Quantifying Replication Slippage Error in Cryptosporidium Metabarcoding Studies.

Genetic variation in Cryptosporidium, a common protozoan gut parasite in humans, is often based on marker genes containing trinucleotide repeats, which differentiate subtypes and track outbreaks. However, repeat regions have high replication slippage rates, making it difficult to discern biological diversity from error. Here, we synthesized Cryptosporidium DNA in clonal plasmid vectors, amplified them in different mock community ratios, and sequenced them using next-generation sequencing to determine the rate of replication slippage with dada2. Our results indicate that slippage rates increase with the length of the repeat region and can contribute to error rates of up to 20%.

Ectoparasite and bacterial population genetics and community structure indicate extent of bat movement across an island chain.

Few studies have examined the genetic population structure of vector-borne microparasites in wildlife, making it unclear how much these systems can reveal about the movement of their associated hosts. This study examined the complex host­vector­microbe interactions in a system of bats, wingless ectoparasitic bat flies (Nycteribiidae), vector-borne microparasitic bacteria (Bartonella) and bacterial endosymbionts of flies (Enterobacterales) across an island chain in the Gulf of Guinea, West Africa. Limited population structure was found in bat flies and Enterobacterales symbionts compared to that of their hosts. Significant isolation by distance was observed in the dissimilarity of Bartonella communities detected in flies from sampled populations of Eidolon helvum bats. These patterns indicate that, while genetic dispersal of bats between islands is limited, some non-reproductive movements may lead to the dispersal of ectoparasites and associated microbes. This study deepens our knowledge of the phylogeography of African fruit bats, their ectoparasites and associated bacteria. The results presented could inform models of pathogen transmission in these bat populations and increase our theoretical understanding of community ecology in host­microbe systems.

A review and analysis of cryptosporidiosis outbreaks in New Zealand.

Cryptosporidium is a leading global cause of diarrhoea with many reported outbreaks related to water and zoonotic transmission. This study summarizes data from Public Health Surveillance reports since 2010 in New Zealand to describe exposures associated with human diarrhoea outbreaks caused by Cryptosporidium. We investigate the species and subtypes of cases involved in some of the outbreaks to elucidate transmission routes and the predominant aetiological agents of cryptosporidiosis. For the period 2010­2017, 318 cryptosporidiosis outbreaks were reported in New Zealand resulting in 1634 cases and 20 hospitalizations. The most important mode of transmission was person-to-person (primary infections and secondary or close contacts infections), relating to 260 outbreaks and 1320 cases, followed by 113 outbreaks associated with animals, resulting in 436 human cases. From 2018 to 2021, there were 37 cryptosporidiosis outbreaks associated with 324 cases. We identified the subtypes by using polymerase chain reaction targeting the gp60 gene and the likelihood of mixed subtype infections with the Tracking of Indels by DEcomposition (TIDE) algorithm. Subtype families Ib and Ig of Cryptosporidium hominis and IIa and IId of Cryptosporidium parvum were found among cases; however, C. hominis subtypes occurred in 8 of the 11 outbreaks reviewed where molecular data were available. Examination of the chromatograms showed no mixed subtype infections in the samples assessed. Subtyping data need to be routinely incorporated into national surveillance programmes to better understand the epidemiology, sources, transmission and extent of cryptosporidiosis outbreaks in New Zealand. Our study highlights the value of integrating epidemiological information and molecular typing to investigate and manage clusters of cryptosporidiosis cases.

Mammal-related Cryptosporidium infections in endemic reptiles of New Zealand.

New Zealand's endemic reptile fauna is highly threatened and pathogens causing infectious diseases may be a significant risk to already endangered species. Here, we investigate Cryptosporidium infection in captive endemic New Zealand reptiles. We found two mammal-related Cryptosporidium species (C. hominis and C. parvum) and six subtypes from three gp60 families (Ib, Ig and IIa) in 12 individuals of captive endemic Tuatara, Otago and Grand skinks, and Jewelled and Rough geckos. Cryptosporidium serpentis was identified in two Jewelled geckos using 18S. In New Zealand, C. hominis and C. parvum are associated with infections in humans and introduced domestic animals but have also been recently found in wildlife. Our finding of Cryptosporidium infection in endemic reptiles can help inform strategies to monitor the conservation of species and manage potential introductions of pathogens to in-situ and ex-situ populations.

Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health.

Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of viral spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus), given that several closely related viruses have been discovered and sarbecovirus-host interactions have gained attention since SARS-CoV-2 emergence. We assessed sampling biases and modelled current distributions of bats based on climate and landscape relationships and project future scenarios for host hotspots. The most important predictors of species distributions were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in locations greater than 2°C hotter in a fossil-fuelled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.

Possibility for reverse zoonotic transmission of SARS-CoV-2 to free-ranging wildlife: A case study of bats.

The COVID-19 pandemic highlights the substantial public health, economic, and societal consequences of virus spillover from a wildlife reservoir. Widespread human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also presents a new set of challenges when considering viral spillover from people to naïve wildlife and other animal populations. The establishment of new wildlife reservoirs for SARS-CoV-2 would further complicate public health control measures and could lead to wildlife health and conservation impacts. Given the likely bat origin of SARS-CoV-2 and related beta-coronaviruses (ß-CoVs), free-ranging bats are a key group of concern for spillover from humans back to wildlife. Here, we review the diversity and natural host range of ß-CoVs in bats and examine the risk of humans inadvertently infecting free-ranging bats with SARS-CoV-2. Our review of the global distribution and host range of ß-CoV evolutionary lineages suggests that 40+ species of temperate-zone North American bats could be immunologically naïve and susceptible to infection by SARS-CoV-2. We highlight an urgent need to proactively connect the wellbeing of human and wildlife health during the current pandemic and to implement new tools to continue wildlife research while avoiding potentially severe health and conservation impacts of SARS-CoV-2 "spilling back" into free-ranging bat populations.

Genomic and phenotypic comparison of two Salmonella Typhimurium strains responsible for consecutive salmonellosis outbreaks in New Zealand.

Salmonella enterica serovar Typhimurium DT160 was the predominant cause of notified human salmonellosis cases in New Zealand from 2000 to 2010, before it was superseded by another S. Typhimurium strain, DT56 variant (DT56v). Whole genome sequencing and phenotypic testing were used to compare 109 DT160 isolates with eight DT56v isolates from New Zealand animal and human sources. Phylogenetic analysis provided evidence that DT160 and DT56v strains were distantly related with an estimated date of common ancestor between 1769 and 1821. The strains replicated at different rates but had similar antimicrobial susceptibility profiles. Both strains were resistant to the phage expressed from the chromosome of the other strain, which may have contributed to the emergence of DT56v. DT160 contained the pSLT virulence plasmid, and the sseJ and sseK2 genes that may have contributed to the higher reported prevalence compared to DT56v. A linear pBSSB1-family plasmid was also found in one of the DT56v isolates, but there was no evidence that this plasmid affected bacterial replication or antimicrobial susceptibility. One of the DT56v isolates was also sequenced using long-read technology and found to contain an uncommon chromosome arrangement for a Typhimurium isolate. This study demonstrates how comparative genomics and phenotypic testing can help identify strain-specific elements and factors that may have influenced the emergence and supersession of bacterial strains of public health importance.

Comparative genetic diversity of Cryptosporidium species causing human infections.

Parasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation in Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of Cryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominis and Cryptosporidium parvum. A deviation of expected values of neutrality using Tajima's D was observed in C. cuniculus and C. meleagridis. The high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima's D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.

Species and genotypes causing human cryptosporidiosis in New Zealand.

Cryptosporidium is one of the most common causes of diarrhoea around the world. Successful management and prevention of this infectious disease requires knowledge of the diversity of species and subtypes causing human disease. We use sequence data from 2598 human faecal samples collected during an 11-year period (2009-2019) to better understand the impact of different species and subtypes on public health and to gain insights into the variation of human cryptosporidiosis in New Zealand. Human cryptosporidiosis in New Zealand is caused by a high diversity of species and subtypes. Six species cause human disease in New Zealand: C. hominis, C. parvum, C. cuniculus, C. erinacei, C. meleagridis and C. tyzzeri. Sequence analysis of the gp60 gene identified 16 subtype families and 101 subtypes. Cryptosporidium hominis IbA10G2 and C. parvum IIaA18G3R1 were the most frequent causes of human cryptosporidiosis with 27% and 29% of infections, respectively. Cryptosporidium hominis presented a peak of notified human cases during autumn (March-May) whereas most cases of human cryptosporidiosis caused by C. parvum are found during the calving and lambing season in spring (September-November). We also reported some subtypes that have been rarely detected in other countries such as IbA20G2 and IIoA13G1 and a low prevalence of the hypertransmissible and virulent IIaA15G2R1. This study provides insight into the variability of cryptosporidiosis in New Zealand essential for disease management and surveillance to prevent the introduction or spread of new species and subtypes in the country.

