We searched PubMed, Web of Science, and Scopus databases for molecular studies on human cryptosporidiosis conducted in Spain published during January 2010–December 2020 (Appendix). Search terms included Cryptosporidium, human, hominis, parvum, gp60, subtype, and Spain. We identified 7 studies reporting molecular data on Cryptosporidium from laboratory-confirmed clinical samples collected in Spain during 2000‒2016; a total of 806 isolates were characterized (Appendix Table). Among C. hominis (76.1%), subtype family Ib predominated (90.7%); subtype IbA10G2 accounted for 99.6% of isolates. Among C. parvum (24.0%), subtype family IIa predominated (87.1%), followed by IIn (7.3%) and IId (5.2%).

During December 2013–December 2019, we collected Cryptosporidium-positive clinical fecal samples routinely submitted for genotyping to the National Reference Laboratory at the Spanish National Centre for Microbiology from 7 regions (Table 1). We obtained additional prepandemic samples through a dedicated multicenter nonoutbreak study across 4 tertiary hospitals in 2 regions (Table 1). During March–December 2023, we collected postpandemic Cryptosporidium-positive clinical samples through a dedicated multicenter nonoutbreak study across 8 tertiary hospitals in 2 regions (Table 2). Upon receipt, all samples were subjected to confirmatory testing and genotyping at the gp60 marker in accordance with established protocols and current subtype nomenclature recommendations (7,8). We considered only samples identified as C. hominis or C. parvum in our analysis.

Our analysis included 389 prepandemic clinical samples (Table 1). Among C. hominis (85.3%), subtype family Ib predominated (96.7%); subtype IbA10G2 accounted for 96.6% of isolates. Among C. parvum (14.7%), subtype family IIa was most common (59.6%), followed by IId (36.8%) and IIc (3.5%).

Our analysis included 126 postpandemic clinical samples (Table 2). Among C. hominis (96.0%), the most common subtype families were If (70.2%) and Ib (22.3%). All If isolates belonged to subtype IfA12G1R5, whereas IbA10G2 represented 7.4% and IbA13G3 represented 88.9% of isolates within subtype family Ib. C. parvum accounted for the remaining 4.0% of isolates, all of which belonged to subtype family IIa.

The distribution of C. hominis subtypes in 2023 differed markedly from that observed during 2000–2019, both in diversity (10 vs. 2–5 subtypes) and frequency rates, as determined by comparison to clinical samples genotyped at the National Reference Laboratory and deposited to GenBank during 2013‒2023 (Table 3). Subtype IfA12G1R5 accounted for 67.5% of cases despite being detected only once previously, whereas the historically predominant subtype IbA10G2 declined dramatically from 79.7% to 1.6%. C. parvum was rarely detected in 2023.

Before the COVID-19 pandemic (2000–2019), C. hominis was the predominant species in Spain, accounting for ≈76%–85% of cases; subtype family Ib was overwhelmingly dominant (91%–97%) (Table 1; Appendix Table). Within family Ib, IbA10G2 was most frequently identified across multiple studies and settings (97%–99%), suggesting a well-established and stable anthroponotic transmission network. C. parvum accounted for a smaller percentage of infections; family IIa predominated, particularly IIaA15G2R1 (Table 1; Appendix Table). That pattern is consistent with ongoing zoonotic transmission linked to livestock or wildlife exposure.

The COVID-19 pandemic appears to have altered this equilibrium. Evidence from several countries indicates that nonpharmaceutical interventions disproportionally affected C. hominis, whose transmission relies primarily on person-to-person contact and common-source exposures. Indeed, postpandemic reductions or even interruptions in C. hominis transmission have been reported in England and Wales (3,4), New Zealand (6), Scotland (5), and Sweden (9). In contrast, transmission of the largely zoonotic C. parvum remained comparatively stable, as observed in New Zealand (6). A similar pattern appears to have occurred in Spain, where all Cryptosporidium-positive samples detected immediately after the pandemic were identified as C. parvum, with no evidence of C. hominis circulation in the investigated population (7).

The postpandemic resurgence observed in 2023 (Table 3), after interruption of C. hominis transmission (7), was accompanied by an unprecedented increase in cryptosporidiosis cases across Europe (10,11). An additional contributing factor might have been an immunity debt effect resulting from reduced Cryptosporidium exposure during COVID-19 restrictions, particularly among children. In Spain, molecular data were initially limited to investigations of waterborne outbreaks in several regions (11), revealing a striking shift in subtype distribution. C. hominis accounted for 94.3% of genotyped samples; the rare subtype IfA12G1R5 was responsible for most (66.1%) infections. Because this subtype had been detected only sporadically before the pandemic (12), its predominance suggests either recent introduction or expansion from previously undetected low-level circulation. Our study expands those observations by providing baseline (nonoutbreak) epidemiologic data showing a similar predominance of C. hominis (96.0%), with IfA12G1R5 accounting for 67.5% of infections. The concordant patterns observed in both outbreak-related and sporadic cases indicate that expansion of IfA12G1R5 is not restricted to outbreaks but reflects sustained communitywide transmission in Spain.

IfA12G1R5 was recognized as a hypertransmissible lineage with a marked capacity for rapid spread, which could explain its predominance in the numerous outbreaks reported in Spain during the second half of 2023. In Europe, IfA12G1R5 was initially detected at low frequencies in the United Kingdom (13), as well as in Germany and Sweden (14) and Spain (12). Of note, IfA12G1R5 had already become the predominant C. hominis subtype in the United States (15) before the pandemic. Phylogenomic evidence indicates that IfA12G1R5 has multiple ancestral origins, involving introductions from East Africa and Europe followed by recombination events, which likely enhanced its fitness and transmission potential (15).

In contrast, the historically dominant IbA10G2 subtype declined sharply in 2023 (1.6%), indicating subtype replacement, consistent with molecular data from outbreak investigations conducted in Spain that year, which identified IbA10G2 in only 1 (0.8%) isolate (11). The shift might reflect a founder effect associated with reestablishment of transmission chains after the pandemic, favoring the expansion of a hypertransmissible subtype such as IfA12G1R5. Similar displacement of IbA10G2 by IfA12G1R5 or other Cryptosporidium subtypes has been documented in the United Kingdom (10) and the United States (15), although the underlying mechanisms and epidemiologic drivers remain unclear and appear unrelated to pandemic-associated disruptions.

C. parvum was detected only sporadically in 2023. The persistence of IIa subtypes at low frequency, together with absence of IIc and IId subtypes, suggests that zoonotic transmission did not undergo postpandemic amplification. That finding supports the hypothesis that nonpharmaceutical interventions selectively altered anthroponotic transmission pathways while largely sparing zoonotic cycles. However, differences in geographic coverage and sampling periods among datasets might have affected the observed patterns, influencing zoonotic transmission dynamics of C. parvum.

Our findings point to a dual epidemiologic scenario in which stable zoonotic transmission of C. parvum coexists with the rapid expansion of highly transmissible, human-adapted C. hominis subtypes such as IfA12G1R5. Clinicians in Spain should be aware of increases in infections caused by this emergent subtype.