Aminoglycoside resistance 16S rRNA methyltransferases block endogenous methylation, affect translation efficiency and fitness of the host

Emergence of NDM-1- and OXA-23-Co-Producing Acinetobacter baumannii ST1 Isolates from a Burn Unit in Spain

The global emergence of carbapenem-resistant Acinetobacter baumanii (CRAB) represents a significant public health threat. In the summer of 2022, a polyclonal CRAB outbreak occurred in our hospital, marking the first detection of an NDM-1 plus OXA-23 co-producing A. baumannii strain in Spain. The aim of this study was to phenotypically and genotypically characterize the clonal spread of NDM-1 and OXA-23 co-producing A. baumannii isolates and to describe the infection control measures implemented to contain the outbreak. Patients with multidrug-resistant A. baumannii isolates (July 2022-May 2023) were included in the study. Isolates were identified via MALDI-TOF, and antimicrobial susceptibility was tested using a broth microdilution method (DKMGN SensititreTM panels). Whole-genome sequencing was performed on 24 representative isolates. Phylogenetic analysis was performed using Ridom SeqSphere+ (cgMLST), while sequence typing was performed using ARIBA (Pasteur and Oxford schemes). A. baumannii isolates from the affected patients belonged to five different sequence types. The two main STs were ST1Pas/ST231Oxf (NDM-1- and OXA-23-co-producing), which accounted for 58%, and ST136Pas/ST406Oxf (OXA-23-producing), which accounted for 21%. All isolates were resistant to fluoroquinolones, trimethoprim/sulfamethoxazole, aminoglycosides, and carbapenems. In addition, 8% were resistant to colistin and 17% to cefiderocol. Finally, the affected patients were cohorted, and a thorough cleaning of the affected units was carried out. This study documents the clonal spread of an NDM-1- and OXA-23-co-producing A. baumannii strain in Spain, linked to a Libyan patient, highlighting the risk of cross-border spread. Although infection control measures successfully contained the outbreak, surveillance is essential as the incidence of CRAB infections is expected to increase.

The newly identified grdA gene confers high-level plazomicin resistance in Salmonella enterica serovars

Plazomicin, a next-generation aminoglycoside, was recently approved by the U.S. Food and Drug Administration for the treatment of multidrug-resistant complicated urinary tract infections. It is highly effective against most aminoglycoside-modifying enzymes (AMEs). Here, we report that Salmonella enterica strains containing the newly identified gentamicin resistance gene (grdA) are highly resistant to plazomicin. Heterologous expression of grdA in Escherichia coli ΔtolC resulted in plazomicin resistance with minimum inhibitory concentration (MIC) > 256 µg/mL. These findings reveal that GrdA confers significantly higher resistance to plazomicin than the previously known plazomicin-resistant AMEs AA (2)-Ia and APH (2″)-Iva.

NpmC - a novel A1408 16S rRNA methyltransferase in the gut of humans and animals

NpmA and NpmB are 16S rRNA methyltransferases that act on residue A1408 and confer high-level resistance to almost all aminoglycosides; however, these methyltransferases are rarely reported. A novel gene, npmC, was identified after analysisng all world-wide available metagenomic projects in a One Health context. This gene has a high level of similarity (91.5%) with npmA and up to 92.7% similarity at amino acidic level. The protein encoded by this gene presents the conserved motifs required for A1408 methylation. npmC was synthesized and its expression in Escherichia coli resulted in a high level of resistance to 4,5-disubstituted 2-deoxystreptamine (2-DOS) and 4-monosubstituted 2-DOS aminoglycosides, as well as moderate resistance to 4,6-disusbstituted 2-DOS aminoglycosides, including the last resort aminoglycoside, plazomicin. Methylation at residue A1408 was confirmed by mass spectrometry assays. Analysis of the npmC gene background revealed that its genetic context was associated with different insertion sequences that could mobilise the gene. Similarities in the genetic context between npmC and npmA indicate that they share a common ancestor. The immediate genetic context of this methyltransferase indicates a high relationship to the Eubacteriales order. This finding reveals the dark matter of the microbiome as a potential source of novel resistance genes, expands the list of the true pan-aminoglycoside 16S rRNA methyltransferases, which threaten the usefulness and development of next-generation aminoglycosides.

Concordance in molecular methods for detection of antimicrobial resistance: A cross sectional study of the influent to a wastewater plant

Methods that are used to characterise microbiomes and antimicrobial resistance genes (ARGs) in wastewater are not standardised. We used shotgun metagenomic sequencing (SM-Seq), RNA sequencing (RNA-seq) and targeted qPCR to compare microbial and ARG diversity in the influent to a municipal wastewater treatment plant in Australia. ARGs were annotated with CARD-RGI and MEGARes databases, and bacterial diversity was characterised by 16S rRNA gene sequencing and SM-Seq, with species annotation in SILVA/GreenGenes databases or Kraken2 and the NCBI nucleotide database respectively. CARD and MEGARes identified evenly distributed ARG profiles but MEGARes detected a richer array of ARGs (richness = 475 vs 320). Qualitatively, ARGs encoding for aminoglycoside, macrolide-lincosamide-streptogramin and multidrug resistance were the most abundant in all examined databases. RNA-seq detected only 32 % of ARGs identified by SM-Seq, but there was concordance in the qualitative identification of aminoglycoside, macrolide-lincosamide, phenicol, sulfonamide and multidrug resistance by SM-Seq and RNA-seq. qPCR confirmed the detection of some ARGs, including OXA, VEB and EREB, that were identified by SM-Seq and RNA-seq in the influent. For bacteria, SM-Seq or 16S rRNA gene sequencing were equally effective in population profiling at phyla or class level. However, SM-Seq identified a significantly higher species richness (richness = 15,000 vs 3750). These results demonstrate that SM-Seq with gene annotation in CARD and MEGARes are equally sufficient for surveillance of antimicrobial resistance in wastewater. For more precise ARG identification and quantification however, MEGARes presented a better resolution. The functionality of detected ARGs was not confirmed, but general agreement on the putative phenotypic resistance profile by antimicrobial class was observed between RNA-Seq and SM-Seq.

