ORIGINAL ARTICLE Antibiotic resistance profile and molecular characterization of Staphylococcus aureus strains isolated in hospitals in Kabul, Afghanistan Haji Mohammad Naimi 1,2 & Camille André 2,4 & Michèle Bes 2,3,4 & Anne Tristan 2,3,4 & Claude-Alexandre Gustave 2,3,4 & François Vandenesch 2,3,4 & Qand Agha Nazari 1 & Frédéric Laurent 2,3,4 & Céline Dupieux 2,3,4 Received: 3 August 2020 /Accepted: 14 December 2020 # The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature 2021 Abstract The aim of this study was to investigate the molecular features and the antibiotic resistance profile of 98 clinical Staphylococcus aureus isolates collected during 6 months in two hospitals of Kabul, Afghanistan. For all isolates, antimicrobial resistance patterns were determined by the disc diffusion method (including methicillin resistance which was detected using cefoxitin). The presence of the mecA/mecC genes was detected by PCR. Strains were then extensively characterized using microarray analysis. Of the 98 S. aureus isolates, methicillin-resistant S. aureus (MRSA) prevalence was high at 66.3%. Antibiotic suscep- tibility testing also revealed a high resistance rate to penicillin (100%), erythromycin (66.3%), ciprofloxacin (55.1%), and cotrimoxazole (40.8%). Resistance to tobramycin was detected in 25.5%, to gentamicin in 16.3%, to chloramphenicol in 34.7%, and to doxycycline in 23.5% of the isolates. All the MRSA isolates were mecA-positive and none of them harbored mecC. Isolates were grouped into twelve clonal complexes and twenty-seven distinct clones. The most frequently detected clones were the Southwest Pacific clone (CC30-MRSA-IV PVL+) (21/65 MRSA, 32.3%), the CC22-MRSA-IV TSST-1+ clone (11/65 MRSA, 16.9%), and the Bengal Bay clone (ST772-MRSA-V PVL+) (11/65 MRSA, 16.9%). The PVL genes were found in 59.2% (46/65 MRSA and 12/33 methicillin-susceptible S. aureus, MSSA) and tst1 gene in 16.3% of isolates. This molecular study highlights the high prevalence of MRSA and the large genetic diversity of the S. aureus isolates circulating and detected in two hospitals of Kabul, with the presence of multiple virulence and antibiotic resistance genes. Keywords Staphylococus aureus . MRSA . Antibiotic resistance . Molecular typing . Kabul . Afghanistan Introduction Staphylococcus aureus is a major human pathogen responsi- ble for serious infections in both community and hospital set- tings [1]. S. aureus can cause a wide range of infections, from minor skin infections, such as carbuncles, folliculitis, and im- petigo, to deep-seated (abscesses or cellulitis) or life- threatening infections such as pneumonia, osteomyelitis, bac- teremia, toxic shock syndrome, or endocarditis. The global emergence and spread of methicillin-resistant S. aureus (MRSA) in hospitals since the 1960s are a public health con- cern and limit the therapeutic arsenal for severe staphylococ- cal infections. Indeed, healthcare-associated (HA-) MRSA are usually resistant to most antimicrobial agents. In the case of severe infections due to these multi-resistant strains, glyco- peptides are often the drugs of last resort; however, isolates with reduced susceptibility to vancomycin are frequently re- ported [2], and some vancomycin-resistant S. aureus (VRSA) Frédéric Laurent and Céline Dupieux contributed equally to this work. * Céline Dupieux celine.dupieux-chabert@chu-lyon.fr 1 Department of Microbiology, Faculty of Pharmacy, Kabul University, Kabul, Afghanistan 2 CIRI – Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France 3 Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France 4 Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, 103 Grande Rue de la Croix-Rousse, 69004 Lyon, France https://doi.org/10.1007/s10096-020-04130-0 / Published online: 3 January 2021 European Journal of Clinical Microbiology & Infectious Diseases (2021) 40:1029–1038