Atypical Mutation in Neisseria gonorrhoeae 23S rRNA Associated with High-Level Azithromycin Resistance

Evaluation of the Allplex NG & DR assay for molecular prediction of ciprofloxacin and azithromycin resistance in Neisseria gonorrhoeae

PURPOSE

Molecular methods to detect antimicrobial resistance in Neisseria gonorrhoeae (Ng) are increasingly needed worldwide to improve diagnostic tests and enable individualized patient treatments. The Allplex™ NG & DR Assay (NG & DR assay) was assessed for its ability to detect Ng and its antimicrobial resistance. The assay predicts ciprofloxacin resistance and susceptibility by targeting the molecular antimicrobial resistance (AMR) determinant gyrA S91F. The AMR determinants 23 S rRNA A2059G and C2611T were investigated to predict azithromycin wild-type and nonwild-type genotypes.

METHODS

After antimicrobial susceptibility testing, 153 Ng isolates were evaluated with the NG & DR assay. Furthermore, 394 clinal specimens, including 76 with corresponding antimicrobial susceptibility results, were analyzed simultaneously by the NG & DR assay and the in-house SYBR-Green assay.

RESULTS

The NG & DR assay predicted ciprofloxacin resistance and susceptibility with a sensitivity and specificity of 98.2% and 100.0%, respectively, and the results were consistent with those of the SYBR-Green assay for the detection of S91F. For the prediction of azithromycin nonwild-type and wild-type genotypes, the NG & DR assay demonstrated a sensitivity and specificity of 50.0% and 100.0%, respectively.

CONCLUSION

The NG & DR assay demonstrated promising results for the molecular prediction of ciprofloxacin resistance and susceptibility, expanding the potential diagnostic tool kit for individualized patient treatment. Furthermore, it might serve as a surveillance tool for azithromycin nonwild-type strains.

Local emergence and global evolution of Neisseria gonorrhoeae with high-level resistance to azithromycin

Antimicrobial resistance in Neisseria gonorrhoeae (Ng) has severely reduced treatment options, including azithromycin (AZM), which had previously been recommended as dual therapy with ceftriaxone. This study characterizes the emergence of high-level resistance to AZM (HLR-AZM) Ng in Baltimore, Maryland, USA, and describes the global evolution of HLR-AZM Ng. Whole genome sequencing (WGS) of 30 Ng isolates with and without HLR-AZM from Baltimore was used to identify clonality and resistance determinants. Publicly available WGS data from global HLR-AZM Ng (n = 286) and the Baltimore HLR-AZM Ng (n = 3) were used to assess the distribution, clonality, and diversity of HLR-AZM Ng. The HLR-AZM Ng isolates from Baltimore identified as multi-locus sequencing typing sequence type (ST) 9363 and likely emerged from circulating strains. ST9363 was the most widely disseminated ST globally represented in eight countries and was associated with sustained transmission events. The number of global HLR-AZM Ng, countries reporting these isolates, and strain diversity increased in the last decade. The majority (89.9%) of global HLR-AZM Ng harbored the A2059G mutation in all four alleles of the 23S rRNA gene, but isolates with two or three A2059G alleles, and alternative HLR-AZM mechanisms were also identified. In conclusion, HLR-AZM in Ng has increased in the last few years, with ST9363 emerging as an important gonococcal lineage globally. The 23S rRNA A2059G mutation is the most common resistance mechanism, but alternative mechanisms are emerging. Continued surveillance of HLR-AZM Ng, especially ST9363, and extensively drug-resistant Ng is warranted.

The novel 2024 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations and superseded WHO N. gonorrhoeae reference strains-phenotypic, genetic and reference genome characterization

OBJECTIVES

MDR and XDR Neisseria gonorrhoeae strains remain major public health concerns internationally, and quality-assured global gonococcal antimicrobial resistance (AMR) surveillance is imperative. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) and WHO Enhanced GASP (EGASP), including metadata and WGS, are expanding internationally. We present the phenotypic, genetic and reference genome characteristics of the 2024 WHO gonococcal reference strains (n = 15) for quality assurance worldwide. All superseded WHO gonococcal reference strains (n = 14) were identically characterized.

MATERIAL AND METHODS

The 2024 WHO reference strains include 11 of the 2016 WHO reference strains, which were further characterized, and four novel strains. The superseded WHO reference strains include 11 WHO reference strains previously unpublished. All strains were characterized phenotypically and genomically (single-molecule PacBio or Oxford Nanopore and Illumina sequencing).

