larval stages of Taenia hydatigena has a significant global impact on livestock production, particularly of goats and sheep. Despite this, global data on prevalence and genetic variance of this parasite are still scarce. In Ghana, as in most African countries, numerous anecdotal observations agree that it is widespread and frequent. To obtain baseline data, we screened 251 goats and 248 sheep in northern Ghana (Upper East Region) for T. hydatigena metacestode and molecularly characterized the isolates using the mtDNA cox1 gene sequence. Prevalence was 58.57% in goats and 60.48% in sheep, confirming the abundance of this parasite in the region. Gene sequences revealed high diversity (π 0.00346, hd 0.809) and significant negative Tajima D and Fu's Fs values, a characteristic of a population experiencing an expansion after a recent bottleneck. This is the first account of the genetic structure of T. hydatigena in Ghana, intended as a basis for subsequent studies in the region.

Ascaridia galli and Heterakis gallinarum prevalence and genetic variance of A. galli in rural chicken from the Northern Region, Ghana.

Rural chicken production in Ghana is predominantly done under the extensive system that exposes birds to parasitic infections. We investigated the prevalence of Ascaridia spp. and Heterakis spp. and as a preliminary study characterized the genetic variance of the Ascaridia galli isolates from rural chicken in Kumbungu, Savelugu and Tolon Districts in the Northern Region, Ghana. A total of 86 chickens aged 6-10 weeks were dissected and GIT inspected for nematodes. Nematode were described based on morphological features to be A. galli and H. gallinarum. Additionally, the mitochondrial cox1 gene (475 bp) of Ascaridia isolates was amplified and sequenced. The overall prevalence of nematodes was 47.67%: A. galli 37.21% and H. gallinarum 20.93%. Prevalence values of A. galli in the Kumbungu, Savelugu and Tolon Districts were 25.00%, 36.00%, 56.00%, respectively, and that of H. gallinarum, respectively were 16.67%, 28.00% and 20.00%. A Chi-square test (x2 = 6.0907, p < 0.048) showed an association of A. galli prevalence to the district of origin of birds. From 20 A. galli cox1 sequences analyzed, all sequences were identified as A. galli. Two haplotypes were recorded, namely, GHA1 and GHA2. Haplotype GHA1 was found to have wide distribution globally, whereas GHA2 appear to be novel in the present study. The data shows the importance of A. galli and H. gallinarum infection in rural chicken in northern Ghana and pave way for further epidemiological study of avian nematodes.

Prevalence and characteristics of Listeria species from selected African countries.

Listeriosis, caused by Listeria spp., presents varying clinical manifestations among individuals, from moderate fecal infections such as diarrhea to severe infections such as septicemia, meningitis and abortion or newborn listeriosis in perinatal patients. In Africa, listeriosis is attributed to poor sanitation and cross-contamination in food processing environments, particularly ready to eat (RTE) foods including dairy products, leafy vegetables, fish and meat. Despite the global increase in reported cases and research on listeriosis, data from Africa remains scarce and this could lead to possible underestimation of the importance of listeriosis on the continent. This paper therefore presents a comprehensive overview of currently available reports on Listeria spp. in Africa with emphasis on molecular characteristics, antimicrobial susceptibility, and prevalence in food, animal and environmental samples. The majority of studies on Listeria spp. in Africa have so far focused on the prevalence and antibiotic susceptibility of L. monocytogenes isolated from RTE foods and raw meat but rarely from humans, animals, and the environment. The overall calculated average prevalence values from the available reports are 23.7 and 22.2% for Listeria spp. and L. monocytogenes, respectively. Listeria spp. isolated from different parts of Africa are generally sensitive to ciprofloxacin, but resistant to penicillin. The majority of these studies employed conventional culture and biochemical tests to characterize Listeria spp. However, the use of modern molecular techniques such as PCR and whole-genome sequencing is on the rise. Most of the studies employing molecular tools were carried out in South Africa and Nigeria, with the predominant strain reported in South Africa being ST6. In order to provide a better understanding of the importance of listeria in Africa, there is the need for extensive and coordinated studies using modern molecular-based techniques to characterize the various Listeria species, and to assess the disease epidemiology using the one health concept.

Taenia hydatigena in goat and sheep in Ghana: a cross-sectional abattoir survey in Northern and Upper West Regions.

