WGS of Commensal Neisseria Reveals Acquisition of a New Ribosomal Protection Protein (MsrD) as a Possible Explanation for High Level Azithromycin Resistance in Belgium

In this study, we characterized all oropharyngeal and anorectal isolates of Neisseria spp. in a cohort of men who have sex with men. This resulted in a panel of pathogenic Neisseria (N. gonorrhoeae [n = 5] and N. meningitidis [n = 5]) and nonpathogenic Neisseria (N. subflava [n = 11], N. mucosa [n = 3] and N. oralis [n = 2]). A high proportion of strains in this panel were resistant to azithromycin (18/26) and ceftriaxone (3/26). Whole genome sequencing (WGS) of these strains identified numerous mutations that are known to confer reduced susceptibility to azithromycin and ceftriaxone in N. gonorrhoeae. The presence or absence of these known mutations did not explain the high level resistance to azithromycin (>256 mg/L) in the nonpathogenic isolates (8/16). After screening for antimicrobial resistance (AMR) genes, we found a ribosomal protection protein, Msr(D), in these highly azithromycin resistant nonpathogenic strains. The complete integration site originated from Streptococcus pneumoniae and is associated with high level resistance to azithromycin in many other bacterial species. This novel AMR resistance mechanism to azithromycin in nonpathogenic Neisseria could be a public health concern if it were to be transmitted to pathogenic Neisseria. This study demonstrates the utility of WGS-based surveillance of nonpathogenic Neisseria.

Phenotypic and genetic barriers to establishment of horizontally transferred genes encoding ribosomal protection proteins

Background Ribosomal protection proteins (RPPs) interact with bacterial ribosomes to prevent inhibition of protein synthesis by tetracycline. RPP genes have evolved from a common ancestor into at least 12 distinct classes and spread by horizontal genetic transfer into a wide range of bacteria. Many bacterial genera host RPP genes from multiple classes but tet(M) is the predominant RPP gene found in Escherichia coli. Objectives We asked whether phenotypic barriers (low-level resistance, high fitness cost) might constrain the fixation of other RPP genes in E. coli. Methods We expressed a diverse set of six different RPP genes in E. coli, including tet(M), and quantified tetracycline susceptibility and growth phenotypes as a function of expression level, and evolvability to overcome identified phenotypic barriers. Results The genes tet(M) and tet(Q) conferred high-level tetracycline resistance without reducing fitness; tet(O) and tet(W) conferred high-level resistance but significantly reduced growth fitness; tetB(P) conferred low-level resistance and while mutants conferring high-level resistance were selectable these had reduced growth fitness; otr(A) did not confer resistance and resistant mutants could not be selected. Evolution experiments suggested that codon usage patterns in tet(O) and tet(W), and transcriptional silencing associated with nucleotide composition in tetB(P), accounted for the observed phenotypic barriers. Conclusions With the exception of tet(Q), the data reveal significant phenotypic and genetic barriers to the fixation of additional RPP genes in E. coli.

Translational control of antibiotic resistance

Many antibiotics available in the clinic today directly inhibit bacterial translation. Despite the past success of such drugs, their efficacy is diminishing with the spread of antibiotic resistance. Through the use of ribosomal modifications, ribosomal protection proteins, translation elongation factors and mistranslation, many pathogens are able to establish resistance to common therapeutics. However, current efforts in drug discovery are focused on overcoming these obstacles through the modification or discovery of new treatment options. Here, we provide an overview for common mechanisms of resistance to translation-targeting drugs and summarize several important breakthroughs in recent drug development.