Past, Present, and Future of RNA Modifications in Infectious Disease Research

In early 2024, the National Academies of Sciences, Engineering, and Medicine (NASEM) released a roadmap for the future of research into mapping ribonucleic acid (RNA) modifications, which underscored the importance of better defining these diverse chemical changes to the RNA macromolecule. As nearly all mature RNA molecules harbor some form of modification, we must understand RNA modifications to fully appreciate the functionality of RNA. The NASEM report calls for massive mobilization of resources and investment akin to the transformative Human Genome Project of the early 1990s. Like the Human Genome Project, a concerted effort in improving our ability to assess every single modification on every single RNA molecule in an organism will change the way we approach biological questions, accelerate technological advance, and improve our understanding of the molecular world. Consequently, we are also at the start of a revolution in defining the impact of RNA modifications in the context of host-microbe and even microbe-microbe interactions. In this perspective, we briefly introduce RNA modifications to the infection biologist, highlight key aspects of the NASEM report and exciting examples of RNA modifications contributing to host and pathogen biology, and finally postulate where infectious disease research may benefit from this exciting new endeavor in globally mapping RNA modifications.

Polymorphism of virulence genes and biofilm associated with in vitro induced resistance to clarithromycin in Helicobacter pylori

BACKGROUND

Clarithromycin-containing triple therapy is commonly used to treat Helicobacter pylori infections. Clarithromycin resistance is the leading cause of H. pylori treatment failure. Understanding the specific mutations that occur in H. pylori strains that have evolved antibiotic resistance can help create a more effective and individualised antibiotic treatment plan. However, little is understood about the genetic reprogramming linked to clarithromycin exposure and the emergence of antibiotic resistance in H. pylori. Therefore, this study aims to identify compensatory mutations and biofilm formation associated with the development of clarithromycin resistance in H. pylori. Clarithromycin-sensitive H. pylori clinical isolates were induced to develop clarithromycin resistance through in vitro exposure to incrementally increasing concentration of the antibiotic. The genomes of the origin sensitive isolates (S), isogenic breakpoint (B), and resistant isolates (R) were sequenced. Single nucleotide variations (SNVs), and insertions or deletions (InDels) associated with the development of clarithromycin resistance were identified. Growth and biofilm production were also assessed.

RESULTS

The S isolates with A2143G mutation in the 23S rRNA gene were successfully induced to be resistant. According to the data, antibiotic exposure may alter the expression of certain genes, including those that code for the Cag4/Cag protein, the vacuolating cytotoxin domain-containing protein, the sel1 repeat family protein, and the rsmh gene, which may increase the risk of developing and enhances virulence in H. pylori. Enhanced biofilm formation was detected among R isolates compared to B and S isolates. Furthermore, high polymorphism was also detected among the genes associated with biofilm production.

CONCLUSIONS

Therefore, this study suggests that H. pylori may acquire virulence factors while also developing antibiotic resistance due to clarithromycin exposure.

Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum

The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.

A panel of diverse Klebsiella pneumoniae clinical isolates for research and development

Klebsiella pneumoniae are a leading cause of healthcare-associated infections worldwide. In particular, strains expressing extended-spectrum β-lactamases (ESBLs) and carbapenemases pose serious treatment challenges, leading the World Health Organization (WHO) to designate ESBL and carbapenem-resistant Enterobacteriaceae as 'critical' threats to human health. Research efforts to combat these pathogens can be supported by accessibility to diverse and clinically relevant isolates for testing novel therapeutics. Here, we describe a panel of 100 diverse K. pneumoniae isolates that are publicly available to assist the research community in this endeavour. Whole-genome sequencing (WGS) was performed on 3878 K. pneumoniae clinical isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. The isolates were cultured from 63 facilities in 19 countries between 2001 and 2020. Core-genome multilocus sequence typing and high-resolution single-nucleotide polymorphism-based phylogenetic analyses captured the genetic diversity of the collection and were used to select the final panel of 100 isolates. In addition to known multidrug-resistant (MDR) pandemic lineages, the final panel includes hypervirulent lineages and isolates with specific and diverse resistance genes and virulence biomarkers. A broad range of antibiotic susceptibilities, ranging from pan-sensitive to extensively drug-resistant isolates, are described. The panel collection, and all associated metadata and genome sequences, are available at no additional cost and will be an important resource for the research community and for the design and development of novel antimicrobial agents and diagnostics against this important pathogen.

Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation

The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.

