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["Sample ID","Material available","Macroscopy","Neutrophilic placentitis","Necrosis","Vasculitis","Mineralization","Bacterial/fungal culture","qPCR Chlamydiales (Abomasal content and/or Placenta)","qPCR Coxiella burnetii (Abomasal content and/or Placenta)","qPCR Leptospira spp. (Abomasal content and/or Placenta)","qPCR Neospora caninum (Brain)","RT-qPCR Schmallenberg virus (Brain stem) ","Detection Schmallenberg virus Ab","Detection of BHV-1 Ab","Detection of BVDV Ag","Sequencing ITS (% of reads and genus)","Pahogens detected","Comments","Most likely etiology"]
["12Ue0622","Complete fetus, placenta and serum","NC","++","++","++","-","Streptococcus uberis in liver, lung, placenta and abomasal content","Placenta positive (Unidentified Chlamydiales)","Placenta and abomasal content positive","Negative","Negative","NA","NA","Negative","Negative","84.4% 'Verticillum in placenta","S. uberis - C. burnetii - unidentified Chlamydiales","-","S. uberis - C. burnetii"]
["12Ue0825","Complete fetus, placenta and serum","NC","++","++","++","++++","Escherichia coli in liver, lung, placenta and abomasal content","Negative","Negative","Negative","Positive","NA","NA","Negative","Negative","Mix fungi in placenta","E. coli - N. caninum","Multifocal necrotizing fetal encephalitis by histopathology.","N.caninum - E.coli"]
["12Ue0839","Complete fetus, placenta and serum","NC","++","+","++","N","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","NA","96.9% Candida in placenta","-","-","-"]
["12Ue0928","Complete fetus, placenta and serum","Yellow cotyledons","+++","+++","+","+++","Streptococcus uberis in placenta and abomasal content","Negative","Negative","Negative","Negative","NA","NA","Negative","Negative","91.8% Malassezia in abomasal content and mix plant fungi in placenta","S. uberis","-","S. uberis "]
["12Ue1096","Complete fetus, placenta and serum","Yellow cotyledons","+","+","+","++","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","Negative","66.6% Unidentified Ascomycota","Pseudomonas spp. detected in Vidal et al, (2017b)","-","Uncultured Pseudomonas spp."]
["12Ue1185","Complete fetus, placenta and serum","NC","+","+","+","++","Negative","Negative","Negative","Placenta and abomasal content positive","Positive","Negative","Negative","Negative","Negative","96.7% Malassezia in abomasal content and mix plant fungi in placenta","Leptospira spp. - N.caninum ","-","Leptospira spp. - N.caninum "]
["12Ue1228","Complete fetus, placenta and serum","Fetal malformation","NA","NA","NA","NA","Negative","Negative","Negative","Negative","NA","Positive","Positive","Negative","Negative","86.3% Cystofilobasidium in placenta"," Schmallenberg virus","-","Schmallenberg virus"]
["12Ue1503","Complete fetus, placenta and serum","NC","++","++","++","++","Negative","Placenta positive (Uncultured Chlamydia sp.)","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Mix plant fungi in placenta","Uncultured Chlamydia","-","Uncultured Chlamydia"]
["12Ue1534","Placenta for bacteriology / Fetus for virology and parasitology / Serum","Fetal malformation","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Positive","Positive","Negative","Negative","Mix plant fungi in placenta","Schmallenberg virus","-","Schmallenberg virus"]
["12Ue1536","Abomasal content for bacteriology / Fetus for virology and parasitology ","Traumatic diaphragmatic hernia","NA","NA","NA","NA","Negative","Abomasal content positive (Unidentified Chlamydiales)","Negative","Negative","Negative","Negative","Negative","NA","Negative","98.2% Actinomucor in abomasal content","unidentified Chlamydiales","-","Non-infectious cause"]
["13Ue0051","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","NA","Mix plant fungi in placenta","-","-","-"]
["13Ue0053","Placenta for bacteriology / Fetus for virology and parasitology / Serum","Fetal malformation","NA","NA","NA","NA","Negative","Placenta positive (Unidentified Chlamydiales)","Negative","Negative","NA","Negative","Negative","Negative","Negative","85.8% Malasseziain placenta","unidentified Chlamydiales","-","Non-infectious cause"]
