Genomic Heterogeneity of Methicillin Resistant Staphylococcus aureus Associated with Variation in Severity of Illness among Children with Acute Hematogenous Osteomyelitis

Anti-Staphylococcus aureus potential of compounds from Ganoderma sp.: A comprehensive molecular docking and simulation approaches

In this study, a series of secondary metabolites from Ganoderma sp. were screened against Staphylococcus aureus protein targets, including as phosphotransacetylase, clumping factor A, and dihydrofolate reductase, using molecular docking simulations. The chemicals that showed the strongest binding energy with the targeted proteins were ganodermanontriol, lucidumol B, ganoderic acid J, ergosterol, ergosterol peroxide, 7-oxoganoderic acid Z, ganoderic acid AM1, ganosinoside A, ganoderic acid D, and 24R-ergosta-7,2E-diene-3β,5α,6β-triol. Interestingly, ganosinoside A showed the greatest affinity for the protein clumping factor A, a result validated by molecular dynamic simulation. Additionally, three natural Ganoderma sp. Strains as Ganoderma lingzhi VNKKK1903, Ganoderma lingzhi VNKK1905A2, and Amauroderma subresinosum VNKKK1904 were collected from Kon Ka Kinh National Park in central land of Vietnam and evaluated for their antibacterial activity against Staphylococcus aureus using an agar well diffusion technique. These results suggest that the fungal extracts and secondary metabolites may serve as valuable sources of antibiotics against Staphylococcus aureus. These findings provided an important scientific groundwork for further exploration of the antibacterial mechanisms of compounds derived from Ganoderma sp. in future research.

Staphylococcus aureus isolates from children with clinically differentiated osteomyelitis exhibit distinct transcriptomic signatures

There is substantial genomic heterogeneity among Staphylococcus aureus isolates of children with acute hematogenous osteomyelitis (AHO) but transcriptional behavior of clinically differentiated strains has not been previously described. This study evaluates transcriptional activity of S. aureus isolates of children with AHO that may regulate metabolism, biosynthesis, or virulence during bacterial growth and pathogenesis. In vitro growth kinetics were compared between three S. aureus clinical isolates from children with AHO who had mild, moderate, and severe illness. Total RNA sequencing was performed for each isolate at six separate time points throughout the logarithmic phase of growth. The NASA RNA-Sequencing Consensus Pipeline was used to identify differentially expressed genes allowing for 54 comparisons between the three isolates during growth. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathways were used to evaluate transcriptional variation in metabolism, biosynthesis pathways and virulence potential of the isolates. The S. aureus isolates demonstrated differing growth kinetics under standardized conditions with the mild isolate having higher optical densities with earlier and higher peak rates of growth than that of the other isolates (p<0.001). Enrichment pathway analysis established distinct transcriptional signatures according to both sampling time and clinical severity. Moderate and severe isolates demonstrated pathways of bacterial invasion, S. aureus infection, quorum sensing and two component systems. In comparison, the mild strain favored biosynthesis and metabolism. These findings suggest that transcriptional regulation during the growth of S. aureus may impact the pathogenetic mechanisms involved in the progression of severity of illness in childhood osteomyelitis. The clinical isolates studied demonstrated a tradeoff between growth and virulence. Further investigation is needed to evaluate these transcriptional pathways in an animal model or during active clinical infections of children with AHO.

Integrating in Silico and In Vitro Studies to Screen Anti-Staphylococcus aureus Activity From Vietnamese Ganoderma multiplicatum and Ganoderma sinense

Background: Staphylococcus aureus is a nosocomial pathogen responsible for many serious infectious diseases in humans. Finding the anti- S. aureus agents is a time-consuming and costly process. Recently, computational methods have provided a better understanding of the interactions between herbal medicine drug targets to help clinical practitioners rationally design herbal formulae. Methods: In this study, molecular docking simulation was applied to screen a list of natural secondary metabolites from Ganoderma sp. on the protein target S. aureus sortase A. Molecular dynamics models were used to assess the stability of protein–ligand complexes during the first 100 ns. To validate the computational results, 2 Ganoderma species, G. multiplicatum VNKKK1901 and G. sinense VNKKK1902, were tested for antibacterial activity against S. aureus using the disk diffusion method. Results: The results showed that, among the selected compounds, ganosinensin B and ganosinoside A generated the highest binding energy on S. aureus sortase A, and demonstrated strong and stable binding capacity to proteins. In addition, the extracts of G. sinense VNKKK1902 and G. multiplicatum VNKKK1901 were bactericidal, with minimum bactericidal concentration (MBC)/minimum inhibitory concentration (MIC) ratios of 2. Conclusion: Our findings provide the first scientific report on the antibacterial activity of Ganoderma sp., which contain 2 promising compounds, ganosinensin B and ganosinoside A, as potential hits for developing novel drugs capable of supporting treatment of S. aureus infection.

