Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

PURPOSE

A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains.

METHODS

T. gondii field isolates were collected from different parts of Europe and assessed by whole genome sequencing (WGS). In comparison to ME49 (a type II reference strain), highly polymorphic regions (HPRs) were identified, showing a considerable number of single nucleotide polymorphisms (SNPs). After confirmation by Sanger sequencing, 18 HPRs were used to design a primer panel for multiplex PCR to establish a multilocus Ion AmpliSeq typing method. Toxoplasma gondii isolates and T. gondii present in clinical samples were typed with the new method. The sensitivity of the method was tested with serially diluted reference DNA samples.

RESULTS

Among type II specimens, the method could differentiate the same number of haplotypes as the reference standard, microsatellite (MS) typing. Passages of the same isolates and specimens originating from abortion outbreaks were identified as identical. In addition, seven different genotypes, two atypical and two recombinant specimens were clearly distinguished from each other by the method. Furthermore, almost all SNPs detected by the Ion AmpliSeq method corresponded to those expected based on WGS. By testing serially diluted DNA samples, the method exhibited a similar analytical sensitivity as MS typing.

CONCLUSION

The new method can distinguish different T. gondii genotypes and detect intra-genotype variability among European type II T. gondii strains. Furthermore, with WGS data additional target regions can be added to the method to potentially increase typing resolution.

The effect of thermal treatments on the viability and infectivity of Cryptosporidium parvum on beef surfaces

AIMS

The aim of this research was to examine the effect of thermal treatments on the viability and infectivity of Cryptosporidium parvum oocysts attached to a beef surface.

METHODS AND RESULTS

This study examined the effects of heat treatment (60 or 75 degrees C) on the viability of C. parvum oocysts inoculated onto the surface of beef muscle estimated by vital dye assay. The infectivity of the oocysts was assessed against monolayers of HCT-8 cells. At 60 degrees C viability of the oocysts decreased from 100% at T0 to 64.2% at T60. At 75 degrees C the viability of the oocysts decreased from 100% at T0 to 53.7% at T15 and finally to 11.2% at T60. Oocysts were rendered noninfective against monolayers of HCT-8 cells following treatments of 60 degrees C/45 s and 75 degrees C/20 s.

CONCLUSION

The washing of carcasses with hot water and standard thermal treatments is sufficient to kill C. parvum on beef.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study found that relatively mild heat, currently used to decontaminate and heat treat beef carcasses and to cook meat products, is capable of inactivating C. parvum.

Genotyping Cryptosporidium parvum by single-strand conformation polymorphism analysis of ribosomal and heat shock gene regions

Polymerase chain reaction (PCR)-coupled single-strand conformation polymorphism (SSCP) approaches utilizing nuclear DNA regions of the small subunit (SSU) of ribosomal RNA and heat shock protein 70 gene (HSP70) were established for genotyping Cryptosporidium parvum. The regions were amplified (individually or in a multiplex reaction) by PCR from DNA extracted from oocysts from ruminant or human hosts, then denatured and subjected to electrophoresis in a mutation detection enhancement (nondenaturing) gel matrix. Single-strand profiles produced in SSCP allowed the unequivocal identification/differentiation of the two common (human, 1 and cattle, 2) genotypes of C. parvum and the direct display of sequence variability within some samples, reflecting population variation. As these are considered among the most closely related genotypes (based on SSU and HSP70 sequence data), these findings and other preliminary results for C. felis (from cat) C. serpentis (from snake) and C. baileyi (from bird) indicate that the SSCP approaches established could be employed to identify any of the currently recognised genotypes and species of Cryptosporidium.

Compositional mapping of mouse chromosomes and identification of the gene-rich regions

The mouse genome is a mosaic of isochores, consisting of long (> 300 kb), compositionally homogeneous DNA segments that can be divided into two GC-poor families, L1 and L2, representing 56% of the genome, and two GC-rich families, H1 and H2, representing 26% and 7% of the genome, respectively, the remaining 11% being formed by satellite and ribosomal DNAs. (GC is the molar fraction of guanine + cytosine in DNA.) The mouse genome differs from the human genome (which is representative of most mammalian genomes) because it shows a narrower compositional spectrum of isochores and it has a karyotype formed exclusively by acrocentric chromosomes. The chromosomal distribution of the four isochore families, as investigated here by in situ hybridization of single-copy sequences from compositional DNA fractions, has shown that G(lemsa) bands are essentially composed of GC-poor isochores, whereas R(everse) bands comprise three subsets of bands: R' bands, containing GC-poor isochores and GC-rich isochores of the H1 family, and T and T' bands, containing all H2 isochores (in addition to other isochores), the former containing a higher proportion of H2 isochores than the latter. Mouse T and T' bands are generally syntenic with, and are compositionally related to, human T and T' bands and have the highest gene concentrations. These findings indicate that the distribution of isochore families and genes in chromosomal bands is basically similar in mouse and in human genomes, in spite of their remarkable differences and their extremely large phylogenetic distance.

MtDNA polymorphisms in a sample of Czechoslovaks and in two groups of Italians

Mitochondrial DNA (mtDNA) variation was investigated in a group of 185 unrelated individuals (64 Czechoslovaks, 99 Northern and 28 Central Italians) using total blood DNA and the six restriction enzymes HpaI, BamHI, HaeII, MspI, AvaII and HincII. Among the 25 patterns (morphs) found, two morphs for HaeII, one for MspI and one for AvaII were new and each was represented by a single individual from Northern Italy. They account for four of the five new types encountered in this survey, being the fifth type characterized by the presence of the very rare morph HaeII-13. The populations analysed confirm the Caucasoid characteristics of certain polymorphisms. A review of the European data available so far is reported.

Molecular phylogeny of bony fishes, based on the amino acid sequence of the growth hormone

Bony fishes (Osteichthyes) comprise over 22,000 species, about half of all vertebrate species. In order to investigate the phylogenetic relationships within this vertebrate class, we have studied the only protein whose primary structure is known in a rather large (27) number of fish species belonging to seven orders--the growth hormone. The phylogeny obtained using the maximum parsimony method based on amino acid sequences represents the first molecular phylogeny of teleostean fishes based on an extensive set of data. This phylogeny agrees remarkably well with the generally accepted phylogeny based on morphological characters and paleontological data.