Mutations in the MepRAB efflux system contribute to the in vitro development of tigecycline resistance in Staphylococcus aureus

Identification of a mepR mutation associated with tigecycline resistance in a clinical Staphylococcus aureus isolate

OBJECTIVES

To identify the role and function of mepR variants in conferring resistance to tigecycline in clinical Staphylococcus aureus.

METHODS

The identification of the mepR and mepA variants in S. aureus DMB26a was performed by whole-genome sequencing and Blast alignment. The effects of the mepRD and mepAD variants of DMB26a on tigecycline susceptibility were evaluated through deletion and complementation analyses, as well as the determination of gene expression levels by RT-qPCR. Minimal inhibitory concentrations (MICs) for DMB26a and its mutants were determined by antimicrobial susceptibility testing.

RESULTS

A mepR variant, designated mepRD, and a mepA variant, designated mepAD, were identified in the clinical tigecycline-resistant S. aureus isolate DMB26a, which showed 78.72% and 84.92% amino acid identity to the MepR and MepA proteins of S. aureus NCTC 8325-4, respectively. Our findings revealed that deletion of mepA in the tigecycline-susceptible S. aureus RN4220 did not lead to a decrease in the MIC of tigecycline, and that there was also no change in the tigecycline MIC after the complementation with mepAD. Furthermore, we constructed a mepR + mepA deletion strain of S. aureus RN4220 and complemented it with mepRD + mepAD. In that case, a 4-fold increase in the tigecycline MIC was observed in S. aureus RN4220ΔmepR + mepA-pLI50_mepRD + mepAD compared with S. aureus RN4220ΔmepR + mepA. In addition, the relative expression of mepAD was increased 6-fold under the regulation of mepRD.

CONCLUSIONS

This study provides the identification of a mepR variant contributing indirectly to tigecycline resistance via mediating increased expression of mepA in a clinical S. aureus isolate.

Induced ciprofloxacin biotransformation and antibiotic-resistance genes control in sulfate-reducing microbial fuel cells: Strategy and mechanism

Ciprofloxacin-containing saline wastewater treatment gains increasing attentions, due to the problems of limited degradation and spreading risk of antibiotic-resistance genes (ARGs). Sulfate reduction is a cost-efficient technology for simultaneous sulfate and antibiotic removal. The microbial fuel cell enhances removal of antibiotics and reduces spreading risk of ARGs in effluents, however, the biotransformation of ciprofloxacin (CIP) in sulfate-reducing microbial fuel cell (SR-MFC) remains unclear. Thus, a SR-MFC is established in this study for treatment of CIP-containing saline wastewater, which achieves simultaneous removal of CIP (50.2%), sulfate (85.1%), and ARGs (17.0%). The Desulfovibrio sp. bacteria become dominant in free biomass (58.8%) and biofilm (73.6%) after CIP exposing, respectively. The CIP can be utilized in prior to lactate for sulfate reduction, while the energy production is initially contributed to sulfate reduction followed by sulfide oxidation. Notably, the expression of ARGs declines probably due to enhanced biotransformation and limited adsorption (2.6%) of CIP on biomass after CIP addition. Long-term exposure to CIP enriches the ARGs of antibiotic efflux pump, implying some CIP is pumped out from intracellular to extracellular. A novel degradation pathway attacking the N15 site in piperazine may be the major and environmental-friendly biotransformation reaction, where the enzyme of ammonia-lyase and acetyltransferase are involved in. To our best knowledge, this is the first report of the novel pathway in bacterial CIP degradation system, which is known as fungal CIP biotransformation pathway. This study provides insights for CIP biotransformation in SR-MFC, and the operational strategy for antibiotic-containing saline wastewater treatment with ARGs control.

