Transient loss of high-level mupirocin resistance in Staphylococcus aureus due to MupA polymorphism

Transiently silent acquired antimicrobial resistance: an emerging challenge in susceptibility testing

Acquisition and expression of antimicrobial resistance (AMR) mechanisms in bacteria are often associated with a fitness cost. Thus, evolutionary adaptation and fitness cost compensation may support the advance of subpopulations with a silent resistance phenotype when the antibiotic selection pressure is absent. However, reports are emerging on the transient nature of silent acquired AMR, describing genetic alterations that can change the expression of these determinants to a clinically relevant level of resistance, and the association with breakthrough infections causing treatment failures. This phenomenon of transiently silent acquired AMR (tsaAMR) is likely to increase, considering the overall expansion of acquired AMR in bacterial pathogens. Moreover, the augmented use of genotypic methods in combination with conventional phenotypic antimicrobial susceptibility testing (AST) will increasingly enable the detection of genotype and phenotype discrepancy. This review defines tsaAMR as acquired antimicrobial resistance genes with a corresponding phenotype within the wild-type distribution or below the clinical breakpoint for susceptibility for which genetic alterations can mediate expression to a clinically relevant level of resistance. References to in vivo resistance development and therapeutic failures caused by selected resistant subpopulations of tsaAMR in Gram-positive and Gram-negative pathogens are given. We also describe the underlying molecular mechanisms, including alterations in the expression, reading frame or copy number of AMR determinants, and discuss the clinical relevance concerning challenges for conventional AST.

Emerging Treatment Strategies for Impetigo in Endemic and Nonendemic Settings: A Systematic Review

PURPOSE

Impetigo affects approximately 162 million children worldwide at any given time. Lack of consensus on the most effective treatment strategy for impetigo and increasing antibiotic resistance continue to drive research into newer and alternative treatment options. We conducted a systematic review to assess the effectiveness of new treatments for impetigo in endemic and nonendemic settings.

METHODS

We searched PubMed, MEDLINE, CINAHL, Web of Science, and Embase via Scopus for studies that explored treatments for bullous, nonbullous, primary, and secondary impetigo published between August 1, 2011, and February 29, 2020. We also searched online trial registries and hand-searched the reference lists of the included studies. We used the revised Cochrane risk of bias (version 2.0) tool for randomized trials and the National Heart, Lung, and Blood Institute for nonrandomized uncontrolled studies to assess the risk of bias.

FINDINGS

We included 10 studies that involved 6651 participants and reported on 9 treatments in the final analysis. Most clinical trials targeted nonbullous impetigo or did not specify this. The risk of bias varied among the studies. In nonendemic settings, ozenoxacin 1% cream appeared to have the strongest evidence base compared with retapamulin and a new minocycline formulation. In endemic settings, oral co-trimoxazole and benzathine benzylpenicillin G injection were equally effective in the treatment of severe impetigo. Mass drug administration intervention emerged as a promising public health strategy to reduce the prevalence of impetigo in endemic settings.

IMPLICATIONS

This review highlights the limited research into new drugs used for the treatment of impetigo in endemic and nonendemic settings. Limited recent evidence supports the use of topical ozenoxacin or retapamulin for impetigo treatment in nonendemic settings, whereas systemic antibiotics and the mass drug administration strategy have evidence for use in endemic settings. Given the troubling increase in resistance to existing treatments, there is a clear need to ensure the judicious use of antibiotics and to develop new treatments and alternative strategies; this is particularly important in endemic settings. PROSPERO identifier: CRD42020173042.

Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure

Sporadic literature reports describe isolates of pathogenic bacteria that harbor an antibiotic resistance determinant but remain susceptible to the corresponding antibiotic as a consequence of a genetic defect. Such strains represent a source from which antibiotic resistance may reemerge to cause treatment failure in patients. Here, we report a systematic investigation into the prevalence and nature of this phenomenon, which we term silencing of antibiotic resistance by mutation (SARM). Instances of SARM were detected among 1,470 Staphylococcus aureus isolates through side-by-side comparison of antibiotic resistance genotype (as determined by whole-genome sequencing) versus phenotype (as assessed through susceptibility testing). Of the isolates analyzed, 152 (10.3%) harbored a silenced resistance gene, including 46 (3.1%) that exhibited SARM to currently deployed antistaphylococcal drugs. SARM resulted from diverse mutational events but most commonly through frameshift mutation of resistance determinants as a result of point deletion in poly(A) tracts. The majority (∼90%) of SARM strains reverted to antibiotic resistance at frequencies of ≥10^-9; thus, while appearing antibiotic sensitive in the clinical microbiology laboratory, most S. aureus isolates exhibiting SARM will revert to antibiotic resistance at frequencies achievable in patients. In view of its prevalence in a major pathogen, SARM represents a significant potential threat to the therapeutic efficacy of antibiotics.IMPORTANCE Antibiotic resistance hinders the treatment of bacterial infection. To guide effective therapy, clinical microbiology laboratories routinely perform susceptibility testing to determine the antibiotic sensitivity of an infecting pathogen. This approach relies on the assumption that it can reliably distinguish bacteria capable of expressing antibiotic resistance in patients, an idea challenged by the present study. We report that the important human pathogen Staphylococcus aureus frequently carries antibiotic resistance genes that have become inactivated ("silenced") by mutation, leading strains to appear antibiotic sensitive. However, resistance can rapidly reemerge in most such cases, at frequencies readily achievable in infected patients. Silent antibiotic resistance is therefore prevalent, transient, and evades routine detection, rendering it a significant potential threat to antibacterial chemotherapy.

High prevalence of direct repeat unit types of 10di, 8 h and 8i among methicillin resistant Staphylococcus aureus strains with staphylococcal cassette chromosome mec type IIIA isolated in Tehran, Iran

Background

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) is a main concern in burn care centers worldwide. The some reports of MRSA in Iran suggested that MRSA with type SCCmec III is common among burn patients. The aim of this study was to determine the prevalence, virulence genes, and antimicrobial susceptibility of the direct repeat units (dru) types of MRSA with SCCmec IIIA isolated from burn wounds in a burn care center in Tehran, Iran.

Methods

In total, 165 S. aureus isolates were collected from clinical samples. In order to detect MRSA isolates, the mecA gene was amplified through the polymerase chain reaction (PCR) method. Antimicrobial susceptibility was tested using the disc agar diffusion test. Moreover, the PCR method was applied to determine SCCmec types, virulence genes, and antimicrobial resistance genes. The dru region was sequenced and thereby, dru types and dru repeats were identified. A similarity matrix was used to create minimum spanning tree (MST).

Results

The prevalence of MRSA was 69% (114 out of 165 isolates). Most of MRSA isolates (61 out of 114, 53.5%) were SCCmec type IIIA. All MRSA isolates were vancomycin-susceptible and more than 68% of MRSA isolates with SCCmec type IIIA were mupirocin resistant. The successful dru typing of isolates with SCCmec type IIIA revealed fourteen different dru types. There were two new dru types, namely dt10di and dt7aj. MST analysis indicated the presence of the three clusters of dt10di (cluster I), dt8i-dt8 h (cluster II), and dt11c-dt10ao-dt11dd-dt11a-dt10a (cluster III). There were significant differences between clusters I and II respecting antimicrobial resistance pattern and virulence genes.

Conclusion

Three main dru clusters are prevalent in the study setting. The main dru types in the setting are dt10di, dt8i, and dt8 h. Dru typing can be used to differentiate MRSA strains with SCCmec IIIA.