Staphylococcus aureus Genomic Analysis and Outcomes in Patients with Bone and Joint Infections: A Systematic Review

Many studies have been published assessing the association between the presence of S. aureus genes and outcomes in patients with bone and joint infections (BJI), but it is not known if they have had similar findings. A systematic literature review was performed. All available data on studies in Pubmed between January 2000 to October 2022 reporting the genetic characteristics of S. aureus and the outcomes of BJIs were analyzed. BJI included prosthetic joint infection (PJI), osteomyelitis (OM), diabetic foot infection (DFI), and septic arthritis. Because of the heterogeneity of studies and outcomes, no meta-analysis was performed. With the search strategy, 34 articles were included: 15 articles on children and 19 articles on adults. In children, most BJI studied were OM (n = 13) and septic arthritis (n = 9). Panton Valentine leucocidin (PVL) genes were associated with higher biological inflammatory markers at presentation (n = 4 studies), more febrile days (n = 3), and more complicated/severe infection (n = 4). Other genes were reported anecdotally associated with poor outcomes. In adults, six studies reported outcomes in patients with PJI, 2 with DFI, 3 with OM, and 3 with various BJI. Several genes were associated with a variety of poor outcomes in adults, but studies found contradictory results. Whereas PVL genes were associated with poor outcomes in children, no specific genes were reported similarly in adults. Additional studies with homogenous BJI and larger sample sizes are needed.

Surveillance of osteoarticular infections caused by Staphylococcus aureus in a paediatric hospital in Mexico City

Staphylococcus aureus is the main aetiologic agent of osteoarticular infections (OAIs) in paediatric patients. The aim of this prospective unicenter study was to describe the phenotypic and genotypic characteristics of S. aureus isolates obtained from OAIs in paediatric patients admitted to tertiary care hospital. Through a surveillance program called OsteoCode, a multidisciplinary team was created and we identified 27 patients with OAIs caused by S. aureus from 2019 to 2021. The susceptibility profile, virulence factors, biofilm formation, pulsed-field gel electrophoresis (PFGE), clonal complex (CC) and sequence type (ST) were determined. In addition, the clinical characteristics and evolution of the patients presented six months after the diagnosis of OAIs were described. Ninety-two percent of the isolates were methicillin-sensitive S. aureus (MSSA). In methicillin-resistant S. aureus (MRSA), SCCmec-II and SCCmec-V were detected. The pvl gene was only observed in MSSA (18.5%) and was associated with highest fever (p=0.015), multiple localization (p=0.017), and soft tissue sites of infection beyond the bone (pyomyositis, pulmonary abscess) (p=0.017). Biofilm formation was detected in 55.6% of isolates. The most common CC were CC5 and CC30 which represent the most common linages for bone and joint infections worldwide. The isolates were distributed in different STs, and ST672 was predominant. MRSA were associated with a longer duration of intravenous treatment and a prolonged hospital stay (p=0.023). Recurrent infection occurred in five children and orthopaedic complications in 33.3% of patients. This is the first study that reflects the epidemiology of S. aureus in OAIs in paediatric patients in Mexico; a clear predominance of MSSA distributed in different STs was observed. Our findings highlight that a multidisciplinary team is required for the diagnosis and treatment of OAIs.

Genomic characterization of Staphylococcus aureus isolates causing osteoarticular infections in otherwise healthy children

Background

Pediatric osteoarticular infections are commonly caused by Staphylococcus aureus. The contribution of S. aureus genomic variability to pathogenesis of these infections is poorly described.

Methods

We prospectively enrolled 47 children over 3 1/2 years from whom S. aureus was isolated on culture—12 uninfected with skin colonization, 16 with skin abscesses, 19 with osteoarticular infections (four with septic arthritis, three with acute osteomyelitis, six with acute osteomyelitis and septic arthritis and six with chronic osteomyelitis). Isolates underwent whole genome sequencing, with assessment for 254 virulence genes and any mutations as well as creation of a phylogenetic tree. Finally, isolates were compared for their ability to form static biofilms and compared to the genetic analysis.

Results

No sequence types predominated amongst osteoarticular infections. Only genes involved in evasion of host immune defenses were more frequently carried by isolates from osteoarticular infections than from skin colonization (p = .02). Virulence gene mutations were only noted in 14 genes (three regulating biofilm formation) when comparing isolates from subjects with osteoarticular infections and those with skin colonization. Biofilm results demonstrated large heterogeneity in the isolates’ capacity to form static biofilms, with healthy control isolates producing more robust biofilm formation.