RESULTS

The 2024 WHO reference strains represent all available susceptible and resistant phenotypes and genotypes for antimicrobials currently and previously used (n = 22), or considered for future use (n = 3) in gonorrhoea treatment. The novel WHO strains include internationally spreading ceftriaxone resistance, ceftriaxone resistance due to new penA mutations, ceftriaxone plus high-level azithromycin resistance and azithromycin resistance due to mosaic MtrRCDE efflux pump. AMR, serogroup, prolyliminopeptidase, genetic AMR determinants, plasmid types, molecular epidemiological types and reference genome characteristics are presented for all strains.

CONCLUSIONS

The 2024 WHO gonococcal reference strains are recommended for internal and external quality assurance in laboratory examinations, especially in the WHO GASP, EGASP and other GASPs, but also in phenotypic and molecular diagnostics, AMR prediction, pharmacodynamics, epidemiology, research and as complete reference genomes in WGS analysis.

Antimicrobial treatment and resistance in sexually transmitted bacterial infections

Sexually transmitted infections (STIs) have been part of human life since ancient times, and their symptoms affect quality of life, and sequelae are common. Socioeconomic and behavioural trends affect the prevalence of STIs, but the discovery of antimicrobials gave hope for treatment, control of the spread of infection and lower rates of sequelae. This has to some extent been achieved, but increasing antimicrobial resistance and increasing transmission in high-risk sexual networks threaten this progress. For Neisseria gonorrhoeae, the only remaining first-line treatment (with ceftriaxone) is at risk of becoming ineffective, and for Mycoplasma genitalium, for which fewer alternative antimicrobial classes are available, incurable infections have already been reported. For Chlamydia trachomatis, in vitro resistance to first-line tetracyclines and macrolides has never been confirmed despite decades of treatment of this highly prevalent STI. Similarly, Treponema pallidum, the cause of syphilis, has remained susceptible to first-line penicillin.

Adaptive Evolution for the Efficient Production of High-Quality d-Lactic Acid Using Engineered Klebsiella pneumoniae

d-Lactic acid serves as a pivotal platform chemical in the production of poly d-lactic acid (PDLA) and other value-added products. This compound can be synthesized by certain bacteria, including Klebsiella pneumoniae. However, industrial-scale lactic acid production in Klebsiella pneumoniae faces challenges due to growth inhibition caused by lactic acid stress, which acts as a bottleneck in commercial microbial fermentation processes. To address this, we employed a combination of evolutionary and genetic engineering approaches to create an improved Klebsiella pneumoniae strain with enhanced lactic acid tolerance and production. In flask fermentation experiments, the engineered strain achieved an impressive accumulation of 19.56 g/L d-lactic acid, representing the highest production yield observed in Klebsiella pneumoniae to date. Consequently, this strain holds significant promise for applications in industrial bioprocessing. Notably, our genome sequencing and experimental analyses revealed a novel correlation between UTP-glucose-1-phosphate uridylyltransferase GalU and lactic acid resistance in Klebsiella pneumoniae. Further research is warranted to explore the potential of targeting GalU for enhancing d-lactic acid production.

Use of genome sequencing to resolve differences in gradient diffusion and agar dilution antimicrobial susceptibility testing performance of Neisseria gonorrhoeae isolates in Alberta, Canada

Agar dilution is the gold standard method for phenotypic antimicrobial susceptibility testing (AST) for Neisseria gonorrhoeae. However, this method is laborious and requires expertise, so laboratories that perform N. gonorrhoeae AST may choose alternative methods such as disk diffusion and gradient diffusion. In this study, we retrospectively compare the performance of gradient diffusion to agar dilution for 2,394 unique N. gonorrhoeae isolates identified in Alberta from 2017 to 2020 against azithromycin, cefixime, ceftriaxone, ciprofloxacin, penicillin, and tetracycline. Genome sequencing was utilized to resolve discrepancies between AST methods, detect antimicrobial resistance markers, and identify trends between error rates and sequence types (STs) of isolates. Over 90% of N. gonorrhoeae isolates were susceptible to azithromycin, cefixime, and ceftriaxone, whereas decreased susceptibility was observed for ciprofloxacin, penicillin, and tetracycline. Categorical (CA) and essential agreement (EA) was poorest between the two methods for penicillin (CA: 86.02%; EA: 77.69%) and tetracycline (CA: 47.22%; EA: 55.96%); however, the low CA was primarily attributed to minor errors. Antimicrobial agents with errors outside of acceptable limits included azithromycin (very major error: 18.42%; major error: 7.73%) and tetracycline (very major error: 6.17%). Genome sequencing on a subset of isolates resolved 30.3% of the azithromycin major errors and confirmed the azithromycin or tetracycline very major errors. Significant associations between certain STs and error types for azithromycin and tetracycline were also identified. Overall, gradient diffusion compared well to agar dilution for cefixime, ceftriaxone, and ciprofloxacin, and genome sequencing was identified as a useful tool to arbitrate discrepant susceptibility testing results between gradient diffusion and agar dilution for N. gonorrhoeae.

Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT.

Emergence of a predominant sequence type ST7363 and the increasing trend of resistance to cefixime and ceftriaxone in Neisseria gonorrhoeae in Southern Taiwan, 2019-2021

BACKGROUND/PURPOSE

Multi-drug resistance and the presence of epidemic lineages of Neisseria gonorrhoeae locally and globally were important clinical and public health issues. We aimed to investigate the molecular epidemiology and the antimicrobial susceptibility profiles of N. gonorrhoeae in Southern Taiwan.

METHODS

Between 2019 and 2021, adult patients who had suspected gonorrhea and attended a urology clinic in southern Taiwan were recruited to participate in this study. Clinical data from medical records and a questionnaire, antimicrobial susceptibility testing using a disk diffusion test in accordance with the guidelines by the Clinical and Laboratory Standards Institute, and Multi-locus sequence typing (MLST) were analyzed.

RESULTS

A total of 500 patients participated in the surveillance study. Among them, 232 N. gonorrhoeae isolates were identified, but only 164 isolates were recovered for further research. ST7363 (n = 83, 50.61%) was found to be the predominant sequence type, followed by ST1583 (n = 24, 14.63%), ST1588 (n = 13, 7.93%), and ST7827 (n = 12, 7.32%). 100% resistance to penicillin and 99.4% non-susceptible rate of ciprofloxacin were observed. The azithromycin resistant rate being 15.24% and the cefixime non-susceptible rate being 17.07% were alarming, both with decreasing trends in susceptibilities during 2019-2021. The 25 azithromycin resistant isolates were mainly belonged to ST7363 (n = 12) and ST7827 (n = 3). Seven (4.2%) isolates were ceftriaxone non-susceptible. Among them, four were assigned to be ST 7827 and three belonged to ST7363.

CONCLUSION

We observed the emergence of a predominant sequence type ST7363 in southern Taiwan. Compared with previous Taiwan studies, the increasing trend of resistance to cefixime and ceftriaxone necessitates clinicians' alertness for clinical treatment response of the extended spectrum cephalosporins and the further surveillance monitor.

What happens when nanoparticles encounter bacterial antibiotic resistance?

Bacterial resistance to antibiotics has become a widespread concern, and poses serious environmental and global health problems. Lots of studies have demonstrated that engineered nanoparticles (NPs) can significantly affect bacterial antibiotic resistance; however, whether NPs promote or inhibit antibiotic resistance remains a complex and well-debated issue. This will constrain environmental antibiotic resistance gene contamination and clinical bacterial resistance problems, resulting in unclear and poorly targeted treatment efficacy. To better understand the relationship between NPs and antibiotic resistance, this review systematically summarizes and reanalyzes published data on the effect of NPs on bacterial antibiotic resistance and related mechanisms. The effects of intrinsic properties of NPs, such as size, concentration, functional groups, and extrinsic properties of NPs on the development of antibiotic resistance were dissected. This review will provide a better understanding of the effects of increasingly released NPs in different environments on bacterial resistance and underlines the direction for employing NPs to control the dissemination of antibiotic resistance genes in the environment. Next, how NPs affect intracellular and extracellular antibiotic resistance needs in-depth exploration. Besides, alternative treatments of NPs and antibiotics in therapy will be a future trend for combating antibiotic resistance, and the follow-up emphasis should determine their dose effects and potential mechanism. This study will expand our understanding of the biosafety of nanomaterials and provides a theoretical reference to guide the proper application of nanomaterials or technologies to environmental pollution control and clinical treatment.

