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Clinical and molecular characteristics of Staphylococcus aureus isolates from patients with COVID-19 in Southwest China

BMC Infectious Diseases volume 25, Article number: 546 (2025) Cite this article

Abstract

Background

This study investigated the clinical and molecular characteristics of Staphylococcus aureus (S. aureus) isolates from patients with coronavirus disease 19 (COVID- 19) at West China Hospital between December 1, 2022 and January 31, 2023.

Methods

In total, 102 strains isolated from sputum, bronchoalveolar lavage fluid, endotracheal aspirates, and blood were collected from 102 patients and subjected to multilocus sequence typing and antimicrobial susceptibility testing. Eighteen virulence genes were also analyzed by polymerase chain reaction.

Results

Seventy-five patients were discharged and 27 died. The predominant comorbidities were hypertension, diabetes mellitus, and cardiac disease. Twenty-eight known sequence types (STs) and 10 novel ones (ST8773/CC398, ST9221/CC5, ST9222/CC59, ST9223/CC8, ST9224/CC22, ST9225/CC1, ST9226/CC5, ST9227/CC59, ST9228/CC59, ST9229/CC398) were identified. The dominant molecular types were ST15 (CC15), ST59 (CC59), and ST5 (CC5). Among the three most prevalent STs, ST5 was significantly more resistant to levofloxacin, moxifloxacin, ciprofloxacin, and sulfamethoxazole than were ST59 and ST15. ST59 and ST5 had higher rates of resistance to erythromycin and clindamycin than ST15. All isolates contained at least eight virulence genes. The hemolysin gene hlb was found to be more prevalent in ST59 (100%) and ST5 (84.6%) than in ST15 (0) (P < 0.001). The prevalence of the enterotoxin gene seb in ST59 (100%) was significantly higher than that in ST5 (23.1%) and ST15 (20%) (P < 0.001), while the carrying rate of the sec gene was significantly higher in ST5 (76.9%) than that in ST59 (0) and ST15 (0) (P < 0.001).

Conclusions

The S. aureus isolates from patients with COVID- 19 in Southwest China exhibited a high degree of genetic diversity. Different STs exhibited different antimicrobial resistance patterns and virulence gene carrying rates.

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Background

Coronavirus disease 2019 (COVID- 19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2), was responsible for a global pandemic with a high mortality rate, particularly among older adults and patients with underlying conditions [1]. Direct damage to the lung epithelium, “cytokine storms,” and a combination of virus- and drug-induced immunosuppression likely increase the susceptibility to secondary infections [2,3,4]. In patients admitted to the intensive care unit (ICU) with COVID- 19, incidences of respiratory and bloodstream coinfections are relatively high, with one study in Wales reporting 40.5% and 15.1%, respectively [5]. Similar to that in patients critically ill with influenza coinfected with bacterial pathogens, Staphylococcus aureus (S. aureus) is the most common co-pathogen in patients with COVID- 19 [5, 6]. The rate of nosocomial methicillin-resistant S. aureus (MRSA) bacteremia in patients admitted with COVID- 19 in a New York City hospital system was reported to be five times higher than that of patients without COVID- 19 [7]. Nori et al. [8] identified 151 clinical isolates of S. aureus from blood and respiratory specimens of patients hospitalized with COVID- 19 in New York City, USA, during from March 1 to April 23, 2020, whereas 279 isolates were identified in patients in the ICU in the same region in 2018 and 2019, suggesting a proportionally higher number of S. aureus infections during the COVID- 19 pandemic. In patients with COVID- 19, bacterial coinfections may exacerbate the immunocompromised state caused by the disease, thereby worsening clinical prognoses [9]. The mortality rate of patients who were severely ill with COVID- 19 and S. aureus coinfection has been 90.9% [10].

