In the Literature Free

Reduced Susceptibility of Staphylococcus Aureus to Vancomycin and Daptomycin: Global Selection by Rifampin

Guérillot R, Gonçalves da Silva A, Monk I, Giulieri S, Tomita T, Alison E, et al. Convergent evolution driven by rifampin exacerbates the global burden of drug-resistant Staphylococcus aureus. mSphere. 2018 Jan 24;3(1). pii: e00550-17. doi:10.1128/mSphere.00550-17. eCollection 2018 Jan-Feb. PubMed PMID: 29404415; PubMed Central PMCID: PMC5784246.

Resistance to rifampin is caused by mutations in rpoB that affect the binding site of the drug. The central role of rpoB, which encodes the ß subunit of the bacterial RNA polymerase, in bacterial gene expression dictates that specific rpoB mutations may not only affect susceptibility to rifampin but may also have a variety of additional consequences. Thus, recent genome-wide studies have found that the strongest genetic marker associated with Staphylococcus aureus exhibiting heterogenous resistance to vancomycin are specific mutations in residue 481 of rpoB. In addition to affecting vancomycin susceptibility, the activities of daptomycin and various ß lactam antibiotics may also be adversely affected. Furthermore, specific alterations at residue 481 and at RelA128 have been associated with persistent methicillin resistant S. aureus (MRSA) infection, increased capsule production, attenuated virulence in a murine model, and reduced susceptibility to elements of the innate immune response [1].

Guérillot and colleagues interrogated 7099 publicly available S. aureus genomes and identified 372 (5.2% of the total) carrying a Rif^r-associated rpoB allele predicted to encode rifampin resistance. These were identified in 6.7% of MRSA and only 0.9% of methicillin susceptible Staphylococcus aureus (MSSA) ones. Eight mutations were associated accounted for 93% of the total.

Only 1 non-Rif^r mutation among the 29 that have previously been associated with increased vancomycin minimum inhibitory concentration (MIC) was found and that in only a single isolate. None of the public mutations derived by in vitro selection and associated with resistance to daptomycin, oxacillin, imipenem, and trimethoprim-sulfamethoxazole were detected among the 7099 genomes. This contrasted with the detection of Rif^r-selected mutations associated with reduced susceptibility to other antibiotics in 160 of 375 Rif^r isolates.

Using large-scale evolutionary convergence analysis of all independent rpoB mutations within the inferred phylogeny of the 7099 isolates, 32 convergent mutations were identified. The most frequent among these was H481N, which was followed by H481Y and which, as mentioned above, is associated with persistence and reduced susceptibility to the innate immune response. Further analysis was consistent with the unsurprising conclusion that rifampin exposure is the major selective pressure exerted on the evolution of rpoB. H481N/Y, which does not adversely affect fitness in vitro, was associated with global expansion of Rif^r clones over several decades. Allelic exchange experiments demonstrated that the H148N mutation enhanced the emergence of Rif^r small colony variants (SCV). Furthermore, 86% of all Rif^r carried specific mutations that promoted cross-resistance to vancomycin, whereas 52% adversely affected both vancomycin and daptomycin susceptibility.

Of concern is that 4 of the most frequent Rif^r mutations confer only low level rifampin resistance with MICs at or below the Clinical and Laboratory Standards Institute resistance breakpoint of ≥4 mcg/mL (the EUCAST resistance breakpoint is ≥0.5 mcg/mL), thus leading to the potential use of rifampin in infections caused be organisms in which resistance mutations already exist.

This study provides robust evidence that, on a global scale, reduced susceptibility of S. aureus to rifampin, vancomycin, and daptomycin has been the consequence of selection of rpoB variants under the pressure of rifampin exposure. It suggests that the frequent persistence of infection, especially due to MRSA, despite what should be adequate antibiotic therapy, may be due to evasion of innate immunity, as well as the development of SCV, both resulting from specific Rif^r mutations (although this same investigative group recently failed to identify specific genomic markers of persistence in a large number of S. aureus isolates [2]). Finally, these results lead to questions regarding the wisdom of using rifampin in combination with vancomycin in the treatment of prosthetic valve endocarditis due to coagulase negative staphylococci or MRSA, as recommended in the current guidelines based on less than robust evidence [3].

