Table 2 Cryptosporidium species and subtypes reported in humans from Africa

Botswana

Children with diarrhoea (< 5 years)

C. parvum (50.0)

[41]

C. hominis (41.0)

Côte d’Ivoire

Individuals with intestinal disorders

C. meleagridis (75.0)

[106]

C. parvum (16.7)

C. hominis (8.3)

Democratic Republic of Congo

HIV-infected adults

C. hominis (80.0)

[28]

C. parvum (20.0)

Egypt

Individuals with livestock in their household

C. hominis (75.0)

[108]

C. parvum (25.0)

IIdA20G1

Egypt

Children with diarrhoea (≤ 10 years)

C. hominis (60.5)

[26]

C. parvum (38.3)

Egypt

Diarrhoeal patients

C. hominis (97.0)

[131]

C. parvum (3.0)

Egypt

Children with diarrhoea (1–14 years)

C. parvum (82.0)

[290]

C. hominis (12.0)

Mixed infections (6.0)

Egypt

Children with diarrhoea (< 10 years)

C. hominis (60.5)

[95]

C. parvum (38.3)

IIaA15G1R1; IIaA15G2R1; IIdA20G1^a

C. parvum + C. bovis (1.2)

Egypt

Diarrhoeal patients

C. hominis (60.0)

[105]

C. parvum (20.0)

C. hominis + C. parvum (20.0)

Egypt

Gastrointestinal symptomatic patients

C. parvum (66.7)

[156]

C. hominis (27.7)

C. meleagridis (5.6)

Egypt

Immunocompromised patients

C. parvum (68.4)

[349]

C. hominis (26.3)

C. parvum + C. hominis (5.3)

Equatorial Guinea

HIV-infected and immunocompetent patients

C. parvum (52.9)

[150]

C. hominis (44.1)

C. meleagridis (2.9)

Equatorial Guinea

HIV-seropositive patients

C. parvum (54.8)

IIcA5G3^b; IIeA10G1

[152]

C. hominis (50.0)

IaA18R3^b; IaA24R3; IbA13G3; IdA15; IdA18^b

C. meleagridis (3.2)

Ethiopia

Diarrhoeal patients (14–71 years)

C. parvum (95.1)

IIaA15G2R1^b; IIaA16G2R1; IIaA16G1R1

[82]

C. hominis (2.4)

IbA9G3

C. hominis + C. parvum (2.4)

Ethiopia

HIV/AIDS patients

C. parvum (65.7)

IIaA13G2R1; IIaA14G2R1; IIaA15G2R1^b; IIaA16G2R1; IIaA16G3R1; IIaA17G2R1; IIaA18G2R1; IIaA19G1R; IIbA12; IIcA5G3a; IIdA17G1; IIdA19G1; IIdA22G1; IIdA24G1; IIeA12G1; If-like

[23]

C. hominis (17.9)

IbA10G2; IdA20^b; IdA24; IdA26; IeA11G3T3

C. viatorum (7.1)

C. felis (3.6)

C. meleagridis (2.1)

C. canis (1.4)

C. xiaoi (1.4)

C. hominis + C. parvum (0.7)

Ethiopia

Patients

C. hominis (100)

IbA9G3

[99]

Ethiopia

Cryptosporidium-positive (7 months to 27 years)

C. viatorum (90.0)

XVaA3d

[161]

Ethiopia

Children (6–15 years)

C. hominis (40.0)

[103]

C. viatorum (40.0)

C. parvum (20.0)

Ghana

Children (≤ 5 years)

C. parvum (100)

[142]

Ghana

Children with and without gastrointestinal symptoms

C. hominis (58.0)

IaA15T1R3; IaA15G1R4; IaA17; IaA18R3; IaA19R3; IaA21R3; IaA22R3; IaA24R3; IbA13G3^b; IdA15; IeA11G3T3

[98]

C. parvum (42.1)

IIcA5G3a^b; IIcA5G3b; IIeA10G1; IIeA10G2

Kenya

HIV patients

C. hominis (66.7)

[146]