Although certain studies have reported the molecular characteristics of S. aureus in China during the COVID- 19 pandemic between 2019 and 2021, when the Delta variant of SARS-CoV- 2 was predominant, most strains were isolated from patients without COVID- 19 due to the low prevalence of the virus at that time [11, 12]. During the COVID- 19 regional epidemic in China between December 1, 2022, and January 31, 2023, where the predominant strain of SARS-CoV- 2 was Omicron, the isolation rate of S. aureus in West China Hospital (the largest hospital in Southwest China, with 4,300 hospital beds) increased notably. Since the COVID- 19 epidemic, the molecular characteristics and antimicrobial resistance profiles of prevalent S. aureus strains isolated in Kunming and Wuhan have substantially changed [11, 12]. Therefore, common clinical pathogens need to be monitored to prevent and control COVID- 19. Unfortunately, studies on S. aureus isolates from patients with COVID- 19 lacked precise clinical and molecular information, particularly regarding the virulence and antimicrobial resistance of these strains. To better understand the epidemiology of S. aureus in Southwest China during the regional Omicron variant epidemic in China, in this study, clinical data were obtained from patients coinfected with COVID- 19 and S. aureus. Furthermore, clinical isolates of S. aureus from patients with COVID- 19 were collected to investigate their molecular characteristics, antimicrobial resistance, and virulence factors.

Methods

Inclusion and exclusion criteria

This retrospective study was conducted between December 1, 2022 and January 31, 2023. In total, 102 patients diagnosed with SARS-CoV- 2 pneumonia and who received medical treatment at West China Hospital were enrolled. All adult and pediatric patients with positive results for SARS-CoV- 2 real-time quantitative polymerase chain reaction (PCR) and positive blood or respiratory cultures for S. aureus were analyzed. All patients experienced lower respiratory tract symptoms in conjunction with radiographic findings. For the sputum specimens, less than 10 squamous epithelial cells and more than 25 neutrophils were observed in the low-power field of view. Laboratory data were obtained using a laboratory information system. Clinical data, including patient demographics, ICU status, mechanical ventilation status, comorbidities, corticosteroid use, and disposition (discharged or deceased), were obtained from electronic medical records. Any repeated positive results for the same organism in the same sample type in any patient were excluded.

Clinical isolates

In total, 102 clinical S. aureus isolates were collected from 102 patients with COVID- 19 from West China Hospital between December 1, 2022 and January 31, 2023. These strains were isolated from sputum, bronchoalveolar lavage fluid (BALF), endotracheal aspirates, and blood. The sputum, endotracheal aspirates, and 10 μl of BALF samples were inoculated into blood and chocolate agar plates (Autobio, Zhengzhou, China) and incubated at 35 °C under 5% CO2 according to the National Guide To Clinical Laboratory Procedures [13]. The suspected colonies were subjected to further identification. Blood samples were collected in the BacT/ALERT FA/FN Plus bottles (bioMérieux, Marcy l’Etoile, France) for aerobic and anaerobic cultures, which were then incubated in the BACT/ALERT 3D automated blood culture system (bioMérieux, Marcy l’Etoile, France). Positive cultures were then transferred to the culture medium, and Gram staining was performed. All isolates were identified via matrix-assisted laser desorption/ionization coupled to time-of-flight mass spectrometry (Bruker Daltonik GmbH, Bremen, Germany).

DNA extraction

Stored S. aureus isolates were cultured on blood agar and incubated at 35 °C overnight, after which a single colony was suspended in 800 μl distilled water. The suspension was harvested via centrifugation at 10,000 rpm for 1 min. According to the manufacturer's protocol, DNA was extracted using the TIANamp Bacteria DNA Kit (TIANGEN, Beijing, China).

Multilocus sequence typing analysis

Seven housekeeping genes, arcC, aroE, glpF, gmk, pta, tpi, and yqiL, were amplified according to the instructions found on the multilocus sequence typing (MLST) website (https://pubmlst.org/organisms/staphylococcus-aureus) [14]. These sequences were uploaded to the MLST website, and each sequence was assigned an allele number. A sequence type (ST) number was assigned to each isolate by combining the allele numbers of the seven loci. Clonal complexes (CCs) were determined based on related STs according to the MLST website.

