Open Access
Table 1
Collection of alveolar and cystic echinococcosis lesion samples stored fresh or frozen or as formalin-fixed paraffin-embedded (FFPE) samples and qPCR results (Cq value and DNA concentration assessment) for the samples.
| Sample code | Geographical origin of patient | Disease | Species | Year of sampling | Tissue type | Lesion location/origin | MLX qPCR tested | Alea |
rrn |
Em |
Eg |
Ec |
Eo |
Tsol |
Toxo |
DNA quantif (ng/μL) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| (qPCR results in mean cycle number) | ||||||||||||||||
| FE-577 | France | AE | Em | 2021 | FFPE | Liver | 1-2-3 | 33.4 | ND | 27.5 | >45 | >45 | >45 | >45 | >45 | 0.9 |
| FE-842 | France | AE | Em | 2021 | Frozen | Liver | 1 | 32.6 | ND | 25.1 | >45 | ND | ND | ND | ND | 5.0 |
| FE-875 | France | AE | Em | 2021 | Frozen | Liver | 1-2-3 | 31.3 | ND | 25.5 | >45 | >45 | >45 | >45 | >45 | 3.9 |
| FE-878 | France | AE | Em | 2021 | Frozen | Liver | 1-2-3 | 34.3 | ND | 24.9 | >45 | >45 | >45 | >45 | >45 | 4.6 |
| FE-907 | France | AE | Em | 2021 | Frozen | Liver | 1-2-3 | 32.7 | ND | 23.9 | >45 | >45 | >45 | >45 | >45 | 12.4 |
| FE-917 | France | AE | Em | 2021 | Frozen | Peritoneal | 1-2-3 | 31.6 | ND | 36.0 | >45 | >45 | >45 | >45 | >45 | 0.002 |
| FE-929 | France | AE | Em | 2021 | FFPE | Liver | 1-2-3 | 32.9 | ND | 33.4 | >45 | >45 | >45 | >45 | >45 | 0.01 |
| LU-O | Luxemburg | AE | Em | 2021 | Frozen | Liver | 1-2-3 | 32.3 | ND | 27.5 | >45 | >45 | >45 | >45 | >45 | 0.9 |
| FE-755 | France | AE | Em | 2020 | FFPE | Peri-duodenal | 1-2-3 | 34.3 | ND | 29.0 | >45 | >45 | >45 | >45 | >45 | 0.3 |
| FE-861 | France | AE | Em | 2020 | Frozen | Liver | 1-2-3 | 31.6 | ND | 27.1 | >45 | >45 | >45 | >45 | >45 | 1.2 |
| FE-908 | France | AE | Em | 2020 | FFPE | Brain | 1-2-3 | 34.2 | ND | 25.8 | >45 | >45 | >45 | >45 | >45 | 3.0 |
| FE-918 | France | AE | Em | 2020 | FFPE | Liver | 1-2-3 | 34.8 | ND | 36.7 | >45 | >45 | >45 | >45 | >45 | 0.001 |
| FE-836 | France | AE | Em | 2019 | Frozen | Liver | 1-2-3 | 34.2 | ND | 31.2 | >45 | >45 | >45 | >45 | >45 | 0.1 |
| FE-652 | France | AE | Em | 2018 | Frozen | Liver | 1-2-3 | 33.7 | ND | 29.4 | >45 | >45 | >45 | >45 | >45 | 0.2 |
| FE-653 | France | AE | Em | 2018 | Frozen | Liver | 1-2-3 | 33.8 | ND | 25.5 | >45 | >45 | >45 | >45 | >45 | 3.7 |
| FE-766 | France | AE | Em | 2018 | Frozen | Foie | 1-2-3 | 34.2 | ND | 26.5 | >45 | >45 | >45 | >45 | >45 | 1.8 |
| FE-792 | France | AE | Em | 2018 | Frozen | Liver | 1-2-3 | 33.8 | ND | 26.5 | >45 | >45 | >45 | >45 | >45 | 1.8 |
| FE-800 | France | AE | Em | 2018 | Frozen | Spleen | 1-2-3 | 34.0 | ND | 25.9 | >45 | >45 | >45 | >45 | >45 | 3.0 |
| FE-805 | France | AE | Em | 2018 | Frozen | Brain | 1-2-3 | 34.2 | ND | 23.7 | >45 | >45 | >45 | >45 | >45 | 14.5 |
| FE-806 | France | AE | Em | 2018 | FFPE | Adrenal | 1-2-3 | 34.7 | ND | 22.9 | >45 | >45 | >45 | >45 | >45 | 25.0 |
