High-level resistance to aminoglycosides and ampicillin among clinical isolates of Enterococcus species in an Iranian referral hospital

A comprehensive One Health investigation of erythromycin and quinupristin/dalfopristin resistant Enterococcus spp. in Iran

Enterococci, flagged by the WHO as a rising cause of antibiotic-resistant infections, make surveillance crucial to control resistant strains. We investigated the resistance to linezolid, quinupristin/dalfopristin (Q/D), and erythromycin in Enterococcus faecalis (n = 251) and Enterococcus faecium (n = 434) isolates collected from patients, healthy carriers, hospitals, poultry, livestock, and municipal wastewater in Ardabil, Iran. The isolates were tested for resistance using phenotypic and genotypic methods. Although none of the isolates were resistant to linezolid, 24.9% of E. faecium isolates were resistant to Q/D, particularly those from patients and poultry slaughterhouse wastewater effluent (P < 0.05). The Q/D resistance genes msrC and ermB were detected in 76.85 and 20.37% of E. faecium isolates, respectively. Erythromycin resistance was common in E. faecalis (51.8%) and E. faecium (37.5%), with no significant difference between sources. However, isolates from patients and livestock wastewater had higher erythromycin MICs. Erythromycin resistance genes, such as ermB, ermC, ermTR, and ermA, were found in 80.7, 41.2, 26.5, and 19% of E. faecium and 80.3, 51.6, 22.4, and 25.8% of E. faecalis isolates, respectively. In conclusion, linezolid is a viable treatment for enterococcal infections in Ardabil, but widespread erythromycin- and Q/D-resistant enterococci pose a public health risk.

CRISPR Elements and Their Association with Macrolide and Aminoglycoside Resistance Genes in Enterococci

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems are common among enterococci and may prevent the acquisition of mobile genetic elements carrying antimicrobial resistance genes. In this study, we correlate the presence of CRISPR with genes associated with macrolide resistance and high-level resistance to aminoglycosides (HLR-A) among 216 Enterococcus faecalis and 82 Enterococcus faecium isolates. We used PCR to detect genes associated with macrolide resistance, HLR-A, and type II-A CRISPR elements. We used two-tailed Fisher's exact test to evaluate correlation between CRISPR and resistance genes. One hundred and seven (35.9%) isolates had at least one HLR-A gene; the prevalent genes were aac(6')-Ie-aph(2″)-Ia and ant(6)-Ia found in 61 (57%) and 46 (43%) isolates, respectively. The macrolide resistance genes erm(A) and erm(B) were found in 116 (38.9%) isolates. Overall, 174 (58.4%) isolates had at least one CRISPR element; the predominant one was CRISPR3-Cas (n = 117; 39.2%). The presence of three genes, two related to HLR-A [aph(2″)-Ic and ant(6)-Ia] and one macrolide resistance gene [erm(B)], was associated with the absence of CRISPR (p < 0.05), mainly in E. faecalis lacking CRISPR3-Cas. We observed the association between the absence of CRISPR and the presence of major aminoglycoside and macrolide resistance determinants, contributing to the understanding of the evolution of resistance in enterococci.

Evaluation of aminoglycoside- and methicillin-resistant Staphylococcus aureus: phenotypic and genotypic insights from clinical specimens in Ardabil, Iran

BACKGROUND

Combination therapy including an aminoglycoside antibiotic and a cell-wall active agent is considered the most suitable option to treat invasive infections with methicillin-resistant Staphylococcus aureus (MRSA). Dual drug therapy enhances the effectiveness of treatment and reduces the risk of resistance development. This study aims to elucidate the phenotypic and molecular resistance to aminoglycosides and methicillin, and the molecular epidemiologic characteristics of S. aureus in Ardabil northwest Iran.

METHODS

Totally, 118 S. aureus isolates collected from clinical specimens were investigated. Identification was performed using standard microbiological and molecular approaches. Aminoglycoside and methicillin resistance were evaluated using the disk diffusion assay, and the minimum inhibitory concentrations (MICs) of aminoglycosides were determined via the agar dilution method. The mecA gene encoding methicillin resistance and aminoglycoside modifying enzymes (AMEs) genes were detected using PCR. Molecular epidemiologic features of the isolates were determined using staphylococcal cassette chromosome mec (SCCmec) typing spa typing and ERIC-PCR assays.

RESULTS

Of the isolates, 42.4% (n = 50) and 57.6% (n = 68) were identified as MRSA and MSSA, respectively. All MRSA isolates were mecA-positive. Among MRSA isolates, SCCmec type IVa (17; 34%) was predominant, followed by types IVc, V, III, II, and I. Resistance rates to gentamicin, kanamycin, tobramycin, and amikacin were 16.1%, 17.8%, 8.5%, and 8.5%, respectively. Overall, the aminoglycoside resistance and most non-aminoglycoside antibiotics were significantly higher in MRSA versus MSSA isolates. The prevalence of AME genes was as follows: aac(6')-Ie-aph(2'') (30; 76.9%), aph(2'')-Ib (22; 56.4%), and ant(4')-Ia (14; 35.9%). About 60% of aminoglycoside-resistant isolates harbored ≥ 2 AME genes. The t030 type was the most common spa type identified. The ERIC-PCR profiles categorized the isolates into 19 unique ERIC types.

CONCLUSIONS

This study reveals high aminoglycoside and methicillin resistance in S. aureus isolates from Ardabil hospitals. Predominant SCCmec type IVa and spa type t030 indicate specific molecular patterns. These findings highlight the need for continuous surveillance and targeted treatment strategies for MRSA infections.

