Climate variation influences host specificity in avian malaria parasites

Parasites with low host specificity (e.g. infecting a large diversity of host species) are of special interest in disease ecology, as they are likely more capable of circumventing ecological or evolutionary barriers to infect new hosts than are specialist parasites. Yet for many parasites, host specificity is not fixed and can vary in response to environmental conditions. Using data on host associations for avian malaria parasites (Apicomplexa: Haemosporida), we develop a hierarchical model that quantifies this environmental dependency by partitioning host specificity variation into region‐ and parasite‐level effects. Parasites were generally phylogenetic host specialists, infecting phylogenetically clustered subsets of available avian hosts. However, the magnitude of this specialisation varied biogeographically, with parasites exhibiting higher host specificity in regions with more pronounced rainfall seasonality and wetter dry seasons. Recognising the environmental dependency of parasite specialisation can provide useful leverage for improving predictions of infection risk in response to global climate change.     

Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species

Bacterial populations can display high levels of genetic structuring but the forces that influence this are incompletely understood. Here, by combining modelling approaches with multilocus sequence data for the zoonotic pathogen Campylobacter, we investigated how ecological factors such as niche (host) separation relate to population structure. We analysed seven housekeeping genes from published C. jejuni and C. coli isolate collections from a range of food and wild animal sources as well as abiotic environments. By reconstructing genetic structure and the patterns of ancestry, we quantified C. jejuni host association, inferred ancestral populations, investigated genetic admixture in different hosts and determined the host origin of recombinant C. jejuni alleles found in hybrid C. coli lineages. Phylogenetically distinct C. jejuni lineages were associated with phylogenetically distinct wild birds. However, in the farm environment, phylogenetically distant host animals shared several C. jejuni lineages that could not be segregated according to host origin using these analyses. Furthermore, of the introgressed C. jejuni alleles found in C. coli lineages, 73% were attributed to genotypes associated with food animals. Our results are consistent with an evolutionary scenario where distinct Campylobacter lineages are associated with different host species but the ecological factors that maintain this are different in domestic animals such that phylogenetically distant animals can harbour closely related strains.     

Antimicrobial resistance profiles of Campylobacter jejuni isolates from wild birds in Sweden

In order to determine the occurrence and frequency of resistant strains of the bacterium Campylobacter jejuni and to establish baseline MICs in isolates from an environmental reservoir, the resistance profiles of 10 antimicrobial substances were determined for 137 C. jejuni isolates from wild birds in Sweden. Observed MICs were generally low, with only low to moderate incidence of resistance to the tested compounds. One isolate, however, was resistant to nalidixic acid and ciprofloxacin, indicating that quinolone-resistant genotypes of C. jejuni have the potential to spread to wild bird hosts.     

Diversities and similarities in PFGE profiles of Campylobacter jejuni isolated from migrating birds and humans

AIMS: To genetically sub-type Campylobacter jejuni strains isolated from migratory birds, and to compare these with clinical strains collected in the same area and corresponding time period, with the aim to increase our knowledge on sub-types occurring among wild birds and their possible impact on human disease. METHODS AND RESULTS: We sub-typed C. jejuni strains from migrating birds (n = 89) and humans (n = 47), using macrorestriction profiling by pulsed-field gel electrophoresis. Isolates from migrant birds often exhibited sub-types with higher levels of similarity to isolates from birds of the same species or feeding guild, than to isolates from other groups of birds. Likewise, could the vast majority of sub-types found among the migrant bird isolates not be identified among sub-types from human cases. Only two bird strains, one from a starling (Sturnus vulgaris) and one from a blackbird (Turdus merula), had sub-types that were similar to some of the human strain sub-types. CONCLUSIONS: Isolates from one bird species, or feeding guild, often exhibited high similarities, indicating a common transmission source for individuals, or an association between certain sub-types of C. jejuni and certain ecological guilds or phylogenetic groups of birds. Sub-types occurring among wild birds were in general distinctively different from those observed in patients. The two bird isolates that were similar to human strains were isolated from bird species that often live in close associations with human settlements. SIGNIFICANCE AND IMPACT OF STUDY: Wild birds have often been mentioned as a potential route for transmission of C. jejuni to humans. Our study demonstrates that strains isolated from birds most often are different from clinical strains, but that some strain similarities occur, notably in birds strongly associated with human activities.     

