Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure

Genotyping and epidemiological distribution of diarrhea-causing isolates of Giardia duodenalis in southeastern part of West Bengal, India

The prevalence and genetic diversity of the protozoan pathogen Giardia duodenalis have been extensively studied worldwide. There is currently a lack of data regarding the genetic variability of the organism in eastern India. Understanding the circulating genotypes and associated risk factors is crucial for effective planning and implementing control measures. Therefore, the objective of the study was to conduct an epidemiological study to determine the prevalence and identify the various genotypes present. This survey adds to our knowledge on the occurrence and distribution of Giardia genotypes in the studied region. The overall prevalence was found to be 6.8%. This parasitic infection was significantly associated with two age groups, i.e., >0-5 years and >5-12 years. Using a multilocus genotyping method, we genotyped 52 human Giardia isolates that were obtained from diarrheal patients. Two distinct assemblages were found in the population-30.8% belonged to assemblage A; 63.5% belonged to assemblage B, prevalent in the population; and 5.7% belonged to a combined assemblage A+B. Sub-assemblage AII was found in 17.3% of the cases, followed by sub-assemblage AI (13.5%). High levels of genetic diversity were found within the population of assemblage B undergoing balancing selection. Overall, the high prevalence of the parasite observed, particularly among children, raises a major concern and necessitates implementation of robust control measures. Furthermore, we report the presence of numerous unique genotypes, circulating in this limited geographical boundary, which can be useful dataset for future studies.

Genetic diversity and molecular diagnosis of Giardia

Giardia is a genus of flagellated protozoan parasites that infect the small intestine of humans and animals, causing the diarrheal illness known as giardiasis. Giardia exhibits significant genetic diversity among its isolates, which can have important implications for disease transmission and clinical presentation. This diversity is influenced by the coevolution of Giardia with its host, resulting in the development of unique genetic assemblages with distinct phenotypic characteristics. Although panmixia has not been observed, some assemblages appear to have a broader host range and exhibit higher transmission rates. Molecular diagnostic methods enable researchers to examine the genetic diversity of Giardia populations, enhancing our understanding of the genetic diversity, population structure, and transmission patterns of this pathogen and providing insights into clinical presentations of giardiasis.

Molecular characterisation and taxon assemblage typing of giardiasis in primary school children living close to the shoreline of Lake Albert, Uganda

As part of an epidemiological survey for gastrointestinal parasites in school children across five primary schools on the shoreline of Lake Albert, the prevalence of giardiasis was 87.0% (n = 254) as determined by real-time PCR analysis of faecal samples with a genus-specific Giardia 18S rDNA probe. Faecal samples were further characterised with taxon assemblage-specific triose phosphate isomerase (TPI) Taqman® probes and by sequence characterisation of the β-giardin gene. While less sensitive than the 18S rDNA assay, general prevalence by TPI probes was 52.4%, with prevalence by taxon assemblage of 8.3% (assemblage A), 35.8% (assemblage B) and 8.3% co-infection (A & B assemblages). While assemblage B was dominant across the sample, proportions of assemblages A and B, and co-infections thereof, varied by school and by age of child; mixed infections were particularly common at Runga school (OR = 6.9 [95% CI; 2.5, 19.3]) and in children aged 6 and under (OR = 2.7 [95% CI; 1.0, 7.3]). Infection with assemblage B was associated with underweight children (OR = 2.0 [95% CI; 1.0, 3.9]). The presence of each assemblage was also confirmed by sequence analysis of the β-giardin gene finding sub-assemblage AII and further genetic diversity within assemblage B. To better explore the local epidemiology of giardiasis and its impact on child health, additional sampling of school children with assemblage typing would be worthwhile.