CLINICAL TRIAL NUMBER

Not applicable.

Evolutionary trajectories of β-lactam resistance in Enterococcus faecalis strains

Resistance to ampicillin and imipenem in Enterococcus faecalis is infrequent. However, the evolution of resistance can occur through prolonged antibiotic exposure during the treatment of chronic infections. In this study, we conducted a long-term evolution experiment using four genetically diverse strains of E. faecalis with varying susceptibilities to ampicillin and imipenem. Each strain was subjected to increasing concentrations of either ampicillin or imipenem over 200 days, with three independent replicates for each strain. Selective pressure from imipenem led to the rapid selection of highly resistant lineages across all genetic backgrounds, compared to ampicillin. In addition to high resistance, we describe, for the first time, the evolution of a β-lactam-dependent phenotype observed in lineages from all backgrounds. Whole-genome sequencing and bioinformatic analysis revealed mutations in three main functional classes: genes involved in cell wall synthesis and degradation, genes in the walK/R two-component system, and genes in the c-di-AMP pathway. Our analysis identified new mutations in genes known to be involved in resistance as well as novel genes potentially associated with resistance. Furthermore, the newly described β-lactam-dependent phenotype was correlated with the inactivation of c-di-AMP degradation, resulting in high levels of this second messenger. Together, these data highlight the diverse genetic mechanisms underlying resistance to ampicillin and imipenem in E. faecalis. The emergence of high resistance levels and β-lactam dependency underscores the importance of understanding evolutionary dynamics in the development of antibiotic resistance.

IMPORTANCE

Enterococcus faecalis is a major human pathogen, and treatment is frequently compromised by poor response to first-line antibiotics such as ampicillin. Understanding the factors that play a role in susceptibility/resistance to these drugs will help guide the development of much-needed treatments.

Important Features for Protein Foldings in Two Acyl Carrier Proteins from Enterococcus faecalis

The emergence of multi-drug resistant Enterococcus faecalis raises a serious threat to global public health. E. faecalis is a gram-positive intestinal commensal bacterium found in humans. E. faecalis can endure extreme environments such as high temperature, pressure, and high salt, which facilitates them to cause infection in hospitals. E. faecalis has two acyl carrier proteins, AcpA (EfAcpA) in de novo fatty acid synthesis (FAS) and AcpB (EfAcpB) which utilizes exogenous fatty acids. Previously, we determined the tertiary structures of these two ACPs and investigated their structure-function relationships. Solution structures revealed that overall folding of these two ACPs is similar to those of other bacterial ACPs. However, circular dichroism (CD) experiments showed that the melting temperature of EfAcpA is 76.3°C and that of EfAcpB is 79.2°C, which are much higher than those of other bacterial ACPs. In this study, to understand the origin of their structural stabilities, we verified the important residues for stable folding of these two ACPs by monitoring thermal and chemical denaturation. Hydrogen/deuterium exchange and chemical denaturation experiments on wild-type and mutant proteins revealed that Ile10 of EfAcpA and Ile14 of EfAcpB mediate compact intramolecular packing and promote high thermostability and stable folding. E. faecalis may maximize efficiency of FAS and increase adaptability to the environmental stress by having two thermostable ACPs. This study may provide insight into bacterial adaptability and development of antibiotics against multi-drug-resistant E. faecalis.

Antimicrobial Biocides Susceptibility and Tolerance-Associated Genes in Enterococcus faecalis and Enterococcus faecium Isolates Collected from Human and Environmental Sources

Enterococci are among the most common causes of nosocomial infections worldwide. Antimicrobial biocides are extensively used to control the growth of microorganisms on different surfaces. The purpose of this study was to determine the susceptibility of Enterococcus faecalis and Enterococcus faecium isolates collected in Iran to biocide agents, formaldehyde (FOR), benzalkonium chloride (BZC), triclosan (TRE), and chlorhexidine digluconate (CHDG). Additionally, the frequency of biocide tolerance-associated (BTA) genes, qacA/B, qacED1, emeA, sigV and gasp65 were investigated. In this study, 222 isolates of E. faecalis and 425 isolates of E. faecium from clinical and non-clinical sources were investigated. Minimum inhibitory concentration (MIC) of biocide agents was determined using agar dilution method. Biocides epidemiological cutoff values (ECOFFs) were determined using 95% rule. BTA genes were identified using PCR testing. ECOFFs for CHDG, BZC, TRE and FOR were 8 µg/mL, 16 µg/mL, 32 µg/mL and 512 µg/mL for both species, respectively. MIC values showed that the distribution of isolates with high level of tolerance to antimicrobial biocides was clearly different, depending on ecological niches. The BTA genes, qacA/B, qacED1, emeA, sigV and gasp65 were detected in 19.4% (43), 19.8% (44), 42.8% (95), 89.6% (199) and 70.2% (156) of E. faecalis and 10.3% (44), 17.2% (73), 27.8% (118), 42.2% (188) and 82.8% (352) of E. faecium isolates, respectively. Based on the distribution pattern of BTA genes 14 and 18 different profiles were identified for E. faecalis and E. faecium isolates respectively. Generally, the isolates carrying at least a single BTA gene showed higher MIC₉₀ against all biocides compared to isolates with no BTA genes. However, there were no clear association between MIC₉₀ values and carrying particular BTA genes profile. The results of this study showed that CHDG was the most effective biocide against E. faecalis and E. faecium isolates. The data presented in current study can be used to define the biocides resistance breakpoints.