Conclusions

S. aureus causing osteoarticular infections are genetically heterogeneous, and more frequently harbor genes involved in immune evasion than less invasive isolates. However, virulence gene carriage overall is similar with infrequent mutations, suggesting that pathogenesis of S. aureus osteoarticular infections may be primarily regulated at transcriptional and/or translational levels.

Virulence Determinants in Staphylococcus aureus Clones Causing Osteomyelitis in Italy

Staphylococcus aureus is the most common pathogen causing osteomyelitis (OM). The aim of this study was to explore the clonal complex (CC) distribution and the pattern of virulence determinants of S. aureus isolates from OM in Italy. Whole-genome sequencing was performed on 83 S. aureus isolates from OM cases in six hospitals. Antibiotic susceptibility tests showed that 30.1% of the isolates were methicillin-resistant S. aureus (MRSA). The most frequent CCs detected were CC22, CC5, CC8, CC30, and CC15, which represent the most common lineages circulating in Italian hospitals. MRSA were limited in the number of lineages (CC22, CC5, CC8, and CC1). Phylogenetic analysis followed the sequence type-CC groupings and revealed a non-uniform distribution of the isolates from the different hospitals. No significant difference in the mean number of virulence genes carried by MRSA or MSSA isolates was observed. Some virulence genes, namely cna, fib, fnbA, coa, lukD, lukE, sak, and tst, were correlated with the CC. However, different categories of virulence factors, such as adhesins, exoenzymes, and toxins, were frequently detected and unevenly distributed among all lineages. Indeed, each lineage carried a variable combination of virulence genes, likely reflecting functional redundancy, and arguing for the importance of those traits for the pathogenicity in OM. In conclusion, no specific genetic trait in the most frequent lineages could explain their high prevalence among OM isolates. Our findings highlight that CCs detected in OM isolates follow the epidemiology of S. aureus infections in the country. It is conceivable that any of the most common S. aureus CC can cause a variety of infections, including OM.

Staphylococcus aureus clones causing osteomyelitis: a literature review (2000-2020)

OBJECTIVES

Staphylococcus aureus is the most common causative organism of osteomyelitis (OM). Nevertheless, the molecular epidemiology of S. aureus causing OM remains ill-defined. This study aimed to address the global epidemiology of S. aureus clones from OM patients.

METHODS

Literature databases were searched for studies reporting the molecular typing of S. aureus involved in OM published between 1 January 2000 and 29 July 2020. Data from 32 articles that fulfilled the inclusion criteria were analysed for year of publication, country of patients, methicillin susceptibility and genotypic characteristics of S. aureus isolates.

RESULTS

Pandemic clones CC5, CC8, CC22, CC30 and CC45 were the most common in OM. The distribution of clones differed greatly among studies owing to the local epidemiology of S. aureus and the MSSA heterogeneity. PVL-positive MRSA clones belonging to ST80/CC80 and ST8/CC8/USA300 were the most common among paediatric patients in Europe and the USA; greater variability was observed in the adult population. In Europe, MRSA belonged to PVL-negative CC5, CC8 and CC22 indicating a nosocomial origin of infections; in Asia PVL-positive ST59/CC59 MRSA was the most frequent. PVL-positive clones were often detected in haematogenous OM in children and adults. Although MSSA were polyclonal, PVL-negative ST398/CC398 MSSA was the most prevalent clone in diabetic foot OM.

CONCLUSION

All major S. aureus clones circulating both in hospital and community settings appear to be capable of causing OM. Future studies reporting molecular typing and genomic data will provide more insights into the epidemiology and pathobiology of S. aureus clones causing OM.

The impact of simultaneous inoculation of Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans on rodent burn wounds

Burn wound infection often involves a diverse combination of bacterial and fungal pathogens. In this study, we characterize the mixed species burn wound infection by inoculating the burn surface with 1 × 10^3/4/5 CFU of Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans in a 1:1:1 ratio. Using the revised Walker-Mason scald burn rat model, 168 male Sprague-Dawley rats (350-450 g) subject to ∼10% TBSA burn injury, with or without inoculation, were evaluated for 11 days after burn. In the wound, P. aeruginosa and S. aureus formed robust biofilms as determined by the bacterial tissue load, ∼1 × 10⁹ CFU/g, and expression of key biofilm genes. Interestingly, within 3 days C. albicans achieved tissue loads of ∼1 × 10⁶ CFU/g, but its numbers were significantly reduced beyond the limit of detection in the burn wound by day 7 in partial-thickness injuries and by day 11 in full-thickness injuries. The pathogenic biofilms contributed to burn depth progression, increased release of HMGB-1 into circulation from injured tissue, and significantly elevated the numbers of circulating innate immune cells (Neutrophils, Monocytes, and Basophils). This robust model of multi-species burn wound infection will serve as the basis for the development of new antimicrobials for combating biofilm-based wound infections.