Antimicrobial susceptibility testing

A VITEK 2 system (bioMérieux, Marcy l’Etoile, France) was utilized to evaluate the antimicrobial susceptibility of isolates, according to the manufacturer’s instructions. The antibiotics tested were penicillin (PEN), oxacillin (OXA), levofloxacin (LEV), ciprofloxacin (CIP), moxifloxacin (MXF), gentamicin (GEN), erythromycin (ERY), clindamycin (CLI), vancomycin (VAN), linezolid (LZD), tigecycline (TGC), tetracycline (TET), teicoplanin (TEC), rifampicin (RIF), and sulfamethoxazole (SXT). Results were interpreted according to the Clinical and Laboratory Standards Institute guidelines [15]. The quality control strain used was ATCC 29213.

Virulence genes detection

Eighteen virulence genes were detected via PCR: hemolysin genes (hla, hlb, hld, and hlg), fibronectin-binding proteins genes (fnbA and fnbB), clumping factor genes (clfA and clfB), Staphylococcal enterotoxin genes (sea, seb, and sec), exfoliative genes (eta and etb), Panton-Valentine Leukocidin (pvl), Sdr protein genes (sdrC, sdrD, and sdrE), and the toxic shock syndrome toxin gene (tst). The hla, hlb, hld, hlg, fnbA, fnbB, clfA, clfB, sea, seb, sec, eta, etb, pvl, sdrC, sdrD, and sdrE genes were detected according to a previously published study [11]. The tst gene was amplified via PCR using a previously described method [16]. Amplicons were analyzed using 1.5% agarose gel electrophoresis. The gel was stained with ethidium bromide and exposed to ultraviolet light for visualizing the amplified products.

Statistical methods

Statistical analyses were performed using IBM SPSS software (version 26.0). Continuous variables were presented as medians (interquartile ranges [IQRs]), whereas categorical variables were presented as counts and proportions. Differences between groups for continuous variables were assessed using either Student’s t-tests for normally distributed data or the Mann–Whitney U-test for non-normally distributed data. Categorical variables were analyzed using the chi-squared test or Fisher’s exact test. Statistical significance was set at P < 0.05.

Results

Demographic and clinical features

Of the 102 patients, 75 were discharged, and 27 died. The mean patient age was 67 ± 20 years (range, 9–98 years). Sixty-seven patients (65.7%) were male. The median age of the deceased group (80 years) was significantly higher than that of the surviving group (68 years) (P = 0.007). The patients presented with diverse comorbidities. Hypertension (37.3%, n = 38), diabetes mellitus (29.4%, n = 30), and cardiac disease (18.6%, n = 19) were the most common comorbidities. Nineteen patients (18.6%) were admitted to the ICU. Forty patients (39.2%) received mechanical ventilation (in the ICU or ward), and 43 patients (42.2%) received corticosteroids. Compared with those in the surviving group, more patients in the deceased group required ICU admission and received mechanical ventilation and corticosteroids. The median length of hospitalization was 16 days (IQR, 17 days). Laboratory data indicated that the median of C-reactive protein (CRP) (78.5, range 2–398 mg/l), interleukin- 6 (IL- 6) (31.3, range 1.7–1209 pg/ml), and procalcitonin (PCT) (0.17, range 0.03–99.7 ng/ml) were all above the normal range. IL- 6 (P = 0.001) and PCT (P = 0.016) levels were significantly higher in the deceased group than in the surviving group, whereas lymphocyte counts were significantly lower in the deceased group than in the surviving group (P = 0.019). Thirty-one patients (30.3%) were infected with MRSA, and 71 (69.7%) with methicillin-sensitive S. aureus (MSSA). Sixty-four S. aureus strains (62.7%) were isolated from patients within 48 h of admission. Ninety-six strains (94.1%) were isolated from sputum, BALF and endotracheal aspirates, whereas six (5.9%) were isolated from blood. The percentage of isolates identified as MRSA was higher in the deceased group than in the surviving group, although this difference was not statistically significant. Among patients, 65.3% of survivors and 84.5% of the deceased had received treatment for S. aureus (Table 1).