Parasitic infections are a major setback to livestock production in Ghana but the disease situation in many localities is poorly understood. A study to determine the prevalence and distribution of Taenia hydatigena in goats and sheep was carried out in two major municipal abattoirs in Tamale and Wa. A total of 538 goats and 256 sheep were screened for cysts during a cross-sectional survey which revealed a prevalence of 22.34% and 33.96% in goats from Tamale and Wa, respectively, and 22.66% in sheep from Tamale. Infection was common in male and female, young and old animals alike. Animals considered in the study originated from various localities within Northern and Upper West Regions and T. hydatigena infection was thought to be autochthonous, depicting a wide distribution of the cestode infection in small ruminants. Our data represent the importance of T. hydatigena infection in goat and sheep production and provide a base for subsequent epidemiological studies in Ghana.

Dicrocoelium spp. in cattle from Wa, Ghana: prevalence and phylogeny based on 28S rRNA.

Dicrocoeliosis is a trematode infection in cattle, sheep and goats caused by the small liver fluke, Dicrocoelium spp. Though endemic in Ghana, its disease situation is poorly understood. In the present study, the prevalence, distribution and worm load of Dicrocoelium spp. in cattle at slaughter in Wa were determined. A total of 389 cattle were screened during meat inspection for liver flukes, and polymerase chain reaction accompanied by DNA sequencing of the 28S rRNA gene was used to identify Dicrocoelium spp. Generally, prevalence of bovine dicrocoeliosis (small liver fluke) stood at 19.54 % with prevalence in males and females being 17.62 % and 21.43 %, respectively. Animals under 2 years suffered more infection than older ones (23.08 % vs. 16.80 %). Dicrocoelium infection was recorded in animals from all the communities where slaughtered cattle came from. On average, 31 flukes per infected animal were recorded. A molecular confirmatory test on seven flukes identified them as D. hospes. This preliminary study highlights the importance of bovine dicrocoeliosis in Ghana and has identified D. hospes as a causal agent. The data provides basis for further studies to appraise the trematode disease situation in animals and phylogeny of Dicrocoelium spp. circulating in Ghana.

Echinococcus ortleppi and Echinococcus canadensis G6/7 affect domestic animals in western Zambia.

Cystic echinococcosis (CE) is endemic in many parts of sub-Saharan Africa. In contrast to the eastern part of the continent, very little data exists on the current disease situation in southern Africa including Zambia. This study determined frequency and species identity of Echinococcus spp. circulating in livestock and dogs in the Western Province of Zambia. Cysts were collected in slaughterhouses at meat inspection (cattle) and during examination of home slaughtered pigs, while dog faecal samples were collected per-rectum and examined microscopically for the presence of taeniid eggs. Individual taeniid eggs from faecal samples and individual protoscoleces from cysts were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and/or sequencing of the NADH-dehydrogenase subunit 1 (nad1) and cytochrome C oxidase 1 (cox1) gene. Fifty-four of 2000 cattle (2.7%) were found infected with a total of 65 cysts, predominantly fertile lungs cysts; all cysts were identified as Echinococcus ortleppi. Two out of 52 home-slaughtered pigs (3.8%) were infected with a fertile lung cyst each; both cysts were also identified as E. ortleppi. Microscopic examination revealed 10/289 dog faecal samples to contain taeniid eggs, of which four samples (two each) contained Echinococcus canadensis (G6/7) or Taenia hydatigena, respectively. This is the first insight in the Echinococcus species circulating in Zambia providing premises for further studies into transmission dynamics of CE in the southern African region.

Diversity of Taenia and Hydatigera (Cestoda: Taeniidae) in domestic dogs in Kenya.

Taenia species of domestic dogs can cause cysticercosis and coenurosis in a wide range of intermediate hosts including humans. Most taeniids of dogs are globally distributed, but some wildlife-transmitted species can be specific for certain regions. Generally, little information exists on the species composition and frequency in most regions of the world, which impairs risk assessment and control strategies. This study determined the range of taeniid species in dogs in four widely spaced areas of Kenya by genetic identification of eggs in faeces collected from the environment. Individual taeniid eggs were characterised by nested polymerase chain reaction of NADH dehydrogenase subunit 1 and cytochrome C oxidase 1 genes, restriction fragment length polymorphism and partial sequencing. Overall 79/1621 (4.9%) faecal samples contained eggs of Taenia or Hydatigera (8.0% in Turkana, 4.8% in Isiolo, 3.8% in Maasai Mara and 1.3% in Meru). Taenia hydatigena and T. multiceps were the most frequent, found in 36 and 15 samples, respectively. Other eggs found in the faeces belonged to T. serialis (sensu lato), T. madoquae (the first record in domestic dogs), T. ovis, T. saginata and Hydatigera taeniaeformis. Polymorphism of nad1 sequences revealed 22 and 8 haplotypes of T. hydatigena and T. multiceps, respectively. The results show the involvement of dogs in both domestic and sylvatic transmission cycles. In addition to the species range, this study provides data on the intraspecific diversity of T. hydatigena and T. multiceps in Kenya, which will serve as baseline information for further studies into cysticercosis and coenurosis in livestock and humans in the region.