Virotyping and genetic antimicrobial susceptibility testing of porcine ETEC/STEC strains and associated plasmid types

Introduction

Enterotoxigenic Escherichia coli (ETEC) infections are the most common cause of secretory diarrhea in suckling and post-weaning piglets. For the latter, Shiga toxin-producing Escherichia coli (STEC) also cause edema disease. This pathogen leads to significant economic losses. ETEC/STEC strains can be distinguished from general E. coli by the presence of different host colonization factors (e.g., F4 and F18 fimbriae) and various toxins (e.g., LT, Stx2e, STa, STb, EAST-1). Increased resistance against a wide variety of antimicrobial drugs, such as paromomycin, trimethoprim, and tetracyclines, has been observed. Nowadays, diagnosing an ETEC/STEC infection requires culture-dependent antimicrobial susceptibility testing (AST) and multiplex PCRs, which are costly and time-consuming.

Methods

Here, nanopore sequencing was used on 94 field isolates to assess the predictive power, using the meta R package to determine sensitivity and specificity and associated credibility intervals of genotypes associated with virulence and AMR.

Results

Genetic markers associated with resistance for amoxicillin (plasmid-encoded TEM genes), cephalosporins (ampC promoter mutations), colistin (mcr genes), aminoglycosides (aac(3) and aph(3) genes), florfenicol (floR), tetracyclines (tet genes), and trimethoprim-sulfa (dfrA genes) could explain most acquired resistance phenotypes. Most of the genes were plasmid-encoded, of which some collocated on a multi-resistance plasmid (12 genes against 4 antimicrobial classes). For fluoroquinolones, AMR was addressed by point mutations within the ParC and GyrA proteins and the qnrS1 gene. In addition, long-read data allowed to study the genetic landscape of virulence- and AMR-carrying plasmids, highlighting a complex interplay of multi-replicon plasmids with varying host ranges.

Conclusion

Our results showed promising sensitivity and specificity for the detection of all common virulence factors and most resistance genotypes. The use of the identified genetic hallmarks will contribute to the simultaneous identification, pathotyping, and genetic AST within a single diagnostic test. This will revolutionize future quicker and more cost-efficient (meta)genomics-driven diagnostics in veterinary medicine and contribute to epidemiological studies, monitoring, tailored vaccination, and management.

The small mycobacterial ribosomal protein, bS22, modulates aminoglycoside accessibility to its 16S rRNA helix-44 binding site

Treatment of tuberculosis continues to be challenging due to the widespread latent form of the disease and the emergence of antibiotic-resistant strains of the pathogen, Mycobacterium tuberculosis. Bacterial ribosomes are a common and effective target for antibiotics. Several second line anti-tuberculosis drugs, e.g. kanamycin, amikacin, and capreomycin, target ribosomal RNA to inhibit protein synthesis. However, M. tuberculosis can acquire resistance to these drugs, emphasizing the need to identify new drug targets. Previous cryo-EM structures of the M. tuberculosis and M. smegmatis ribosomes identified two novel ribosomal proteins, bS22 and bL37, in the vicinity of two crucial drug-binding sites: the mRNA-decoding center on the small (30S), and the peptidyl-transferase center on the large (50S) ribosomal subunits, respectively. The functional significance of these two small proteins is unknown. In this study, we observe that an M. smegmatis strain lacking the bs22 gene shows enhanced susceptibility to kanamycin compared to the wild-type strain. Cryo-EM structures of the ribosomes lacking bS22 in the presence and absence of kanamycin suggest a direct role of bS22 in modulating the 16S rRNA kanamycin-binding site. Our structures suggest that amino-acid residue Lys-16 of bS22 interacts directly with the phosphate backbone of helix 44 of 16S rRNA to influence the micro-configuration of the kanamycin-binding pocket. Our analysis shows that similar interactions occur between eukaryotic homologues of bS22, and their corresponding rRNAs, pointing to a common mechanism of aminoglycoside resistance in higher organisms.

Interactions between host epithelial cells and Acinetobacter baumannii promote the emergence of highly antibiotic resistant and highly mucoid strains

Acinetobacter baumannii is an important nosocomial pathogen. Upon colonizing a host, A. baumannii are subjected to selective pressure by immune defenses as they adapt to the host environment. However, the mechanism of this pathoadaptation is unknown. Here, we established an in vitro system to evolve A. baumannii driven by the continuous selective pressure exerted by epithelial cells, and we used a combination of experimental evolution, phenotypic characterization and multi-omics analysis to address the underlying mechanism. When continuously exposed to selective pressure by pulmonary epithelial cells, A. baumannii showed ptk mutation-mediated mucoid conversion (reduced adhesion and increased anti-phagocytic ability) by enhancement of capsular exopolysaccharide chain length; rsmG mutation-mediated deficiency of 7-methylguanosine modification in the 524th nucleotide of 16S rRNA, which increased ribosome translation efficiency; and rnaseI mutation-mediated changes in outer membrane permeability and efflux pump expression. Together, these mutations altered susceptibility to a variety of antimicrobial agents, including the novel antibiotic cefiderocol, by regulating siderophore and siderophore-receptor biosynthesis. In conclusion, pulmonary epithelial cells modulate A. baumannii pathoadaptation, implicating the host–microbe interaction in the survival and persistence of A. baumannii.