Multilocus genotyping of Giardia duodenalis infecting rabbits in Ogun State, Nigeria

Giardiasis is a cosmopolitan gastrointestinal protozoal parasite that infects humans and various animals worldwide. To assess the zoonotic transmission potential of Giardia, molecular characterization is required. We are unaware of any report on the genotypes of Giardia infecting rabbits in Nigeria. Molecular detection and genotyping of Giardia duodenalis were conducted in a herd of adult Chinchilla rabbits (Oryctolagus cuniculus) managed on the Teaching and Research farm of the Federal University of Agriculture, Abeokuta located in a southwestern state of Nigeria by analysis of the small-subunit ribosomal RNA (ssu rRNA), glutamate dehydrogenase (gdh), triosephosphate isomerase (tpi) and beta-giardin (bg) genes. An overall prevalence of 72.3% (60/83) was recorded in the rabbits with no statistically significant (p > .05) influence of sex on the distribution of the infection in the herd. All the 19 isolates amplified at the four genetic loci were identified as G. duodenalis assemblage BIV by multiple alignment analysis of their consensus sequences. Novel nucleotide substitutions were identified in two isolates at the ssu rRNA locus. Phylogenetic analysis revealed that all ssu rRNA genotypes were closely related to G. duodenalis assemblage B of cattle and human origin. Findings of this study suggest that the rabbits harbour potentially zoonotic assemblage BIV that portends a high risk to students and staff of the University who are in regular contact with the animals.

Genetic variability and transcontinental sharing of Giardia duodenalis infrapopulations determined by glutamate dehydrogenase gene

Microevolutionary data of Giardia duodenalis sub-assemblages is a prerequisite for determining the invasion zoonotic patterns of the parasite. To infer transmission patterns that could not be differentiated by the phenotypic features, a population genetic investigation is crucial for the elucidation of the genetic structure of G. duodenalis among the continents. Forty G. duodenalis positive fecal samples were collected from different foci of Northwest Iran. The specimens were subjected to Trichrome staining and sucrose gradient flotation. DNA samples were extracted, amplified, and sequenced by targeting glutamate dehydrogenase (gdh) gene. The global gdh sequences of sub-assemblages AII and BIV retrieved from NCBI GenBank were analyzed to estimate diversity indices, neutrality indices, and gene migration tests. Sequencing analyses indicated various levels of genetic variability of sub-assemblages AII and BIV among the five continents. Sub-assemblage BIV had greater genetic variability (haplotype diversity: 0.975; nucleotide diversity: 0.04246) than sub-assemblage AII. The statistical Fst value demonstrated that the genetic structure of sub-assemblages AII and BIV are moderately differentiated between European-American populations (Fst: 0.05352-0.15182), whereas a significant differentiation was not seen among other geographical population pairs. We conclude that a high gene flow of G. duodenalis sub-assemblages AII and BIV is unequivocally sharing among the continents. The current findings strengthen our knowledge to assess the evolutionary patterns of G. duodenalis in endemic foci of the world and it will become the basis of public health policy to control human giardiasis.

Multilocus genotyping of Giardia duodenalis in captive non-human primates in Sichuan and Guizhou provinces, Southwestern China

Giardia duodenalis is a common human and animal pathogen. It has been increasingly reported in wild and captive non-human primates (NHPs) in recent years. However, multilocus genotyping information for G. duodenalis infecting NHPs in southwestern China is limited. In the present study, the prevalence and multilocus genotypes (MLGs) of G. duodenalis in captive NHPs in southwestern China were determined. We examined 207 fecal samples from NHPs in Sichuan and Guizhou provinces, and 16 specimens were positive for G. duodenalis. The overall infection rate was 7.7%, and only assemblage B was identified. G. duodenalis was detect positive in northern white-cheeked gibbon (14/36, 38.9%), crab-eating macaque (1/60, 1.7%) and rhesus macaques (1/101, 0.9%). Multilocus sequence typing based on beta-giardin (bg), triose phosphate isomerase (tpi) and glutamate dehydrogenase (gdh) revealed nine different assemblage B MLGs (five known genotypes and four novel genotypes). Based on a phylogenetic analysis, one potentially zoonotic genotype of MLG SW7 was identified in a northern white-cheeked gibbon. A high degree of genetic diversity within assemblage B was observed in captive northern white-cheeked gibbons in Southwestern China, including a potentially zoonotic genotype, MLG SW7. To the best of our knowledge, this is the first report using a MLGs approach to identify G. duodenalis in captive NHPs in Southwestern China.

