Genomic and phenotypic characterization of multidrug-resistant Staphylococcus haemolyticus isolated from burn patients in Chongqing, southwestern China

Abstract

Staphylococcus hemolyticus is one of the frequently isolated nosocomial pathogens in immunocompromised patients; however, its genotypic and phenotypic characteristics in burn patients remain largely unknown. In this study, 146 S. haemolyticus strains were collected from the burn unit of a tertiary hospital in Chongqing, southwestern China. Whole genome sequencing was applied to determine the molecular characteristics of these S. haemolyticus isolates. Results showed that sequence type 1 (ST1; 26.7%, 39/146) was the most prevalent lineage, followed by clones ST42 (17.8%, 25/146), ST3 (15.8%, 23/146), ST25 (9.6%, 14/146), ST29 (4.8%, 7/146), and newly emerged ST152 (6.2%, 9/146). In terms of phenotypes, 90.4% (132/146) of the S. haemolyticus isolates were multidrug-resistant (MDR), and more than 90% strains exhibited resistance to penicillin, erythromycin, oxacillin, and levofloxacin. A total of 145 out of 146 S. haemolyticus isolates harbored at least 10 virulence factor genes. The tested strains with ST1, ST3, ST25, and ST42 presented similar hemolytic activities and biofilm formation capabilities. All detected ST152 isolates were MDR, corresponding to the number of their antimicrobial resistance genes being the largest among all tested STs. Moreover, ST152 isolates had increased hemolytic capacity and biofilm formation capability compared with their counterpart ST29 strains, the parent lineage of ST152 with a single locus variation. Overall, this study showed the genomic and phenotypic characteristics of 146 S. haemolyticus strains isolated in Chongqing and found the newly emerged ST152 MDR lineage with hypervirulence, which may call attention to the control of infections caused by MDR S. haemolyticus strains in hospitals.IMPORTANCEStaphylococcus haemolyticus is a common opportunistic pathogen with multidrug resistance in clinical infections. In this study, we analyzed the molecular epidemiological characteristics of 146 S. haemolyticus strains isolated from the burn patients of a tertiary hospital in Chongqing between 2017 and 2023. The results demonstrated that the phylogenetic evolution of S. haemolyticus strains was diverse and plastic. The majority of the isolates were multidrug-resistant (MDR). The virulence genes, resistance elements, and phenotypes, such as hemolysis and biofilm formation, were determined. A new lineage (ST152) that harbored the highest number of resistance genes was characterized to be 100% (9/9) MDR. The prevalence of ST152 S. haemolyticus strains suggests a new health threat in terms of control and treatment of coagulase-negative staphylococcal infections in Chongqing. This study provides information for clinical control of S. haemolyticus dissemination and infection in hospitals.

Keywords: ST152; Staphylococcus haemolyticus; antimicrobial resistance; biofilm formation; burn unit; hemolytic activity; virulence; whole genome sequencing.

Fig 1

Clinical information of burn inpatients, strain sources, and ST distribution of the S. haemolyticus strains. Clinical information of S. haemolyticus-infected inpatients classified by (A) gender and (B) age. (C) S. haemolyticus strain distribution in ward. (D) Distribution of specimen sources in the S. haemolyticus isolates. (E) Distribution of STs in the S. haemolyticus strains.

Fig 2

Approximate maximum-likelihood phylogenetic tree of S. haemolyticus strains isolated from the burn unit based on core-genomic SNPs. The genome sequence of CGMH-SH53 (a CC3-ST3 strain) was used as the reference. The tree was generated using the iTOL online platform (https://itol.embl.de/). The total branches of the six clades are shown in diverse colors. The inner circle indicates different STs, and the sample source, ward distribution, and the time of strain collected were colored and mapped in the outer rings.

Fig 3

Antimicrobial resistance and AMR gene carriage of the S. haemolyticus isolates belonging to major STs. (A) Antimicrobial resistant rates in S. haemolyticus isolates of the certain STs. (B) Distribution of AMR genes in S. haemolyticus strains of the major STs. (C) Number of AMR genes carried by S. haemolyticus of the major STs. The data are shown as mean ± standard deviation. Statistical analysis was performed using one-way analysis of variance. ****P < 0.0001, ***P < 0.001, **P < 0.01, and *P < 0.05. GEN, gentamicin; ERY, erythromycin; PEN, penicillin; OXA, oxacillin; LVX, levofloxacin; MFX, moxifloxacin; RIF, rifampicin; SXT, trimethoprim/sulfamethoxazole; LZD, linezolid; and VAN, vancomycin.

Fig 4

AMR gene carriage, AMR genetic point mutation, and virulence factor gene distribution of the 146 S. haemolyticus isolates. The presence of an AMR gene, a point mutation, and a virulence factor gene in a strain is shown in blue, purple, and green, respectively, while the absence of an AMR gene, point mutation, and virulence factor gene in the strain is indicated in gray.

Fig 5

Distribution of the virulence factor genes among S. haemolyticus isolates of the major STs. (A) Number of virulence factor genes carried by S. haemolyticus of the major STs. The data are shown as mean ± standard deviation. Statistical analysis was performed using one-way analysis of variance. ****P < 0.0001 and *P < 0.05. (B) Distribution of virulence factor genes in the major STs of S. haemolyticus strains. The percentage of a virulence factor gene in certain ST was indicated.

Fig 6

Hemolytic activity and biofilm formation capacity of the S. haemolyticus isolates belonging to major STs. (A) Erythrocyte lysing ability of the major ST strains. The hemolytic activity was determined by a test tube method at an absorbance of 543 nm. Detection of biofilm formation ability of S. haemolyticus strains of the major STs cultured in (B) BHI, (C) BHI_NaCl, and (D) BHI_glu. Biofilm formation capacity was detected by semiquantitative crystal violet method at an absorbance of 570 nm. Each experiment was independently repeated three times. The data are shown as mean ± standard deviation. Statistical analysis was performed using one-way analysis of variance. **P < 0.01 and *P < 0.05.