Table 1 Demographic and clinical characteristics of patients with COVID- 19 coinfected with Staphylococcus aureus
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Multilocus sequence typing

Twenty-eight STs were identified among the 92 S. aureus isolates, and 10 isolates were assigned to novel STs; these included ST8773 (CC398), ST9221 (CC5), ST9222 (CC59), ST9223 (CC8), ST9224 (CC22), ST9225 (CC1), ST9226 (CC5), ST9227 (CC59), ST9228 (CC59), and ST9229 (CC398). The most prevalent ST was ST15 (CC15) (14.7%, 15/102), followed by ST59 (CC59) (12.7%, 13/102) and ST5 (CC5) (12.7%, 13/102). There were 12 STs (4 novel STs) among the MRSA and 31 STs (6 novel STs) among the MSSA isolates. The most common ST among the MRSA isolates was ST59 (38.7%, 12/31), followed by ST5 (16.1%, 5/31) and ST398 (CC398) (9.7%, 3/31). Among the MSSA isolates, ST15 (21.1%, 15/71) was the most prevalent, followed by ST5 (11.3%, 8/71) and ST188 (CC1) (9.9%, 7/71) (Table 2). Twenty-five STs and five novel STs were isolated from the surviving group, with ST15 being the most prevalent (16%, 12/75), whereas 12 STs and five novel STs were isolated from the deceased group, with ST59 being the most prevalent (14.8%, 4/27).

Table 2 Sequence types of 102 Staphylococcus aureus isolates
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Antimicrobial susceptibilities of S. aureus isolates

All isolates were susceptible to VAN, LZD, TGC, and TEC. The antimicrobial resistance rates varied among different STs (Table 3). ST5 was significantly more resistant to LEV, MXF, CIP, and SXT than were ST59 and ST15. ST59 and ST5 exhibited higher rates of resistance to ERY and CLI than did ST15. Of the ST5 (n = 13) and ST59 (n = 13) isolates, 38.5% and 92.3% were identified as MRSA, respectively. All ST15 isolates were MSSA. Resistance to PEN alone and to PEN, ERY, and CLI were the most common resistance profiles of ST15 isolates. Resistance to PEN, ERY, CLI, and OXA was the most common resistance profile of ST59 isolates. Resistance to PEN, ERY, CLI, LEV, MXF, CIP, and SXT was the most common resistance profile of ST5 isolates. The antimicrobial resistance rates of ST59, ST5, and ST15 are provided in Table 4.

Table 3 Virulence genes and antimicrobial resistance profiles among the molecular types of 102 Staphylococcus aureus isolates
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Table 4 Antimicrobial resistance rates of the three most prevalent STs of Staphylococcus aureus isolates
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Virulence genes

All isolates carried hld, clfA, clfB, and sdrE. The prevalence of exfoliative genes (eta and etb), pvl, and tst was low. The eta gene was found in only one isolate (ST121/CC121), and no isolate carried etb. The carrying rates of pvl and tst were both 4.9%. The pvl gene was detected in ST59, ST22 (CC22), and ST88 (CC88), and the tst gene was found in ST5, ST188 (CC1), and ST30 (CC30). The carrying rate of the hlg gene was 16.7%, and it was found only in CC398, CC22, and CC30. The carrying rate of seb (43.1%, 44/102) was higher than that of sea (10.8%, 11/102) and sec (17.6%, 18/102) (Table 3). All isolates carried at least eight virulence genes. Among the three most prevalent STs, hlb was found to be more prevalent in ST59 (100%) and ST5 (84.6%) than in ST15 (0) (P < 0.001), whereas sec and tst were only found in ST5. The carrying rate of sec was significantly higher in ST5 (76.9%) than that in ST59 (0) and ST15 (0) (P < 0.001). Only ST59 carried the pvl gene, and the prevalence of seb in ST59 (100%) was significantly higher than that in ST5 (23.1%) and ST15 (20%) (P < 0.001) (Table 5).

