Antimicrobial Resistance Genes Analysis of Publicly Available Staphylococcus aureus Genomes

Analysis of co-occurrence of type II toxin-antitoxin systems and antibiotic resistance determinants in Staphylococcus aureus

Toxin-antitoxin (TA) systems consist of toxic proteins and their inhibitors, and were originally shown to ensure plasmid maintenance in bacterial populations. Over time, however, TA systems have also been identified on bacterial chromosomes, raising questions about their roles unrelated to plasmid stability. Among the eight currently recognized types of TA systems, type II has been the most extensively investigated. Type II systems are often found in pathogenic bacterial species, including staphylococci. Staphylococcus aureus, a notorious human pathogen, harbors multiple type II TA systems, both plasmid- and chromosome-encoded, while their potential relation to virulence remains to be addressed. Here, we investigate the co-occurrence of TA systems and antibiotic resistance (AR) determinants in S. aureus, focusing on the potential negative impact of type II toxin RNases on antibiotic resistance. We considered both well-characterized and newly characterized TA loci of S. aureus. Our findings demonstrate a relationship between TA systems and AR determinants, wherein TA systems negatively affect antibiotic resistance. Due to substantial selective pressure, the migration of TA systems from plasmids to chromosomes results in their inactivation. This observation may be an important factor shaping the spread and evolution of both TA systems and AR determinants in bacteria. We exemplify this phenomenon in detail using the well-known PemIK-Sa1 system and a newly identified SCCmec-related PemIK-Sa6 system characterized in this study.

IMPORTANCE

Toxin-antitoxin (TA) systems are entities unique to bacteria. They are involved in the maintenance of mobile genetic elements (MGEs), regulation of gene expression and bacterial virulence. Staphylococcus aureus is a dangerous human pathogen with increasing antibiotic resistance (AR). The maintenance and dissemination of AR determinants is often driven by MGEs, which link AR and TA systems. Our study identified a negative correlation between TA systems and AR determinants in S. aureus. Furthermore, we have shown that the expression of a toxic component of an exemplary TA system negatively affects antibiotic resistance. We argue that in particular strains, a selective pressure maintains either the TA system or AR determinant. Alternatively, TA systems are inactivated by mutations when present together with AR determinants to maintain the functionality of the latter. Our observations uncover an important factor shaping the spread and evolution of both TA systems and AR determinants in bacteria, which is especially relevant to pathogenic species.

The interplay between mobilome and resistome in Staphylococcus aureus

Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.

Global Trends of Antibiotic Resistance Genes in Staphylococcus aureus: A Comprehensive Genomic Analysis

Staphylococcus aureus (S. aureus) is a pathogen capable of causing severe diseases and exhibiting resistance to multiple antibiotics. However, there is a significant lack of comprehensive research on the global prevalence of its antibiotic resistance genes (ARGs). This study provided a comprehensive analysis of ARGs in S. aureus, using 113,842 S. aureus genome sequences from the National Center for Biotechnology Information database. The results revealed that a significant majority (84%) of these genomes harbored at least one ARG, with a total of 389,464 ARG sequences identified across 19 major types and 103 subtypes. These ARGs exhibited varied abundances and diversities, linked primarily to clinical cases worldwide. ARGs for fluoroquinolones, multidrug resistance, bacitracin, tetracyclines, beta-lactams, and aminoglycosides were notably abundant, ranging from 3.16 × 10-5 to 1.49 copies of ARG per million bp. Variations in the abundance and diversity of ARGs were observed between countries, with middle- and low-income countries showing higher gene abundance but lower diversity compared with high-income countries. Temporal analysis over 30 years showed a fluctuating decline in ARG abundance alongside an increase in diversity, suggesting evolving resistance mechanisms. The study also explored the role of mobile genetic elements in ARG dissemination, finding a substantial proportion of ARG subtypes associated with plasmids and insertion sequence elements, indicating their potential for spread across borders. The global distribution of mobile ARGs was further analyzed, revealing the extensive reach of certain ARGs across countries. This research provides valuable insights into the prevalence and dissemination of antibiotic resistance in S. aureus on a global scale, aiding in the development of effective monitoring and control strategies to combat ARGs in S. aureus and other pathogens.

Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study

Staphylococcus aureus is an opportunistic pathogen and a leading cause of bloodstream infections, with its capacity to acquire antibiotic resistance genes posing significant treatment challenges. This pilot study characterizes the genomic profiles of S. aureus isolates from patients with bloodstream infections in KwaZulu-Natal, South Africa, to gain insights into their resistance mechanisms, virulence factors, and clonal and phylogenetic relationships. Six multidrug-resistant (MDR) S. aureus isolates, comprising three methicillin-resistant S. aureus (MRSA) and three methicillin-susceptible S. aureus (MSSA), underwent whole genome sequencing and bioinformatics analysis. These isolates carried a range of resistance genes, including blaZ, aac(6')-aph(2″), ant(9)-Ia, ant(6)-Ia, and fosB. The mecA gene, which confers methicillin resistance, was detected only in MRSA strains. The isolates exhibited six distinct spa types (t9475, t355, t045, t1265, t1257, and t7888) and varied in virulence gene profiles. Panton-Valentine leukocidin (Luk-PV) was found in one MSSA isolate. Two SCCmec types, IVd(2B) and I(1B), were identified, and the isolates were classified into four multilocus sequence types (MLSTs), with ST5 (n = 3) being the most common. These sequence types clustered into two clonal complexes, CC5 and CC8. Notably, two MRSA clones were identified: ST5-CC5-t045-SCCmec_I(1B) and the human-associated endemic clone ST612-CC8-t1257-SCCmec_IVd(2B). Phylogenomic analysis revealed clustering by MLST, indicating strong genetic relationships within clonal complexes. These findings highlight the value of genomic surveillance in guiding targeted interventions to reduce treatment failures and mortality.

Innovative Elastomers with Antimicrobial Activity May Decrease Infection Risks during Milking

Contagious pathogens are very costly to dairy herds, and they may have zoonotic and reverse-zoonotic potentials and may contribute to the spread of antimicrobial resistance. One of the most important risk factors for spreading these infections is milking, when liner contamination may transfer the pathogens from infected to healthy cows. There is no effective protocol to prevent the transmission of infection without the segregation of infected cows. Recently, the availability of elastomers with patented antimicrobial components in their formulations has allowed the exploration of alternative methods to reduce the risk of infection. Two different types of elastomers (rubber and silicone) and nine different formulations were challenged with three major mastitis pathogens (S. aureus, S. agalactiae, and E. coli). The results that were obtained in this study were interesting and unexpected. Indeed, to our knowledge, this is the first study to show that basic rubber materials have intrinsic antimicrobial activity. Silicone elastomers did not exhibit the same levels of bactericidal activity, although they did exhibit some antibacterial capacity. A significant decrease in bacterial survival curves was observed for all the formulations tested when antimicrobial components were added. The different results observed for the various products are likely due to the different formulations and diverse manufacturing processes. The availability of these new materials that significantly reduce the bacterial load on the liner surface may reduce the risk of spreading intramammary infections during milking. This would be an important step forward in achieving global sustainability of dairy herds, consistent with the objectives of One Health, by reducing the risks of zoonotic diseases and antimicrobial treatments.

SHIP: identifying antimicrobial resistance gene transfer between plasmids

MOTIVATION

Plasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of plasmids, as they show large DNA sequence variability. Identifying and quantifying such transfer can provide novel insight into the role of small mobile elements and resistant plasmid regions in the spread of AMR.