A survey for potentially zoonotic gastrointestinal parasites in domestic cavies in Cameroon (Central Africa)

Background

Farm animals are usually suspected to transmit infections to humans. Domestic cavies (Cavia porcellus) are hosts to a variety of pathogens, some of which are zoonotic. Several parasites including the protozoa Giardia spp. and Cryptosporidium spp. may be causative agents of gastrointestinal disorders in domestic cavies and humans. The aim of the study was to investigate the occurrence of potentially zoonotic protozoa as well as any potential zoonotic gastrointestinal parasite in domestic cavies raised under a semi extensive system in the rural areas of Cameroon.

Results

Giardia/Cryptosporidium antigens were detected in 12.90% of cavies. Helminthe eggs were found in 1.52% of animals. The prevalence of Paraspidodera uncinata, Heligmosomoides polygyrus (also known as Nematospiroides dubius) and Trichuris sp. was 1% (4/397), 0.3% (1/397), and 0.3% (1/397), respectively. Presence of Giardia/Cryptosporidium was unrelated to the occurrence of diarrhea, as none of the positive samples was from a diarrheic individual.

Conclusion

Domestic cavies are hosts of Giardia/Cryptosporidium and appear as potential source of human giardiasis, cryptosporidiosis and infection with H. polygyrus in Cameroon. In keeping with the One Health Initiative, veterinarians and medical doctors should collaborate to address the problem of Giardia and Cryptosporidium infection in cavies and cavy breeders both in Cameroon and other countries with a similar cavy breeding system. Follow-up studies are required to further taxonomically characterize these cavy parasites and to determine their routes of transmission to humans.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-017-1096-2) contains supplementary material, which is available to authorized users.

Molecular diversity and frequency of the diarrheagenic enteric protozoan Giardia duodenalis and Cryptosporidium spp. in a hospital setting in Northern Spain

Background

Human giardiosis and cryptosporidiosis are caused by the enteric protozoan parasites Giardia duodenalis and Cryptosporidium spp. Both pathogens are major contributors to the global burden of diarrhoeal disease, affecting primarily children and immunodebilitated individuals in resource-poor settings. Giardiosis and cryptosporidiosis also represent an important, often underestimate, public health threat in developed countries. In Spain only limited information is currently available on the epidemiology of these infections. Molecular data on the diversity, frequency, geographical distribution, and seasonality of G. duodenalis assemblages/sub-assemblages and Cryptosporidium species/sub-genotypes are particularly scarce.

Methods

A longitudinal molecular epidemiological survey was conducted between July 2015 to September 2016 in patients referred to or attended at the Hospital San Pedro (La Rioja, Northern Spain) that tested positive for G. duodenalis (N = 106) or Cryptosporidium spp. (N = 103) by direct microscopy and/or a rapid lateral flow immunochromatographic assay. G. duodenalis infections were subsequently confirmed by real-time PCR and positive isolates assessed by multi-locus sequence genotyping of the glutamate dehydrogenase and β-giardin genes of the parasite. Cryptosporidium species and sub-genotypes were investigated at the 60 kDa glycoprotein or the small subunit ribosomal RNA genes of the parasite. Sociodemographic and clinical parameters of infected patients were also gathered and analysed.

Principal findings

Out of 90 G. duodenalis-positive isolates by real-time PCR a total of 16 isolates were successfully typed. AII (44%, 7/16) was the most prevalent sub-assemblage found, followed by BIV (31%, 5/16) and BIII (19%, 3/16). A discordant genotype result AII/AIII was identified in an additional (6%, 1/16) isolate. No mixed infections A+B were detected. Similarly, a total of 81 Cryptosporidium spp. isolates were successfully typed, revealing the presence of C. hominis (81%, 66/81) and C. parvum (19%, 15/81). Obtained GP60 sequences were assigned to sub-type families Ib (73%, 59/81) within C. hominis, and IIa (7%, 6/81) and IId (2%, 2/81) within C. parvum. A marked inter-annual variation in Cryptosporidium cases was observed.

Conclusions

Human giardiasis and cryptosporidiosis are commonly identified in patients seeking medical care in Northern Spain and represent a more important health concern than initially thought. Assemblage A within G. duodenalis and sub-genotype IbA10G2 within C. hominis were the genetic variants of these parasite species more frequently found circulating in the population under study. Molecular data presented here seem to suggest that G. duodenalis and Cryptosporidium infections arise through anthroponotic rather than zoonotic transmission in this Spanish region.