["13Ue0054","Placenta for bacteriology / Fluids for virology / Serum","NA","NA","NA","NA","NA","Serratia marcescens in placenta","Placenta positive (Unidentified Chlamydiales)","Negative","Negative","NA","Negative","Negative","Negative","NA","Mix rumen fungi in placenta","S. marcescens and unidentified Chlamydiales","-","-"]
["13Ue0056","Abomasal content for bacteriology / Fluids for virology / Serum","Fetal malformation","NA","NA","NA","NA","Negative","Negative","Negative","Negative","NA","Positive","Positive","Negative","Negative","Mix fungi in abomasal content","Schmallenberg virus","Virus detected in the spleen by PCR","Schmallenberg virus"]
["13Ue0141","Complete fetus and placenta","Fetal malformation","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Positive","NA","Negative","Mix fungi in abomasal content and 99.9% Unidentified Fungi in placenta","Schmallenberg virus","-","Schmallenberg virus"]
["13Ue0197","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","NA","Mix fungi in placenta","-","-","-"]
["13Ue0200","Complete fetus, placenta and serum","NC","++","++","+","+","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Abomasal content 88.2% Candida and mix plant fungi in placenta","-","-","Unclear"]
["13Ue0217","Complete fetus, placenta and serum","Fetal malformation","(+)","(+)","(+)","(+)","Bacillus licheniformis in placenta and abomasal content","Negative","Negative","Negative","Negative","Negative","Positive","Negative","Negative","Mix fungi in abomasal content and placenta","B.. licheniformis and Schmallenberg virus","-","Schmallenberg virus"]
["13Ue0218","Placenta for bacteriology / Fetus for virology and parasitology / Serum","Yellow cotyledons - crumbly consistency","(+)","(+)","(+)","+","Negative","Placenta positive (Unidentified Chlamydiales)","Negative","Negative","Negative","Negative","Positive","Negative","Negative","69% Unidentified Capnodialesin placenta","unidentified Chlamydiales and Schmallenberg virus","Commensal microbiota detected in Vidal et al, (2017b)","Schmallenberg virus"]
["13Ue0219","Placenta for bacteriology / Fluids for virology / Serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","NA","NA","NA","Negative","NA","Mix plant fungi in placenta","-","-","-"]
["13Ue0236","Complete fetus, placenta and serum","NC","NA","NA","NA","NA","Negative","Negative","Negative","Negative","NA","Positive","Positive","Negative","Negative","53.3% Unidentified Fungi in abomasal content and 98.9% Cryptococcus in placenta","Schmallenberg virus","-","Schmallenberg virus"]
["13Ue0238","Placenta for bacteriology / Fetus for virology and parasitology / Serum","Fetal malformation","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Positive","Negative","Negative","Mix soil fungi","Schmallenberg virus"," Autolytic microbiota detected in Vidal et al, (2017b)","Schmallenberg virus"]
["13Ue0253","Placenta for bacteriology / Fetus for virology and parasitology / Serum","Yellow cotyledons","+++","+++","++","++","Negative","Negative","Negative","Negative","Positive","NA","NA","Negative","Negative","Mix plant fungi in placenta","N. caninum","Protozoal cysts in placenta by histopathology","N. caninum"]
["13Ue0268","Complete fetus, placenta and serum","Yellow cotyledons; crumbly consistency","+++","+++","++","+++","Negative","Negative","Negative","Negative","Positive","Negative","Negative","Negative","Negative","Mix fungi in placenta","N. caninum","Protozoal cysts in placenta by histopathology","N. caninum"]
["13Ue0274","Complete fetus, placenta and serum","Fetal malformation","NA","NA","NA","NA","Negative","Negative","Negative","Negative","NA","Negative","Positive","Negative","Negative","69.1% Alternaria","Schmallenberg virus","-","Schmallenberg virus"]
["13Ue0348","Complete fetus, placenta and serum","Yellow cotyledons","++","++","++","+++","Streptococcus pluranimalium in placenta and abomasal content","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","98% Cryptococcusin abomasal content and 90.1% Candida","S. pluranimalium","-","S. pluranimalium"]
["13Ue0448","Complete fetus, placenta and serum","Fetal malformation","NA","NA","NA","NA","Negative","Negative","Negative","Negative","NA","Positive","Positive","Negative","Negative","Mix plant fungi in placenta","Schmallenberg virus","Virus detected in the spleen by PCR","Schmallenberg virus"]