Genetic characteristics of azithromycin-resistant Neisseria gonorrhoeae collected in Hyogo, Japan during 2015-2019

Introduction. Azithromycin (AZM) is a therapeutic drug for sexually transmitted infections and is used for Neisseria gonorrhoeae when first- and second-line drugs are not available. Recently, the susceptibility of N. gonorrhoeae against AZM has been decreasing worldwide.Hypothesis/Gap Statement. Azithromycin-resistance (AZM-R) rates among N. gonorrhoeae in Japan are increasing, and the gene mutations and epidemiological characteristics of AZM-R in N. gonorrhoeae have not been fully investigated.Aim. We determined the susceptibility to AZM and its correlation with genetic characteristics of N. gonorrhoeae.Methodology. We investigated the susceptibility to AZM and genetic characteristics of N. gonorrhoeae. Mutations in domain V of the 23S rRNA gene and mtrR were examined in 93 isolates, including 13 AZM-R isolates. Spread and clonality were examined using sequence types (STs) of multi-antigen sequence typing for N. gonorrhoeae (NG-MAST), and whole genome analysis (WGA) to identify single nucleotide polymorphisms.Results. The number of AZM-R isolates increased gradually from 2015 to 2019 in Hyogo (P=0.008). C2599T mutations in 23S rRNA significantly increased in AZM-R isolates (P<0.001). NG-MAST ST4207 and ST6762 were frequently detected in AZM-R isolates, and they had higher MICs to AZM from 6 to 24 µg/ml. The phylogenic tree-based WGA showed that all isolates with ST4207 were contained in the same clade, and isolates with ST6762 were divided into two clades, AZM-S isolates and AZM-R isolates, which were different from the cluster containing ST1407.Conclusion. Our study showed yearly increases in AZM-R rates in N. gonorrhoeae. NG-MAST ST4207 and ST6762 were not detected in our previous study in 2015 and were frequently identified in isolates with higher MICs to AZM. WGA confirmed that isolates with these STs are closely related to each other. Continued surveillance is needed to detect the emergence and confirm the spread of NG-MAST ST4207 and ST6762.

Increasing azithromycin resistance in Neisseria gonorrhoeae due to NG-MAST 12302 clonal spread in Canada, 2015-2018

Objectives: Azithromycin resistant (AZIR) gonorrhea has been steadily increasing in Canada over the past decade which is cause for alarm as azithromycin (AZI) has been part of the combination therapy recommended by the Canadian Guidelines on Sexually Transmitted Infections (CGSTI) since 2012.

Method: Neisseria gonorrhoeae (NG) with AZI MICs ≥ 1 mg/L collected between 2015 and 2018 as part of the Gonococcal Antimicrobial Surveillance Program-Canada underwent antimicrobial susceptibility testing, molecular typing and whole genome sequencing. Regional, demographic and clinical isolation site comparisons were made to aid in our understanding of AZI susceptibility trending.

Results: 3,447 NG with AZI MICs ≥ 1 mg/L were identified in Canada, increasing from 6.3% in 2015 to 26.5% of isolates in 2018. Central Canada had the highest proportion rising from 9.2% in 2015 to 31.2% in 2018. 273 different NG-MAST sequence types were identified among these isolates with ST-12302 the most prevalent (50.9%). Whole genome sequencing identified the Neisseria lactamica -like mosaic mtr locus as the mechanism of AZIR in isolates of ST-12302 and isolates genetically similar (differ by ≤ 5 base pairs) designated as the ST-12302 genogroup, accounting for 65.2% of study isolateswhich were originally identified in central Canada but spread to other regions by 2018.

Conclusion: Genomic analysis indicated that AZIR in Canadian NG expanded rapidly due to clonal spread of the ST-12302 genogroup. The rapid expansion of this AZIR clonal group in all regions of Canada is of concern. CGSTI are currently under review to address the increase in AZIR in Canada.

