DataSheet_1_Resistome, mobilome, and virulome explored in clinical isolates derived from acne patients in Egypt: unveiling unique traits of an emerging coagulase-negative Staphylococcus pathogen.docx

Coagulase-negative staphylococci (CoNS) are a group of gram-positive staphylococcal species that naturally inhabit the healthy human skin and mucosa. The clinical impact of CoNS-associated infections has recently been regarded as a challenge for diagnosis and therapeutic options. CoNS-associated infections are primarily caused by bacterial resistance to antibiotics and biofilm formation. As antibiotics are still the most used treatment, this problem will likely persist in the future. The present study aimed to investigate the resistance and virulence of CoNS recovered from various acne lesions and explore their genetic basis. Skin swab samples were collected from participants with acne and healthy skin. All samples underwent conventional culture for the isolation of CoNS, MALDI-TOF confirmation, antibiotic susceptibility, and biofilm formation testing. A total of 85 CoNS isolates were recovered from the samples and preliminarily identified as Staphylococcus epidermidis. Isolates from the acne group (n = 60) showed the highest rates of resistance to penicillin (73%), cefoxitin (63%), clindamycin (53.3%), and erythromycin (48%), followed by levofloxacin (36.7%) and gentamycin (31.7%). The lowest rates of resistance were observed against tetracycline (28.3%), doxycycline (11.7%), and minocycline (8.3%). CoNS isolated from mild, moderate acne and healthy isolates did not show strong biofilm formation, whereas the isolates from the severe cases of the acne group showed strong biofilm formation (76.6%). Four extensively drug-resistant and strong biofilm-forming staphylococcal isolates recovered from patients with severe acne were selected for whole-genome sequencing (WGS), and their genomes were investigated using bioinformatics tools. Three of the sequenced genomes were identified as S. epidermidis; however, isolate 29AM was identified as Staphylococcus warneri, which is a newly emerging pathogen that is not commonly associated with acne and was not detected by MALDI-TOF. All the sequenced strains were multidrug-resistant and carried multiple resistance genes, including blaZ, mecA, tet(K), erm(C), lnuA, vgaA, dfrC, fusB, fosBx1, norA, and vanT, which were found to be located on plasmids and chromosomes. Virulence features were detected in all genomes in the presence of genes involved in adherence and biofilm formation (icaA, icaB, icaC, sdrG, sdrH, atl, ebh, and ebp). Only the S. warneri isolate 29AM contained immune evasion genes (capB, capC, acpXL, and manA), an anti-phagocytosis gene (cdsA), and other unique features. As a result of their potential pathogenicity and antibiotic resistance, CoNS must be monitored as an emerging pathogen associated with acne infections. To the best of our knowledge, this is the first report to isolate, identify, and correlate S. warneri with severe acne infections among Egyptian patients using WGS and bioinformatic analysis.

凝固酶阴性葡萄球菌（Coagulase-negative staphylococci, CoNS）是一类革兰阳性葡萄球菌属物种，自然定植于健康人体皮肤与黏膜表面。近年来，凝固酶阴性葡萄球菌相关感染的临床诊疗已成为诊断与治疗方案选择的一大挑战。该类感染的发生主要与细菌对抗生素的耐药性及生物膜形成能力相关。由于抗生素仍是目前最常用的治疗手段，该问题在未来仍将持续存在。

本研究旨在探究从各类痤疮皮损中分离得到的凝固酶阴性葡萄球菌的耐药性与毒力特征，并解析其遗传基础。研究从痤疮患者与健康人群的皮肤处采集拭子样本，所有样本均通过常规培养法分离凝固酶阴性葡萄球菌，并经基质辅助激光解吸电离飞行时间质谱（MALDI-TOF）验证，同时开展药敏试验与生物膜形成能力检测。最终从样本中分离得到85株凝固酶阴性葡萄球菌，经初步鉴定为表皮葡萄球菌（Staphylococcus epidermidis）。

痤疮组分离株（n=60）对青霉素（73%）、头孢西丁（63%）、克林霉素（53.3%）与红霉素（48%）的耐药率最高，其次为左氧氟沙星（36.7%）与庆大霉素（31.7%）；而对四环素（28.3%）、多西环素（11.7%）与米诺环素（8.3%）的耐药率最低。从轻度、中度痤疮患者及健康人群中分离的菌株未表现出较强的生物膜形成能力，而痤疮组重度痤疮患者分离株的强生物膜形成率达76.6%。

本研究选取4株从重度痤疮患者体内分离的泛耐药且强生物膜形成能力葡萄球菌株开展全基因组测序（Whole-genome sequencing, WGS），并借助生物信息学工具对其基因组进行分析。经测序的基因组中有3株被鉴定为表皮葡萄球菌，而菌株29AM被鉴定为沃氏葡萄球菌（Staphylococcus warneri）——这是一种新兴致病菌，此前极少与痤疮感染相关，且未被MALDI-TOF质谱检出。

所有测序菌株均为多重耐药株，携带多种耐药基因，包括blaZ、mecA、tet(K)、erm(C)、lnuA、vgaA、dfrC、fusB、fosBx1、norA及vanT，上述基因均位于质粒与染色体上。所有菌株基因组中均检测到与黏附及生物膜形成相关的毒力特征基因，包括icaA、icaB、icaC、sdrG、sdrH、atl、ebh及ebp。仅沃氏葡萄球菌株29AM携带免疫逃逸基因（capB、capC、acpXL及manA）、抗吞噬基因（cdsA）及其他独特的遗传特征。

鉴于凝固酶阴性葡萄球菌潜在的致病性与抗生素耐药性，需将其作为与痤疮感染相关的新兴致病菌进行监测。据我们所知，本研究是首个通过全基因组测序与生物信息学分析，在埃及患者体内分离、鉴定并证实沃氏葡萄球菌与重度痤疮感染相关的研究报告。