["13Ue0458","Complete fetus, placenta and serum","Whyte cotyledons with small hemorrhagies ","++","++","+","+","Candida catenulata in placenta and abomasal content","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","68.7% Mucor","-","-","Unclear"]
["13Ue0486","Complete fetus, placenta and serum","Yellow cotyledons","+","+","+","-","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Mix plant fungi in placenta","-","-","Unclear"]
["13Ue0491","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","NA","Mix fungi in abomasal content and placenta","-","-","-"]
["13Ue0526","Complete fetus, placenta and serum","NC","+","+","(+)","+","Aspergillus sp. in placenta","Placenta positive (Unidentified Chlamydiales)","Negative","Negative","Positive","Negative","Negative","Negative","Negative","Mix plant fungi in abomasal content and placenta","N. caninum - unidentified Chlamydiales","-","N. caninum"]
["13Ue0536","Complete fetus, placenta and serum","Fetal malformation","++","+++","+++","+++","Negative","Negative","Placenta positive","Negative","Negative","Negative","Negative","Negative","Negative","81.9% Candida in abomasal content and 32.5% Candida in placenta","C. burnetii ","-","C. burnetii "]
["13Ue0659","Complete fetus, placenta (no cotyledons) and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","NA","Mix fungi in abomasal content","-","-","-"]
["13Ue0660","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Streptococcus uberis in placenta and abomasal content","Placenta positive (Unidentified Chlamydiales)","Negative","Negative","Negative","Negative","Negative","Negative","NA","Mix fungi in abomasal content","S. uberis and unidentified Chlamydiales","-","-"]
["13Ue0751","Complete fetus, placenta (no cotyledons) and serum","NA","NA","NA","NA","NA","Escherichia coli in placenta and abomasal content","Placenta positive (Unidentified Chlamydiales)","Negative","Negative","Negative","Negative","Negative","Negative","NA","71.2% Cryptococcus in abomasal content","E. coli and unidentified Chlamydiales","-","-"]
["13Ue0752","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","NA","22.4% Penicillium in abomasal content and 46.6% Penicillium in placenta","-","-","-"]
["13Ue0754","Complete fetus, placenta and serum","NC","+++","+++","+++","+++","Negative","Negative","Negative","Negative","Positive","Negative","Negative","Negative","Negative","76.6% Peyronellaea in abomasal content","N. caninum","-","N. caninum"]
["13Ue0755","Complete fetus, placenta and serum","NC","+++","+++","+","+","Escherichia coli in liver, lung, placenta and abomasal content","Negative","Negative","Negative","Positive","Negative","Negative","Negative","Negative","90.4% Cryptococcus in placenta","N. caninum - E. coli","+++ rods detected in placenta by histopathology","N. caninum - E. coli"]
["13Ue0851","Complete fetus, placenta and serum","NC","+++","+++","+++","(+)","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Mix fungi in placenta","-","Enterobacteriaceae, Enterobacteriales and Trueperella detected in Vidal et al, (2017b)","Enterobacteriaceae, Enterobacteriales and Trueperella "]
["13Ue0858","Complete fetus, placenta and serum","Diffuse necrosis with a red rim in placenta","++","+++","++","+++","Negative","Negative","Placenta and abomasal content positive","Negative","Negative","Negative","Negative","Negative","Negative","Mix plant fungi in abomasal content","C.burnetii ","-","C.burnetii "]
["13Ue0862","Complete fetus, placenta and serum","Fetal malformation","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Mix fungi in abomasal content","-","-","Non-infectious cause"]
["13Ue0974","Complete fetus, placenta and serum","NC","+++","+++","+++","+++","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Mix plant fungi in placenta","-","-","Unclear"]
["13Ue1009","Complete fetus, placenta and serum","Fetal malformation","+++","+++","+","+++","Negative","Placenta positive (Chlamydia abortus)","Placenta positive","Negative","Negative","Negative","Negative","Negative","Negative","44.4% Penicillium in placenta","C.burnetii - C. abortus","-","C.burnetii - C. abortus"]