Table 5 Distribution of virulence genes in the three most prevalent sequence types (STs)
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Discussion

Patients with COVID- 19 coinfected with S. aureus were primarily elderly, with a higher prevalence of coinfection observed in males compared to females. Hypertension, diabetes mellitus, and cardiac disease were the most common comorbidities. These results are consistent with those in previous reports [17]. In patients with cardiovascular disease and diabetes, bacterial and fungal coinfections increase the risk of death compared to patients with these comorbidities but without coinfections [10]. The median age of deceased patients in this study was significantly higher than that of the surviving patients, which is consistent with the results of a previous study that found the mortality rate of severely ill COVID- 19 patients coinfected with bacterial and fungal to be 81.0% in the group aged > 75 years and 51.9% in the group aged 66–75 years [10]. A more significant number of patients in the deceased group were admitted to the ICU (P = 0.004) and received mechanical ventilation (P < 0.001) and corticosteroids (P < 0.001) than those in the surviving group. Among patients with COVID- 19 who were on ICU ventilation for more than one week, 50.5% developed respiratory coinfections [18]. Patients with bacterial and fungal coinfections and who had undergone invasive mechanical ventilation were 3.8 times more likely to die than those who underwent the same procedure without coinfections [10]. In this study, IL- 6 and PCT were significantly higher in deceased patients than in those who survived, indicating that these patients suffered from severe infections and immune imbalances. Zhang et al. [19] reported that the levels of high-sensitivity C-reactive protein (hs-CRP), PCT, and IL- 6 in patients with COVID- 19 and coinfection were significantly elevated compared with those in the non-coinfected patients. IL- 6 and PCT levels in critically ill patients were significantly higher on the first day of admission, and IL- 6 levels are independently associated with death in patients with COVID- 19 [20]. The elevation in IL- 6, PCT, and CRP levels at hospital admission was highly significantly associated with ventilator requirement or death within 30 days, and IL- 6 ≥ 52.8 pg/ml, PCT ≥ 0.11 ng/ml, and CRP ≥ 71.1 mg/L were predictive of a severe course of COVID- 19 [21]. Accordingly, IL- 6, PCT, and CRP were suggested as biomarkers to predict the severity and poor prognosis of COVID- 19 [22]. Pandey et al. [5] reported that most coinfections in patients with COVID- 19 were late respiratory tract infections, consistent with our finding that 94.1% of the isolates were from the respiratory tract. A review by Adalbert et al. [17] reported that nearly half of the patients tested were coinfected with MRSA; however, in our study, MRSA only accounted for 30% of coinfections. This discrepancy may be related to different regions and infection types. Data from the China Antimicrobial Surveillance Network (https://www.chinets.com/) showed that the MRSA rate in China dropped from 69% in 2005 to 29.6% in 2023, indicating a decreasing trend. The detection rate of MRSA (30.3%) in this study was comparable to the national average rate. The detection rate for MSSA (69.7%) in this study was considerably higher than that for MRSA (30.3%), suggesting that MSSA was the most common cause of coinfection among patients with COVID- 19 in Southwest China. Furthermore, in the deceased group, more than half of the patients (63.0%, 17/27) were infected with MSSA. Cox et al. [23] reported that MSSA coinfection in adolescent patients with Delta-variant SARS-CoV- 2 can lead to increased morbidity and mortality. Therefore, in patients with COVID- 19, MSSA should not be disregarded in favor of focusing solely on MRSA. Among the patients with COVID- 19 on mechanical ventilation, 19 infected with MRSA (47.5%) and 21 with MSSA (52.5%) were identified. De Pascale et al. [24] found that, for S. aureus ventilator-associated pneumonia, patients with COVID- 19 were more likely to experience MRSA infections than were patients without COVID- 19.