Phenotypic and genetic stepwise changes in Staphylococcus aureus during in vitro adaptive laboratory evolution under the selective pressure of tigecycline

Compared with tigecycline-resistant gram-negative bacteria, tigecycline adaptive laboratory evolution (ALE) has been preliminarily performed in Staphylococcus aureus. This study aims to develop higher-level tigecycline-resistant S. aureus mutants (TRSAms) and explore the mechanisms behind decreasing susceptibility to tigecycline. In this study, S. aureus strains were cultured in serial-increasing concentrations of tigecycline and successfully obtained high-level TRSAms. Different phenotypic changes in high-level TRSAms were assessed by growth rate measurement, autolysis assays, mutant frequency determination, and virulence evaluations in vivo and in vitro. The phenotypes of fitness cost showed significant differences in these high-level TRSAms. Whole-genome sequencing analysis detected synchronous mutations between yycH and fakA repeatedly in three high-level TRSAms from different parent strains. Further cloning experiments demonstrated that the complementary yycH gene increased susceptibility to tigecycline in TRSAms, and deletion mutant construction and complementation of Glu283Ter YycH confirm its critical role in tigecycline susceptibility in S. aureus. We also scanned the global genome to evaluate clinical importance; mutations on rpsJ detected in this study are associated with the MRSA ST5-t002 isolates and omadacycline selective mutants. In summary, we described a complete trajectory of phenotypic and genotypic changes in the ALE process for decreasing susceptibility to tigecycline in S. aureus. It is considered that the yycH gene has been involved in decreasing tigecycline susceptibility in S. aureus.

Efflux pumps: gatekeepers of antibiotic resistance in Staphylococcus aureus biofilms

Staphylococcus aureus, a versatile human pathogen, poses a significant challenge in healthcare settings due to its ability to develop antibiotic resistance and form robust biofilms. Understanding the intricate mechanisms underlying the antibiotic resistance is crucial for effective infection treatment and control. This comprehensive review delves into the multifaceted roles of efflux pumps in S. aureus, with a focus on their contribution to antibiotic resistance and biofilm formation. Efflux pumps, integral components of the bacterial cell membrane, are responsible for expelling a wide range of toxic substances, including antibiotics, from bacterial cells. By actively extruding antibiotics, these pumps reduce intracellular drug concentrations, rendering antibiotics less effective. Moreover, efflux pumps have emerged as significant contributors to both antibiotic resistance and biofilm formation in S. aureus. Biofilms, structured communities of bacterial cells embedded in a protective matrix, enable S. aureus to adhere to surfaces, evade host immune responses, and resist antibiotic therapy. Efflux pumps play a pivotal role in the development and maintenance of S. aureus biofilms. However, the interplay between efflux pumps, antibiotic resistance and biofilm formation remains unexplored in S. aureus. This review aims to elucidate the complex relationship between efflux pumps, antibiotic resistance and biofilm formation in S. aureus with the aim to aid in the development of potential therapeutic targets for combating S. aureus infections, especially those associated with biofilms. The insights provided herein may contribute to the advancement of novel strategies to overcome antibiotic resistance and disrupt biofilm formation in this clinically significant pathogen.

Tigecycline Resistance-Associated Mutations in the MepA Efflux Pump in Staphylococcus aureus

Tigecycline is an important antibacterial drug for treating infection by clinical multidrug-resistant bacteria, and tigecycline-resistant Staphylococcus aureus (TRSA) has been increasingly reported in recent years. Notably, only rpsJ and mepA are associated with the tigecycline resistance of S. aureus. The mepA gene encodes MepA efflux pumps, and the overexpression of mepA has been confirmed to be directly related to tigecycline resistance. Although the mutations of MepA widely occur, the associations between TRSA and mutations of MepA are still unclear. In this study, we explored mutations in the mepA genes from various sources. Then, tigecycline resistance-associated mutations T29I, E287G, and T29I+E287G in MepA were identified, and their effects were evaluated through mutant deletion and complementation, tigecycline accumulation assay, and molecular docking experiments. Results showed that the MICs of tigecycline, gentamicin, and amikacin increased in special complementary transformants and recovered after the addition of the efflux pump inhibitor carbonyl cyanide 3-chlorophenylhydrazone (CCCP). The tigecycline accumulation assay of the mepA-deleted mutant strain and its complementary transformants showed that T29I, E287G, and T29I+E287G mutations promoted tigecycline efflux, and molecular docking showed that mutations T29I, E287G, and T29I+E287G decreased the binding energy and contributed to ligand binding. Moreover, we inferred the evolutionary trajectory of S. aureus under the selective pressure of tigecycline in vitro. Overall, our study indicated that mutations in MepA play important roles in tigecycline resistance in S. aureus. IMPORTANCE Previous analysis has shown that overexpression of MepA is an exact mechanism involved in tigecycline resistance apart from the rpsJ mutation and is usually dependent on the mutant mepR. However, no research has evaluated the effects of diverse mutations discovered in TRSA in MepA. This study demonstrates that the mutations in MepA confer resistance to tigecycline without overexpression and provides genotypic references for identifying TRSA. Although tigecycline resistance-associated mutations in MepA identified in this study have not been observed in clinical isolates, the mechanism should be explored given that S. aureus strains are prevalent in the environment. Measures should be implemented to contain TRSA within the time window before tigecycline resistance-associated mutations in MepA are prevalent.