["13Ue1143","Complete fetus, placenta and serum","Multifocal red areas in allantochorion","+++","+++","(+)","++","Escherichia coli in placenta and abomasal content","Negative","Negative","Negative","NA","NA","NA","Negative","Negative","Mix fungi in abomasal content and 81.1% Candida in placenta","E. coli","Enterobacteriaceae detected in Vidal et al, (2017b)","E. coli"]
["13Ue1180","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","NA","Mix fungi in placenta","-","-","-"]
["13Ue1218","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","NA","NA","-","-","-"]
["13Ue1275","Complete fetus, placenta and serum","NC","+","+","++","+","Streptococcus uberis in placenta and abomasal content","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","100% unidentified Capnodiales in abomasal content ","S. uberis","Streptococcus detected in Vidal et al, (2017b)","S. uberis "]
["13Ue1360","Complete fetus, placenta and serum","NC","++","+","-","+++","Aspergillus sp. and Candida tropicalis in placenta","Negative","Negative","Negative","Positive","NA","NA","Negative","Negative","96.6% unidentified Capnodiales in abomasal content annd 50.5% Candida in placenta","N. caninum","-","N. caninum"]
["13Ue1414","Complete fetus, placenta and serum","NC","+","++","(+)","+++","Escherichia coli in placenta and abomasal content","Negative","Placenta and abomasal content positive","Negative","Negative","Negative","Negative","Negative","Negative","68.1% Cryptococcusin abomasal content","C. burnetii - E. coli ","-","C.burnetii "]
["13Ue1524","Complete fetus, placenta and serum","NC","+","+","+","+","Unidentified yeast","Negative","Placenta and abomasal content positive","Negative","Negative","Negative","Negative","Negative","Negative","93.2% Malasseziain abomasal content and mix plant fungi in placenta","C. burnetii ","Trophoblasts with intracytoplasmatic bacteria detected by histopathology","C.burnetii "]
["13Ue1631","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","NA","89.3% Penillium in placenta","-","-","-"]
["13Ue1756","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","NA","Mix fungi in abomasal content and placenta","-","-","-"]
["14A0007","Complete fetus, placenta and serum","NC","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Mix plant fungi in abomasal content","-","Intrauterine stress","Non-infectious cause"]
["14A0008","Complete fetus and placenta ","Yellow cotyledons","+","+","+","++","Negative","Negative","Negative","Negative","Negative","NA","NA","NA","Negative","Mix fungi in abomasal content and 50.9% Cryptococcus in placenta","-","-","Unclear"]
["14A0009","Complete fetus, placenta and serum","One cotyledon had cystic cavities filled with clear liquid - yellow cotyledons","(+)","(+)","-","+","Negative","Negative","Negative","Negative","NA","NA","NA","Negative","Negative","43.8 % Penicillium in abomasal content","-","-","Unclear"]
["14A00014","Complete fetus and placenta ","NC","+","+++","+","+","Streptococcus pluranimalium in placenta and abomasal content","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Negative","Mix fungi in abomasal content ","S. pluranimalium","-","S. pluranimalium"]
["14A0015","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","NA","99.8% unidentified Capnodiales in abomasal content","-","-","-"]
["14A00020","Complete fetus and placenta ","Cotyledons with dark-red decoloration ","+","+","+","+","Negative","Negative","Negative","Negative","Negative","NA","NA","NA","Negative","75.1 % Candida in abomasal content","-","Dam with septicemia","Non-infectious cause"]
["14A0023","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Trueperella pyogenes in placenta and abomasal content","Negative","Negative","Negative","Negative","NA","NA","Negative","NA","Mix fungi in abomasal content and 95.9% unidentified Capnodiales in placenta","T. Pyogenes","-","-"]
["14A00026","Complete fetus and placenta ","Hemorrhagic cotyledons","++","++","+++","-","Campylobacter fetus subsp. fetus in placenta and abomasal content","Negative","Negative","Negative","Negative","NA","NA","NA","Negative","Mix fungi in abomasal content ","Campylobacter fetus subsp. fetus","-","Campylobacter fetus sp. fetus"]