In this study, S. aureus isolates from patients with COVID- 19 are genetically diverse. The most prevalent STs were ST15, ST59, and ST5, which accounted for 40.2% of all isolates. ST59 was the most prevalent for MRSA, and ST15 was the most prevalent for MSSA. A multicenter study wherein 565 MRSA isolates were collected from seven provinces in China indicated that ST59, ST5, ST239, ST764, and ST398 were the most frequently encountered MRSA isolates [25]. Among these epidemic MRSA strains, ST5 and ST239 are the typical hospital-associated MRSA (HA-MRSA) clones prevalent in China and other Asian countries [26,27,28]. Notably, we did not identify any ST239 isolates in our study. This result aligns with that of a study showing a decreasing prevalence of ST239 and an increasing prevalence of ST5 in China [25]. ST5 and its variant ST764 displayed a jagged growth trend in China over the preceding seven years [25]. A recent study reported that ST5/ST764 was the most prevalent type of HA-MRSA isolate in southern China [29]. Furthermore, ST5 is one of the global HA-MRSA clones (New York/Japan clone) [27]. Community-acquired MRSA (CA-MRSA) strains were found to be heterogenetic and region-specific. More than 20 genetic lineages have been found to be associated with CA-MRSA worldwide [30, 31]. In Europe, ST80 clones were prevalent, ST1 and ST8 clones were mainly found in the United States and Canada, and ST59 clones were the most common CA-MRSA in China and other Asian countries [32]. Several studies have indicated that ST398 is the predominant molecular type of MSSA isolates from humans in China [33,34,35]. Li et al. [36] reported that ST398 and ST15 were the most predominant STs among the MSSA isolates from the intestinal tracts of adult patients in China. In northern Japan, ST15 was the most common MSSA from the oral cavity and skin surface [37]. Ma et al. [12] reported that, following the COVID- 19 epidemic, the molecular characteristics of S. aureus isolated from children in Kunming have changed significantly. In 2019 and 2021, ST22 was the most prevalent ST, whereas in 2020, it was ST59. After 2019, the dominant MRSA ST shifted from ST338 to ST59. In another study, ST7 isolates exhibited an increasing trend in prevalence in Wuhan, China, after the COVID- 19 pandemic [11].

The antimicrobial agents VAN, LZD, TGC, and TEC exhibited high in vitro antibiotic activities against S. aureus isolates in our study, which is consistent with other findings reported during the COVID- 19 pandemic [11, 12, 38]. Different antimicrobial resistance profiles were observed in different STs. Among the three most prevalent STs in our study, ST15 was the most susceptible to antibiotics. Most of the ST59 isolates were MRSA, and all were susceptible to GEN, LEV, MXF, CIP, SXT, and RIF. Among the ST5 isolates, 38.5% were MRSA, and all ST5 MRSA isolates were resistant to LEV, MXF, and CIP, except for one isolate that was intermediately susceptible to MXF. Most of the HA-MRSA strains found in China comprised ST5-MRSA, whereas ST59 was the most prominent CA-MRSA. The different rates of resistance to quinolone antimicrobial agents between the ST59 and ST5 MRSA isolates found in our study were consistent with those reported in previous studies, which revealed that CA-MRSA isolates were more susceptible to CIP, TET, SXT, RIF, GEN, and LEV [32, 39].