RESULTS

We developed SHIP, a novel method to quantify plasmid similarity based on the dynamics of plasmid evolution. This allowed us to find conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, which is evidence for lateral transfer. Our results show that regions carrying AMR genes are highly mobilizable between plasmids through transposons, integrons, and recombination events, and contribute to the spread of AMR. Identified transferred fragments include a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae, and a region encoding tetracycline resistance transferred through recombination in Enterococcus faecalis.

AVAILABILITY AND IMPLEMENTATION

The code developed in this work is available at https://github.com/AbeelLab/plasmidHGT.

Antibiotic Resistance/Susceptibility Profiles of Staphylococcus equorum Strains from Cheese, and Genome Analysis for Antibiotic Resistance Genes

In food, bacteria carrying antibiotic resistance genes could play a prominent role in the spread of resistance. Staphylococcus equorum populations can become large in a number of fermented foods, yet the antibiotic resistance properties of this species have been little studied. In this work, the resistance/susceptibility (R/S) profile of S. equorum strains (n = 30) from cheese to 16 antibiotics was determined by broth microdilution. The minimum inhibitory concentration (MIC) for all antibiotics was low in most strains, although higher MICs compatible with acquired genes were also noted. Genome analysis of 13 strains showed the S. equorum resistome to be composed of intrinsic mechanisms, acquired mutations, and acquired genes. As such, a plasmidic cat gene providing resistance to chloramphenicol was found in one strain; this was able to provide resistance to Staphylococcus aureus after electroporation. An msr(A) polymorphic gene was identified in five strains. The Mrs(A) variants were associated with variable resistance to erythromycin. However, the genetic data did not always correlate with the phenotype. As such, all strains harbored a polymorphic fosB/fosD gene, although only one acquired copy was associated with strong resistance to fosfomycin. Similarly, a plasmid-associated blaR1-blaZI operon encoding a penicillinase system was identified in five ampicillin- and penicillin G-susceptible strains. Identified genes not associated with phenotypic resistance further included mph(C) in two strains and norA in all strains. The antibiotic R/S status and gene content of S. equorum strains intended to be employed in food systems should be carefully determined.

Molecular Characteristics of Methicillin-Resistant and Susceptible Staphylococcus aureus from Pediatric Patients in Eastern China

Staphylococcus aureus is an opportunistic pathogen that causes invasive infections in humans. In recent years, increasing studies have focused on the prevalence of S. aureus infections in adults; however, the epidemiology and molecular characteristics of S. aureus from Chinese pediatric patients remain unknown. The present study examined the population structure, antimicrobial resistance, and virulent factors of methicillin-resistant and -susceptible S. aureus isolated from Chinese pediatric patients from one medical center in eastern China. A total of 81 cases were screened with positive S. aureus infections among 864 pediatric patients between 2016 and 2022 in eastern China. Molecular analysis showed that ST22 (28.4%) and ST59 (13.6%) were the most typical strains, and associations between different clonal complex (CC) types/serotype types (ST) and the age of pediatric patients were observed in this study. CC398 was the predominant type in neonates under 1 month of age, while CC22 was mainly found in term-infant (under 1 year of age) and toddlers (over 1 year of age). Additionally, 17 S. aureus isolates were resistant to at least three antimicrobials and majority of them belonged to CC59. The blaZ gene was found in 59 isolates and mecA gene was present in 26 strains identified as methicillin-resistant. Numerous virulent factors were detected in S. aureus isolated from present pediatric patients. Remarkably, lukF-PV and lukS-PV were dominantly carried by CC22, tsst-1 genes were detected in CC188, CC7, and CC15, while exfoliative toxin genes were found only in CC121. Only 41.98% of the S. aureus isolates possessed scn gene, indicating that the sources of infections in pediatric patients may include both human-to-human transmissions as well as environmental and nosocomial infections. Together, the present study provided a phylogenetic and genotypic comparison of S. aureus from Chinese pediatric patients in Suzhou city. Our results suggested that the colonization of multi-drug resistant isolates of S. aureus may raise concern among pediatric patients, at least from the present medical center in eastern China.