Molecular evidence for host specificity of parasitic nematode microfilariae in some African rainforest birds

Here we describe, determine the prevalence, and examine the host-specificity of some parasitic nematode microfilariae in selected bird species from West and Central Africa. We used microscopy to determine the prevalence of microfilariae in 969 host individuals representing 121 rainforest bird species from Cameroon, Côte d’Ivoire and Equatorial Guinea. Thirteen (11%) of these potential host species harboured microfilariae, and 35 individuals (3.6%) were infected. From the 35 infected individuals, we identified eight distinct morphological microfilarial forms. Sixteen of the 35 infected individuals were of one host species, the Fire-crested Alethe (Alethe diademata), at a prevalence rate of 62%. To examine host and geographical specificity, we sequenced a portion of the LSU rDNA gene from representative microfilariae drawn from different hosts and collecting locations. Identical sequences of the nematode LSU rDNA gene were found in A. diademata collected from locations in Côte d’Ivoire and Equatorial Guinea, locations separated by the Dahomey Gap and associated with different hypothesized refugial areas. In contrast, several other bird species collected at the same sites harboured different microfilaria lineages. We sequenced the mitochondrial ATP synthase genes of the host species A. diademata, and found a 5.4% sequence divergence between the birds sampled in Côte d’Ivoire, and those from Cameroon. Thus, despite this split between the two populations, they harbour microfilariae with identical lineages. These data provide evidence that the microfilariae found in A. diademata may be highly host specific. This apparent specificity may have important implications for the evolutionary and ecological interactions between parasitic nematodes and their avian hosts.     

Evolution of the population structure of Venturia inaequalis,the apple scab fungus,associated with the domestication of its host

Evaluating the impact of plant domestication on the population structure of the associated pathogens provides an opportunity to increase our understanding of how and why diseases emerge. Here, we investigated the evolution of the population structure of the apple scab fungus Venturia inaequalis in response to the domestication of its host. Inferences were drawn from multilocus microsatellite data obtained from samples collected on (i) the Central Asian Malus sieversii, the main progenitor of apple, (ii) the European crabapple, Malus sylvestris, a secondary progenitor of apple, and (iii) the cultivated apple, Malus×domestica, in orchards from Europe and Central Asia. Using clustering methods, we identified three distinct populations: (i) a large European population on domesticated and wild apples, (ii) a large Central Asian population on domesticated and wild apples in urban and agricultural areas, and (iii) a more geographically restricted population in M. sieversii forests growing in the eastern mountains of Kazakhstan. Unique allele richness and divergence time estimates supported a host‐tracking co‐evolutionary scenario in which this latter population represents a relict of the ancestral populations from which current populations found in human‐managed habitats were derived. Our analyses indicated that the domestication of apple induced a significant change in the genetic differentiation of populations of V. inaequalis in its centre of origin, but had little impact on its population dynamics and mating system. We discuss how the structure of the apple‐based agrosystem may have restricted changes in the population structure of the fungus in response to the domestication of its host.     

Expanding host specificity and pathogen sharing beyond viruses

Most emerging pathogens of humans can infect multiple host species (Woolhouse & Gowtage‐Sequeria, 2005). This simple fact has motivated multiple large‐scale, comparative analyses of the drivers of pathogen sharing and zoonotic pathogen richness among hosts as well as the factors determining the zoonotic potential of pathogens themselves. However, most of this work focuses on viruses, limiting a broader understanding of how host range varies within and between pathogen groups. In this issue of Molecular Ecology, Shaw et al. (2020) compile a comprehensive data set of host–pathogen associations across viruses and bacteria and test whether previous patterns observed in the former occur in the latter. They find most viruses and bacteria are specialists, and viruses are more likely to be generalists; however, generalist bacteria encompass multiple host orders, whereas viral sharing occurs more within host orders. Lastly, the authors demonstrate that many factors previously identified as predictors of zoonotic richness for viruses occur for bacteria and that host phylogenetic similarity is a primary determinant of cross‐species transmission. However, pathogen sharing with humans was more common and more weakly related to phylogenetic distance to Homo sapiens for bacteria compared to viruses, suggesting the former could pose greater spillover risks across host orders. This work represents a key advance in our understanding of host specificity and pathogen sharing beyond viruses.     