Emergence and spread of antibiotic-resistant foodborne pathogens from farm to table

Antibiotics have been overused and misused for preventive and therapeutic purposes. Specifically, antibiotics are frequently used as growth promoters for improving productivity and performance of food-producing animals such as pigs, cattle, and poultry. The increasing use of antibiotics has been of great concern worldwide due to the emergence of antibiotic resistant bacteria. Food-producing animals are considered reservoirs for antibiotic resistance genes (ARGs) and residual antibiotics that transfer from the farm through the table. The accumulation of residual antibiotics can lead to additional antibiotic resistance in bacteria. Therefore, this review evaluates the risk of carriage and spread of antibiotic resistance through food chain and the potential impact of antibiotic use in food-producing animals on food safety. This review also includes in-depth discussion of promising antibiotic alternatives such as vaccines, immune modulators, phytochemicals, antimicrobial peptides, probiotics, and bacteriophages.

An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and blaNDM: evaluation of the global dissemination of these resistance determinants

The spread of extremely-drug resistant Klebsiella pneumoniae has become a major health threat worldwide. This is largely mediated by certain lineages, recognized as high-risk clones dispersed in all the world. The analysis of an outbreak of nine ST15, NDM-1 metallo-β-lactamase producing K. pneumoniae was performed. An IncC plasmid carrying the bla_NDM-1 gene also carried the rare rmtC gene, encoding for a 16S rRNA methyltransferases (16RMTases), conferring resistance to all aminoglycosides. We studied the global spread of NDM variants and their association with the 16RMTases among K. pneumoniae complete genomes available in GenBank, producing a complete overview of the association of 16RMTases and NDM in K. pneumoniae genomics. NDM is more and more often associated with16RMTases and both are spreading in K. pneumoniae, conferring resistance to every beta-lactam and aminoglycoside. Our analysis suggest that aminoglycosides have limited future as second line treatment against NDM-producing K. pneumoniae.

Public health implications of plasmid-mediated quinolone and aminoglycoside resistance genes in Escherichia coli inhabiting a major anthropogenic river of India

Presence of antimicrobial resistance (AMR) genes in Escherichia coli inhabiting anthropogenic rivers is an important public health concern because plasmid-mediated AMR genes can easily spread to other pathogens by horizontal gene transfer. Besides β -lactams, quinolones and aminoglycosides are the major antibiotics against E. coli. In the present study, we have investigated the presence of plasmid-mediated quinolone resistance (PMQR) and aminoglycoside resistance genes in E. coli isolated from a major river of northern India. Our results revealed that majority of the strains were phenotypically susceptible for fluoroquinolones and some aminoglycosides like amikacin, netilmicin, tobramycin and gentamicin. However, 16.39% of the strains were resistant for streptomycin, 8.19% for kanamycin and 3.30% for gentamicin. Of the various PMQR genes investigated, only qnrS1 was present in 24.59% of the strains along with ISEcl2 . Aminoglycoside-resistance genes like strA-strB were found to be present in 16.39%, aphA1 in 8.19% and aacC 2 in only 3.30% of the strains. Though, no co-relation was observed between phenotypic resistance for fluorquinolones and presence of PMQR genes, phenotypic resistance for streptomycin, kanamycin and gentamicin exactly co-related with the presence of the genes strA-strB , aphA1 and aacC2 , respectively. Moreover, all the AMR genes discerned in aquatic E. coli were found to be situated on conjugative plasmids and, thus easily transferrable. Our study accentuates the importance of routine surveillance of urban rivers to curtail the spread of AMR genes in aquatic pathogens.

Elevated expression of rsmI can act as a reporter of aminoglycoside resistance in Escherichia coli using kanamycin as signal molecule

We aimed to design and analyse expressional response of endogenous and exogenous 16S rRNA methyl transferase genes under sub inhibitory concentration stress of different clinically relevant aminoglycoside antibiotics in Escherichia coli to identify an endogenous marker. One hundred twenty nine aminoglycoside resistant E. coli of clinical origin were collected for detection of 16S rRNA methyl transferase genes by PCR assay and each gene type was cloned within E. coli JM107. Parent isolates were subjected to plasmid elimination by SDS treatment. Expression analysis of both acquired and endogenous 16S rRNA methyl transferase genes were performed by quantitative real-time PCR in clones and parent isolates under aminoglycoside stress (4 mg/L). Majority of the isolates were harbouring rmtC (35/129), followed by rmtB (32/129), rmtA (21/129), rmtE (13/129), armA (11/129) rmtF (9/129) and rmtH (8/129). Plasmid was successfully eliminated for all the isolates with 6% of SDS. Expression analysis indicates that kanamycin, tobramycin and netilmicin stress could increase the expression of 16S rRNA methyltransferese genes. In the presence of kanamycin stress the expression of rsmI was consistently elevated for all the wild type isolates and clones tested. Except for isolates harbouring rmtB and rmtC expression of rsmE and rsmF was increased in the presence of all aminoglycosides. For all the cured mutants it was apparently observed that expression of endogenous methyl transferases were marginally increased. Elevated expression of constitutive rsmI can be used as a potential biomarker for detection of acquired 16S rRNA methyl transferase mediated aminoglycoside resistance by using sub inhibitory concentration of kanamycin as signal molecule.

RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence

RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications regulating host-pathogen interactions have been demonstrated. They show how RNA modifications can regulate immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence. Here, we illustrate some of these findings, and highlight the strategies used to characterize RNA modifications, and their potential for new therapeutic applications.

rRNA Methylation and Antibiotic Resistance

Methylation of nucleotides in rRNA is one of the basic mechanisms of bacterial resistance to protein synthesis inhibitors. The genes for corresponding methyltransferases have been found in producer strains and clinical isolates of pathogenic bacteria. In some cases, rRNA methylation by housekeeping enzymes is, on the contrary, required for the action of antibiotics. The effects of rRNA modifications associated with antibiotic efficacy may be cooperative or mutually exclusive. Evolutionary relationships between the systems of rRNA modification by housekeeping enzymes and antibiotic resistance-related methyltransferases are of particular interest. In this review, we discuss the above topics in detail.