ABC-F Proteins Mediate Antibiotic Resistance through Ribosomal Protection

ABSTRACTMembers of the ABC-F subfamily of ATP-binding cassette proteins mediate resistance to a broad array of clinically important antibiotic classes that target the ribosome of Gram-positive pathogens. The mechanism by which these proteins act has been a subject of long-standing controversy, with two competing hypotheses each having gained considerable support: antibiotic efflux versus ribosomal protection. Here, we report on studies employing a combination of bacteriological and biochemical techniques to unravel the mechanism of resistance of these proteins, and provide several lines of evidence that together offer clear support to the ribosomal protection hypothesis. Of particular note, we show that addition of purified ABC-F proteins to anin vitrotranslation assay prompts dose-dependent rescue of translation, and demonstrate that such proteins are capable of displacing antibiotic from the ribosomein vitro. To our knowledge, these experiments constitute the first direct evidence that ABC-F proteins mediate antibiotic resistance through ribosomal protection.IMPORTANCEAntimicrobial resistance ranks among the greatest threats currently facing human health. Elucidation of the mechanisms by which microorganisms resist the effect of antibiotics is central to understanding the biology of this phenomenon and has the potential to inform the development of new drugs capable of blocking or circumventing resistance. Members of the ABC-F family, which includelsa(A),msr(A),optr(A), andvga(A), collectively yield resistance to a broader range of clinically significant antibiotic classes than any other family of resistance determinants, although their mechanism of action has been controversial since their discovery 25 years ago. Here we present the first direct evidence that proteins of the ABC-F family act to protect the bacterial ribosome from antibiotic-mediated inhibition.

Safety Evaluation Of Sjenica Cheese With Regard To Coagulase-Positive Staphylococci And Antibiotic Resistance Of Lactic Acid Bacteria And Staphylococci

Sjenica cheese is an artisanal cheese stored in brine, traditionally produced from raw sheep’s milk in the southern part of Serbia - Sjenica Pester plateau.The aim of this study was to perform the safety evaluation of Sjenica cheese. As one of the safety criteria we considered the number of coagulase positive staphylococci and their enterotoxigenic potential. Antibiotic susceptibility/resistance patterns of autochthonous lactic acid bacteria and coagulase-positive staphylococci isolated from Sjenica cheese was also investigated.During the monitoring period of the cheese-making process, coagulase positive staphylococci did not reach the value of 105cfu/g. Among coagulase positive staphylococci, 12 (46,15%) isolates showed enterotoxigenic potential and were identified asStaphylococcus intermedius(11 isolates) andStaphylococcus aureus(1 isolate). Vancomycin resistance was the most prevalent phenotypic resistance profile in coagulase positive staphylococci.Lactococci present the most dominant population among lactic acid bacteria. The most prevalent resistance phenotype in lactococci was resistance to streptomycin (83.33%), ampicillin and penicillin (70.83%); lactobacilli were characterized by resistance to vancomycin (62.5%) and tetracycline (54.17%), while resistance to streptomycin (82.46%) was the most prevalent phenotypic profile in enterococci.All coagulase positive staphylococci and lactic acid bacteria isolates that showed resistance to tetracycline on disc diffusion and E-test, were tested for the presence of ribosomal protection proteins,tet(M) andtet(K) genes. All isolates were positive for ribosomal protection proteins genes; 14 (60.87%) isolates showedtet(M) gene presence, while 2 lactobacilli isolates revealed the presence oftet(K) gene.

Structure-Activity Relationship of the Aminomethylcyclines and the Discovery of Omadacycline

ABSTRACTA series of novel tetracycline derivatives were synthesized with the goal of creating new antibiotics that would be unaffected by the known tetracycline resistance mechanisms. New C-9-position derivatives of minocycline (the aminomethylcyclines [AMCs]) were tested forin vitroactivity against Gram-positive strains containing known tetracycline resistance mechanisms of ribosomal protection (Tet M inStaphylococcus aureus,Enterococcus faecalis, andStreptococcus pneumoniae) and efflux (Tet K inS. aureusand Tet L inE. faecalis). A number of aminomethylcyclines with potentin vitroactivity (MIC range of ≤0.06 to 2.0 μg/ml) were identified. These novel tetracyclines were more active against one or more of the resistant strains than the reference antibiotics tested (MIC range, 16 to 64 μg/ml). The AMC derivatives were active against bacteria resistant to tetracycline by both efflux and ribosomal protection mechanisms. This study identified the AMCs as a novel class of antibiotics evolved from tetracycline that exhibit potent activityin vitroagainst tetracycline-resistant Gram-positive bacteria, including pathogenic strains of methicillin-resistantS. aureus(MRSA) and vancomycin-resistant enterococci (VRE). One derivative, 9-neopentylaminomethylminocycline (generic name omadacycline), was identified and is currently in human trials for acute bacterial skin and skin structure infections (ABSSSI) and community-acquired bacterial pneumonia (CABP).