Strong genetic structure revealed by multilocus patterns of variation in Giardia duodenalis isolates of patients from Galicia (NW-Iberian Peninsula)

We report a survey of genetic variation at three coding loci in Giardia duodenalis of assemblages A and B obtained from stool samples of patients from Santiago de Compostela (Galicia, NW-Iberian Peninsula). The mean pooled synonymous diversity for assemblage A was nearly five times lower than for assemblage B (0.77%±0.30% and 4.14%±1.65%, respectively). Synonymous variation in both assemblages was in mutation-drift equilibrium and an excess of low-frequency nonsynonymous variants suggested the action of purifying selection at the three loci. Differences between isolates contributed to 40% and 60% of total genetic variance in assemblages A and B, respectively, which revealed a significant genetic structure. These results, together with the lack of evidence for recombination, support that (i) Giardia assemblages A and B are in demographic equilibrium and behave as two genetically isolated populations, (ii) infections are initiated by a reduced number of individuals, which may be genetically diverse and even belong to different assemblages, and (iii) parasites reproduce clonally within the host. However, the observation of invariant loci in some isolates means that mechanisms for the homogenization of the genetic content of the two diploid nuclei in each individual must exist.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.

Prevalence and Genetic Diversity of Giardia duodenalis and Cryptosporidium spp. among School Children in a Rural Area of the Amhara Region, North-West Ethiopia

Backgroud

Giardia duodenalis and Cryptosporidium spp. are enteric protozoan causing gastrointestinal illness in humans and animals. Giardiasis and cryptosporidiosis are not formally considered as neglected tropical diseases, but belong to the group of poverty-related infectious diseases that impair the development and socio-economic potential of infected individuals in developing countries.

Methods

We report here the prevalence and genetic diversity of G. duodenalis and Cryptosporidium spp. in children attending rural primary schools in the Bahir Dar district of the Amhara Region, Ethiopia. Stool samples were collected from 393 children and analysed by molecular methods. G. duodenalis was detected by real-time PCR, and the assemblages and sub-assemblages were determined by multilocus sequence-based genotyping of the glutamate dehydrogenase and β-giardin genes of the parasite. Detection and identification of Cryptosporidium species was carried out by sequencing of a partial fragment of the small-subunit ribosomal RNA gene.

Principal Findings

The PCR-based prevalences of G. duodenalis and Cryptosporidium spp. were 55.0% (216/393) and 4.6% (18/393), respectively. A total of 78 G. duodenalis isolates were successfully characterized, revealing the presence of sub-assemblages AII (10.3%), BIII (28.2%), and BIV (32.0%). Discordant typing results AII/AIII and BIII/BIV were identified in 7.7% and 15.4% of the isolates, respectively. An additional five (6.4%) isolates were assigned to assemblage B. No mixed infections of assemblages A+B were found. Extensive genetic variation at the nucleotide level was observed within assemblage B (but no within assemblage A), resulting in the identification of a large number of sub-types. Cryptosporidium diversity was demonstrated by the occurrence of C. hominis, C. parvum, and C. viatorum in the population under study.

Conclusions

Our data suggest an epidemiological scenario with an elevated transmission intensity of a wide range of G. duodenalis genetic variants. Importantly, the elevated degree of genetic diversity observed within assemblage B is consistent with the occurrence of intra-assemblage recombination in G. duodenalis.

Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections

Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.

Population expansion and gene flow in Giardia duodenalis as revealed by triosephosphate isomerase gene

Background

Giardia duodenalis is a protozoan parasite that can cause significant diarrhoeal diseases. Knowledge of population genetics is a prerequisite for ascertaining the invasion patterns of this parasite. In order to infer evolutionary patterns that could not be uncovered based on the morphological features, a population genetic study with the incorporation of molecular marker was carried out to access the genetic structure of G. duodenalis isolated from the Malaysian population and the global populations.

Methods

A total of 154 samples positive for Giardia, collected from different Malaysian communities, were subjected to DNA amplification and sequencing targeting three genetic loci (tpi, gdh, and bg). The tpi sequences together with sequences from the global data obtained from the NCBI GenBank were used for genetic diversity analyses including identification of haplotypes, haplotype diversity, nucleotide diversity, Tajima’s D and Fu and Li’s D, gene flow and genetic differentiation tests.