Substitutions in SurA and BamA Lead to Reduced Susceptibility to Broad Range Antibiotics in Gonococci

There is growing concern about the emergence and spread of multidrug-resistant Neisseria gonorrhoeae. To effectively control antibiotic-resistant bacterial pathogens, it is necessary to develop new antimicrobials and to understand the resistance mechanisms to existing antibiotics. In this study, we discovered the unexpected onset of drug resistance in N. gonorrhoeae caused by amino acid substitutions in the periplasmic chaperone SurA and the β-barrel assembly machinery component BamA. Here, we investigated the i19.05 clinical isolate with mutations in corresponding genes along with reduced susceptibility to penicillin, tetracycline, and azithromycin. The mutant strain NG05 (surAmut bamAmut, and penAmut) was obtained using the pan-susceptible n01.08 clinical isolate as a recipient in the transformation procedure. Comparative proteomic analysis of NG05 and n01.08 strains revealed significantly increased levels of other chaperones, Skp and FkpA, and some transport proteins. Efflux pump inhibition experiments demonstrated that the reduction in sensitivity was achieved due to the activity of efflux pumps. We hypothesize that the described mutations in the surA and bamA genes cause the qualitative and quantitative changes of periplasmic chaperones, which in turn alters the function of synthesized cell envelope proteins.

Emergence of a Neisseria gonorrhoeae clone with reduced cephalosporin susceptibility between 2014 and 2019 in Amsterdam, The Netherlands, revealed by genomic population analysis

BACKGROUND

Emerging resistance to cephalosporins in Neisseria gonorrhoeae (Ng) is a major public health threat, since these are considered antibiotics of last resort. Continuous surveillance is needed to monitor the circulation of resistant strains and those with reduced susceptibility.

OBJECTIVES

For the purpose of epidemiological surveillance, genomic population analysis was performed on Ng isolates from Amsterdam with a focus on isolates with reduced susceptibility to ceftriaxone.

METHODS

WGS data were obtained from 318 isolates from Amsterdam, the Netherlands between 2014 and 2019. Isolates were typed according to MLST, Ng Multi-Antigen Sequence Typing (NG-MAST) and Ng Sequence Typing for Antimicrobial Resistance (NG-STAR) schemes and additional resistance markers were identified. Phylogenetic trees were created to identify genetic clusters and to compare Dutch and non-Dutch MLST7827 isolates.

RESULTS

MLST7363 and MLST1901 were the predominant strains having reduced susceptibility to ceftriaxone during 2014-16; MLST7827 emerged and dominated during 2017-19. NG-STAR38 and NG-MAST2318/10386 were predominant among MLST7827 isolates. MLST7827 reduced susceptibility isolates carried a non-mosaic 13.001 penA allele with an A501V mutation and porB1b G120K/A121D mutations, which were lacking in susceptible MLST7827 isolates. Phylogenetic analysis of all publicly available MLST7827 isolates showed strong genetic clustering of Dutch and other European MLST7827 isolates.

CONCLUSIONS

MLST7827 isolates with reduced ceftriaxone susceptibility have emerged during recent years in Amsterdam. Co-occurrence of penA A501V and porB1b G120K/A121D mutations was strongly associated with reduced susceptibility to ceftriaxone. Genetic clustering of Dutch and other European MLST7827 isolates indicates extensive circulation of this strain in Europe. Close monitoring of the spread of this strain having an alarming susceptibility profile is needed.

Evidence of Horizontal Gene Transfer of 50S Ribosomal Genes rplB, rplD, and rplY in Neisseria gonorrhoeae

Horizontal gene transfer (HGT) in the penA and multidrug efflux pump genes has been shown to play a key role in the genesis of antimicrobial resistance in Neisseria gonorrhoeae. In this study, we evaluated if there was evidence of HGT in the genes coding for the ribosomal proteins in the Neisseria genus. We did this in a collection of 11,659 isolates of Neisseria, including N. gonorrhoeae and commensal Neisseria species (N. cinerea, N. elongata, N. flavescens, N. mucosa, N. polysaccharea, and N. subflava). Comparative genomic analyses identified HGT events in three genes: rplB, rplD, and rplY coding for ribosomal proteins L2, L4 and L25, respectively. Recombination events were predicted in N. gonorrhoeae and N. cinerea, N. subflava, and N. lactamica were identified as likely progenitors. In total, 2,337, 2,355, and 1,127 isolates possessed L2, L4, and L25 HGT events. Strong associations were found between HGT in L2/L4 and the C2597T 23S rRNA mutation that confers reduced susceptibility to macrolides. Whilst previous studies have found evidence of HGT of entire genes coding for ribosomal proteins in other bacterial species, this is the first study to find evidence of HGT-mediated chimerization of ribosomal proteins.