Molecular Characteristics of Cryptosporidium spp. in Human Cases in Five Finnish Hospital Districts during 2021
Description
Aims of this study were to characterise the species and subtype distribution of Cryptosporidium infections in Five Finnish hospital districts during 2021. This dataset contains data on 60 clinical Cryptosporidium cases from the hospital districts of Helsinki and Uusimaa, Vaasa, Kymenlaakso, South Karelia, and Central Finland. Data includes patient information from the Finnish Infectious Diseases Register (FIDR) (age, sex, hospital district, sampling date), as well as species and subtype and identification method of samples received. Over 70% of samples were identified as Cryptosporidium parvum and 20% as C. mortiferum (previously known as Cryptosporidium chipmunk genotype I), which has not been identified in Finland before. Two cases of Cryptosporidium hominis were identified. C. parvum infections were associated with the Vaasa district (P = 0.034), while C. mortiferum was associated with Helsinki and Uusimaa district (P = 0.015). Additionally, C. mortiferum infections were more common in over 50-year old patients. The C. parvum subtype IIaA15G2R1 and the C. mortiferum subtype XIVaA20G2T1 were the most common subtypes identified.
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Data was gathered with the aid of HUS Helsinki University Hospital Diagnostics Center, which supplied samples from human patients with confirmed Cryptosporidium infections sampled in 2021. Received samples were matched to data in the Finnish Infectious Diseases Register (FIDR) via personal identity code. The age, gender, sampling date, and hospital district were collected for each case. Received DNA samples underwent species determination, which were carried out using quantitative real-time polymerase chain reaction (qPCR) (Jothikumar et al., 2008) and 18S sequencing via nested PCR. For 18S amplification, primers SHP1 and SHP2 were used for primary PCR, while SHP3 (Silva et al., 2013) and SSU-R3 (Xiao et al., 1999) were used for secondary PCR. The PCR program was used as presented in Kivistö et al. (2021), while the reaction mix was slightly modified. The 50 µl mix contained 1x DreamTaq™ buffer and the DreamTaq™ Hot Start DNA polymerase (Thermo Fisher Scientific, USA) and BSA was not used. Amplification of a ~850 bp segment of the 60kD glycoprotein (gp60) was performed with nested PCR. The ~850 bp fragment was amplified with primers AL3531 (Peng et al., 2001) and AL3535 (Alves et al., 2003) in the primary PCR and AL3532 and AL3534 in the secondary PCR (Peng et al., 2001). If the amplification of the ~850 bp segment was unsuccessful, a shorter ~350 bp segment was amplified instead, with AL351 and AL353 in the primary PCR and with AL3532 and LX0029 in the secondary PCR (Sulaiman et al., 2005). Statistical analyses on the data were performed with with the IBM SPSS Statistics for Windows, version 29 (IBM Corp., USA). And a binary logistic regression model was used to identify associations between species and collected patient data. Results were considered statistically significant at P < 0.05. Nucleotide sequence data on a new gp60 type identified is available in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB65470.