Table 1.
Species, number of sample types and number of individual birds per total number of birds tested for Chlamydiaceae using real-time PCR in this study
| Order | Family | Species name (Latin) | Species name (English) | Number of available and Chlamydiaceae*-positive swab samples per anatomical site | Chlamydiaceae-positive birds (%, 95% CI) | Mean Ct value, Chlamydiaceae quantitative PCR | Chlamydia psittaci-positive birds (%) | Accession number of ompA study sequence | ||
| Faeces | Choana | Cloaca | ||||||||
| Anseriformes | Anatidae | Anas platyrhynchos | Mallard | 0/26 | 0/4 | 0/4 | 0/29 (0, 0–11.7) | n.d. | ||
| Cygnus olor | Mute swan | 0/0 | 0/1 | 0/1 | 0/1 (0, 0–79.4) | n.d. | ||||
| Mergus merganser | Common merganser | 0/9 | 0/0 | 0/0 | 0/9 (0, 0–29.9) | n.d. | ||||
| Apodiformes | Apodidae | Apus apus | Common swift | 0/15 | 0/7 | 0/7 | 0/20 (0, 0–16.1) | n.d. | ||
| Tachymarptis melba | Alpine swift | 0/3 | 0/0 | 0/0 | 0/3 (0, 0–56.2) | n.d. | ||||
| Charadriiformes | Laridae | Larus michahellis | Yellow-legged gull | 0/3 | 0/1 | 0/1 | 0/4 (0, 0–49.0) | n.d. | ||
| Ciconiiformes | Ciconiidae | Ciconia ciconia | White stork | 0/3 | 0/2 | 0/2 | 0/5 (0, 0–43.5) | n.d. | ||
| Columbiformes | Columbidae | Columba livia domestica | Fancy pigeon | 0/4 | 1/1 | 1/1 | 1/5 (20, 3.6–62.5) | Choana: 28.0 Cloaca: 29.3 |
1/1 (100) | MT450277 |
| Columba livia domestica | Feral pigeon | 0/5 | 0/2 | 0/2 | 0/6 (0, 0–39.0) | n.d. | ||||
| Columba palumbus | Common wood pigeon | 1/4 | 0/1 | 0/1 | 1/5 (20, 3.6–62.5) | Faeces: 37.9 | 0/1 (0) | |||
| Streptopelia decaocto | Eurasian collared dove | 0/2 | 1/2 | 1/2 | 1/4 (25, 4.6–69.9) | Choana: 36.0 Cloaca: 16.9 |
1/1 (100) | MT450278 | ||
| Gruiformes | Rallidae | Crex crex | Corn crake | 0/1 | 0/0 | 0/0 | 0/1 (0, 0–79.4) | n.d. | ||
| Fulica atra | Eurasian coot | 0/2 | 0/1 | 0/1 | 0/3 (0, 0–56.2) | n.d. | ||||
| Passeriformes | Acrocephalidae | Acrocephalus scirpaceus | Eurasian reed warbler | 0/0 | 0/1 | 0/1 | 0/1 (0, 0–79.4) | n.d. | ||
| Emberizidae | Emberiza citrinella | Yellowhammer | 0/1 | 0/1 | 0/1 | 0/1 (0, 0–79.4) | n.d. | |||
| Fringillidae | Carduelis carduelis | Goldfinch | 0/8 | 0/1 | 0/1 | 0/8 (0, 0–32.4) | n.d. | |||
| Chloris chloris | European greenfinch | 0/4 | 0/4 | 0/4 | 0/7 (0, 0–35.4) | n.d. | ||||
| Coccothraustes coccothraustes | Hawfinch | 0/1 | 0/1 | 0/1 | 0/2 (0, 0–65.8) | n.d. | ||||
| Fringilla coelebs | Common chaffinch | 0/4 | 0/1 | 0/1 | 0/4 (0, 0–49.0) | n.d. | ||||
| Serinus serinus | European serin | 0/1 | 0/0 | 0/0 | 0/1 (0, 0–79.4) | n.d. | ||||
| Hirundinidae | Delichon urbicum | Common house martin | 0/2 | 0/0 | 0/0 | 0/2 (0, 0–65.8) | n.d. | |||
