| Summary: | <i>Chlamydia</i> (<i>C.</i>) <i>felis</i> primarily replicates in feline conjunctival epithelial cells and is an important cause of conjunctivitis in cats. Data on <i>C. felis</i> infection rates in stray cats in Switzerland has been missing so far. We performed a qPCR-based <i>Chlamydiaceae</i>-screening on 565 conjunctival and 387 rectal samples from 309 stray and 86 pet cats followed by <i>Chlamydia</i> species identification and <i>C. felis</i> typing using the gene <i>pmp9</i>, which encodes a polymorphic membrane protein. Overall, 19.1% of the stray and 11.6% of the pet cats were <i>Chlamydiaceae</i>-positive with significantly higher rates in cats displaying signs of conjunctivitis (37.1%) compared to healthy animals (6.9%). Rectal shedding of <i>Chlamydiaceae</i> occurred in 25.0% of infected cats and was mostly associated with concurrent ocular positivity (87.5%). In 92.2% of positive conjunctival and rectal samples, the <i>Chlamydia</i> species was identified as <i>C. felis</i> and in 2.6% as <i>C. abortus</i>. The <i>C. felis pmp9</i> gene was very conserved in the sampled population with only one single-nucleotide polymorphism (SNP) in one conjunctival sample. In conclusion, <i>C. felis</i> strains are circulating in Swiss cats, are associated with conjunctivitis, have a low <i>pmp9</i> genetic variability, and are rectally shed in about 16% of positive cases.
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