Fasciola spp. in Armenia: Genetic diversity in a global context.

Fasciolosis, a food- and waterborne infection caused by the trematodes Fasciola hepatica and F. gigantica, is recognized by WHO as a neglected zoonotic disease. Whereas F. hepatica is distributed worldwide in cooler climates, F. gigantica occurs mainly in the tropics of Africa and Asia. The southern Caucasus, with Armenia, is one of the most northern regions where both species occur and may produce hybrids. In this study, livestock in central Armenia was surveyed for fasciolosis, the causative species were determined and the genetic diversity of both species was estimated. Total prevalence in sheep (1794), cattle (324) and goats (9) was 21.2%, 15.7% and 44.4%, respectively. After morphological identification and sequencing of a mitochondrial (nad1) and a nuclear marker gene (28S rRNA), 62 collected specimens were allocated to F. hepatica (n = 55) and F. gigantica (n = 7). Intraspecific diversity was evaluated for the complete nad1 gene, resulting in 29 haplotypes of F. hepatica and six haplotypes of F. gigantica. Diversity was higher among F. gigantica than F. hepatica in the Armenian sample set, a difference that was confirmed analyzing available sequences for both species worldwide. Maximum genetic distance between haplotypes in global networks was 49 nucleotide steps for F. gigantica compared to 15 for F. hepatica. In the available sample sets, F. hepatica showed higher diversity in western Asia and the Middle East compared to Europe and eastern Asia, while for F. gigantica loosely structured clusters comprising mainly western/southern Asian and African haplotypes could be identified. A distinct clade comprising haplotypes from Zambia was basal in the phylogenetic tree. Biogeographical implications of these data are discussed.

Molecular characterization of Echinococcus species in dogs from four regions of Kenya.

Cystic echinococcosis is endemic both in livestock and humans in many parts of Kenya. However, very little data exists on Echinococcus infections in dogs, and therefore their role in maintaining the transmission cycles and environmental contamination with eggs of Echinococcus species is unknown. The study aimed to establish the prevalence and distribution of Echinococcus granulosus sensu lato causing infection in dogs in Kenya. A total of 1621 dog faecal samples were collected from the environment in four different regions and examined microscopically for the presence of taeniid eggs. Up to 20 individual taeniid eggs per faecal sample were picked, lysed and genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequencing of the NADH dehydrogenase subunit 1 (nad1) gene. Eleven percent (178/1621) of faecal samples had taeniid eggs, while 4.4% (71/1621) contained Echinococcus spp. eggs. Area-wise, the faecal prevalence of Echinococcus spp. was 9.2% (48/524) in Turkana, 4.0% (20/500) in Maasai Mara, 0.7% (2/294) in Isiolo and 0.3% (1/303) in Meru. E. granulosus sensu stricto (s. s.) was the dominant Echinococcus taxon, followed by E. canadensis (G6/7) that was detected in 51 and 23 faecal samples, respectively. E. ortleppi was detected in only 5 faecal samples. We report for the first time the presence of E. felidis eggs in two dog faecal samples (from Maasai Mara region). Mixed infections of these taxa were also found in faecal samples, including: E. granulosus s. s. and E. canadensis (G6/7) (n = 7), E. granulosus s. s. and E. ortleppi (n = 1) and all three species (n = 1). The dog data presented here confirm the differences in diversity and abundance of Echinococcus spp. between regions of Kenya, correspond well with previously published data from livestock, and tentatively suggest a role of domestic dogs as a link between domestic and sylvatic cycles of Echinococcus spp.

Genetic characterisation of Fasciola gigantica from Ghana.