Spatial epidemiology and natural population structure of Campylobacter jejuni colonizing a farmland ecosystem

Recent progress in determining the population structure of Campylobacter jejuni, and discerning associations between genotypes and specific niches, has emphasized the shortfall in our understanding of the ecology and epidemiology of this bacterium. We examined the natural structure of the C. jejuni community associated with cattle farmland in the UK by structured spatiotemporal sampling of habitats, including livestock and wild animal faeces, environmental water and soil, over a 10-week period within a 100 km2 area. A total of 172 isolates were characterized using multilocus sequence typing into 65 sequence types (STs). Isolates from cattle faeces were significantly over-represented in the ST-61 complex, whereas isolates from wildlife faeces and water were more likely to belong to the ST-45 complex and a number of unusual STs, many of which were first encountered during this study. Sampling within a narrow spatiotemporal window permitted the application of novel statistical methods exploring the relationship between the genetic relatedness and spatial separation of isolates. This approach showed that isolates from the same sampling squares and squares separated by <1.0 km were genetically more similar than isolates separated by greater distances. Our study demonstrates the potential of multilocus sequence typing combined with spatial modelling in exploring natural transmission pathways for C. jejuni.     

Prevalence of Campylobacter jejuni,Campylobacter lari,and Campylobacter coli in different ecological guilds and taxa of migrating birds

A total of 1,794 migrating birds trapped at a coastal site in southern Sweden were sampled for detection of Campylobacter spp. All isolates phenotypically identified as Campylobacter jejuni and a subset of those identified as non-C. jejuni were identified to the species level by PCR-based techniques. C. jejuni was found in 5.0% of the birds, Campylobacter lari was found in 5.6%, and Campylobacter coli was found in 0.9%. An additional 10.7% of the tested birds were infected with hippurate hydrolysis-negative Campylobacter spp. that were not identified to the species level. The prevalence of Campylobacter spp. differed significantly between ecological guilds of birds. Shoreline-foraging birds feeding on invertebrates and opportunistic feeders were most commonly infected (76.8 and 50.0%, respectively). High prevalence was also shown in other ground-foraging guilds, i.e., ground-foraging invertebrate feeders (11.0%), ground-foraging insectivores (20.3%), and plant-eating species (18.8%). Almost no Campylobacter spp. were found in ground-foraging granivores (2.3%), arboreal insectivores (0.6%), aerial insectivores (0%), or reed- and herbaceous plant-foraging insectivores (3.5%). During the autumn migration, a high proportion of samples from juveniles were positive (7.1% in passerines, 55.0% in shorebirds), indicating transmission on the breeding grounds or during the early part of migration. Prevalence of Campylobacter spp. was associated with increasing body mass among passerine bird species. Furthermore, prevalence was higher in short-distance migrants wintering in Europe than in long-distance migrants wintering in Africa, the Middle East, or Asia. Among ground-foraging birds of the Muscicapidae, those of the subfamily Turdinae (i.e., Turdus spp.) showed a high prevalence of Campylobacter spp., while the organism was not isolated in any member of the subfamily Muscicapinae (i.e., Erithacus and Luscinia). The prevalence of Campylobacter infection in wild birds thus seems to be linked to various ecological and phylogenetic factors, with great variations in carriership between different taxa and guilds.     

High population connectivity across the Indo-Pacific: Congruent lack of phylogeographic structure in three reef fish congeners

We used the mitochondrial control region and a comparative approach to study the genetic population structure of two surgeonfishes, Naso brevirostris and Naso unicornis, across their Indo-central Pacific ranges. Our purpose was to compare our results with those of a previous study of Naso vlamingii [Klanten, S.O., van Herwerden, L., Choat J.H., 2007. Extreme genetic diversity and temporal rather than spatial partitioning in a widely distributed coral reef fish. Mar. Biol. 150, 659-670] another widely distributed Indo-central Pacific Naso species. We found no evidence of a barrier to gene flow between the Indian and Pacific Oceans for either species, consistent with what was shown for N. vlamingii. Overall, both target species lacked spatial population partitions and probably have complex patterns of gene flow on several spatial scales. Despite the lack of geographic population structure distinct clades were observed in N. brevirostris, similar to those found in N. vlamingii. Coalescence times for intraspecific clades of N. brevirostris and N. vlamingii approximate each other, suggesting parallel evolutionary histories. A bimodal mismatch distribution in N. brevirostris indicates that a biogeographic barrier separated N. brevirostris populations sometime during its species history. Naso unicornis, in contrast, lacked genetic structure of any kind, although it has what could represent a single surviving clade. Congruent lack of spatial population structure among all three species suggest that such patterns are not due to stochastic processes of DNA mutation and are most likely driven by ecological and environmental factors.     

