Whole-genome sequencing of dog-specific assemblages C and D of Giardia duodenalis from single and pooled cysts indicates host-associated genes

Zoonotic Cryptosporidium and Giardia in marsupials-an update

Marsupials, inhabiting diverse ecosystems, including urban and peri-urban regions in Australasia and the Americas, intersect with human activities, leading to zoonotic spill-over and anthroponotic spill-back of pathogens, including Cryptosporidium and Giardia. This review assesses the current knowledge on the diversity of Cryptosporidium and Giardia species in marsupials, focusing on the potential zoonotic risks. Cryptosporidium fayeri and C. macropodum are the dominant species in marsupials, while in possums, the host-specific possum genotype dominates. Of these three species/genotypes, only C. fayeri has been identified in two humans and the zoonotic risk is considered low. Generally, oocyst shedding in marsupials is low, further supporting a low transmission risk. However, there is some evidence of spill-back of C. hominis into kangaroo populations, which requires continued monitoring. Although C. hominis does not appear to be established in small marsupials like possums, comprehensive screening and analysis are essential for a better understanding of the prevalence and potential establishment of zoonotic Cryptosporidium species in small marsupials. Both host-specific and zoonotic Giardia species have been identified in marsupials. The dominance of zoonotic G. duodenalis assemblages A and B in marsupials may result from spill-back from livestock and humans and it is not yet understood if these are transient or established infections. Future studies using multilocus typing tools and whole-genome sequencing are required for a better understanding of the zoonotic risk from Giardia infections in marsupials. Moreover, much more extensive screening of a wider range of marsupial species, particularly in peri-urban areas, is required to provide a clearer understanding of the zoonotic risk of Cryptosporidium and Giardia in marsupials.

Phylogenomics of Acinetobacter species and analysis of antimicrobial resistance genes

Introduction

Non-baumannii Acinetobacter species are increasingly isolated in the clinical setting and the environment. The aim of the present study was to analyze a genome database of 837 Acinetobacter spp. isolates, which included 798 non-baumannii Acinetobacter genomes, in order to define the concordance of classification and discriminatory power of 7-gene MLST, 53-gene MLST, and single-nucleotide polymorphism (SNPs) phylogenies.

Methods

Phylogenies were performed on Pasteur Multilocus Sequence Typing (MLST) or ribosomal Multilocus Sequence Typing (rMLST) concatenated alleles, or SNPs extracted from core genome alignment.

Results

The Pasteur MLST scheme was able to identify and genotype 72 species in the Acinetobacter genus, with classification results concordant with the ribosomal MLST scheme. The discriminatory power and genotyping reliability of the Pasteur MLST scheme were assessed in comparison to genome-wide SNP phylogeny on 535 non-baumannii Acinetobacter genomes assigned to Acinetobacter pittii, Acinetobacter nosocomialis, Acinetobacter seifertii, and Acinetobacter lactucae (heterotypic synonym of Acinetobacter dijkshoorniae), which were the most clinically relevant non-baumannii species of the A. baumannii group. The Pasteur MLST and SNP phylogenies were congruent at Robinson-Fould and Matching cluster tests and grouped genomes into four and three clusters in A. pittii, respectively, and one each in A. seifertii. Furthermore, A. lactucae genomes were grouped into one cluster within A. pittii genomes. The SNP phylogeny of A. nosocomialis genomes showed a heterogeneous population and did not correspond to the Pasteur MLST phylogeny, which identified two recombinant clusters. The antimicrobial resistance genes belonging to at least three different antimicrobial classes were identified in 91 isolates assigned to 17 distinct species in the Acinetobacter genus. Moreover, the presence of a class D oxacillinase, which is a naturally occurring enzyme in several Acinetobacter species, was found in 503 isolates assigned to 35 Acinetobacter species.

Conclusion

In conclusion, Pasteur MLST phylogeny of non-baumannii Acinetobacter isolates coupled with in silico detection of antimicrobial resistance makes it important to study the population structure and epidemiology of Acinetobacter spp. isolates.