Molecular survey of aminoglycoside-resistant Acinetobacter baumannii isolated from tertiary hospitals in Qazvin, Iran

Aminoglycoside-modifying enzymes (AMEs) and 16S rRNA methylases (16S RMTase) are two main resistance mechanisms against aminoglycosides. This study aimed to evaluate the frequency of AMEs and 16S rRNA methylase genes among aminoglycoside non-susceptible Acinetobacter baumannii isolates and to assess their clonal relationship using repetitive extragenic palindromic-PCR (rep-PCR). In this cross-sectional study, a total of 192 A. baumannii isolates were collected from the patients hospitalized in Qazvin, Iran (January 2016 to January 2018). Identification of isolates was performed by standard laboratory methods and API 20E strips. Antimicrobial susceptibility was determined by Kirby–Bauer method followed by examination of the genes encoding the AMEs and 16S RMTase by PCR and sequencing methods. The clonal relationship of isolates was carried out by rep-PCR. In total, 98.4% of isolates were non-susceptible to aminoglycosides, 98.4%, 97.9% and 83.9% of isolates were found to be non-susceptible against gentamicin, tobramycin and amikacin, respectively. The frequencies of aph(3′)-VI, aac(6′)-Ib, aac(3)-II, aph(3′)-Ia and armA genes were 59.3%, 39.2%, 39.2%, 31.7% and 69.8%, respectively, either alone or in combination. Rep-PCR results showed that the aminoglycoside non-susceptible isolates belonged to three distinct clones: A (79.4%), B (17.5%) and C (3.2%). The findings of this study showed a high frequency for AMEs with the emergence of armA genes among the aminoglycoside non-susceptible A. baumannii isolates. Rational administration of aminoglycosides as well as using an appropriate infection control policy may reduce the presence of resistance to antibiotics in medical centres.

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Little is known regarding carbapenem resistance mechanisms in A. baumannii in our region.

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More than 85% of our isolates were non-susceptible to carbapenems in Qazvin hospitals, Iran.

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bla_OXA-23, bla_OXA-24, bla_IMP-1, and bla_VIM-1 genes is established in carbapenem resistant A. baumannii isolates.

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Clonal distribution of carbapenem resistant A. baumannii was demonstrated in investigated hospital settings.

Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data

Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology (GO) enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of C. beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however, their validation is required.

Aminoglycoside Resistance: Updates with a Focus on Acquired 16S Ribosomal RNA Methyltransferases

The clinical usefulness of aminoglycosides has been revisited as an effective choice against β-lactam-resistant and fluoroquinolone-resistant gram-negative bacterial infections. Plazomicin, a next-generation aminoglycoside, was introduced for the treatment of complicated urinary tract infections and acute pyelonephritis. In contrast, bacteria have resisted aminoglycosides, including plazomicin, by producing 16S ribosomal RNA (rRNA) methyltransferases (MTases) that confer high-level and broad-range aminoglycoside resistance. Aminoglycoside-resistant 16S rRNA MTase-producing gram-negative pathogens are widespread in various settings and are becoming a grave concern. This article provides up-to-date information with a focus on aminoglycoside-resistant 16S rRNA MTases.

Plazomicin: an intravenous aminoglycoside antibacterial for the treatment of complicated urinary tract infections

INTRODUCTION

Antimicrobial resistance continues to be a major public health concern due to the emergence and spread of multi-drug resistant (MDR) organisms, including extended spectrum ß-lactamase (ESBL) and carbapenemase producing Enterobacterales. Plazomicin is a novel aminoglycoside that demonstrates activity against MDR gram-negatives, including those producing ESBLs and most carbapenemases, and retains activity against aminoglycoside modifying enzymes as a result of structural modifications. The information discussed is meant to assist in identifying plazomicin's place in therapy and to expand the clinician's armamentarium.

AREAS COVERED

Herein, we review the pharmacology, microbiology, clinical efficacy, and safety of plazomicin. To gather relevant information, a literature search was performed using PubMed, Ovid, and Google Scholar electronic databases. Search terms used include plazomicin, ACHN-490, extended spectrum ß-lactamase, ESBL, CRE, aminoglycoside modifying enzymes, and AME. Additional information was obtained from FDA review documents and research abstracts presented at international conferences.

EXPERT OPINION

Plazomicin is a promising carbapenem or β-lactam/β-lactamase inhibitor-sparing alternative for the treatment of complicated urinary tract infections caused by MDR Enterobacterales. Although robust data for bloodstream infections and bacterial pneumonias are lacking, plazomicin may be considered in individual clinical scenarios if combination therapy is warranted provided supportive microbiological data and therapeutic drug monitoring are available.