["14A00027","Complete fetus, placenta and serum","Yellow cotyledons - crumbly consistency","++","+++","++","++","Streptococcus pluranimalium in placenta and abomasal content","Negative","Negative","Negative","Positive","NA","NA","Negative","NA","Mix fungi in placenta","N. caninum - S. pluranimalium","Protozoal cysts detected in placenta by histopathology","N. caninum and S. pluranimalium"]
["14A0028","Complete fetus and placenta ","NA","NA","NA","NA","NA","Streptococcus uberis in placenta and abomasal content","Negative","Negative","Negative","Negative","NA","NA","NA","NA","Mix fungi in abomasal content and placenta","S. uberis  ","-","-"]
["14A00046","Complete fetus, placenta and serum","Yellow cotyledons - crumbly consistency","++","++","+","+++","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","Negative","85.3% Candida in abomasal content and 20.5% Candida in placenta","-","-","Unclear"]
["14A00051","Complete fetus, placenta and serum","Whyte cotyledons","++","++","+","+","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","Negative","37.1% Aspergillus in placenta","-","-","Unclear"]
["14A0054","Complete fetus, placenta and serum","NA","NA","NA","NA","NA","Streptococcus pluranimalium in placenta and abomasal content","Negative","Negative","Negative","Negative","NA","NA","Negative","NA","58.3% Orpinomyces in placenta","S. pluranimalium","-","-"]
["14A00056","Complete fetus, placenta and serum","NC","++","+","+","-","Streptococcus uberis and Candida krusei in placenta","Negative","Negative","Negative","Negative","NA","NA","Negative","Negative","60.6% Penicillium in placenta","S. uberis","-","S. uberis"]
["14A00057","Complete fetus, placenta and serum","NC","++","++","+","+","Negative","Negative","Negative","Negative","Negative","NA","NA","Negative","Negative","Mix plant fungi in placenta","-","Dam was sick for an extended period","Non-infectious cause"]
["14A0076","Complete fetus, placenta and serum","Fetal malformation","++","(+)","(+)","+++","Negative","Negative","Placenta positive","Negative","Negative","Negative","Positive","Negative","Negative","Mix fungi in placenta","C. burnetii - Schmallenberg virus","-","Schmallenberg virus"]
["14A0090","Complete fetus, placenta and serum","Internal bleeding from umbilical arteries","+","(+)","-","(+)","Negative","Negative","Placenta and abomasal content positive","Negative","Negative","NA","NA","NA","Negative","Mix fungi in abomasal content and placenta","C. burnetii ","-","Non-infectious cause"]
["14A0145","Placenta for bacteriology","NC","++","++","++","(+)","Escherichia coli in placenta ","Negative","Negative","Negative","NA","NA","NA","NA","NA","NA","E. coli",null,"-"]
["14A0154","Complete fetus, placenta and serum","Yellow cotyledons","+","++","++","+++","Negative","Negative","Negative","Negative","Negative","NA","NA","NA","Negative","Mix fungi in placenta","-","-","Unclear"]
["15A0002","Placenta for bacteriology","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","NA","NA","NA","NA","NA","44.5% Cryptococcus in placenta","-","-","-"]
["15A0009","Placenta for bacteriology","NA","NA","NA","NA","NA","Aspergillus fumigatus in placenta ","Negative","Negative","Negative","NA","NA","NA","NA","NA","84.6% Zymoseptoria in placenta","-","-","-"]
["15A0015","Placenta for bacteriology ","NA","NA","NA","NA","NA","Negative","Negative","Negative","Negative","NA","NA","NA","NA","NA","74.4% Candida in placenta","A. fumigatus","-","-"]
[]
["74 cases","yellow: not possible to assess because high degree of autolysis or not cotyledons available for analysis"]
[]
[]
[]
["Bacterial culture (n = 20)","Fungal culture (n = 6, one case with two)"]
["Escherichia coli = 6 cases","Aspergillus sp. = 2 cases"]
["Streptococcus uberis = 6 cases","Aspergillus fumigatus = 1 case"]
["Streptococcus pluranimalium = 4 cases","Candida catenulata = 1 case"]
["Bacillus licheniformis = 1 ","Candida krusei = 1 case"]
["Campylobacter fetus subsp. fetus = 1","Candida tropicalis = 1 case"]
["Serratia marcescens = 1","Unidentified yeast = 1 case"]
["Trueperella pyogenes = 1"]
[]
[]
[]
["qPCR Bacteria","qPCR Neospora caninum = 9 cases"]
["Chlamydiales = 10 cases"]
["Coxiella burnetii = 8 cases"]
["Pathogenic Leptospira spp. = 1 case"]
[]
[]
["qPCR Schmallenberg virus = 5 cases","Detection Schmallenberg virus Ab = 11 cases"]

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