Bats are not squirrels: Revisiting the cost of cooling in hibernating mammals.

Many species use stored energy to hibernate through periods of resource limitation. Hibernation, a physiological state characterized by depressed metabolism and body temperature, is critical to winter survival and reproduction, and therefore has been extensively quantified and modeled. Hibernation consists of alternating phases of extended periods of torpor (low body temperature, low metabolic rate), and energetically costly periodic arousals to normal body temperature. Arousals consist of multiple phases: warming, euthermia, and cooling. Warming and euthermic costs are regularly included in energetic models, but although cooling to torpid body temperature is an important phase of the torpor-arousal cycle, it is often overlooked in energetic models. When included, cooling cost is assumed to be 67% of warming cost, an assumption originally derived from a single study that measured cooling cost in ground squirrels. Since this study, the same proportional value has been assumed across a variety of hibernating species. However, no additional values have been derived. We derived a model of cooling cost from first principles and validated the model with empirical energetic measurements. We compared the assumed 67% proportional cooling cost with our model-predicted cooling cost for 53 hibernating mammals. Our results indicate that using 67% of warming cost only adequately represents cooling cost in ground squirrel-sized mammals. In smaller species, this value overestimates cooling cost and in larger species, the value underestimates cooling cost. Our model allows for the generalization of energetic costs for multiple species using species-specific physiological and morphometric parameters, and for predictions over variable environmental conditions.

Long-term Colonization by Campylobacter jejuni Within a Human Host: Evolution, Antimicrobial Resistance, and Adaptation.

Background: Campylobacteriosis is inflammation of the gastrointestinal tract as a result of Campylobacter infection. Most campylobacteriosis cases are acute and self-limiting, with Campylobacter excretion ceasing a few weeks after symptoms cease. We identified a patient with fecal specimens positive for Campylobacter jejuni (ST45) intermittently during a 10-year period. Methods: Sixteen Campylobacter isolates were collected from the patient during 2006-2016. The isolates' genomes were sequenced to determine their relatedness, and their antimicrobial susceptibility patterns and motility were measured to determine the effects of antibiotic therapy and long-term excretion on the Campylobacter population. Results: Phylogenetic analyses estimated that the isolates shared a date of common ancestor between 1998 and 2006, coinciding with the onset of symptoms for the patient. Genomic analysis identified selection for changes in motility, and antimicrobial susceptibility testing suggested that the Campylobacter population developed resistance to several antibiotics coinciding with periods of antibiotic therapy. Conclusions: The patient was consistently colonized with organisms from a Campylobacter population that adapted to the internal environment of the patient. Genomic and phylogenetic analyses can give insight into a patient's infection history and the effect of antimicrobial treatment on Campylobacter populations in this unusual situation of long-term colonization of an individual.

Genomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012.

During 1998-2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time. The genetic heterogeneity was evenly distributed across multiple predicted functional protein groups, and we found no evidence of host group differentiation between isolates collected from human, poultry, bovid, and wild bird sources, indicating ongoing transmission between these host groups. Our findings demonstrate how a comparative genomic approach can be used to gain insight into outbreaks, disease transmission, and the evolution of a multihost pathogen after a probable point-source introduction.

Behavior of bats at wind turbines.