Virulence genes, such as hemolysin genes (hla, hlb, and hld), fibronectin-binding protein genes (fnbA and fnbB), clumping factor genes (clfA and clfB), and Sdr protein genes (sdrC, sdrD, and sdrE) exhibited high prevalence rates among the isolates in our study. The hemolysin genes encode hemolysin, which destroys host cell types, promotes inflammation, and causes pneumonia and sepsis in clinical practice [12]. The fibronectin-binding protein genes, clumping factor genes, and Sdr protein genes are adhesion genes. The proteins encoded by these genes play an important role in pathogen recognition and adhesion of host cells and extracellular matrix proteins, which are the first steps in biofilm formation and disease development [40, 41]. The carrying rates of hemolysin and adhesive factor virulence genes were significantly higher among clinical isolates than that among carriage isolates [42]. Among enterotoxin genes, sea and seb were the most prevalent ones [43]. In the present study, seb exhibited a higher carrying rate than sea and sec, which was in contrast with that reported in foodborne S. aureus, where the most prevalent enterotoxin gene is sea [44, 45]. Our results were consistent with the previous study which showed seb (84.4%) was the most common gene followed by sea (49.4%) among the MRSA isolates associated with bloodstream infections [29]. Staphylococcal enterotoxins A-E (SEA-SEE) are known to exhibit superantigenic properties, and superantigens trigger excessive and aberrant activation of T cells that results in the release of proinflammatory cytokines, initially tumour necrosis factor alpha, followed by IL- 6, interferon gamma, leading to symptoms of toxic shock and even death in the patient [46]. SEB is the most potent superantigen among the SEs, and aerosolized SEB can cause pulmonary edema and respiratory failure in animals [47]. Exfoliative toxins (ETs), also known as epidermolytic toxins, are related to Staphylococcal scalded skin syndrome (SSSS), and SSSS predominantly affects neonates and infants, but immunosuppression and renal impairment are reported to be risk factor for SSSS in adults [48]. In the present study, one isolate with the eta gene, belonging to ST121 (CC121), was isolated from the sputum of a woman diagnosed with classical Hodgkin lymphoma and pneumonia. PVL plays an essential role in pneumonia development and is associated with severe invasive infections [49, 50]. An association between PVL-secreting S. aureus and influenza virus has been reported [51, 52]. Claire Duployez et al. [53] reported a case of necrotizing pneumonia induced by PVL-secreting MSSA in a young adult infected with COVID- 19, indicating that similar to the influenza virus, SARS-CoV- 2 is a facilitating factor for PVL-producing S. aureus necrotizing pneumonia. In the present study, among the five patients infected with S. aureus isolates carrying pvl, four were diagnosed with severe pneumonia, while one was a young woman with no underlying disease who was admitted to the ICU. The previous study and our research indicated that in previously healthy young patients admitted to the ICU for COVID- 19 and S. aureus pneumonia, a PVL-producing strain should be considered, and treatment should be administered accordingly. Specific STs are associated with virulence genes. The ST6 (CC5) isolates had a high carrying rate for the sea gene while the seb gene was highly prevalent in ST59 isolates. The sec and tst genes were found to be more prevalent in ST5 than other STs. Cai et al. [54] reported that the sea gene was prevalent in the ST6 and ST30 clones; the ST59 clone had a high carrying rate for the seb gene, and the sec gene was prevalent in ST45, ST25, and ST5, consistent with our results. The carrying rates of hemolysin genes and adhesion genes were also different among different types of S. aureus. The genes hla-hld-fnbA-fnbB were prevalent in CC15; hla-hlb-hld-fnbA-fnbB were prevalent in CC59, and hld-hlg-fnbB were prevalent in CC398. Several studies have reported that the pvl gene is highly prevalent in ST22 isolates [11, 12, 54, 55]. In our study, only five isolates carried pvl — two isolates were ST22, two were ST59, and one was ST88. Gu et al. [11] reported that the ST7 isolates exhibited increased positivity rates for various virulence genes, including hlb, fnbB, seb, and sdrE, after the COVID- 19 pandemic in Wuhan, China. Ma et al. [12] reported that ST59 exhibited higher carrying rates for various virulence genes than ST22 and ST338 in Kunming in 2020. These characteristics made ST7 and ST59 the dominant strains during the COVID- 19 pandemic in Wuhan and Kunming, respectively.

Despite its strengths, this study has certain limitations. First, the sample size was small. In addition, the findings were obtained from a single center, which may affect the representativeness of the S. aureus isolates. In the future large-sample, multi-center studies will be required to confirm the results of the present study.

