Characterization of staphylococci sampled from diabetic foot ulcer of Jordanian patients

Studying Microbial Ecology of Diabetic Foot Infections: Significance of PCR Analysis for Prudent Antimicrobial Stewardship

This study presents a comprehensive investigation into the microbial ecology of diabetic foot infections (DFIs), using molecular-polymerase chain reaction (PCR) analysis to accurately identify the causative agents. One hundred DFI patients were recruited and classified using the Depth Extent Phase and Associated Etiology (DEPA) score according to their severity. Results revealed polymicrobial infections in 75% of cases, predominantly featuring Staphylococcus epidermidis (83%) and Staphylococcus aureus (63%). Importantly, 20% of samples exhibited facultative anaerobes Bacteroides fragilis or Clostridium perfringens, exclusively in high DEPA score ulcers. Candida albicans coinfection was identified in 19.2% of cases, underscoring the need for mycological evaluation. Empirical antimicrobial therapy regimens were tailored to DEPA severity, yet our findings highlighted a potential gap in methicillin-resistant Staphylococcus aureus (MRSA) coverage. Despite an 88% prevalence of methicillin-resistant Staphylococci, vancomycin usage was suboptimal. This raises concerns about the underestimation of MRSA risk and the need for tailored antibiotic guidelines. Our study demonstrates the efficacy of molecular-PCR analysis in identifying diverse microbial communities in DFIs, influencing targeted antibiotic choices. The results advocate for refined antimicrobial guidelines, considering regional variations in microbial patterns and judiciously addressing multidrug-resistant strains. This research contributes crucial insights for optimizing DFIs management and helps the physicians to have a fast decision in selection the suitable antibiotic for each patient and to decrease the risk of bacterial resistance from the improper use of broad-spectrum empirical therapies.

Emergence and Genomic Characterization of a spa Type t4407 ST6-SCCmec Type IVa Methicillin-Resistant Staphylococcus aureus Strain Isolated from Al-Karak Hospital, Jordan

Background and Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) is a major concern in Jordanian hospitals in terms of infection control. The purpose of this study was to identify the resistance patterns of Staphylococcus aureus strains isolated from surfaces of critical locations within the Al-Karak Governmental Hospital in 2019. Additionally, the study aimed to conduct whole-genome sequencing on the isolates. Materials and Methods: In February 2019, fourteen S. aureus strains were isolated from surfaces in critical sites in the Al-Karak Governmental Hospital. These isolates underwent antibiogram testing to determine their resistance profile. Genome sequencing using the Illumina MiSeq platform was applied to the extracted DNA from these isolates. The genomic data, including coding sequences, were analyzed to identify lineage, resistance genes, and plasmids. Results: The antibiogram results revealed that 11 of the 14 isolates were resistant to oxacillin, 6 to linezolid, and 1 to rifampicin, while none showed resistance to chloramphenicol. Eleven isolates were identified as MRSA, with a novel spa type (t4407) not previously reported in Jordan. High-quality sequencing data were obtained for only one isolate, i.e., A29, the genome showed 2,789,641 bp with a 32.7% GC content and contained 2650 coding sequences. Genomic analysis indicated the ST6 lineage, mecA gene (SCCmec type IVa(2B)), and a hybrid plasmid (pJOR_blaZ) carrying the blaZ gene for β-lactam resistance. Genomic data were deposited in NCBI (CP104989). The A29 genome closely resembled an MRSA genome isolated from a Danish hospital in 2011. The SNP analysis revealed identical antimicrobial resistance genes in these two genomes. Conclusions: This study unveils the first genomic sequence of an MRSA isolate from Jordan, marked by distinctive genotypic traits. The findings enhance our understanding of the MRSA types circulating in Jordan and the region and substantiate the phenomenon of intercontinental MRSA transmission.

Proportion of toxin and non-toxin virulence factors of Staphylococcus aureus isolates from diabetic foot infection: a systematic review and meta-analysis

BACKGROUND

Staphylococcus aureus isolates are the leading cause of diabetic foot infections (DFIs). Identification of specific virulence factors of S. aureus involved in the pathogenesis of DFIs may help control the infection more effectively. Since the most prevalent virulence factor genes are probably related to the DFI pathogenesis, the aim of this study is to evaluate the proportion of virulence factor genes of S. aureus isolates from DFIs.

MATERIALS AND METHODS

We conducted a systematic search of PubMed, Embase, Web of Science, and Scopus to identify all articles reporting the proportion of different types of virulence factors of S. aureus isolates from DFI samples.

RESULTS

Seventeen studies were eligible, in which 1062 S. aureus isolates were obtained from 1948 patients and 2131 DFI samples. Among the toxin virulence factors, hld 100.0% (95% CI: 97.0, 100.0%), hlg 88.0% (95% CI: 58.0, 100.0%), hla 80.0% (95% CI: 31.0, 100.0%), hlgv 79.0% (95% CI: 35.0, 100.0%) and luk-ED 72.0% (95% CI: 42.0, 95.0%) had the highest proportion respectively. Among the genes associated with biofilm formation, both icaA and icaD had the highest proportion 100.0% (95% CI: 95.6, 100.0%).

CONCLUSION

The results of the present study showed that among the toxin virulence factors, hemolysins (hld, hlg, hla, hlgv) and luk-ED and among the non-toxin virulence factors, icaA and icaD have the greatest proportion in S. aureus isolates from DFIs. These prevalent genes may have the potential to evaluate as virulence factors involved in DFI pathogenesis. Finding these probable virulence factor genes can help control diabetic foot infection more effectively via anti-virulence therapy or preparation of multi-epitope vaccines.