| Hirundo rustica | Barn swallow | 0/4 | 0/2 | 0/2 | 0/6 (0, 0–39.0) | n.d. | ||||
| Motacillidae | Motacilla alba | White wagtail | 0/3 | 0/0 | 0/0 | 0/3 (0, 0–56.2) | n.d. | |||
| Muscicapidae | Erithacus rubecula | European robin | 0/0 | 0/1 | 0/1 | 0/1 (0, 0–79.4) | n.d. | |||
| Ficedula hypoleuca | European pied flycatcher | 0/1 | 0/0 | 0/0 | 0/1 (0, 0–79.4) | n.d. | ||||
| Muscicapa striata | Spotted flycatcher | 0/3 | 0/0 | 0/0 | 0/3 (0, 0–56.2) | n.d. | ||||
| Phoenicurus ochruros | Black redstart | 0/6 | 0/2 | 0/2 | 0/8 (0, 0–32.4) | n.d. | ||||
| Paridae | Cyanistes caeruleus | Eurasian blue tit | 0/18 | 0/7 | 0/7 | 0/25 (0, 0–13.3) | n.d. | |||
| Parus major | Great tit | 0/15 | 0/3 | 0/3 | 0/18 (0, 0–17.6) | n.d. | ||||
| Passeridae | Passer domesticus | House sparrow | 0/40 | 0/11 | 0/11 | 0/48 (0, 0–7.4) | n.d. | |||
| Passer montanus | Eurasian tree sparrow | 0/5 | 0/1 | 0/1 | 0/6 (0, 0–39.0) | n.d. | ||||
| Sittidae | Sitta europaea | Eurasian nuthatch | 0/0 | 0/1 | 0/1 | 0/1 (0, 0–79.4) | n.d. | |||
| Sturnidae | Sturnus vulgaris | Common starling | 0/4 | 0/2 | 0/2 | 0/6 (0, 0–39.0) | n.d. | |||
| Sylviidae | Sylvia atricapilla | Eurasian blackcap | 0/7 | 0/1 | 0/1 | 0/7 (0, 0–35.4) | n.d. | |||
| Sylvia borin | Garden warbler | 0/1 | 0/0 | 0/0 | 0/1 (0, 0–79.4) | n.d. | ||||
| Turdidae | Turdus merula | Blackbird | 0/50 | 0/22 | 0/21 | 0/67 (0, 0–5.4) | n.d. | |||
| Turdus philomelos | Song thrush | 0/3 | 0/3 | 0/3 | 0/4 (0, 0–49.0) | n.d. | ||||
| Turdus pilaris | Fieldfare | 0/2 | 0/1 | 0/1 | 0/3 (0, 0–56.2) | n.d. | ||||
| Turdus viscivorus | Mistle thrush | 0/1 | 0/0 | 0/0 | 0/1 (0, 0–79.4) | n.d. | ||||
| Pelecaniformes | Ardeidae | Ardea cinerea | Grey heron | 0/0 | 0/2 | 0/2 | 0/2 (0, 0–65.8) | n.d. | ||
| Piciformes | Picidae | Dendrocopos major | Great spotted woodpecker | 0/3 | 0/1 | 0/1 | 0/3 (0, 0–56.2) | n.d. | ||
| Picus viridis | European green woodpecker | 0/3 | 0/0 | 0/1 | 0/4 (0, 0–49.0) | n.d. | ||||
| Total | 1/267 | 2/91 | 2/91 | 3/339 (0.9, 0.3–2.6) | 2/3 (66.7) | |||||
*All faecal swabs were obtained from living birds after defecation. Both choanal and cloacal swabs were available from 89 deceased birds. From one blackbird only a choanal swab was available. From one Eurasian blue tit a faecal and a choanal swab were available. Only a cloacal swab was obtained from one Eurasian blue tit and one European green woodpecker. All three swab types were obtained from 20 birds that died or were euthanased during treatment due to trauma or disease.
CI, confidence interval; Ct, cycle threshold; n.d., not determined; ompA, outer membrane protein A.