Clinical epigenetics and multidrug-resistant bacterial infections: host remodelling in critical illness

The inappropriate use of antibiotics in man is driving to insurgence of pathogenic bacteria resistant to multiple drugs (MDR) representing a challenge in critical illness. The interaction of MDR bacteria with host cells can guide molecular perturbations of host transcriptional programmes involving epigenetic-sensitive mechanisms, mainly DNA methylation, histone modifications, and non-coding RNAs leading to pathogen survival. Clinical evidence of epigenetic manipulation from MDR bacteria mainly arises from Mycobacterium tuberculosis as well as Helicobacter pylori, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, and Legionella pneumophila infection suggesting possible biomarkers of disease. For example, DNA hypermethylation of E-cadherin (CDH1), upstream transcription factor 1/2 (USF1/2), WW domain containing oxidoreductase (WWOX), and mutL homolog 1 (MLH1) genes in gastric mucosa is correlated with malignancy suggesting useful biomarkers of early disease state. Moreover, upregulated circulating miR-361-5p, miR-889, miR-576-3p may be useful biomarkers to discriminate tuberculosis patients. Moreover, Listeria monocytogenes can indirectly induce H3 hyperacetylation leading to inflammation in human endothelial cells whereas Pseudomonas aeruginosa excretes QS 2-AA to directly induce H3 deacetylation leading to bacterial persistence in human monocytes. Remarkably, epigenetic-sensitive drugs may aid to counteract MDR in clinical setting. Trichostatin A, a histone deacetyltransferase inhibitor (HDACi), leads to AMP β-defensin 2 (HBD2) gene up-regulation in human epithelial cells suggesting a useful 'epi-therapy' for Escherichia coli-induced intestinal diseases. We update on the most current clinical studies focusing on epigenetic changes involved in bacterial-host interactions and their putative role as biomarkers or drug targets to improve precision medicine and personalized therapy in critical illness and transplantation setting.

High distribution of 16S rRNA methylase genes rmtB and armA among Enterobacter cloacae strains isolated from an Ahvaz teaching hospital, Iran

The emergence of 16S rRNA methylase genes encoded on plasmids confers high-level aminoglycoside resistance (HLAR). This study aimed to investigate the prevalence of 16S rRNA methylases among Enterobacter cloacae strains isolated from an Ahvaz teaching hospital, Iran. A total of 68 E. cloacae clinical strains were collected between November 2017 and September 2018. The MICs of aminoglycosides were assessed using the agar dilution method. The presence of 16S rRNA methylase genes, including armA, rmtA to rmtH, and nmpA was evaluated by PCR. The transferability of 16S rRNA methylase-harboring plasmids was evaluated by conjugation assay. The genetic diversity of all isolates was evaluated by ERIC-PCR. The armA and rmtB genes were the only 16S rRNA methylase genes detected in this study (29 out of 68 isolates; 42.64%). The transferability by conjugation was observed in 23 rmtB or/and armA positive donors. HLAR phenotype was in 33 of 68 strains. Ten clonal types were obtained by ERIC-PCR and significant associations (p < 0.05) were between the clone types and aminoglycoside susceptibility, as well as with profile of the 16S rRNA methylase genes. In conclusion, both horizontal transfer and clonal spread are responsible for dissemination of the rmtB and armA genes among E. cloacae strains.

De Novo Emergence of Peptides That Confer Antibiotic Resistance

The origin of novel genes and beneficial functions is of fundamental interest in evolutionary biology. New genes can originate from different mechanisms, including horizontal gene transfer, duplication-divergence, and de novo from noncoding DNA sequences. Comparative genomics has generated strong evidence for de novo emergence of genes in various organisms, but experimental demonstration of this process has been limited to localized randomization in preexisting structural scaffolds. This bypasses the basic requirement of de novo gene emergence, i.e., lack of an ancestral gene. We constructed highly diverse plasmid libraries encoding randomly generated open reading frames and expressed them in Escherichia coli to identify short peptides that could confer a beneficial and selectable phenotype in vivo (in a living cell). Selections on antibiotic-containing agar plates resulted in the identification of three peptides that increased aminoglycoside resistance up to 48-fold. Combining genetic and functional analyses, we show that the peptides are highly hydrophobic, and by inserting into the membrane, they reduce membrane potential, decrease aminoglycoside uptake, and thereby confer high-level resistance. This study demonstrates that randomized DNA sequences can encode peptides that confer selective benefits and illustrates how expression of random sequences could spark the origination of new genes. In addition, our results also show that this question can be addressed experimentally by expression of highly diverse sequence libraries and subsequent selection for specific functions, such as resistance to toxic compounds, the ability to rescue auxotrophic/temperature-sensitive mutants, and growth on normally nonused carbon sources, allowing the exploration of many different phenotypes.IMPORTANCE De novo gene origination from nonfunctional DNA sequences was long assumed to be implausible. However, recent studies have shown that large fractions of genomic noncoding DNA are transcribed and translated, potentially generating new genes. Experimental validation of this process so far has been limited to comparative genomics, in vitro selections, or partial randomizations. Here, we describe selection of novel peptides in vivo using fully random synthetic expression libraries. The peptides confer aminoglycoside resistance by inserting into the bacterial membrane and thereby partly reducing membrane potential and decreasing drug uptake. Our results show that beneficial peptides can be selected from random sequence pools in vivo and support the idea that expression of noncoding sequences could spark the origination of new genes.

Antimicrobial Resistance in Escherichia coli

Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.

