The ability of Mycoplasma hyopneumoniae to persist despite fluoroquinolone treatments was investigated with pigs. Groups of specific-pathogen-free pigs were experimentally infected with M. hyopneumoniae strain 116 and treated with marbofloxacin at the therapeutic dose (TD) or half of the therapeutic dose (TD/2) for 3 days. Results showed that, despite tissue penetration of marbofloxacin, particularly in the trachea and the tracheal secretions, the treatments did not have any influence on M. hyopneumoniae recovery from tracheal swabs. Mycoplasmas were also isolated from inner organs and tissues such as liver, spleen, kidneys, and bronchial lymph nodes. Recontamination of pigs via environment could not explain mycoplasma persistence after medication, as decontamination of pigs and allocation to a new disinfected environment did not have any significant effect on the phenomenon. A significant decrease in the susceptibility level to marbofloxacin of 12 mycoplasma clones reisolated after the treatments (TD/2 and TD) was observed. Two point mutations were found in the ParC quinolone resistance-determining region (QRDR) of DNA topoisomerase IV (Ser803Phe and Asp843Asn), and one point mutation was observed just behind the QRDR of ParC (Ala1163Glu). This is the first time that mutations in a gene coding for topoisomerase IV have been described for M. hyopneumoniae after in vivo marbofloxacin treatments in experimentally infected pigs. However, development of resistance is not sufficient to explain M. hyopneumoniae persistence in vivo since (i) marbofloxacin concentrations were above the marbofloxacin MIC of the wild-type strain and (ii) mycoplasmas reisolated after a single injection of marbofloxacin did not display an increased marbofloxacin MIC.Mycoplasma hyopneumoniae is one of the primary pathogens associated with the porcine respiratory disease complex, one of the most common and economically important diseases for swine producers worldwide (43). M. hyopneumoniae is the etiological agent of enzootic pneumonia in swine, a chronic respiratory disease characterized by high morbidity and low mortality rates (15). The principal clinical but not constant sign is a chronic cough. Mycoplasmal pneumonia is located mainly in the anterior lobes of the lung. In the acute phase of the disease, catarrhal pneumonia is observed, with exudates in the airways. The bronchial and mediastinal lymph nodes are often enlarged. In the chronic stage of the disease, recovering lesions, consisting of fissures of collapsed alveoli adjoining areas of alveolar emphysema, are observed (26). M. hyopneumoniae is a very contagious bacterium and may be transmitted via direct contact between pigs (43) or via environment (14, 48).In vitro, M. hyopneumoniae is susceptible to various antibiotics, including fluoroquinolones, tetracyclines, spiramycin, and tiamulin (17,18,19,25,42,49). However, although antibiotic treatments are usually able to control the disease (49), persistence is observed under field conditions (43) and experimental infections (16,25)....