Virulence-factor encoding genes (VFGs) and antimicrobial resistance genes (ARGs) of ocular Methicillin-Resistant Staphylococcus aureus (MRSA), are the reason behind the common cause of severe and untreatable ocular infection and are largely unknown. The unavailability of the complete genome sequence of ocular MRSA strains hinders the unambiguous determination of ARGs and VRGs role in disease pathogenesis and their genomic location. To fulfill this critical need, we achieved the high-quality complete genome of four ocular MRSA strains (AMRF3 – AMRF6) by combining MinION nanopore sequencing technology, followed by polishing with Illumina sequence reads. We obtained a single chromosome and a plasmid in each strain. Sequence typing revealed that AMRF3 and AMRF5 strains harbored ST772, whereas AMRF4 and AMRF6 harbored ST 2066. All plasmids carried heavy metal cadmium resistance genes cadC and cadD, while cadA was detected only in the plasmid pSaa6159 of AMRF4 and AMRF6 strains. Further, pSaa6159 contains a complete Tn552 transposon with beta-lactamase genes, blaI, blaR1, and blaZ. Interestingly, pSaa6159 in AMRF6 carried five copies of Tn552 transposon. Several exotoxins and enterotoxins were identified across ocular MRSA strains and ST2066 strains found to be not carried any enterotoxins; this finding suggests that these two strains are exotoxigenic. Besides, ST2066 strains carried serine proteases (splA, splB, splD, splE and spIF) and exotoxin (seb and set 21) for their virulence, while ST772 carried antimicrobial resistance genes (blaZ, dfrG, msrA, mphC and fosB) and enterotoxin sec for virulence, suggesting sequence type-specific resistance and virulence. Also, we identified many VFGs and ARGs, that provided multi-drug resistance, enterotoxigenic, exotoxigenic, biofilm-forming, host tissue adhesion and immune response evasion in ocular MRSA strains. Thus, our study provides a better insight into the genomes of ocular MRSA strains that would provide more effective treatment strategies for ocular MRSA infection.

眼部耐甲氧西林金黄色葡萄球菌的毒力因子编码基因（VFGs）和抗菌素耐药基因（ARGs）(MRSA)，是导致严重且无法治愈的眼部感染的常见原因，并且在很大程度上是未知的。眼部 MRSA 菌株的完整基因组序列的不可用阻碍了对 ARG 和 VRG 在疾病发病机制及其基因组位置中的作用的明确确定。为了满足这一关键需求，我们通过结合 MinION 纳米孔测序技术获得了四种眼部 MRSA 菌株 (AMRF3 – AMRF6) 的高质量完整基因组，然后使用 Illumina 序列读数进行抛光。我们在每个菌株中获得了一条染色体和一个质粒。序列分型显示，AMRF3和AMRF5菌株携带ST772，而AMRF4和AMRF6携带ST 2066。所有质粒均携带重金属镉抗性基因cadC和cadD，而仅在 AMRF4 和 AMRF6 菌株的质粒 pSaa6159 中检测到cadA。此外，pSaa6159 包含一个完整的 Tn552 转座子，带有 β-内酰胺酶基因blaI、blaR1和blaZ。有趣的是，AMRF6 中的 pSaa6159 携带了 5 个 Tn552 转座子拷贝。在发现不携带任何肠毒素的眼部 MRSA 菌株和 ST2066 菌株中鉴定出几种外毒素和肠毒素；这一发现表明这两种菌株是产毒的。此外，ST2066菌株携带丝氨酸蛋白酶（splA、splB、splD、splE和spIF）和外毒素（seb和set 21) 的毒力，而 ST772 携带抗菌素抗性基因 ( blaZ、dfrG、msrA、mphC和fosB ) 和肠毒素 sec 的毒力，表明序列类型特异性抗性和毒力。此外，我们鉴定了许多 VFG 和 ARG，它们在眼部 MRSA 菌株中提供了多药耐药性、产肠毒素、产外毒素、生物膜形成、宿主组织粘附和免疫反应逃避。因此，我们的研究可以更好地了解眼部 MRSA 菌株的基因组，这将为眼部 MRSA 感染提供更有效的治疗策略。