The impact of Staphylococcus aureus genomic variation on clinical phenotype of children with acute hematogenous osteomyelitis

Background

Children with acute hematogenous osteomyelitis (AHO) have a broad spectrum of illness ranging from mild to severe. The purpose of this study is to evaluate the impact of genomic variation of Staphylococcus aureus on clinical phenotype of affected children and determine which virulence genes correlate with severity of illness.

Methods

De novo whole genome sequencing was conducted for a strain of Community Acquired Methicillin Resistant Staphylococcus aureus (CA-MRSA), using PacBio Hierarchical Genome Assembly Process (HGAP) from 6 Single Molecule Real Time (SMRT) Cells, as a reference for DNA library assembly of 71 Staphylococcus aureus isolates from children with AHO. Virulence gene annotation was based on exhaustive literature review and genomic data in NCBI for Staphylococcus aureus. Clinical phenotype was assessed using a validated severity score. Kruskal-Wallis rank sum test determined association between clinical severity and virulence gene presence using False Discovery Rate (FDR), significance <0.01.

Results

PacBio produced an assembled genome of 2,898,306 bp and 2054 Open Reading Frames (ORFs). Annotation confirmed 201 virulence genes. Statistical analysis of gene presence by clinical severity found 40 genes significantly associated with severity of illness (FDR ≤0.009). MRSA isolates encoded a significantly greater number of virulence genes than did MSSA (p < 0.0001). Phylogenetic analysis by maximum likelihood (PAML) demonstrated the relatedness of genomic distance to clinical phenotype.

Conclusions

The Staphylococcus aureus genome contains virulence genes which are significantly associated with severity of illness in children with osteomyelitis. This study introduces a novel reference strain and detailed annotation of Staphylococcus aureus virulence genes. While this study does not address bacterial gene expression, a platform is created for future transcriptome investigations to elucidate the complex mechanisms involved in childhood osteomyelitis.

Seasonal Variation and Weather Changes Related to the Occurrence and Severity of Acute Hematogenous Osteomyelitis in Children

BACKGROUND

Acute hematogenous osteomyelitis (AHO) demonstrates regional variability in incidence and severity. In this study, we evaluated seasonal variations of AHO and assessed the effects of weather trends on the occurrence and severity of illness in affected children.

METHODS

National Weather Service data from the dates of symptom onset and of admission of children with AHO were gathered. Seasonal occurrence rates and the weather patterns were studied according to severity-of-illness category. Statistical analysis was performed with Pearson and Spearman correlations and analysis of variance.

RESULTS

A total of 209 children with AHO were admitted within 21 days of symptom onset (average, 5.0 ± 3.8 days). Severity-of-illness scores ranged from 0 to 10 (average, 3.2 ± 3.2). Symptom onset occurred most commonly in summer (73 [34.9%]) or spring (54 [25.8%]). We found a significant correlation between severity of illness and minimum temperature at symptom onset during the summer season (P = .020). A significant change in average humidity (21.6%) occurred during the winter between the date of symptom onset and the date of admission for children with severe illness (P = .020).

DISCUSSION

This study identified seasonal variation in the occurrence of AHO in children; summer was the most common season for occurrence. To our knowledge, this is the first detailed evaluation of weather parameters and trends in weather changes from symptom onset to admission with consideration of the effects of weather on the occurrence of infection and severity of illness.

Procalcitonin and Pancreatic Stone Protein Function as Biomarkers in Early Diagnosis of Pediatric Acute Osteomyelitis

Background

High plasma levels of procalcitonin (PCT) are typically seen in children with severe bacterial infection, particularly in cases of septic shock or bacteremia. Similarly, pancreatic stone protein (PSP) is associated with inflammation, infection, and other disease-related stimuli. However, the prognostic value of PSP in critically ill pediatric patients is unknown. This study investigated the early diagnostic value of PCT and PSP in pediatric acute osteomyelitis.

Material/Methods

A total of 187 patients with suspected acute osteomyelitis and 80 healthy control children were enrolled. The serum expression of PTC and PSP was measured. Pearson correlation analysis was conducted to correlate PTC with PSP. ROC analysis was used to test the value of PTC and PSP in early diagnosis of pediatric acute osteomyelitis.