In conclusion, patients coinfected with COVID- 19 and S. aureus were predominantly older adults and male, with most infections being caused by MSSA (69.7%). S. aureus isolates from patients with COVID- 19 exhibited diverse genetic backgrounds, and the three most prevalent STs were ST15, ST59, and ST5. The genetic diversity based on STs was considerably higher for MSSA (31 STs) than for the MRSA isolates (12 STs). Different STs exhibited different antimicrobial resistance patterns and virulence gene carrying rates. These findings fill the knowledge gap regarding the epidemiological characteristics of coinfecting S. aureus in China and contribute to the advancement of the global epidemiology data, providing an epidemiological basis for the treatment and prevention of S. aureus coinfections with COVID- 19.

Data availability

The 102 S. aureus sequencing data is available on NCBI with GenBank PQ001151-PQ001354 and GenBank PQ015696-PQ016205 accession numbers. Other datasets generated and analyzed during the current study are available from the corresponding author upon reasonable request.

Abbreviations

S. aureus :

Staphylococcus aureus

COVID- 19:

Coronavirus disease 19

PCR:

Polymerase chain reaction

BALF:

Bronchoalveolar lavage fluid

MLST:

Multilocus sequence typing

STs:

Sequence types

SARS-CoV- 2:

Severe acute respiratory syndrome coronavirus type 2

ICU:

Intensive care unit

MRSA:

Methicillin-resistant S. aureus

MSSA:

Methicillin-sensitive S. aureus

CCs:

Clonal complexes

SSSS:

Staphylococcal scalded skin syndrome

COPD:

Chronic obstructive pulmonary disease

PEN:

Penicillin

OXA:

Oxacillin

LEV:

Levofloxacin

CIP:

Ciprofloxacin

MXF:

Moxifloxacin

GEN:

Gentamicin

ERY:

Erythromycin

CLI:

Clindamycin

VAN:

Vancomycin

LZD:

Linezolid

TGC:

Tigecycline

TET:

Tetracycline

TEC:

Teicoplanin

RIF:

Rifampicin

SXT:

Sulfamethoxazole

hla,  hlb,  hld, and hlg :

Hemolysin genes

fnbA and fnbB :

Fibronectin-binding proteins genes

clfA and  clfB :

Clumping factor genes

sea,  seb, sec :

Staphylococcal Enterotoxin genes

eta and etb :

Exfoliative genes

pvl :

Panton-Valentine Leukocidin

sdrC,  sdrD, and  sdrE :

Sdr protein genes

tst :

The toxic shock syndrome toxin gene

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Acknowledgements

We acknowledged the original manuscript describing the MLST technique for S. aureus as detailed on the pubMLST website. This MLST scheme was developed by Mark Enright in the laboratory of Brian Spratt, Imperial College London, in collaboration with the laboratories of Nick Day and Sharon Peacock.

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Authors and Affiliations

  1. Division of Clinical Microbiology, Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37 Guoxue Lane, Chengdu, 610041, Sichuan, China

    Siying Wu, Mei Kang, Ya Liu, Yuling Xiao, Jin Deng, Weili Zhang & Quanfeng Liao

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  1. Siying Wu
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  2. Mei Kang
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  3. Ya Liu
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  4. Yuling Xiao
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  7. Quanfeng Liao
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Contributions

SW: Conceptualization, Data curation, Formal analysis, Methodology, Writing – original draft. MK: Conceptualization, Supervision, Project administration, Writing – review & editing. YL: Data curation, Methodology. JD: Validation, Methodology. YX: Formal analysis. WZ: Investigation. QL: Investigation. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Mei Kang.

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Ethics approval and consent to participate

This is a retrospective study; the research does not involve personal privacy or commercial interests. The data has been de-identified and cannot be traced. This study did not contact the human subjects and only investigated the S. aureus isolated from the patients. Therefore, ethical approval was obtained, and the informed consent to participate was waived by the Ethics Committee of West China Hospital, Sichuan University (registration no. 2023–1475).

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Not applicable.

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The authors declare no competing interests.

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Wu, S., Kang, M., Liu, Y. et al. Clinical and molecular characteristics of Staphylococcus aureus isolates from patients with COVID-19 in Southwest China. BMC Infect Dis 25, 546 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12879-025-10868-9

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BMC Infectious Diseases

ISSN: 1471-2334

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