| FE-829 | France | AE | Em | 2018 | Frozen | Liver | 1-2-3 | 33.0 | ND | 26.2 | >45 | >45 | >45 | >45 | >45 | 2.2 |
| FE-768 | France | AE | Em | 2017 | FFPE | Peritoneal | 1 | 34.5 | ND | 28.4 | >45 | ND | ND | ND | ND | 0.5 |
| FE-782 | France | AE | Em | 2017 | FFPE | Liver | 1 | 36.4 | ND | 22.9 | >45 | ND | ND | ND | ND | 26.2 |
| P16-1535 | France | AE | Em | 2016 | FFPE | Liver | 1 | 34.5 | 35.5 | 30.9 | >45 | ND | ND | ND | ND | 0.08 |
| P16-2314 | France | AE | Em | 2016 | FFPE | Liver | 1 | 35.0 | 39.2 | 36.3 | >45 | ND | ND | ND | ND | 0.002 |
| P16-5377 | France | AE | Em | 2016 | FFPE | Liver | 1 | 34.9 | 29.3 | 29.3 | >45 | ND | ND | ND | ND | 0.25 |
| FE-769 | France | AE | Em | 2015 | FFPE | Liver | 1 | 34.5 | ND | 28.9 | >45 | ND | ND | ND | ND | 0.3 |
| P15-11460 | France | AE | Em | 2015 | FFPE | Liver | 1 | 35.4 | 40.8 | 39.2 | >45 | ND | ND | ND | ND | 0.0002 |
| P1515434.50 | France | AE | Em | 2015 | FFPE | Liver | 1 | 34.8 | 31.7 | 31.9 | >45 | ND | ND | ND | ND | 0.04 |
| P15-15434 | France | AE | Em | 2015 | FFPE | Liver | 1 | 35.4 | 38.9 | 34.8 | >45 | ND | ND | ND | ND | 0.005 |
| P14-3252 | France | AE | Em | 2014 | FFPE | Liver | 1 | 35.1 | 36.1 | 31.9 | >45 | ND | ND | ND | ND | 0.04 |
| P14-8880 | France | AE | Em | 2014 | FFPE | Liver | 1 | 35.0 | 31.5 | 31.5 | >45 | ND | ND | ND | ND | 0.05 |
| P1315022.50 | France | AE | Em | 2013 | FFPE | Liver | 1 | 34.8 | 27.4 | 27.3 | >45 | ND | ND | ND | ND | 1.05 |
| P13-4653IIC | France | AE | Em | 2013 | FFPE | Liver | 1-2 | 35.1 | 41.1 | >45 | >45 | >45 | >45 | ND | ND | >45 |
| FE-904 | Poland | AE | Em | 2012 | FFPE | Liver | 1-2-3 | 34.2 | ND | 29.7 | >45 | >45 | >45 | >45 | >45 | 0.2 |
| P12-16504ES | France | AE | Em | 2012 | FFPE | Liver | 1 | 34.9 | 38.4 | 34.6 | >45 | ND | ND | ND | ND | 0.01 |
| P1215706III | France | AE | Em | 2012 | FFPE | Liver | 1 | 34.8 | 36.4 | 32.9 | >45 | ND | ND | ND | ND | 0.02 |
| P11-12405 | France | AE | Em | 2011 | FFPE | Liver | 1 | 34.9 | 40.8 | >45 | >45 | ND | ND | ND | ND | >45 |
| P1112967.50 | France | AE | Em | 2011 | FFPE | Liver | 1-2 | 35.1 | 35.0 | 35.8 | >45 | >45 | >45 | ND | ND | 0.002 |
| P08-1905I | France | AE | Em | 2008 | FFPE | Liver | 1 | 34.9 | 38.6 | 35.5 | >45 | ND | ND | ND | ND | 0.003 |
| P06-11605I | France | AE | Em | 2006 | FFPE | Liver | 1 | 34.9 | 35.9 | 38.7 | >45 | ND | ND | ND | ND | 0.0003 |
| P06-4509III | France | AE | Em | 2006 | FFPE | Liver | 1 | 34.9 | 35.6 | 34.6 | >45 | ND | ND | ND | ND | 0.01 |
| P05-14960II | France | AE | Em | 2005 | FFPE | Liver | 1 | 35.1 | 33.9 | 33.2 | >45 | ND | ND | ND | ND | 0.01 |
| S00-15720II | France | AE | Em | 2000 | FFPE | Sub cutan. | 1 | 35.2 | 32.2 | 31.9 | >45 | ND | ND | ND | ND | 0.04 |
| S99-6011IIA | France | AE | Em | 1999 | FFPE | Liver | 1 | 34.7 | 36.3 | 39.0 | >45 | ND | ND | ND | ND | 0.0002 |