Atopic dermatitis-derived Staphylococcus aureus strains: what makes them special in the interplay with the host

Background

Atopic dermatitis (AD) is a chronic inflammatory skin condition whose pathogenesis involves genetic predisposition, epidermal barrier dysfunction, alterations in the immune responses and microbial dysbiosis. Clinical studies have shown a link between Staphylococcus aureus and the pathogenesis of AD, although the origins and genetic diversity of S. aureus colonizing patients with AD is poorly understood. The aim of the study was to investigate if specific clones might be associated with the disease.

Methods

WGS analyses were performed on 38 S. aureus strains, deriving from AD patients and healthy carriers. Genotypes (i.e. MLST, spa-, agr- and SCCmec-typing), genomic content (e.g. virulome and resistome), and the pan-genome structure of strains have been investigated. Phenotypic analyses were performed to determine the antibiotic susceptibility, the biofilm production and the invasiveness within the investigated S. aureus population.

Results

Strains isolated from AD patients revealed a high degree of genetic heterogeneity and a shared set of virulence factors and antimicrobial resistance genes, suggesting that no genotype and genomic content are uniquely associated with AD. The same strains were characterized by a lower variability in terms of gene content, indicating that the inflammatory conditions could exert a selective pressure leading to the optimization of the gene repertoire. Furthermore, genes related to specific mechanisms, like post-translational modification, protein turnover and chaperones as well as intracellular trafficking, secretion and vesicular transport, were significantly more enriched in AD strains. Phenotypic analysis revealed that all of our AD strains were strong or moderate biofilm producers, while less than half showed invasive capabilities.

Conclusions

We conclude that in AD skin, the functional role played by S. aureus may depend on differential gene expression patterns and/or on post-translational modification mechanisms rather than being associated with peculiar genetic features.

Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Associated with Hospitalized Newborn Infants

Multidrug resistance (MDR) is a significant challenge in healthcare management, and addressing it requires a comprehensive approach. In this study, we employed a combination of phenotypic and genotypic approaches, along with whole genome sequencing (WGS) to investigate five hospital-associated MDR methicillin-resistant Staphylococcus aureus (MRSA) strains that were isolated from newborn infants. Our analysis revealed the following for the MDR-MRSA strains: SauR31 was resistant to three antimicrobial classes; SauR12, SauR91 and SauR110 were resistant to four antimicrobial classes; and SauR23 exhibited resistance to seven classes. All the MDR-MRSA strains were capable of producing slime and biofilms, harbored SCCmec type IV, and belonged to different spa types (t022, t032, and t548), with varying profiles for microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) and virulence genes. The WGS data for the MDR SauR23 and SauR91 strains revealed that most of the antimicrobial resistance genes were present in the chromosomes, including blaZ, mecA, norA, lmrS, and sdrM, with only the ermC gene found in a small (<3 kb) plasmid. The presence of MDR-MRSA strains among neonates raises public concern, hence implementation of multifaceted interventions is recommended to address this issue. In addition, metadata is needed to improve the investigation of antimicrobial resistance genes in MDR isolates.

In vitro antimicrobial activity and resistance mechanisms of the new generation tetracycline agents, eravacycline, omadacycline, and tigecycline against clinical Staphylococcus aureus isolates

