Abstract Title Plasmid-mediated resistance to macrolides in some Staphylococcus isolates recovered from patients with lower respiratory tract infection. Background Staphylococcus aureus and coagulase-negative staphylococci are considered to be among the major causes of nosocomial and community-acquired infections. Macrolides, lincosamides and streptogramin type B (MLS) antibiotics are widely indicated for the treatment of staphylococcal infections. A great concern is the increase in the prevalence of macrolide resistance among Staphylococcus spp. The aim of our study was to detect plasmid-harbored genes responsible for macrolide resistance in staphylococci involved in lower respiratory tract infections (LRIs) in Egypt. Methods and findings A total of 189 bacterial isolates were recovered from 180 sputum and bronchoalveolar lavage specimens obtained from patients with LRIs. The specimens were collected during the period of 2010 to 2012 from Microbiological diagnostic laboratories of two governmental hospitals specialized in the treatment of chest infections, Al-Sadr (Abbassia) and Al-Demerdash hospitals. The antibiogram analysis revealed that 64, out of 189 isolates (33.9%) were resistant to the tested antibiotics (Erythromycin, Clarithromycin, Azithromycin and Clindamycin). Among the resistant isolates, only 8 isolates (12.5%) were identified to be Staphylococcus spp. Among these isolates, four showed constitutive (cMLS) phenotype, while the other isolates exhibited inducible (iMLS) phenotype. The molecular analysis of resistant isolates revealed the presence of plasmids in the eight test isolates. By using PCR, two genes suspected to be responsible for plasmid-mediated resistance could be detected using two specific primer pairs for erythromycin ribosomal methylase (erm) and erythromycin resistance ATP-binding protein (coded as msr). The erm gene was detected in four isolates (50%), while the prevalence of msr gene constituted 25% (detected in two isolates only). Further verification of msr gene was performed by DNA sequencing of the PCR product obtained by using the plasmid extract of one isolate as a template. The nucleotide sequence of msr gene was submitted to the GenBank database, and given the accession code KJ710361. Conclusion Plasmid-mediated resistance to macrolides prevails among Staphylococcus isolates involved in LRIs as the 8 resistant isolates of this genus was shown to harbor plasmids, with prevalence of 50% (erm gene) and 25% (msr gene). Therefore, the reasons behind the prevalence of plasmid-mediated resistance to macrolides have to be studied, and control measures should be undertaken.