Results

Analysis of the Malaysian and global data showed that assemblages A, B, and E (the most prevalent assemblages in humans and animals), have different levels of genetic diversity. Assemblage B had the highest level of both haplotype diversity and nucleotide diversity, followed by assemblage E. The analysis also revealed population expansion and high gene flow in all assemblages. No clear genetic structure was observed across five continents (i.e., the Americas, Europe, Asia, Australia and Africa). However, median joining network of assemblage B formed a cluster that was exclusively isolated from Asia while other haplotypes were well dispersed across the continents.

Conclusions

This study provides new insight into the genetic diversity of Giardia assemblages in different geographical regions. The significant result shown by gene flow and genetic differentiation analyses as well as test of neutrality among the populations should have brought a clearer picture to the dynamics and distribution of Giardia infection.

Prevalence of Zoonotic Giardia duodenalis Assemblage B and First Identification of Assemblage E in Rabbit Fecal Samples Isolates from Central China

Giardia duodenalis is an important zoonotic pathogen, causes diarrhea in humans and animals worldwide. To date, few data are available on the prevalence of G. duodenalis in rabbits in China. In total, 955 fecal samples were collected from rabbits during 2008-2011 in Henan Province, Central China. The overall prevalence of G. duodenalis was 8.4% (80/955) on microscopic analysis, with the highest infection rate (11.3%) in rabbits aged 91-200 d. All G. duodenalis-positive isolates were characterized at the small subunit ribosomal RNA, β-giardin (bg), glutamate dehydrogenase (gdh), and triosephosphate isomerase genes. Two assemblages and a mixed assemblage were detected in the rabbits: assemblage B (n = 26), assemblage E (n = 2), and a mixed assemblage of B and E (n = 4). Assemblage B isolates showed variability at the nucleotide sequences belonging to the so-called subtype BIV, based on analysis of multiple genes. This is the first report of G. duodenalis assemblage E in rabbits, and one novel subtype of assemblage E was identified through sequence analysis of gdh and bg genes, respectively. Our data suggest that rabbits may be reservoirs of G. duodenalis cysts potentially infectious to humans.

Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis

Ichthyophthirius multifiliis is the etiologic agent of "white spot", a commercially important disease of freshwater fish. As a parasitic ciliate, I. multifiliis infects numerous host species across a broad geographic range. Although Ichthyophthirius outbreaks are difficult to control, recent sequencing of the I. multifiliis genome has revealed a number of potential metabolic pathways for therapeutic intervention, along with likely vaccine targets for disease prevention. Nonetheless, major gaps exist in our understanding of both the life cycle and population structure of I. multifiliis in the wild. For example, conjugation has never been described in this species, and it is unclear whether I. multifiliis undergoes sexual reproduction, despite the presence of a germline micronucleus. In addition, no good methods exist to distinguish strains, leaving phylogenetic relationships between geographic isolates completely unresolved. Here, we compared nucleotide sequences of SSUrDNA, mitochondrial NADH dehydrogenase subunit I and cox-1 genes, and 14 somatic SNP sites from nine I. multifiliis isolates obtained from four different states in the US since 1995. The mitochondrial sequences effectively distinguished the isolates from one another and divided them into at least two genetically distinct groups. Furthermore, none of the nine isolates shared the same composition of the 14 somatic SNP sites, suggesting that I. multifiliis undergoes sexual reproduction at some point in its life cycle. Finally, compared to the well-studied free-living ciliates Tetrahymena thermophila and Paramecium tetraurelia, I. multifiliis has lost 38% and 29%, respectively, of 16 experimentally confirmed conjugation-related genes, indicating that mechanistic differences in sexual reproduction are likely to exist between I. multifiliis and other ciliate species.

Reproductive clonality in protozoan pathogens--truth or artefact?