Wind turbines are causing unprecedented numbers of bat fatalities. Many fatalities involve tree-roosting bats, but reasons for this higher susceptibility remain unknown. To better understand behaviors associated with risk, we monitored bats at three experimentally manipulated wind turbines in Indiana, United States, from July 29 to October 1, 2012, using thermal cameras and other methods. We observed bats on 993 occasions and saw many behaviors, including close approaches, flight loops and dives, hovering, and chases. Most bats altered course toward turbines during observation. Based on these new observations, we tested the hypotheses that wind speed and blade rotation speed influenced the way that bats interacted with turbines. We found that bats were detected more frequently at lower wind speeds and typically approached turbines on the leeward (downwind) side. The proportion of leeward approaches increased with wind speed when blades were prevented from turning, yet decreased when blades could turn. Bats were observed more frequently at turbines on moonlit nights. Taken together, these observations suggest that bats may orient toward turbines by sensing air currents and using vision, and that air turbulence caused by fast-moving blades creates conditions that are less attractive to bats passing in close proximity. Tree bats may respond to streams of air flowing downwind from trees at night while searching for roosts, conspecifics, and nocturnal insect prey that could accumulate in such flows. Fatalities of tree bats at turbines may be the consequence of behaviors that evolved to provide selective advantages when elicited by tall trees, but are now maladaptive when elicited by wind turbines.

Evolutionary processes in populations of Cryptosporidium inferred from gp60 sequence data.

Cryptosporidiosis is one of the most common human infectious diseases globally. The gp60 gene has been adopted as a key marker for molecular epidemiological investigations into this protozoan disease because of the capability to characterize genotypes and detect variants within Cryptosporidium species infecting humans. However, we know relatively little about the potential spatial and temporal variation in population demography that can be inferred from this gene beyond that it is recognized to be under selective pressure. Here, we analyzed the genetic variation in time and space within two putative populations of Cryptosporidium in New Zealand to infer the processes behind the patterns of sequence polymorphism. Analyses using Tajima's D, Fu, and Li's D* and F* tests show significant departures from neutrality in some populations and indicate the selective maintenance of alleles within some populations. Demographic analyses showed distortions in the pattern of the genetic variability caused by high recombination rates and population expansion, which was observed in case notification data. Our results showed that processes acting on populations that have similar effects can be distinguished from one another and multiple processes can be detected acting at the same time. These results are significant for prediction of the parasite dynamics and potential mechanisms of long-term changes in the risk of cryptosporidiosis in humans.

Origin of a major infectious disease in vertebrates: The timing of Cryptosporidium evolution and its hosts.

Protozoan parasites of the genus Cryptosporidium infect all vertebrate groups and display some host specificity in their infections. It is therefore possible to assume that Cryptosporidium parasites evolved intimately aside with vertebrate lineages. Here we propose a scenario of Cryptosporidium-Vertebrata coevolution testing the hypothesis that the origin of Cryptosporidium parasites follows that of the origin of modern vertebrates. We use calibrated molecular clocks and cophylogeny analyses to provide and compare age estimates and patterns of association between these clades. Our study provides strong support for the evolution of parasitism of Cryptosporidium with the rise of the vertebrates about 600 million years ago (Mya). Interestingly, periods of increased diversification in Cryptosporidium coincides with diversification of crown mammalian and avian orders after the Cretaceous-Palaeogene (K-Pg) boundary, suggesting that adaptive radiation to new mammalian and avian hosts triggered the diversification of this parasite lineage. Despite evidence for ongoing host shifts we also found significant correlation between protozoan parasites and vertebrate hosts trees in the cophylogenetic analysis. These results help us to understand the underlying macroevolutionary mechanisms driving evolution in Cryptosporidium and may have important implications for the ecology, dynamics and epidemiology of cryptosporidiosis disease in humans and other animals.

Can survival analyses detect hunting pressure in a highly connected species? Lessons from straw-coloured fruit bats.

Animal behaviour, social structure and population dynamics affect community structure, interspecific interactions, and a species' resilience to harvesting. Building on new life history information for the straw-coloured fruit bat (Eidolon helvum) from multiple localities across Africa, we used survival analyses based on tooth-cementum annuli data to test alternative hypotheses relating to hunting pressure, demography and population connectivity. The estimated annual survival probability across Africa was high (≥ 0.64), but was greatest in colonies with the highest proportion of males. This difference in sex survival, along with age and sex capture biases and out-of-phase breeding across the species' distribution, leads us to hypothesize that E. helvum has a complex social structure. We found no evidence for additive mortality in heavily hunted populations, with most colonies having high survival with constant risk of mortality despite different hunting pressure. Given E. helvum's slow life history strategy, similar survival patterns and rate among colonies suggest that local movement and regional migration may compensate for local excess hunting, but these were also not clearly detected. Our study suggests that spatio-temporal data are necessary to appropriately assess the population dynamics and conservation status of this and other species with similar traits.