Comparison of genotypes and serotypes of Campylobacter jejuni isolated from Danish wild mammals and birds and from broiler flocks and humans.

The incidence of human infection with Campylobacter jejuni is increasing in most developed countries and the reason for this is largely unknown. Although poultry meat is considered to be a major source, it is evident that other reservoirs exist, possibly common to humans and poultry. Environmental sources are believed to be important reservoirs of Campylobacter infection in broiler chicken flocks. We investigated the potential importance of wildlife as a source of infection in commercial poultry flocks and in humans by comparing the serotype distributions, fla types, and macrorestriction profiles (MRPs) of C. jejuni isolates from different sources. The serotype distribution in wildlife was significantly different from the known distributions in broilers and humans. Considerable sero- and genotype diversity was found within the wildlife collection, although two major groups of isolates within serotype O:12 and the O:4 complex were found. Common clonal lines among wildlife, chicken, and/or human isolates were identified within serotype O:2 and the O:4 complex. However, MRPs of O:12 and O:38 strains isolated from wildlife and other sources indicated that some clonal lines propagated in a wide selection of animal species but were not detected in humans or broilers in this study. The applied typing methods successfully identified different clonal groups within a strain collection showing large genomic diversity. However, the relatively low number of wildlife strains with an inferred clonal relationship to human and chicken strains suggests that the importance of wildlife as a reservoir of infection is limited.     

High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms

A method for high-resolution genomic fingerprinting of the enteric pathogens Campylobacter jejuni and Campylobacter coli, based on the determination of amplified fragment length polymorphism, is described. The potential of this method for molecular epidemiological studies of these species is evaluated with 50 type, reference, and well-characterised field strains. Amplified fragment length polymorphism fingerprints comprised over 60 bands detected in the size range 35-500 bp. Groups of outbreak strains, replicate subcultures, and 'genetically identical' strains from humans, poultry and cattle, proved indistinguishable by amplified fragment length polymorphism fingerprinting, but were differentiated from unrelated isolates. Previously unknown relationships between three hippurate-negative C. jejuni strains, and two C. coli var. hyoilei strains, were identified. These relationships corresponded to available epidemiological data. We conclude that this amplified fragment length polymorphism fingerprinting method may be a highly effective tool for molecular epidemiological studies of Campylobacter spp.     

Multi‐locus sequence typing of Salmonella enterica serovar Typhimurium isolates from wild birds in northern England suggests host‐adapted strain

Aims: Recent studies have suggested that Salmonella Typhimurium strains associated with mortality in UK garden birds are significantly different from strains that cause disease in humans and livestock and that wild bird strains may be host adapted. However, without further genomic characterization of these strains, it is not possible to determine whether they are host adapted. The aim of this study was to characterize a representative sample of Salm. Typhimurium strains detected in wild garden birds using multi‐locus sequence typing (MLST) to investigate evolutionary relationships between them. Methods and Results: Multi‐locus sequence typing was performed on nine Salm. Typhimurium strains isolated from wild garden birds. Two sequence types were identified, the most common of which was ST568. Examination of the public Salmonella enterica MLST database revealed that only three other ST568 isolates had been cultured from a human in Scotland. Two further isolates of Salm. Typhimurium were determined to be ST19. Conclusions: Results of MLST analysis suggest that there is a predominant strain of Salm. Typhimurium circulating among garden bird populations in the United Kingdom, which is rarely detected in other species, supporting the hypothesis that this strain is host adapted. Significance and Impact of the Study: Host–pathogen evolution is often assumed to lead to pathogens becoming less virulent to avoid the death of their host; however, infection with ST568 led to high mortality rates among the wild birds examined, which were all found dead at wild bird‐feeding stations. We hypothesize that by attracting unnaturally high densities of birds, wild bird‐feeding stations may facilitate the transmission of ST568 between wild birds, therefore reducing the evolutionary cost of this pathogen killing its host, resulting in a host‐adapted strain with increased virulence.     