Genomic comparisons confirm Giardia duodenalis sub-assemblage AII as a unique species

Giardia duodenalis is a parasitic flagellated protozoan which infects a wide range of mammalian hosts, including humans, and is subdivided into at least eight genetic assemblages commonly thought to represent cryptic species. Molecular studies have shown that G. duodenalis assemblage A, which parasitizes humans and animals, contains several phylogenetically distinct groupings known as sub-assemblages. Molecular studies employing poor phylogenetic-resolution markers routinely recover these sub-assemblages, implying that they represent evolutionarily distinct clades and possibly cryptic species, a hypothesis which is supported by epidemiologic trends. Here, we further tested this hypothesis by using available data from 41 whole genomes to characterize sub-assemblages and coalescent techniques for statistical estimation of species boundaries coupled to functional gene content analysis, thereby assessing the stability and distinctiveness of clades. Our analysis revealed two new sub-assemblage clades as well as novel signatures of gene content geared toward differential host adaptation and population structuring via vertical inheritance rather than recombination or panmixia. We formally propose sub-assemblage AII as a new species, Giardia hominis, while preserving the name Giardia duodenalis for sub-assemblage AI. Additionally, our bioinformatic methods broadly address the challenges of identifying cryptic microbial species to advance our understanding of emerging disease epidemiology, which should be broadly applicable to other lower eukaryotic taxa of interest. Giardia hominis n. sp. Zoobank LSID: urn:lsid: zoobank.org:pub:4298F3E1-E3EF-4977-B9DD-5CC59378C80E.

Multilocus Genotyping of Giardia duodenalis in Alpine Musk Deer (Moschus chrysogaster) in China

Giardia duodenalis is the underlying cause of a significant number of outbreaks of gastrointestinal illness in humans and animals worldwide. The purpose of this study was to elucidate the prevalence and genetic diversity of G. duodenalis in captive alpine musk deer (Moschus chrysogaster) in China. A total of 202 fecal samples were collected from three farms in Gansu Province, China. Identification of G. duodenalis was conducted by nested PCR targeting the genes coding for SSU rRNA, β-giardin (bg), glutamate dehydrogenase (gdh) and triosephosphate isomerase (tpi). The overall prevalence of G. duodenalis in captive alpine musk deer in surveyed area was 19.3% (39/202). Two G. duodenalis genetic assemblages were identified, namely assemblage A and E. Mixed genotype infections (A+E) were found in 15.4% (6/39) of positive samples. Multilocus genotyping (MLG) analysis of G. duodenalis isolates revealed six novel assemblage A MLGs formed by two newly-described MLG-subtypes which belonged to sub-assemblage AI. To the best of our knowledge, this is the first report on MLG of G. duodenalis isolates in captive alpine musk deer in China. The presence of zoonotic assemblages and sub-assemblages of G. duodenalis in deer species suggests that these animals may potentially act as a reservoir of this protozoan for humans.

Giardia duodenalis Virulence - "To Be, or Not To Be"

Purpose of review

Here, we review recent progress made on the genetic characterization of Giardia duodenalis assemblages and their relationship with virulence. We also discuss the implications of virulence factors in the pathogenesis of giardiasis, and advances in the development of vaccines and drugs based on knowledge of virulence markers.

Recent findings

The use of transcriptomic and proteomic technologies as well as whole genome sequencing (WGS) from single cysts has allowed the assembly of the draft genome sequences for assemblages C and D of G. duodenalis. These findings, along with the published genomes for assemblages A, B, and E, have allowed comparative genomic investigations. In addition, the use of these methodologies for the characterization of the secretomes of trophozoite-epithelial cell interactions for assemblages A/B has led to the identification of virulence markers including energy metabolism enzymes, proteinases, high-cysteine membrane proteins (HCMPs), and variant surface proteins (VSPs). Recently, some drugs and vaccines, targeting virulence factors have been developed, offering possible alternatives to current treatment and prevention options against giardiasis.

