Cryptosporidium species and subtypes identified in human domestic cases through the national microbiological surveillance programme in Sweden from 2018 to 2022.

"representative nucleotide sequences that were generated were submitted to the genbank database under the following accession numbers: ol598537-ol598578 om146534-om146540 om160950-om160951 or491772-or491782 and or790948-or790949.; table 2 c parvum subtype families and subtypes identified in sweden from 2018 to 2022 subtype family (n) subtype (n) 12 genbank acc no 3 comment 45 iia (692) iiaa12g1r1r1 (1) or491776 new subtype 2018 iiaa13g1r1 (14) gu111578 only detected in halland county iiaa13g2r1 (3) ku852706 - iiaa13r1 (8) ku852702 - iiaa14r1 (25) jx183797 associated with a local outbreak 2022 ( n = 4) iiaa14g1r1 (14) kf128737 - iiaa14g1r1r1 (14) ku852703 associated with a local outbreak 2022 ( n = 2) iiaa15g1r1 (2) ol598550 2018 iiaa15g1r1 (1) ol598568 2019 iiaa15g1r1 (2) jf727794 2021 iiaa15g1r1_variant (5) ku852704 2022 iiaa15g1r1r1_variant (1) or491775 new subtype 2022 iiaa15g2r1 (216) af164490 associated with a local outbreak in 2022 ( n = 2) and a national outbreak in 2022 ( n = 107) iiaa16g1r1b (163) eu647727 associated with a local outbreak in 2019 ( n = 4) and 2021 ( n = 1) iiaa16g1r1b_variant (7) kt895368 - iiaa16g2r1 (4) dq192505 - iiaa16g3r1 (1) dq192506 2018 iiaa17g1r1 (4) gq983359 - iiaa17g1r1c (71) jx183801 associated with a local outbreak in 2020 ( n = 7) iiaa17g1r1c_variant (8) af403168 - iiaa17g2r1 (4) af164493 - iiaa17g2r1_variant (1) or491772 new subtype 2020 iiaa17r1 (4) jx183800 - iiaa18g1r1b (11) kf289039 - iiaa18g1r1b_variant (18) kt895369 associated with a local outbreak in 2021 ( n = 3) iiaa18g1r1d (5) jx183803 only detected in uppsala county iiaa18g2r1 (1) dq630515 2018 iiaa18g3r1 (1) dq192508 2019 iiaa18g5r1 (1) mf142037 2019 iiaa18r1 (1) ku852705 2022 iiaa19g1r1 (2) kc679056 2022 iiaa19g2r1 (1) dq630514 2021 iiaa19r1 (3) ol598555 new subtype iiaa20g1r1 (20) jx183804 - iiaa20g1r1 (1) ol598549 2018 iiaa20g1r1 (1) ol598553 2019 iiaa20g1r1_variant (1) ol598567 new subtype 2019 iiaa20r1 (1) jq028867 2021 iiaa21g1r1 (27) fj917373 - iiaa21r1 (1) ol598556 2019 iiaa22g1r1 (14) jx183806 - iiaa22g1r1 (1) ol598539 2018 iiaa23g1r1 (4) kc995126 - iiaa24g1r1 (4) or491777 only detected in halland county may in 2019 iic (4) iica5g3j (1) hq005749 2022 iica5g3o (3) ku670812 only detected in halland county in 2021 iid (663) iida7 (1) or491780 new subtype 2022 iida16g1 (13) jx183808 - iida16g1b (9) 6 fj17372 - iida17g1 (6) ku852708 - iida18g1 (4) ku852709 - iida18g1 (2) ef576975 - iida18g1 (1) mh796389 - iida19g1 (18) dq280496 associated with a local outbreak in 2022 ( n = 1) iida19g1 (4) or491778 - iida20g1 (3) ol598548 - iida20g1b (2) ay738185 - iida20g1d (1) ay738186 2018 iida20g1e (72) jq028866 associated with a local outbreak in 2019 ( n = 2) iida21g1 (12) dq280497 - iida21g1 (48) ol598545 associated with local outbreaks in 2019 ( n = 2) 2020 ( n = 4) and 2021 ( n = 1) iida22g1 (15) ay166806 associated with a local outbreak in 2019 ( n = 4) iida22g1 (5) kr349103 - iida22g1 (3) or491774 - iida22g1c (211) fj917374 associated with a national outbreak 2019 ( n = 122) and a local outbreak 2022 ( n = 2) iida23g1 (17) eu868625 associated with a local outbreak in 2021 ( n = 12) iida23g1 (12) fj917376 - iida23g1 (2) kr349095 - iida23g1 (1) kp997136 2021 iida24g1 (160) jq028865 associated with a national outbreak in 2019 ( n = 65) iida24g1 (2) eu549714 2018 iida24g1c (1) jx183810 2018 iida25g1 (23) jx043492 - iida25g1 (1) ol598537 2018 iida26g1b (1) jx183811 2019 iida27g1 (7) ol598546 only detected in ostergotland county iida27g1_variant (2) ol598571 new subtype 2020 iida28g1 (4) ol598551 new subtype iie (8) iiea11g1 (5) ol598540 only detected in stockholm county iiea11g1 (1) ol598561 2019 iiea11g1 (1) ol598572 2022 iiea14g1 (1) or491779 new subtype 2019 iil (3) iila16r2 (2) am937007 - iila17r2 (1) ol598577 2021 iiy 7 (2) iiya23g1r1 (2) ol598564 new subtype family iiz 7 (2) iiza14r2 (2) ol598569 new subtype family 1 the four most common c parvum subtypes are indicated in bold 2 gp60 pcr negative ( n = 38) 3 sequences submitted to genbank are indicated in bold.; non bold accession numbers refer to reference sequences from genbank 4 association with outbreak(s) are indicated in bold 5 when a county is stated it refers to subtypes (n = > 1) that have only been detected in one county 6 one sample of this subtype was part of an investigation of zoonotic transmission published by bujila et al 2021 [ ] 7 rrna sequences have been deposited in genbank with acc no om146538 and om146539 respectively within subtype family iid 22 different subtypes were detected.; table 3 c hominis subtype families and subtypes identified in sweden from 2018 to 2022 subtype family (n) subtype (total n) 12 genbank acc no 3 comment ia (5) iaa11r3 (2) mt009623 2019 iaa16r4 (1) ol598578 new subtype 2021 iaa28r3 (1) ol598538 new subtype 2018 iaa30r3 (1) or491782 2018 ib (38) iba10g2 (32) ay262031 - iba10g2 (1) ol598563 2019 iba12g3 (5) ky990894 2018 id (3) ida17 (2) ku852721 2022 ida21 (1) fj707316 2019 ie (8) iea11g3t3 (8) gu214354 - 1 the three most common c hominis subtypes are indicated in bold 2 gp60 pcr negative ( n = 2) 3 sequences submitted to genbank are indicated in bold.; table 4 additional cryptosporidium spp subtype families and subtypes identified in sweden from 2018 to 2022 species (n) subtype families/subtypes (n) 1 genbank acc no 2 comment c mortiferum (59) 3 xivaa20g2t1 (32) ku852739 associated with a local outbreak in 2019 ( n = 3) c erinacei (11) xiiiaa12r13 (1) ol598574 new subtype 2020 xiiiaa17r7 (1) om160950 new subtype 2020 xiiiaa17r13 (1) ol598566 new subtype 2019 xiiiaa19r7 (2) ol598547 new subtype 2018 xiiiaa22r9 (1) om160951 2020 xiiiaa22r11 (1) ol598565 2019 xiiiaa23r10 (1) ol598542 new subtype 2018 c cuniculus (5) vaa22 (3) ol598554 - vba29r4 (1) gu097639 2021 vba30r4 (1) or491773 new subtype 2021 c meleagridis (3) iiiaa20g4r1 (1) ol598544 new subtype 2018 iiika6r1 (1) 4 ol598552 new subtype family 2018 c equi (2) vida10g1 (1) 4 ol598562 new subtype family 2019 viaa11g3 (1) ku200960 - 1 gp60 pcr negative: c mortiferum ( n = 3) c erinacei ( n = 3) and c meleagridis ( n = 1) 2 sequences submitted to genbank are indicated in bold.; non bold accession numbers refer to reference sequences from genbank 3 20 cases published by bujila et al 2021 [ ] 4 rrna sequences have been deposited in genbank with acc no om146536 and om146537 respectively a phylogenetic tree that contained one representative gp60 sequence from each subtype family detected within the national surveillance programme ( n = 19) was constructed (fig 4 )."

"Declarations Ethics approval and informed consentThis work was performed in accordance with the Swedish Disease Act (2004:168) and part of the Public Health Agency of Sweden assignment to monitor communicable diseases and evaluate infection control measures in accordance with Sect. 18 of the ordinance (2021:248) issued by the Swedish Parliament. For this reason, specific ethical clearance and informed consent is not required for the results presented from the national surveillance programme for Cryptosporidium. Consent for publicationNot applicable. Competing interestsThe authors declare no competing interests. Competing interests The authors declare no competing interests."

"Funding This work was funded by the administrative grant of the Public Health Agency of Sweden."