Results

Acute osteomyelitis was diagnosed in 49.2% of the patients (n=92) based on the layered bone puncture. The serum levels of PTC and PSP in pediatric acute osteomyelitis were higher than in the non-acute osteomyelitis group (P<0.01). Serum PTC concentrations showed a significantly positive correlation with PSP levels (P<0.001). ROC analysis showed that the AUC values of PTC and PSP were 0.767 (95% CI, 0.700–0.826), and 0.796 (95% CI, 0.731–0.855), respectively. The AUC value of PTC & PSP was 0.903 (95% CI: 0.851–0.941), which was markedly increased compared with PTC or PSP (P<0.01).

Conclusions

Serum levels of PCT and PSP are promising biomarkers for early diagnosis of pediatric acute osteomyelitis.

Examining the association of MMP-1 gene -1607 (2G/1G) and -519 (A/G) polymorphisms with the risk of osteomyelitis: A case-control study

To investigate the effects of matrix metalloproteinase-1 (MMP-1) gene polymorphisms on the onset of osteomyelitis in Chinese Han population.In all, 80 osteomyelitis patients (case group) and 81 healthy people (control group) were recruited into this case-control study. Polymerase chain reaction-restriction fragment length polymorphism method was utilized to examine the genotypes of MMP-1 polymorphisms (-1607 2G/1G and -519A/G) in the 2 groups. Genotype and allele differences between the case and control groups were analyzed by chi-square test. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated to present the association strength between MMP-1 gene polymorphisms and osteomyelitis.Frequencies of -1607 2G/2G genotype between the case and control groups were statistically significant (P = .025). Compared with 1G/1G genotype carriers, the 2G/2G genotype carriers had 1.605 times risk of developing osteomyelitis (OR 2.605, 95% CI 1.116-6.082). Meanwhile, the 2G allele significantly associated with the risk of osteomyelitis (OR 1.735, 95% CI 1.115-2.701). In addition, frequency of -519GG genotype was obviously higher in case group than that in control group (P = .024), and GG genotype related to an increased risk of osteomyelitis (OR 2.792, 95% CI 1.127-6.917). Whereas, the -519G allele may be a susceptible factor for osteomyelitis (OR 1.622, 95% CI 1.038-2.536).The MMP-1 -1607 (2G/1G) and -519 (A/G) polymorphisms may contribute to the onset of osteomyelitis.

Acute Hematogenous Osteomyelitis in Children: Pathogenesis, Diagnosis, and Treatment

Acute hematogenous osteomyelitis (AHO) in children is an ideal condition to study due to its representation of a wide spectrum of disorders that comprise pediatric musculoskeletal infection. Proper care for children with AHO is multidisciplinary and collaborative. AHO continues to present a significant clinical challenge due to evolving epidemiology and complex pathogenesis. A guideline-driven, multidisciplinary approach has been introduced and shown to effectively reduce hospital stay, improve the timing and selection of empirical antibiotic administration, reduce delay to initial MRI, reduce the rate of readmission, and shorten antibiotic duration.

Cefazolin and Ertapenem, a Synergistic Combination Used To Clear Persistent Staphylococcus aureus Bacteremia

Ertapenem and cefazolin were used in combination to successfully clear refractory methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia. In addition, recent work has demonstrated activity of combination therapy with beta-lactams from different classes against methicillin-resistant S. aureus (MRSA). The ertapenem-plus-cefazolin combination was evaluated for synergy in vitro and in vivo in a murine skin infection model using an index MSSA bloodstream isolate from a patient in whom persistent bacteremia was cleared with this combination and against a cadre of well-described research strains and clinical strains of MSSA and MRSA. Against the index MSSA bloodstream isolate, ertapenem and cefazolin showed synergy using both checkerboard (fractional inhibitory concentration [FIC] index = 0.375) and time-kill assays. Using a disk diffusion ertapenem potentiation assay, the MSSA isolate showed a cefazolin disk zone increased from 34 to 40 mm. In vitro pharmacokinetic/pharmacodynamic modeling at clinically relevant drug concentrations demonstrated bactericidal activity (>3 log₁₀-CFU/ml reduction) of the combination but bacteriostatic activity of ether drug alone at 48 h. A disk diffusion potentiation assay showed that ertapenem increased the cefazolin zone of inhibition by >3 mm for 34/35 (97%) MSSA and 10/15 (67%) MRSA strains. A murine skin infection model of MSSA showed enhanced activity of cefazolin plus ertapenem compared to monotherapy with these agents. After successful use in clearance of MSSA bacteremia, the combination of ertapenem and cefazolin showed synergy against MSSA in vitro and in vivo. This combination may warrant consideration for future clinical study in MSSA bacteremia.