Summary

Among the nine recognized species of Giardia, G. duodenalis stands out because of its broad spectrum of hosts and its socio-economic importance. This species comprises eight genetic assemblages (A to H), of which A and B are zoonotic, and the other assemblages have narrow host specificities. Assemblages A and B may be considered as the most virulent ones, but the existence of asymptomatic carriers and considerable genetic variability within and among these assemblages hampers the definition of common virulence factors. The attachment of Giardia trophozoites to epithelial cells and structural cytoskeleton components of the adhesive disk, such as giardins or tubulins, is proposed to play key roles, but toxins have not yet been precisely defined. However, recent transcriptomic and proteomic analyses of the secretomes of trophozoites representing assemblages A and B and interacting with particular epithelial cell lines have defined a series of virulence factors, including glycolytic (e.g., enolase) and arginolytic (e.g., arginine deiminase) enzymes, cysteine proteases (e.g., giardipain-1) and VSPs (e.g., VSP9B10A). Other factors, such as HCMPs and tenascins, have been consistently found to be excreted/secreted, but their role(s) in the pathogenesis of giardiasis has not yet been elucidated. Interestingly, recent investigations of single cysts representing assemblages C and D using advanced sequencing and informatic methods have suggested that the transcription/expression profiles of virulence factors vary both within and between assemblages, thus assemblage-specific molecules might allow adaptation to the microenvironment within the host. Importantly, some drugs active against cysteine-rich proteins of Giardia, including giardipain-1, VSPs and arginine deiminase, have been shown to be targeted by cysteine-modifying compounds as disulfiram, L-canavanin and allicin. On the other hand, VSPs are presently considered as key vaccine candidates because they induce protection against Giardia in rodents and dogs. Overall, this review reveals that much more work is needed to identify, characterize, and understand the roles of virulence factors in Giardia and to assess their validity as drug and vaccine targets. Clear, advanced omics and informatic tools should assist in this future endeavor, with a focus on targeting virulence factors that are common and/or unique to distinct assemblages to develop new and effective interventions against Giardia.

Zoonotic giardiasis: an update

Giardia duodenalis is a common intestinal parasite in various hosts, with the disease giardiasis being a zoonosis. The use of molecular typing tools has improved our understanding of the distribution and zoonotic potential of G. duodenalis genotypes in different animals. The present review summarizes recent data on the distribution of G. duodenalis genotypes in humans and animals in different areas. The dominance of G. duodenalis assemblages A and B in humans and common occurrence of host-adapted assemblages in most domesticated animals suggests that zoonotic giardiasis is probably less common than believed and could be attributed mainly to contact with or contamination from just a few species of animals such as nonhuman primates, equines, rabbits, guinea pigs, chinchillas, and beavers. Future studies should be directed to advanced genetic characterization of isolates from well-designed epidemiological investigations, especially comparative analyses of isolates from humans and animals living in the same household or community. This will likely lead to better understanding of zoonotic transmission of G. duodenalis in different environmental and socioeconomic settings.

Giardia duodenalis: Biology and Pathogenesis

Giardia duodenalis captured the attention of Leeuwenhoek in 1681 while he was examining his own diarrheal stool, but, ironically, it did not really gain attention as a human pathogen until the 1960s, when outbreaks were reported. Key technological advances, including in vitro cultivation, genomic and proteomic databases, and advances in microscopic and molecular approaches, have led to an understanding that this is a eukaryotic organism with a reduced genome rather than a truly premitochondriate eukaryote. This has included the discovery of mitosomes (vestiges of mitochondria), a transport system with many of the features of the Golgi apparatus, and even evidence for a sexual or parasexual cycle. Cell biology approaches have led to a better understanding of how Giardia survives with two nuclei and how it goes through its life cycle as a noninvasive organism in the hostile environment of the lumen of the host intestine. Studies of its immunology and pathogenesis have moved past the general understanding of the importance of the antibody response in controlling infection to determining the key role of the Th17 response. This work has led to understanding of the requirement for a balanced host immune response that avoids the extremes of an excessive response with collateral damage or one that is unable to clear the organism. This understanding is especially important in view of the remarkable ranges of early manifestations, which range from asymptomatic to persistent diarrhea and weight loss, and longer-term sequelae that include growth stunting in children who had no obvious symptoms and a high frequency of postinfectious irritable bowel syndrome (IBS).

Suitability of current typing procedures to identify epidemiologically linked human Giardia duodenalis isolates

Background

Giardia duodenalis is a leading cause of gastroenteritis worldwide. Humans are mainly infected by two different subtypes, i.e., assemblage A and B. Genotyping is hampered by allelic sequence heterozygosity (ASH) mainly in assemblage B, and by occurrence of mixed infections. Here we assessed the suitability of current genotyping protocols of G. duodenalis for epidemiological applications such as molecular tracing of transmission chains.

Methodology/Principal findings

Two G. duodenalis isolate collections, from an outpatient tropical medicine clinic and from several primary care laboratories, were characterized by assemblage-specific qPCR (TIF, CATH gene loci) and a common multi locus sequence typing (MLST; TPI, BG, GDH gene loci). Assemblage A isolates were further typed at additional loci (HCMP22547, CID1, RHP26, HCMP6372, DIS3, NEK15411).