Efficacy of Apramycin against Multidrug-Resistant Acinetobacter baumannii in the Murine Neutropenic Thigh Model

Apramycin, an aminocyclitol aminoglycoside, was rapidly bactericidal against Acinetobacter baumannii In a neutropenic murine thigh infection model, treatment-associated A. baumannii CFU reductions of >4 log₁₀ per thigh were observed for all exposures for which area under the curve (AUC)/MIC ratio was >50 and maximum concentration of drug in serum (C_max)/MIC was ≈10 or higher. Based on these findings, we suggest that apramycin deserves further preclinical exploration as a repurposed therapeutic for multidrug-resistant Gram-negative pathogens, including A. baumannii.

Environmental and genetic modulation of the phenotypic expression of antibiotic resistance

Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic ‘dark matter’) that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA

The aminoglycoside resistance conferred by an N1-methylation of A1408 in 16S rRNA by a novel plasmid-mediated methyltransferase NpmA can be a future health threat. In the present study, we have determined crystal structures of the bacterial ribosomal decoding A site with an A1408m¹A antibiotic-resistance mutation both in the presence and absence of aminoglycosides. G418 and paromomycin both possessing a 6′-OH group specifically bind to the mutant A site and disturb its function as a molecular switch in the decoding process. On the other hand, binding of gentamicin with a 6′-NH₃⁺ group to the mutant A site could not be observed in the present crystal structure. These observations agree with the minimum inhibitory concentration of aminoglycosides against Escherichia coli. In addition, one of our crystal structures suggests a possible conformational change of A1408 during the N1-methylation reaction by NpmA. The structural information obtained explains how bacteria acquire resistance against aminoglycosides along with a minimum of fitness cost by the N1-methylation of A1408 and provides novel information for designing the next-generation aminoglycoside.

The chemistries and consequences of DNA and RNA methylation and demethylation

Chemical modification of nucleobases plays an important role for the control of gene expression on different levels. That includes the modulation of translation by modified tRNA-bases or silencing and reactivation of genes by methylation and demethylation of cytosine in promoter regions. Especially dynamic methylation of adenine and cytosine is essential for cells to adapt to their environment or for the development of complex organisms from a single cell. Errors in the cytosine methylation pattern are associated with most types of cancer and bacteria use methylated nucleobases to resist antibiotics. This Point of View wants to shed light on the known and potential chemistry of DNA and RNA methylation and demethylation. Understanding the chemistry of these processes on a molecular level is the first step towards a deeper knowledge about their regulation and function and will help us to find ways how nucleobase methylation can be manipulated to treat diseases.

Post-transcriptional Modifications Modulate rRNA Structure and Ligand Interactions

Post-transcriptional modifications play important roles in modulating the functions of RNA species. The presence of modifications in RNA may directly alter its interactions with binding partners or cause structural changes that indirectly affect ligand recognition. Given the rapidly growing list of modifications identified in noncoding and mRNAs associated with human disease, as well as the dynamic control over modifications involved in various physiological processes, it is imperative to understand RNA structural modulation by these modifications. Among the RNA species, rRNAs provide numerous examples of modification types located in differing sequence and structural contexts. In addition, the modified rRNA motifs participate in a wide variety of ligand interactions, including those with RNA, protein, and small molecules. In fact, several classes of antibiotics exert their effects on protein synthesis by binding to functionally important and highly modified regions of the rRNAs. These RNA regions often display conservation in sequence, secondary structure, tertiary interactions, and modifications, trademarks of ideal drug-targeting sites. Furthermore, ligand interactions with such regions often favor certain modification-induced conformational states of the RNA. Our laboratory has employed a combination of biophysical methods such as nuclear magnetic resonance spectroscopy (NMR), circular dichroism, and UV melting to study rRNA modifications in functionally important motifs, including helix 31 (h31) and helix h44 (h44) of the small subunit rRNA and helix 69 (H69) of the large subunit rRNA. The modified RNA oligonucleotides used in these studies were generated by solid-phase synthesis with a variety of phosphoramidite chemistries. The natural modifications were shown to impact thermal stability, dynamic behavior, and tertiary structures of the RNAs, with additive or cooperative effects occurring with multiple, clustered modifications. Taking advantage of the structural diversity offered by specific modifications in the chosen rRNA motifs, phage display was used to select peptides that bind with moderate (low micromolar) affinity and selectivity to modified h31, h44, and H69. Interactions between peptide ligands and RNAs were monitored by biophysical methods, including electrospray ionization mass spectrometry (ESI-MS), NMR, and surface plasmon resonance (SPR). The peptides compare well with natural compounds such as aminoglycosides in their binding affinities to the modified rRNA constructs. Some candidates were shown to exhibit specificity toward different modification states of the rRNA motifs. The selected peptides may be further optimized for improved RNA targeting or used in screening assays for new drug candidates. In this Account, we hope to stimulate interest in bioorganic and biophysical approaches, which may be used to deepen our understanding of other functionally important, naturally modified RNAs beyond the rRNAs.

Mechanisms of Resistance to Aminoglycoside Antibiotics: Overview and Perspectives

Aminoglycoside (AG) antibiotics are used to treat many Gram-negative and some Gram-positive infections and, importantly, multidrug-resistant tuberculosis. Among various bacterial species, resistance to AGs arises through a variety of intrinsic and acquired mechanisms. The bacterial cell wall serves as a natural barrier for small molecules such as AGs and may be further fortified via acquired mutations. Efflux pumps work to expel AGs from bacterial cells, and modifications here too may cause further resistance to AGs. Mutations in the ribosomal target of AGs, while rare, also contribute to resistance. Of growing clinical prominence is resistance caused by ribosome methyltransferases. By far the most widespread mechanism of resistance to AGs is the inactivation of these antibiotics by AG-modifying enzymes. We provide here an overview of these mechanisms by which bacteria become resistant to AGs and discuss their prevalence and potential for clinical relevance.