The debate around the frequency and importance of genetic exchange in parasitic protozoa is now several decades old. Recently, fresh assertions have been made that predominant clonal evolution explains the population structures of several key protozoan pathogens. Here, we present an alternative perspective. On the assumption that much apparent clonality may be an artefact of inadequate sampling and study design, we review current research to define why sex might be so difficult to detect in protozoan parasite populations. In doing so, we contrast laboratory models of genetic exchange in parasitic protozoa with natural patterns of genetic diversity and consider the fitness advantage of sex at different evolutionary scales. We discuss approaches to improve the accuracy of efforts to characterize genetic exchange in the field. We also examine the implications of the first population genomic studies for the debate around sex and clonality in parasitic protozoa and discuss caveats for the future.

Epidemiology of Giardia duodenalis infection in ruminant livestock and children in the Ismailia province of Egypt: insights by genetic characterization

Background

Giardia duodenalis is a common flagellated protozoan parasite that infects the small intestine of a wide range of vertebrate hosts. This study aimed to determine whether tracing of G. duodenalis isolates by current genetic typing tools is possible using an exemplary set of samples from infected cattle, buffalo and children from the Ismailia province, Egypt.

Method

A total of 804 fecal samples from ruminant animals was collected from 191 herds and 165 samples from diarrheal children below the age of 10 years. Parasites were detected in these samples using the copro-antigen RIDA^®QUICK test and by real-time PCR. Samples were then genetically characterized based on the triosephosphate isomerase, glutamate dehydrogenase and β-giardin genes.

Results

The prevalence of G. duodenalis was 53% in ruminants and 21% in symptomatic children and infection was not positively correlated with diarrheal symptoms. Sequence typing analysis confirmed predominance of B-type sequences (>67%) in humans and E-type sequences (>81%) in ruminants over A-type sequences. For 39 samples the complete sequence information of the three marker gene fragments could be derived. Integration of the concatenated sequence information of the three marker gene fragments with the spatial data of the respective sample revealed that identical or near identical (only up to 1 out of 1358 bp different) concatenated sequencing types were spatially related in 4 out of 5 cases.

Conclusion

The risk of zoonotic infection emanating from ruminants even in high prevalence areas is negligible. Genetic characterization indicated a predominant anthropogenic cycle of infection within the pediatric population studied. Integration of sequence typing data with information on geographic origins of samples allows parasite sub-population tracing using current typing tools.

Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE) recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination), are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately (“Russian doll pattern”). Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections (“starving sex hypothesis”). We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

Micropathogen species definition is extremely difficult, since concepts applied to higher organisms (the biological species concept) are inadequate. In particular, the pathogens here surveyed have given rise to long-lasting controversies about their species status and that of the genotypes that subdivide them. The population genetic approach based on the predominant clonal evolution (PCE) concept proposed by us could bring simple solutions to these controversies, since it permits the description of clearly defined evolutionary entities (clonal multilocus genotypes and near-clades [incompletely isolated clades]) that could be the basis for species description, if the concerned specialists find it justified for applied research. The PCE model also provides a convenient framework for applied studies (molecular epidemiology, vaccine and drug design, clinical research) dealing with these pathogens and others.

Occurrence and molecular typing of Giardia isolates in pet rabbits, chinchillas, guinea pigs and ferrets collected in Europe during 2006-2012

A total of 1180 faecal samples (528 from rabbits, 531 from chinchillas and 121 from guinea pigs) collected during 2006-2012 by veterinarians in Germany and in other European countries were submitted to a diagnostic laboratory for Giardia testing by means of coproantigen ELISA. Of these samples, 40 rabbits (7.6 per cent), 326 chinchillas (61.4 per cent) and five guinea pigs (4.1 per cent ) were found to be positive. To gain insights into the genetic identity of Giardia in small mammals, ELISA-positive samples from 23 chinchillas, five ferrets, a rabbit, and a Desmarest's hutia were investigated by PCR and sequencing of fragments of the small subunit ribosomal DNA (ssu), the triose phosphate isomerase (tpi) and the β-giardin (bg) genes. At the ssu locus, assemblage B was identified in 28 of 30 isolates, whereas assemblage A and D were each detected in one sample. The majority of isolates from chinchillas and those from ferrets had Giardia duodenalis sequences identical to sub-assemblages AI or BIV, based on either a single locus (tpi or bg) or multiple loci (tpi and bg). As sub-assemblages AI or BIV are associated with human infection, these results indicate that small mammals can act as reservoirs of cysts potentially infectious to humans.