Current and Emerging Topical Antibacterials and Antiseptics: Agents, Action, and Resistance Patterns

Bacterial skin infections represent some of the most common infectious diseases globally. Prevention and treatment of skin infections can involve application of a topical antimicrobial, which may be an antibiotic (such as mupirocin or fusidic acid) or an antiseptic (such as chlorhexidine or alcohol). However, there is limited evidence to support the widespread prophylactic or therapeutic use of topical agents. Challenges involved in the use of topical antimicrobials include increasing rates of bacterial resistance, local hypersensitivity reactions (particularly to older agents, such as bacitracin), and concerns about the indiscriminate use of antiseptics potentially coselecting for antibiotic resistance. We review the evidence for the major clinical uses of topical antibiotics and antiseptics. In addition, we review the mechanisms of action of common topical agents and define the clinical and molecular epidemiology of antimicrobial resistance in these agents. Moreover, we review the potential use of newer and emerging agents, such as retapamulin and ebselen, and discuss the role of antiseptic agents in preventing bacterial skin infections. A comprehensive understanding of the clinical efficacy and drivers of resistance to topical agents will inform the optimal use of these agents to preserve their activity in the future.

Correlation of mupirocin resistance with biofilm production in methicillin-resistant Staphylococcus aureus from surgical site infections in a tertiary centre, Egypt

The aim of this study was to detect mupirocin-resistant isolates from pus/wound swabs taken postoperatively in a tertiary centre in Egypt and to determine their ability to form biofilm in order to establish its correlation with mupirocin resistance. This was a prospective study including 513pus/wound swabs from patients suffering from postoperative surgical site infections over the period July 2013-January 2015. Samples were cultured and isolates were identified by coagulase activity, DNase test, mannitol fermentation by mannitol salt agar followed by API Staph 32. Oxacillin agar screen test, agar dilution test for mupirocin, and mupA gene detection by PCR were performed for all methicillin-resistant Staphylococcus aureus (MRSA) isolates. Biofilm detection was carried out by the microtitre plate and Congo red agar methods. Of the 161 S. aureus isolates identified, 73 (45.3%) were MRSA, among which 82.2% were mupirocin-susceptible and 17.8% were mupirocin-resistant. Among the resistant isolates, 38.5% showed low-level resistance and 61.5% were high-level mupirocin-resistant. The mupA gene was detected in 75.0% of high-level mupirocin-resistant strains and in none of the low-level mupirocin-resistant strains. Among the mupirocin-susceptible isolates, 95.0% were biofilm-producers and 5.0% did not produce biofilm. All mupirocin-resistant isolates produced biofilm. Moreover, 15.3% of high-level mupirocin-resistant strains were negative for the mupA gene but showed evidence of biofilm formation. In conclusion, biofilm formation may be suggested to play a role in mupirocin resistance besides the presence of a genetic element encoding abnormal isoleucyl-tRNA synthetase, however further studies are needed to confirm these findings.

Clonal variation in high- and low-level phenotypic and genotypic mupirocin resistance of MRSA isolates in south-east London

OBJECTIVES

Both low-level mupirocin resistance (LMR) and high-level mupirocin resistance (HMR) have been identified. The aim of this study was to determine the epidemiology of LMR and HMR in MRSA isolates at five hospitals that have used mupirocin for targeted decolonization as part of successful institutional control programmes.

METHODS

All MRSA identified in three microbiology laboratories serving five central and south-east London hospitals and surrounding communities between November 2011 and February 2012 were included. HMR and LMR were determined by disc diffusion testing. WGS was used to derive multilocus sequence types (MLSTs) and the presence of HMR and LMR resistance determinants.

RESULTS

Prevalence of either HMR or LMR amongst first healthcare episode isolates from 795 identified patients was 9.69% (95% CI 7.72-11.96); LMR was 6.29% (95% CI 4.70-8.21) and HMR was 3.40% (95% CI 2.25-4.90). Mupirocin resistance was not significantly different in isolates identified from inpatients at each microbiology laboratory, but was more common in genotypically defined 'hospital' rather than 'community' isolates (OR 3.17, 95% CI 1.36-9.30, P = 0.002). LMR was associated with inpatient stay, previous history of MRSA and age ≥65 years; HMR was associated with age ≥65 years and residential postcode outside London. LMR and HMR varied by clone, with both being low in the dominant UK MRSA clone ST22 compared with ST8, ST36 and ST239/241 for LMR and with ST8 and ST36 for HMR. V588F mutation and mupA carriage had high specificity (>97%) and area under the curve (>83%) to discriminate phenotypic mupirocin resistance, but uncertainty around the sensitivity point estimate was large (95% CI 52.50%-94.44%). Mutations in or near the mupA gene were found in eight isolates that carried mupA but were not HMR.