C. parvum (16.7)

C. meleagridis (16.7)

Kenya

Not stated

C. hominis (C. parvum human) (90.0)

Ib; Ie^b

[155]

C. meleagridis (10.0)

Kenya

An HIV-infected adult with diarrhoea

C. muris “rock hyrax”

[139]

Kenya

HIV-positive and negative children and adults

C. parvum human (69.7)

[147]

C. parvum bovine (21.2)

C. meleagridis (3.0)

C. muris (3.0)

Kenya

Children (< 5 years)

C. hominis (87.4)

[129]

C. parvum (8.6)

C. canis (1.7)

C. felis (1.1)

C. muris (0.6)

C. meleagridis (0.6)

Kenya

Children (≤ 5 years)

C. hominis (82.1)

[88]

C. parvum (17.9)

Kenya

HIV/AIDS patients with and without diarrhoea (≥ 18 years)

C. hominis (60.7)

Ia; Ib^b; Id; Ie; If

[25]

C. parvum (23.2)

IIa^b; IIb; IIe^b; IIc

C. canis (7.1)

C. meleagridis (5.3)

C. suis (3.6)

Kenya

HIV infected and uninfected children (5 years)

C. hominis (82.8)

IaA25R5; IaA27R3; IaA30R3; IaA7R1; IbA9G3; IbA9G3R2; IdA22; IdA24; IdA19; IdA25; IdA21; IdA20; IdA17G1; IdA18; IdA15G1; IdA23G1; IeA11G3T3R1^b; IeA11G3T3; IfA19G1; IfA14G1; IfA12G1

[115]

C. parvum (11.9)

IIcA5G3R2

C. felis (2.6)

C. meleagridis (1.3)

C. parvum + C. hominis (0.7)

Kenya

Cryptosporidium spp.-positive female (25 years)

C. viatorum

XVaA3d

[161]

Kenya

Children (≤ 5 years)

C. hominis (38.9)

[153]

C. parvum (36.1)

C. meleagridis (16.7)

C. canis (5.6)

Unknown genotype (2.8)

Madagascar

Children with acute diarrhoeal disease (≤ 16 years)

C. hominis (91.7)

IaA22R3; IdA15G1^b; IeA11G3T3

[350]

C. parvum (8.3)

IIcA5G3

Madagascar

Humans from rural south-eastern Madagascar

C. suis (100)

[97]

Malawi

HIV-positive and negative children

C. hominis (63.6)

[147]

C. parvum (36.4)

Malawi

Children HIV-positive and seronegative (≤ 30 months)

C. hominis (95.3)

Ia; Ib; Id^b; Ie

[351]

C. parvum (4.7)

IIc; IIe

Malawi

Diarrhoeal children (< 5 years)

C. hominis (58.1)

[149]

C. parvum (23.3)

C. parvum + C. hominis (2.3)

C. parvum/C. hominis (9.3)

C. meleagridis (4.7)

C. muris/C. andersoni (2.3)

Nigeria

HIV-infected (majority) and non-infected patients

C. hominis (47.2)

IaA14R3; IaA16R3; IaA24R3; IaA25R3; IbA13G3; IeA11T3G3^b

[83]

C. parvum (44.4)

IIcA5G3a; IIcA5G3h; New subtype family 1^b; New subtype family 2

C. felis (5.6)

C. canis (2.8)

Nigeria

Children (6 months to 6 years)

C. hominis (44.2)

IaA18R2; IaA22R2; IaA24R2; IaA25R2; IaA28R2; IaA21R1; IbA10G2; IbA13G3^b; IdA11; IdA17; IeA11G3T3^b; Ih (Novel subtype); IhA14G1

[141]

C. parvum (32.5)

IIaA15G2R1; IIaA16G1R1; IIcA5G3a^b; IIcA5G3b; IIiA11; IImA14G1

C. parvum plus C. hominis (5.2)

C. meleagridis (6.5)

C. cuniculus (C. rabbit genotype) (6.5)

C. ubiquitum (C. cervine genotype) (3.9)

C. canis (1.3)

Nigeria

Children (19.5–72 months)