| S97-9110IV | France | AE | Em | 1997 | FFPE | Liver | 1 | 35.0 | 28.0 | 27.9 | >45 | ND | ND | ND | ND | 0.68 |
| EK-A20 | Morocco | CE | Eg | 2021 | frozen | Liver | 1-2-3 | 31.6 | ND | >45 | 21.7 | >45 | >45 | >45 | >45 | 139.5 |
| EK-B21 | ND | CE | Eg | 2021 | FFPE | Liver | 1-2-3 | 34.4 | ND | >45 | 37.1 | >45 | >45 | >45 | >45 | 0.003 |
| EK-B22 | France | CE | Eg | 2021 | FFPE | Lung | 1-2-3 | 32.7 | ND | >45 | 39.0 | >45 | >45 | >45 | >45 | 0.001 |
| EK-G23 | France | CE | Eg | 2021 | FFPE | Lung | 1 | 38.4# | ND | >45 | 27.1 | ND | ND | ND | ND | 3.3 |
| EK-G24 | Romania | CE | Eg | 2021 | Frozen | Liver | 1-2-3 | 32.9 | ND | >45 | 25.4 | >45 | >45 | >45 | >45 | 10.4 |
| EK-K25 | Turkey | CE | Eg | 2021 | Frozen | Liver | 1-2-3 | 32.9 | ND | >45 | 22.3 | >45 | >45 | >45 | >45 | 94.6 |
| EK-H13 | Algeria | CE | Eg | 2020 | Frozen | Liver | 1-2-3 | 33.8** | ND | >45 | 23.4 | >45 | >45 | >45 | >45 | 42.6 |
| EK-L14 | Morocco | CE | Eg | 2020 | FFPE | Intra-abdominal | 1-2-3 | 31.6 | ND | >45 | 36.6 | >45 | >45 | >45 | >45 | 0.004 |
| EK-L15 | Morocco | CE | Eg | 2020 | Frozen | Kidney | 1-2-3 | 31.9 | ND | >45 | 22.3 | >45 | >45 | >45 | >45 | 94.2 |
| EK-M16 | Algeria | CE | Eg | 2020 | FFPE | Liver | 1-2-3 | 33.5 | ND | >45 | 35.8 | >45 | >45 | >45 | >45 | 0.01 |
| EK-M17 | Morocco | CE | Eg | 2020 | Frozen | Bottom | 1-2-3 | 34.2** | ND | >45 | 25.6 | >45 | >45 | >45 | >45 | 9.0 |
| EK-M18 | Morocco | CE | Eg | 2020 | FFPE | Bone | 1 | 34.8 | ND | >45 | 33.0 | ND | ND | ND | ND | 0.05 |
| EK-S19 | France | CE | Eg | 2020 | Frozen | Spleen | 1-2-3 | 34.2** | ND | >45 | 21.0 | >45 | >45 | >45 | >45 | 239.9 |
| EK-M11 | Tunisia | CE | Eg | 2019 | Frozen | Lung | 1-2-3 | >45 | ND | >45 | 16.0 | >45 | >45 | >45 | >45 | 8300.4 |
| EK-M12 | Tunisia | CE | Eg | 2019 | Frozen | Lung | 1-2-3 | 34.1 | ND | >45 | 21.8 | >45 | >45 | >45 | >45 | 134.1 |
| EK-D28 | Mali | CE | Ec | 2019 | Frozen | Lung | 1-2-3 | 32.2 | ND | >45 | >45 | 14.7 | >45 | >45 | >45 | 2617.2 |
| EK-H29 | ND | CE | Ec | 2019 | Frozen | Lung | 1-2-3 | 33.2 | ND | >45 | >45 | 28.2 | >45 | >45 | >45 | 0.2 |
| EK-B1 | Algeria | CE | Eg | 2018 | FFPE | Liver | 1-2-3 | 34.7 | ND | >45 | 27.6 | >45 | >45 | >45 | >45 | 2.3 |
| EK-C2 | Moldova | CE | Eg | 2018 | Frozen | Bone | 1-2-3 | 33.9 | ND | >45 | 33.2 | >45 | >45 | >45 | >45 | 0.04 |
| EK-C3 | Moldova | CE | Eg | 2018 | Frozen | Bone | 1-2-3 | 33.3 | ND | >45 | 32.8 | >45 | >45 | >45 | >45 | 0.06 |
| EK-H4 | France | CE | Eg | 2018 | FFPE | NR | 1-2-3 | 34.4 | ND | >45 | 32.9 | >45 | >45 | >45 | >45 | 0.05 |
| EK-H5 | France | CE | Eg | 2018 | FFPE | NR | 1-2-3 | 34.1 | ND | >45 | 35.9 | >45 | >45 | >45 | >45 | 0.01 |
| EK-K6 | Morocco | CE | Eg | 2018 | Frozen | Bedsore | 1-2-3 | 33.9 | ND | >45 | 31.9 | >45 | >45 | >45 | >45 | 0.1 |