Effect of on-farm use of antimicrobial drugs on resistance in fecal Escherichia coli of preweaned dairy calves

Respiratory disease and diarrhea are the 2 most common diseases that result in the use of antimicrobial drugs in preweaned calves. Because the use of drugs in food animals, including dairy calves, has the potential for generating cross-resistance to drugs used in human medicine, it is vital to propose farm practices that foster the judicious use of antimicrobials while assuring animal health and productivity. The objective of this study was to use dairy farm calf treatment records to identify antimicrobial drug treatments in calves and to evaluate their effects on the prevalence of antimicrobial-resistant Escherichia coli from rectal swabs of preweaned dairy calves. Eight farms from central New York participated in the study, 3 farms using individual pen housing management and 5 farms using group pen housing management. Eligible study farms could not add antimicrobial drugs to the milk fed to preweaned calves and were required to have farm records documenting antimicrobial drug treatment of calves from birth to weaning. Three fecal E. coli isolates per calf were tested for susceptibility to 12 antimicrobial drugs using a Kirby-Bauer disk diffusion assay. A total of 473 calves were sampled, from which 1,423 commensal E. coli isolates were tested. Of the 9 antimicrobial drugs used on study farms, only enrofloxacin was significantly associated with reduced antimicrobial susceptibility of E. coli isolates, although treatment with ceftiofur was associated with reduced susceptibility to ceftriaxone. The median numbers of days from treatment with ceftiofur and enrofloxacin to rectal swab sampling of calves were 16 d (range: 1-39) and 12 d (range: 6-44), respectively. At the isolate level, treatment with enrofloxacin resulted in odds ratios of 2 [95% confidence interval (CI): 1-4] and 3 (95% CI: 2-6), respectively, for isolation of nonsusceptible E. coli to nalidixic acid and ciprofloxacin compared with calves not treated with enrofloxacin. Treatment with ceftiofur resulted in an odds ratio of 3 (95% CI: 0.9-12) for isolation of nonsusceptible E. coli to ceftriaxone compared with calves not treated with ceftiofur. Treatment with enrofloxacin resulted in selection of isolates that presented phenotypic resistance to both ciprofloxacin and ceftriaxone. Treatment with ceftiofur resulted in a higher prevalence of isolates resistant to ≥3 antimicrobial drugs (97%) compared with no treatment with ceftiofur (73%). These findings reinforce the necessity for continued implementation of practices at the dairy farm that support the sustainable and judicious use of antimicrobial drugs in dairy calves.

Genetic basis of high level aminoglycoside resistance in Acinetobacter baumannii from Beijing, China

The objective of this study was to investigate the genetic basis of high level aminoglycoside resistance in Acinetobacter baumannii clinical isolates from Beijing, China. 173 A. baumannii clinical isolates from hospitals in Beijing from 2006 to 2009 were first subjected to high level aminoglycoside resistance (HLAR, MIC to gentamicin and amikacin>512 µg/mL) phenotype selection by broth microdilution method. The strains were then subjected to genetic basis analysis by PCR detection of the aminoglycoside modifying enzyme genes (aac(3)-I, aac(3)-IIc, aac(6')-Ib, aac(6')-II, aph(4)-Ia, aph(3')-I, aph(3')-IIb, aph(3')-IIIa, aph(3')-VIa, aph(2″)-Ib, aph(2″)-Ic, aph(2″)-Id, ant(2″)-Ia, ant(3″)-I and ant(4')-Ia) and the 16S rRNA methylase genes (armA, rmtB and rmtC). Correlation analysis between the presence of aminoglycoside resistance gene and HLAR phenotype were performed by SPSS. Totally 102 (58.96%) HLAR isolates were selected. The HLAR rates for year 2006, 2007, 2008 and 2009 were 52.63%, 65.22%, 51.11% and 70.83%, respectively. Five modifying enzyme genes (aac(3)-I, detection rate of 65.69%; aac(6')-Ib, detection rate of 45.10%; aph(3')-I, detection rate of 47.06%; aph(3')-IIb, detection rate of 0.98%; ant(3″)-I, detection rate of 95.10%) and one methylase gene (armA, detection rate of 98.04%) were detected in the 102 A. baumannii with aac(3)-I+aac(6')-Ib+ant(3″)-I+armA (detection rate of 25.49%), aac(3)-I+aph(3')-I+ant(3″)-I+armA (detection rate of 21.57%) and ant(3″)-I+armA (detection rate of 12.75%) being the most prevalent gene profiles. The values of chi-square tests showed correlation of armA, ant(3″)-I, aac(3)-I, aph(3')-I and aac(6')-Ib with HLAR. armA had significant correlation (contingency coefficient 0.685) and good contingency with HLAR (kappa 0.940). The high rates of HLAR may cause a serious problem for combination therapy of aminoglycoside with β-lactams against A. baumannii infections. As armA was reported to be able to cause high level aminoglycoside resistance to most of the clinical important aminoglycosides (gentamicin, amikacin, tobramycin, etc), the function of aminoglycoside modifying enzyme gene(s) in A. baumannii carrying armA deserves further investigation.