Whole genome sequencing and pan-genome analysis of Staphylococcus/Mammaliicoccus spp. isolated from diabetic foot ulcers and contralateral healthy skin of Algerian patients

BACKGROUND

Diabetic foot infections (DFIs) are the most common complications of diabetic foot ulcers (DFUs), and a significant cause of lower extremity amputation. In this study we used whole genome sequencing to characterize the clonal composition, virulence and resistance genetic determinants of 58 Staphylococcus/Mammaliicoccus spp. isolates from contralateral healthy skin and DFU from 44 hospitalized patients.

RESULTS

S. aureus (n = 32) and S. epidermidis (n = 10) isolates were recovered from both DFUs and healthy skin, whereas, S. haemolyticus (n = 8), M. sciuri (n = 1), S. hominis (n = 1) and S. simulans (n = 3) were recovered exclusively from healthy skin. In contrast, S. caprae (n = 2) and S. saprophyticus (n = 1) were recovered only from DFUs. Among S. aureus isolates, MRSA were present with high prevalence (27/32, 84.4%), 18 of which (66.7%) were from DFUs and 9 (33.3%) from healthy skin. In contrast, the coagulase-negative Staphylococcus (CoNS)/Mammaliicoccus isolates (n = 26), in particular S. epidermidis and S. haemolyticus were more prevalent in healthy skin, (10/26, 38.5%) and (8/26, 30.8%), respectively. MLST, spa and SCCmec typing classified the 32 S. aureus isolates into 6 STs, ST672, ST80, ST241, ST1, ST97, ST291 and 4 unknown STs (STNF); 8 spa types, t044, t037, t3841, t1247, t127, t639, t937 and t9432 and 2 SCCmec types, type IV and type III(A). Among CoNS, the S. epidermidis isolates belonged to ST54, ST35 and ST640. S. haemolyticus belonged to ST3, ST25, ST29, ST1 and ST56. The sole M. sciuri isolate was found to carry an SCCmec type III(A). A wide range of virulence genes and antimicrobial resistance genes were found among our isolates, with varying distribution between species or STs. The pan-genome analysis revealed a highly clonal population of Staphylococcus isolates, particularly among S. aureus isolates. Interestingly, the majority of S. aureus isolates including MRSA, recovered from the healthy skin and DFUs of the same patient belonged to the same clone and exhibited similar virulence/resistance genotype.

CONCLUSIONS

Our study provides clinically relevant information on the population profile, virulence and antibiotic resistance of Staphylococcus/Mammaliicoccus spp. in DFIs, which could serve as a basis for further studies on these as well as other groups of pathogens associated with DFIs.

Current types of staphylococcal cassette chromosome mec (SCCmec) in clinically relevant coagulase-negative staphylococcal (CoNS) species

Coagulase-negative staphylococci (CoNS) colonize human skin and mucosal membranes, which is why they are considered harmless commensal bacteria. Two species, Staphylococcus epidermidis and Staphylococcus haemolyticus belong to the group of CoNS species and are most frequently isolated from nosocomial infections, including device-associated healthcare-associated infections (DA-HAIs) and local or systemic body-related infections (FBRIs). Methicillin resistance, initially described in Staphylococcus aureus, has also been reported in CoNS species. It is mediated by the mecA gene within the staphylococcal cassette chromosome (SCCmec). SCCmec typing, primarily using PCR-based methods, has been employed as a molecular epidemiological tool. However, the introduction of whole genome sequencing (WGS) and next-generation sequencing (NGS) has enabled the identification and verification of new SCCmec types. This review describes the current distribution of SCCmec types, subtypes, and variants among CoNS species, including S. epidermidis, S. haemolyticus, and S. capitis. The literature review focuses on recent research articles from the past decade that discuss new combinations of SCCmec in coagulase-negative Staphylococcus. The high genetic diversity and gaps in CoNS SCCmec annotation rules underscore the need for an efficient typing system. Typing SCCmec cassettes in CoNS strains is crucial to continuously updating databases and developing a unified classification system.

Methicillin-Resistant Staphylococcus aureus from Diabetic Foot Infections in a Tunisian Hospital with the First Detection of MSSA CC398-t571

This study sought to analyze the antimicrobial resistant phenotypes and genotypes as well as the virulence content of S. aureus isolates recovered from patients with diabetic foot infections (DFIs) in a Tunisian hospital. Eighty-three clinical samples of 64 patients were analyzed, and bacterial isolates were identified by MALDI-TOF. The antimicrobial resistance phenotypes were determined by the Kirby-Bauer disk diffusion susceptibility test. Resistance and virulence genes, agr profile, spa and SCCmec types were determined by PCR and sequencing. S. aureus was detected in 14 of the 64 patients (21.9%), and 15 S. aureus isolates were recovered. Six out of the fifteen S. aureus isolates were methicillin-resistant (MRSA, mecA-positive) (40%). The isolates harbored the following resistance genes (number of isolates): blaZ (12), erm(B) (2), erm(A) (1), msrA (2), tet(M) (2), tet(K) (3), tet(L) (1), aac(6')-aph(2″) (2), ant(4″) (1) and fexA (1). The lukS/F-PV and tst genes were detected in three isolates. Twelve different spa-types were identified and assigned to seven clonal complexes with the predominance of agr-type III. Furthermore, the SCCmec types III, IV and V were found among the MRSA isolates. Moreover, one MSSA CC398-t571-agr-III isolate was found; it was susceptible to all antimicrobial agents and lacked luk-S/F-PV, tst, eta and etb genes. This is the first report on the prevalence and molecular characterization of S. aureus from DFIs and also the first detection of the MSSA-CC398-t571 clone in human infections in Tunisia. Our findings indicated a high prevalence S. aureus in DFIs with genetic diversity among the MSSA and MRSA isolates.