References

Editor’s Note (written by Ferric C. Fang, MD): The emergence of stable lineages of rifampin-resistant Staphylococcus aureus is a concern. Combination therapy is thought to reduce the likelihood that rifampin resistance will emerge during therapy, but rifampin is available without prescription in many parts of the world and is sometimes employed as monotherapy for the treatment of tuberculosis or non-tuberculous infections. Although most single rpoB mutations conferring rifampin resistance are associated with reduced fitness, intragenic compensatory mutations to ameliorate the fitness cost may arise, possibly accounting for the clones carrying multiple rpoB mutations observed in this study. The desire to limit rifampin use and the spread of resistance will have to be balanced against the present lack of effective options for the treatment of biofilm-associated staphylococcal infections. If rifampin combinations are employed, care must be taken with regard to timing, dosing, and adjunctive surgical debridement (Sendi and Zimmerli. The use of rifampin in staphylococcal orthopedic-device-related infections. Clin Microbiol Infect 23:349–50, 2017).

Autologous Fecal Microbiota Transplantation Restores the Gut Microbiome of Allogeneic Hematopoietic Stem Cell Transplant Recipients

Taur Y, Coyte K, Schluter J, Robilotti E, Figueroa C, Gjonbalaj M, et al. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci Transl Med. 2018 Sep 26;10(460). pii: eaap9489. doi:10.1126/scitranslmed.aap9489. PubMed PMID: 30257956.

Recipients of allogeneic hematopoietic stem cell transplants (HSCT) commonly have profoundly altered fecal microbiomes. Altered composition and reduced diversity of the microbiome, as occurs after antibiotic exposure, have been associated in such patients with an increased risk of acute graft versus host disease and mortality and the loss of colonization resistance is associated with an increased risk of systemic infections as well as gastrointestinal infection due to Clostridioides difficile. One means of determining whether these observations indicate causality, rather than mere association, is to perform a therapeutic intervention directed at restoration of the fecal microbiome to its “normal” state and to observe clinical outcomes relative to those in a control group.

Taur et al examined frozen serially collected feces from a large number of patients undergoing allo-HSCT and, using 16S rRNA amplification and sequencing, confirmed that their average microbiota diversity was initially high but decreased as they received prophylactic or therapeutic antibiotics. Diversity reached a nadir at approximately day +5 post-transplantation and remained low for approximately 6 weeks. Despite subsequent slow recovery, diversity rarely achieved pre-allograft levels by day +100.

Taur and colleagues have initiated a trial designed to first determine the feasibility of restoration of the pre-transplant gut flora and, subsequently, to determine whether this associated with a decrease in post-transplantation complications. Patients undergoing HSCT were randomized to receive autologous fecal microbiota transplants (auto-FMT) or no treatment in a single center, open-label randomized controlled trial. Fecal samples were screened initially and again a median of 13 days later at the time of allo-HSCT and, if the latter samples had reduced numbers of “healthy bacteria” of the Bacteriodetes phylum, the patients underwent randomization.

The study reviewed here provides data on the first 25 patients (14 auto-FMT recipients and 11 controls) concerning the ability of the allo-FMT to restore the baseline fecal microbiome. The investigators report that this procedure was associated with increased microbiota diversity relative to controls and restoration of its composition to its pre-antibiotic state. This finding suggests that the clinical endpoint portion of the study may prove to be a valid test of the effect of reduced diversity and altered composition of the fecal microbiota on complications of all-HSCT and whether restoration of the microbiota to its predisruption state accounts for improved clinical outcomes. In the meantime, patient accrual into the study continues.