In this study, we investigated the in vitro activity and resistance mechanisms of the new generation tetracycline agents, namely eravacycline, omadacycline, and tigecycline, against Staphylococcus aureus isolates. A total of 1,017 non-duplicate S. aureus isolates were collected and subjected to susceptibility testing against eravacycline, omadacycline, and tigecycline using the broth microdilution method. Tetracyclines-resistant (eravacycline/omadacycline/tigecycline-resistant) isolates were selected to elucidate the resistance mechanisms using polymerase chain reaction (PCR), cloning experiment, efflux pump inhibition, and quantitative real-time PCR. The results of the antibacterial susceptibility testing showed that compared with omadacycline, eravacycline and tigecycline had superior antibacterial activity against S. aureus isolates. Among 1,017 S. aureus, 41 tetracyclines-resistant isolates were identified. These resistant isolates possessed at least one tetracycline resistance gene and genetic mutation in the MepRAB efflux pump and 30S ribosome units. A frameshift mutation in mepB was detected in most tetracyclines-resistant strains (except for JP3349) compared with tetracyclines-susceptible (eravacycline/omadacycline/tigecycline-susceptible) strains. This was first shown to decrease susceptibility to omadacycline, but not to eravacycline and tigecycline. After treatment with eravacycline, omadacycline or tigecycline, overexpression of mepA, tet38, tet(K) and tet(L) was detected. Moreover, multi-locus sequence typing showed a major clonal dissemination type, ST5, and its variant ST764 were seen in most tetracyclines-resistant strains. To conclude, eravacycline and tigecycline exhibited better activity against S. aureus including tetracycline-resistant isolates than omadacycline. The resistance to these new generation tetracyclines due to an accumulation of many resistance mechanisms.

In vitro activity of tigecycline and proteomic analysis of tigecycline adaptation strategies in clinical Enterococcus faecalis isolates from China

OBJECTIVES

This study aimed to investigate the in vitro activities of tigecycline (TGC) and the underlying molecular mechanisms of TGC stress response and resistance in clinical Enterococcus faecalis isolates from China.

METHODS

Antimicrobial susceptibility and antibiofilm activities of TGC in 399 E. faecalis isolates were evaluated. Heteroresistance was evaluated by population analysis profiling. Resistance and heteroresistance mechanisms were investigated by identifying genetic mutations in tetracycline (tet) target sites and through analysis of efflux protein inhibitors (EPIs). Furthermore, quantitative proteomics was used to investigate the global proteomic response of E. faecalis to TGC stress, as well as the resistance mechanisms of TGC within in vitro induced resistant isolate.

RESULTS

TGC minimum inhibitory concentrations (MICs) against clinical E. faecalis isolates were ≤0.5 mg/L. TGC displayed remarkable inhibitory activity against biofilm formation. The occurrence rate of TGC heteroresistance was 1.75% (7/399), and the increased TGC MIC values of heteroresistance-derived clones could be reversed by EPI. TGC resistance was associated with mutations in the 16S rRNA site or 30S ribosomal protein S10. A total of 105 and 356 differentially expressed proteins was identified after being exposed to 1/2× MIC concentrations of TGC, while 356 differentially expressed proteins was identified in TGC-resistant isolate. The differentially expressed proteins were enriched in the translation and DNA replication process. In addition, multiple adenosine triphosphate (ATP)-binding cassette (ABC) transporters were upregulated.

CONCLUSIONS

TGC exhibited excellent activity against a substantial proportion of clinical isolates from China. However, E. faecalis exhibited a strong adaptation mechanism during TGC exposure: mutation of TGC target sites and elevated expression of efflux pumps under TGC selection, resulting in TGC resistance.

Efflux Pump Mediated Antimicrobial Resistance by Staphylococci in Health-Related Environments: Challenges and the Quest for Inhibition

The increasing emergence of antimicrobial resistance in staphylococcal bacteria is a major health threat worldwide due to significant morbidity and mortality resulting from their associated hospital- or community-acquired infections. Dramatic decrease in the discovery of new antibiotics from the pharmaceutical industry coupled with increased use of sanitisers and disinfectants due to the ongoing COVID-19 pandemic can further aggravate the problem of antimicrobial resistance. Staphylococci utilise multiple mechanisms to circumvent the effects of antimicrobials. One of these resistance mechanisms is the export of antimicrobial agents through the activity of membrane-embedded multidrug efflux pump proteins. The use of efflux pump inhibitors in combination with currently approved antimicrobials is a promising strategy to potentiate their clinical efficacy against resistant strains of staphylococci, and simultaneously reduce the selection of resistant mutants. This review presents an overview of the current knowledge of staphylococcal efflux pumps, discusses their clinical impact, and summarises compounds found in the last decade from plant and synthetic origin that have the potential to be used as adjuvants to antibiotic therapy against multidrug resistant staphylococci. Critically, future high-resolution structures of staphylococcal efflux pumps could aid in design and development of safer, more target-specific and highly potent efflux pump inhibitors to progress into clinical use.