Fasciola hepatica and Fasciola gigantica are the causal agents of the zoonotic food-born disease fascioliasis. Africa is primarily endemic to F. gigantica, although sympatric presence of F. hepatica is known for some countries. The present situation of fascioliasis in western Africa, and Ghana in particular, is still poorly understood, and studies including molecular identification of species and variants are lacking. In this explorative study we genotyped 19 Fasciola isolates obtained by opportunistic sampling in the Upper East and Upper West Regions of Ghana. All isolates were identified as F. gigantica based on a partial sequence of the 28S rRNA (548 bp) gene. In addition, the complete mtDNA nad1 (903 bp) gene was employed to infer intraspecific microvariation among isolates. Six nad1 haplotypes were identified that clustered into two West African haplogroups when compared with previous records from Nigeria. These preliminary data suggest that fascioliasis in Ghana is (at least) mainly caused by F. gigantica, and that transmission may be principally autochthonous. However, the small number of isolates prevents firm conclusions, and this study is intended to stimulate molecular surveys on this neglected disease in a neglected region.

Genetic differentiation of the G6/7 cluster of Echinococcus canadensis based on mitochondrial marker genes.

Among the genotype/species causing cystic echinococcosis, the taxonomic status of Echinococcus canadensis is only partially resolved. Within E. canadensis, four genotypes (G6, G7, G8 and G10) have been described based on short mitochondrial sequences, of which G6 and G7 (the 'camel' and the 'pig' strain, respectively) are closely related and variously regarded as microvariants of a single strain G6/7. Globally, this G6/7 cluster is the second most important agent of human cystic echinococcosis and is the predominant Echinococcus taxon in large parts of sub-Saharan Africa. To add data on the internal structure and the geographical distribution of this cluster, we analysed diversity and population structure of 296 isolates of E. canadensis from sub-Saharan Africa, the Middle East and Europe using the complete mitochondrial cytochrome c oxidase subunit 1 (cox1) (1,608bp) and NADH dehydrogenase subunit 1 (nad1) (894bp) gene sequences. Polymorphism of the mtDNA loci gave 51 (cox1), 33 (nad1) and 73 (cox1-nad1 concatenated) haplotypes. African and Middle Eastern isolates mainly grouped in a star-like structure around a predominant haplotype, while the European isolates produced more diversified networks. Although the cox1 diagnostic sequence for G6 is frequent in the African/Middle Eastern sub-cluster, and that for G7 is common in the European isolates, numerous intermediate variants prevent a clear distinction into 'G6' or 'G7', and the entire taxon is best treated as a common haplotype cluster G6/7. Meanwhile, the G6/7 cluster is clearly distinct from sequences of wildlife isolates of G8 and G10 from the northern hemisphere, and sequences of the latter genotypes were remarkably distant from each other. It is clear from the present study that, based on mitochondrial data, G6/7 is a coherent genotypic entity within E. canadensis that retains substantial intraspecific variance, and sub-populations share common ancestral polymorphisms and haplotypes. This study provides the basis for wider biogeographic comparison and population genetics studies of this taxon.

Prevalence and diversity of cystic echinococcosis in livestock in Maasailand, Kenya.

Cystic echinococcosis (CE) is a zoonotic disease caused by several members of the Echinococcus granulosus species complex. In East Africa, several species/strains are known to occur in livestock and humans, but host preferences, relative frequencies and spatial distribution of these taxa are poorly known. Here, we contribute livestock data for Maasailand of southern Kenya. Total CE prevalence was 25.8 % in cattle (151/587), 16.5 % in sheep (71/430) and 10.8 % in goats (21/194), which is a significant increase compared to surveys done about three decades ago. The majority of cysts occurred in the liver (56 % in cattle, 70 % in sheep and 65 % in goats). Molecular characterization by PCR-RFLP and sequencing of parts of the mitochondrial nad-1 gene was done for a subsample of 285 cysts. E. granulosus G1 was dominant in all host species (200 of 201 cysts from cattle, 68 of 69 from sheep and 11 of 15 from goats); the remaining taxa were Echinococcus canadensis G6 (one cyst from sheep, four from goats) and Echinococcus ortleppi (one cyst from cattle). Considering cyst fertility, sheep appear to be the most important hosts for E. granulosus G1, while goats were found to be suitable hosts for E. canadensis G6 (three of four cysts were fertile). For the first time, E. ortleppi was found in cattle from southern Kenya. Our data show an intense and possibly increasing level of CE transmission in southern Kenya, and the predominance of E. granulosus G1, which appears to be particularly pathogenic to humans, calls for urgent control measures.