CONCLUSIONS

Mupirocin resistance was identified in <10% of patients and varied significantly by clone, implying that changes in clonal epidemiology may have an important role in determining the prevalence of resistance in conjunction with selection due to mupirocin use.

Mupirocin and chlorhexidine resistance in Staphylococcus aureus in patients with community-onset skin and soft tissue infections

Decolonization measures, including mupirocin and chlorhexidine, are often prescribed to prevent Staphylococcus aureus skin and soft tissue infections (SSTI). The objective of this study was to determine the prevalence of high-level mupirocin and chlorhexidine resistance in S. aureus strains recovered from patients with SSTI before and after mupirocin and chlorhexidine administration and to determine whether carriage of a mupirocin- or chlorhexidine-resistant strain at baseline precluded S. aureus eradication. We recruited 1,089 patients with community-onset SSTI with or without S. aureus colonization. In addition to routine care, 483 patients were enrolled in a decolonization trial: 408 received intranasal mupirocin (with or without antimicrobial baths), and 258 performed chlorhexidine body washes. Patients were followed for up to 12 months with repeat colonization cultures. All S. aureus isolates were tested for high-level mupirocin and chlorhexidine resistance. At baseline, 23/1,089 (2.1%) patients carried a mupirocin-resistant S. aureus strain and 10/1,089 (0.9%) patients carried chlorhexidine-resistant S. aureus. Of 4 patients prescribed mupirocin, who carried a mupirocin-resistant S. aureus strain at baseline, 100% remained colonized at 1 month compared to 44% of the 324 patients without mupirocin resistance at baseline (P = 0.041). Of 2 patients prescribed chlorhexidine, who carried a chlorhexidine-resistant S. aureus strain at baseline, 50% remained colonized at 1 month compared to 48% of the 209 patients without chlorhexidine resistance at baseline (P = 1.0). The overall prevalence of mupirocin and chlorhexidine resistance is low in S. aureus isolates recovered from outpatients, but eradication efforts were less successful in patients carrying a mupirocin-resistant S. aureus strain at baseline.

Emergence of high-level mupirocin resistance in coagulase-negative staphylococci associated with increased short-term mupirocin use

In our hospital, mupirocin has increasingly been used for peri-operative decolonization of Staphylococcus aureus. The target for mupirocin is isoleucyl tRNA synthetase (ileS). High-level resistance to mupirocin is conferred by acquisition of plasmids expressing a distinct ileS gene (ileS2). Here we evaluated the longitudinal trends in high-level mupirocin resistance in coagulase-negative staphylococci (CoNS) and linked this to the presence of ileS2 genes and mupirocin use. We assessed mupirocin resistance in CoNS bloodstream isolates from 2006 to 2011 tested by Phoenix automated testing (PAT). We evaluated the reliability of PAT results using Etest. PAT species determination was confirmed by MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry. We investigated the presence of ileS2 in the first 100 consecutive CoNS bloodstream isolates of each year using RT-PCR. Mupirocin use increased from 3.6 kg/year in 2006 to 13.3 kg/year in 2010 and correlated with the increase in the percentage of CoNS isolates carrying ileS2 (8% in 2006 to 22% in 2011; Spearman's rho, 0.137; P = 0.01). The sensitivity and specificity of PAT for detecting high-level mupirocin resistance were 0.97 and 0.97, respectively. ileS2 was detected in 81 of 82 phenotypically highly mupirocin-resistant strains and associated with resistance to ciprofloxacin, erythromycin, and clindamycin. In conclusion, we found a rapid increase in high-level resistance to mupirocin and resistance to other antibiotics in CoNS associated with an increase in mupirocin use. The associated resistance to other antibiotics may result in a reduction of oral antibiotic options for prolonged treatment of prosthetic infections with CoNS.