Interplay of host specificity and biogeography in the population structure of a cosmopolitan endoparasite: microsatellite study of Ligula intestinalis (Cestoda)

Organisms with wide geographical or phenotypic diversity often constitute assemblages of genetically distinct species or lineages. Within parasites, an emergence of host-specific lineages is assumed to create such cryptic variability; however, empirical evaluation of these processes is scarce. Here, we analyse populations of a parasite with a complex life cycle, wide host spectrum and global distribution, with the aim to reveal factors underlying the evolution of host- or geography-dependent lineages. Using 15 microsatellite loci, deep genetic distances were observed between populations from distant geographical areas. On the local scale, host-mediated genetic structure was found among sympatric samples. Two lineages differing in the spectrum of infected hosts co-occurred in the Euro-Mediterranean area, and two distinct lineages were recovered from Lake Tana in Ethiopia. Although sampled across several host taxa and multiple localities, a lack of marked genetic structure was seen in the populations belonging to one of the European lineages. Only weak genetic differentiation between sympatric samples from two host species was found. Complexity of the parasite life-cycle contributed to such a stratified pattern. Differences in the immune response between fish hosts were suggested as the factor diversifying the populations locally; conversely, high mobility of the parasite due to migration with its bird (definitive) host were assessed to homogenize populations across the area of distribution. However, despite the high mobility, large bodies of salt water prevent the parasite from long-distance migrations, as was demonstrated in an example of the Mediterranean Sea which represented an effective barrier to gene flow.     

Host specificity and incidence of Trypanosoma in some African rainforest birds: a molecular approach

Studies of host-parasite interactions in birds have contributed greatly to our understanding of the evolution and ecology of disease. Here we employ molecular techniques to determine the incidence and study the host-specificity of parasitic trypanosomes in the African avifauna. We developed a polymerase chain reaction (PCR)-based diagnostic test that amplified the small subunit ribosomal RNA gene (SSU rRNA) of Trypanosoma from avian blood samples. This nested PCR assay complements and corroborates information obtained by the traditional method of blood smear analysis. The test was used to describe the incidence of trypanosomes in 479 host individuals representing 71 rainforest bird species from Cameroon, the Ivory Coast and Equatorial Guinea. Forty-two (59%) of these potential host species harboured trypanosomes and 189 individuals (35%) were infected. To examine host and geographical specificity, we examined the morphology and sequenced a portion of the SSU rRNA gene from representative trypanosomes drawn from different hosts and collecting locations. In traditional blood smear analyses we identified two trypanosome morphospecies, T. avium and T. everetti. Our molecular and morphological results were congruent in that these two morphospecies had highly divergent SSU rRNA sequences, but the molecular assay also identified cryptic variation in T. avium, in which we found seven closely allied haplotypes. The pattern of sequence diversity within T. avium provides evidence for widespread trypanosome mixing across avian host taxa and across geographical locations. For example, T. avium lineages with identical haplotypes infected birds from different families, whereas single host species were infected by T. avium lineages with different haplotypes. Furthermore, some conspecific hosts from geographically distant sampling locations were infected with the same trypanosome lineage, but other individuals from those locations harboured different trypanosome lineages. This apparent lack of host or geographical specificity may have important consequences for the evolutionary and ecological interactions between parasitic trypanosomes and their avian hosts.     

Evolution in a multi-host parasite: Chronobiological circadian rhythm and population genetics of Schistosoma japonicum cercariae indicates contrasting definitive host reservoirs by habitat

Schistosomiasis japonica is a disease of profound medical and veterinary importance which has remained endemic in many regions and has re-emerged where previously controlled in China. Although over 40 mammalian species are suspected as reservoirs for Schistosoma japonicum, their relative roles, particularly wildlife, remain to be ascertained. As cercarial emergence is a heritable trait shaped by the definitive hosts’ behaviour, three chronobiological trials of cercarial emergence from field-collected snails from two contrasting ecological regions within China were performed, followed by genetic analyses of the parasites. Two distinct modes were identified, with late afternoon emergence mainly found in the hill region, compatible with a nocturnal rodent reservoir, and early emergence within the marshland consistent with a diurnal cattle reservoir. Furthermore, genetic analyses pointed to a clear separation between cercariae with different biological traits. The phenotypic and genotypic differentiation of the parasites identified here between and within two regions may indicate a strain complex. Such parasite diversity could, in turn, provide an explanation for the different infection scenarios observed between the two regions, and hence have important applied implications in terms of targeted control of key reservoirs.     

Knockout mutagenesis of the kpsE gene of Campylobacter jejuni 81116 and its involvement in bacterium-host interactions

Campylobacter jejuni is a common cause of bacterial enteritis. The surface capsular polysaccharides are important for this bacterium to survive in the environment, but little is known about their involvement in bacterium-host interactions. This study showed that the C. jejuni capsular polysaccharides play an important role in adherence to and invasion of human embryonic epithelial cells. However, no significant role of capsular polysaccharides was shown in colonization of the chicken gut.