C. hominis (37.3)

[86]

C. parvum (35.3)

C. parvum + C. hominis (7.8)

C. meleagridis (7.8)

C. cuniculus (C. rabbit genotype) (3.9)

C. ubiquitum (C. cervine genotype) (2.0)

C. canis (2.0)

Nigeria

Diarrhoeal and non-diarrhoeal children (1 to > 12 months)

C. hominis (60.0)

IaA24R3^b; IbA13G3

[87]

C. parvum (40.0)

IIcA5G3k

Nigeria

Patients (2 months to 70 years)

C. hominis (66.7)

IaA23R3; IaA25R3

[166]

C. parvum (33.3)

IIeA10G1

Nigeria

HIV-infected patients (22–65 years)

C. hominis (50.0)

IeA11G3T3

[101]

C. parvum (25.0)

IIcA5G3k

C. meleagridis + C. hominis (25.0)

São Tomé and Príncipe

Children (2 months to 10 years)

C. hominis (73.7)

IeA11G3T3R1; IeA11G3T3; IaA27R3^b; IaA23R3

[96]

C. parvum (26.3)

IIdA21G1a; IIdA26G1^b; IIaA16G2R1; IIaA15G2R1

South Africa

Children (< 5 years)

C. hominis (75.0)

IbA12G3R2; IbA10G2; IeA11G3T3

[154]

C. meleagridis (25.0)

South Africa

Children (< 5 years)

C. hominis (76.0)

IaA20R3; IaA25G1R3; IaA17R3; IbA9G3; IbA10G1; IdA20; IdA25IdA26; IdA24; IeA11G3T3^b; IfA14G1; IfA12G1

[89]

C. parvum (20.0)

IIbA11; IIcA5G3b^b; IIeA12G1

C. meleagridis (4.0)

IIIdA4

South Africa

School children and hospital patients (≤ 88 years)

C. hominis (81.8)

[77]

C. parvum (18.2)

South Africa

HIV-infected children

C. hominis (75.0)

Ia; Ib; Id; Ie

[352]

C. parvum (25.0)

IIc

Tanzania

People living in and around Gombe National Park

C. hominis (100)

IfA12G2

[102]

Tanzania

Diarrhoeal children and controls (< 2 years old)

C. hominis (84.7)

[72]

C. parvum (7.6)

C. parvum or C. hominis (7.6)

Tanzania

HIV patients (18–65 years)

C. hominis (71.4)

[162]

C. parvum (28.6)

Tunisia

Children (< 5 years old)

C. parvum (57.1)

IIaA15G2R1^b; IIdA16G1

[114]

C. meleagridis (42.9)

Tunisia

Children with primary immune deficiencies

C. hominis (40.0)

[151]

C. parvum (20.0)

C. meleagridis (20.0)

C. hominis/C. meleagridis (20.0)

Tunisia

Immunocompetent and immunodeficiency children

C. parvum (42.1)

[140]

C. hominis (36.8)

C. meleagridis (21.1)

Uganda

Volunteers (1.9 months to 75 years)

C. parvum (97.1)

[107]

C. parvum or C. hominis or C. cuniculus (2.9)

Uganda

Children (2–84 months)

C. hominis (74.4)

Ia; Ib; Id; Ie^b

[148]

C. parvum (18.3)

IIc^b; IIg; IIh; Iii

C. hominis + C. parvum (3.7)

C. meleagridis (3.7)

Uganda

Children with persistent diarrhoea, with and without HIV/AIDS (< 6 months)

C. hominis (73.7)

[70]

C. parvum (18.4)

C. parvum + C. hominis (3.9)

C. meleagridis (3.9)

Uganda

People who share habitats with free-ranging gorillas

C. parvum (100)

[191]

Zambia

Dairy farm workers and their household members

C. parvum (80.0)

[118]

C. hominis (20.0)