MupB, a new high-level mupirocin resistance mechanism in Staphylococcus aureus

Mupirocin is a topical antibiotic used for the treatment of skin infections and the eradication of methicillin-resistant Staphylococcus aureus carriage. It inhibits bacterial protein synthesis by interfering with isoleucyl-tRNA synthetase activity. High-level mupirocin resistance (MIC of ≥ 512 μg/ml) is mediated by the expression of mupA (ileS2), which encodes an alternate isoleucyl-tRNA synthetase. In this study, we describe high-level mupirocin resistance mediated by a novel locus, mupB. The mupB gene (3,102 bp) shares 65.5% sequence identity with mupA but only 45.5% identity with ileS. The deduced MupB protein shares 58.1% identity (72.3% similarity) and 25.4% identity (41.8% similarity) with MupA and IleS, respectively. Despite this limited homology, MupB contains conserved motifs found in class I tRNA synthetases. Attempts to transfer high-level mupirocin resistance via conjugation or transformation (using plasmid extracts from an mupB-containing strain) were unsuccessful. However, by cloning the mupB gene into a shuttle vector, it was possible to transfer the resistance phenotype to susceptible S. aureus by electroporation, proving that mupB was responsible for the high-level mupirocin resistance. Further studies need to be done to determine the prevalence of mupB and to understand risk factors and outcomes associated with resistance mediated by this gene.

Mupirocin resistance in Staphylococcus aureus causing recurrent skin and soft tissue infections in children

Staphylococcus aureus resistance to mupirocin is often caused by acquisition of a novel isoleucyl-tRNA synthetase encoded on the plasmid gene mupA. We tested S. aureus isolates from children at Texas Children's Hospital with recurrent skin and soft tissue infections for mupirocin resistance and mupA. Of 136 isolates, 20 were resistant to mupirocin (14.7%). Fifteen isolates (11%) carried mupA, and the gene was more common in methicillin-susceptible S. aureus (21.4%) than methicillin-resistant S. aureus (8.3%; P=0.03). Seven of 20 mupirocin-resistant isolates displayed clindamycin resistance.

Risk factors associated with mupirocin resistance in meticillin-resistant Staphylococcus aureus

Implementation of meticillin-resistant Staphylococcus aureus (MRSA) decolonisation programmes has been increasing and the emergence of mupirocin resistance has been reported. However, the patient-level risk factors associated with mupirocin resistance are not clear. In this study, independent predictors of mupirocin resistance in MRSA among Providence Veterans Affairs Medical Center patients with MRSA-positive culture dates between 1 July 2004 and 30 June 2008 were identified using a frequency-matched case-control study. Forty cases (mupirocin-resistant) were matched on culture date quarter and year to 270 controls (mupirocin-susceptible). The adjusted conditional logistic regression model identified three significant independent predictors associated with mupirocin resistance in MRSA: (1) exposure to mupirocin in the year prior to the culture date [odds ratio (OR): 9.84; 95% confidence interval (CI): 2.93-33.09]; (2) Pseudomonas aeruginosa infection in the year before the culture-related admission (4.85; 1.20-19.61); and (3) cefepime use in the year prior to culture (2.80; 1.03-7.58). In sensitivity analyses, previous mupirocin exposure was associated with low-level [minimum inhibitory concentration (MIC) 8-128mg/L; 23 cases, 202 controls; OR: 6.32; 95% CI: 1.58-25.33] and high-level (MIC ≥256mg/L; 17 cases, 151 controls; OR: 11.18; 95% CI: 1.89-66.30) mupirocin resistance. To our knowledge, this is the first case-control study to reveal a strong association between previous mupirocin exposure and subsequent mupirocin resistance in MRSA, with demonstrated robustness in low- and high-level mupirocin resistance. Mupirocin susceptibility monitoring is critical for facilities instituting decolonisation with mupirocin as increased use may reduce effectiveness through resistance.