| EK-K7 | Morocco | CE | Eg | 2018 | Frozen | Bedsore | 1-2-3 | 34.2 | ND | >45 | 31.7 | >45 | >45 | >45 | >45 | 0.1 |
| EK-L8 | France | CE | Eg | 2018 | FFPE | Lung | 1-2-3 | 34.9 | ND | >45 | 37.9 | >45 | >45 | >45 | >45 | 0.002 |
| EK-M9 | Moldova | CE | Eg | 2018 | Frozen | Intraperitoneal | 1-2-3 | 34.1 | ND | >45 | 32.1 | >45 | >45 | >45 | >45 | 0.09 |
| EK-T10 | Tibet | CE | Eg | 2018 | Frozen | NR | 1-2-3 | 33.9 | ND | >45 | 24.9 | >45 | >45 | >45 | >45 | 15.6 |
| EK-S27 | Mauritania | CE | Ec | 2018 | Frozen | NR | 1-2-3 | 31.9 | ND | >45 | >45 | 26.9 | >45 | >45 | >45 | 0.6 |
| EK-S26 | ND | CE | Ec | 2017 | Frozen | Lung | 1-2-3 | 37.5 | ND | >45 | >45 | 21.0 | >45 | >45 | >45 | 34.2 |
| EK-M30* | France | CE | Eo | 2017 | FFPE | Bone | 1-2-3 | 34.4 | ND | >45 | >45 | >45 | 34.7 | >45 | >45 | 0.03 |
| EK-R31* | France | CE | Eo | 2017 | FFPE | Bone | 1-2-3 | 34.2 | ND | >45 | >45 | >45 | 25.8 | >45 | >45 | 59.4 |
| P10-8854†,$ | Turkey | CE | Eg | 2010 | FFPE | NA | 1-2 | 35.2 | >45 | >45 | 39.9# | >45 | >45 | ND | ND | 0.0004 |
| P06-5181.50 | ND | CE | Eg | 2006 | FFPE | NA | 1-2 | 35.4 | >45 | >45 | 38.8 | >45 | >45 | ND | ND | 0.001 |
| P0517231.50 | ND | CE | Eg | 2005 | FFPE | Liver | 1-2 | 35.1 | >45 | >45 | 36.9 | >45 | >45 | ND | ND | 0.003 |
| P05-17231 | ND | CE | Eg | 2005 | FFPE | Liver | 1-2 | 35.4 | >45 | >45 | 37.0 | >45 | >45 | ND | ND | 0.003 |
| Em | France | Control | Em | 2005 | Frozen | Fox | 1-2-3 | 35.1 | ND | 22.9 | >45 | >45 | >45 | >45 | >45 | 25.8 |
| 5872 | France | Control | Eg | 2012 | Frozen | Ovine | 1-2-3 | 33.0 | ND | >45 | 24.7 | >45 | >45 | >45 | >45 | 17.5 |
| 3734 | France | Control | Ec | 2010 | Frozen | Pig | 1-2-3 | 34.7 | ND | >45 | >45 | 23.2 | >45 | >45 | >45 | 8.0 |
| 6697 | France | Control | Eo | 2012 | Frozen | Bovine | 1-2-3 | 34.1 | ND | >45 | >45 | >45 | 23.8 | >45 | >45 | 337.5 |
| Ts-Pasteur | France | Control | Tsol | ND | Frozen | ND | 1-2-3 | 34.8 | ND | >45 | >45 | >45 | >45 | 15.9 | >45 | 86.2 |
| Tcati | France | Control | Tcat | ND | Frozen | Cat | 1-2-3 | 34.3 | ND | >45 | >45 | >45 | >45 | >45 | 24.5 | 0.4 |
| Tcanis | France | Control | Tcan | ND | Frozen | Fox | 1-2-3 | 34.8 | ND | >45 | >45 | >45 | >45 | >45 | 20.8 | 1.9 |
AE, alveolar echinococcosis; CE, cystic echinococcosis; rrn, qPCR targeting fragment of the mitochondrial 16S-rrnL gene [20]; Em, Echinococcus multilocularis; Eg, E. granulosus; Ec, E. canadensis; Eo, E. ortleppi; Tsol, Taenia solium; Tcat, Toxocara cati; Tcan, T. canis. qPCR tested: T for 3 multiplex qPCR tested on the sample, qPCR MLX 1, Em–Eg–Alea, 2, Ec–Eo–Alea, 3, Tsol–Toxo.
ND for no data.
†
Sample not described in Knapp et al. [19] but tested with the same PCR techniques.
$
Sample positive for the multiplex PCR from Trachsel et al. [37].
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