Of 175/202 (86.6%) patients the G. duodenalis assemblage could be identified: Assemblages A 25/175 (14.3%), B 115/175 (65.7%) and A+B mixed 35/175 (20.0%). By incorporating allelic sequence heterozygosity in the analysis, the three marker MLST correctly identified 6/9 (66,7%) and 4/5 (80.0%) consecutive samples from chronic assemblage B infections in the two collections, respectively, and identified a cluster of five independent patients carrying assemblage B parasites of identical MLST type. Extended MLST for assemblage A altogether identified 5/6 (83,3%) consecutive samples from chronic assemblage A infections and 15 novel genotypes. Based on the observed A+B mixed infections it is estimated that only 75% and 50% of assemblage A or B only cases represent single strain infections, respectively. We demonstrate that typing results are consistent with this prediction.

Conclusions/Significance

Typing of assemblage A and B isolates with resolution for epidemiological applications is possible but requires separate genotyping protocols. The high frequency of multiple infections and their impact on typing results are findings with immediate consequences for result interpretation in this field.

Giardia duodenalis is a leading cause of gastroenteritis worldwide. Humans are mainly infected by the two different genetic subtypes, assemblage A and B. Molecular typing tools for epidemiological applications such as tracking transmission, attribution to a source and outbreak investigations have been developed and are highly desirable. However, to what degree the tetraploid genome with allelic sequence heterogeneity (ASH), and the frequent occurrence of mixed, assemblage A and B infections hamper performance is unclear. Here, we assessed the suitability of current genotyping protocols for deciphering the molecular epidemiology of G. duodenalis. Against a common reporting bias, we incorporated ASH in the analysis and we show that typing with resolution for epidemiological applications is possible for both, assemblage A and B isolates, but requires separate protocols. We also demonstrate how the high frequency of multiple infections overall impacts on typing results, which has immediate consequences for result interpretation in this field.

Update on Giardia: Highlights from the seventh International Giardia and Cryptosporidium Conference

Although Giardia duodenalis is recognized as one of the leading causes of parasitic human diarrhea in the world, knowledge of the mechanisms of infection is limited, as the pathophysiological consequences of infection remain incompletely elucidated. Similarly, the reason for and consequences of the very specific genome-organization in this parasite with 2 active nuclei is only partially known. Consistent with its tradition, the 7th International Giardia and Cryptosporidium Conference (IGCC 2019) was held from June 23 to 26, 2019, at the Faculty of Medicine and Pharmacy of the University of Rouen-Normandie, France, to discuss current research perspectives in the field. This renowned event brought together an international delegation of researchers to present and debate recent advances and identify the main research themes and knowledge gaps. The program for this interdisciplinary conference included all aspects of host-parasite relationships, from basic research to applications in human and veterinary medicine, as well as the environmental issues raised by water-borne parasites and their epidemiological consequences. With regard to Giardia and giardiasis, the main areas of research for which new findings and the most impressive communications were presented and discussed included: parasite ecology and epidemiology of giardiasis, Giardia-host interactions, and cell biology of Giardia, genomes and genomic evolution. The high-quality presentations discussed at the Conference noted breakthroughs and identified new opportunities that will inspire researchers and funding agencies to stimulate future research in a “one health” approach to improve basic knowledge and clinical and public health management of zoonotic giardiasis.

A chromosome-scale reference genome for Giardia intestinalis WB

Giardia intestinalis is a protist causing diarrhea in humans. The first G. intestinalis genome, from the WB isolate, was published more than ten years ago, and has been widely used as the reference genome for Giardia research. However, the genome is fragmented, thus hindering research at the chromosomal level. We re-sequenced the Giardia genome with Pacbio long-read sequencing technology and obtained a new reference genome, which was assembled into near-complete chromosomes with only four internal gaps at long repeats. This new genome is not only more complete but also better annotated at both structural and functional levels, providing more details about gene families, gene organizations and chromosomal structure. This near-complete reference genome will be a valuable resource for the Giardia community and protist research. It also showcases how a fragmented genome can be improved with long-read sequencing technology completed with optical maps.

Measurement(s)	DNA • sequence_assembly • sequence feature annotation
Technology Type(s)	DNA sequencing • sequence assembly process • sequence annotation
Sample Characteristic - Organism	Giardia intestinalis

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11695659