Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications

Neisseria commensals are an indisputable source of resistance for their pathogenic relatives. However, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leverage in vitro selection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (≥ 2 μg/mL) in the Neisseria commensal, N. elongata. Across multiple lineages (n = 7/16), we find mutations that reduce susceptibility to azithromycin converge on the locus encoding the 50S ribosomal L34 protein (rpmH) and the intergenic region proximal to the 30S ribosomal S3 protein (rpsC) through short tandem duplication events. Interestingly, one of the laboratory evolved mutations in rpmH is identical (7LKRTYQ12), and two nearly identical, to those recently reported to contribute to high-level azithromycin resistance in N. gonorrhoeae. Transformations into the ancestral N. elongata lineage confirmed the causality of both rpmH and rpsC mutations. Though most lineages inheriting duplications suffered in vitro fitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Ultimately, studies like this will be critical for predicting commensal alleles that could rapidly disseminate into pathogen populations via allelic exchange across recombinogenic microbial genera.

Analysis of an IncR Plasmid Carrying bla NDM-1 Linked to an Azithromycin Resistance Region in Enterobacter hormaechei Involved in an Outbreak in Quebec

Analyzing the genetic environment of clinically relevant MDR genes can provide information on the way in which such genes are maintained and disseminated. Understanding this phenomenon is of interest for clinicians as it can also provide insight on where these genes might have been sourced, possibly supporting outbreak investigations.

Azithromycin resistance in Shiga-toxin Producing Escherichia coli in France between 2004 and 2020 and detection of mef (C)- mph (G) genes.

We described and characterized Shiga-toxin-producing Escherichia coli (STEC) strains with high levels of resistance to azithromycin isolated in France, between 2004 and 2020. Nine of 1715 (0.52%) STEC strains were resistant to azithromycin, with an increase since 2017. One isolate carried a plasmid-borne mef (C)- mph( G) genes association, described here for the first time in E. coli. Azithromycin resistance, although rare, needs consideration as this treatment may be useful in case of STEC infection.

The antimicrobial resistance landscape of Neisseria gonorrhoeae in New Zealand from November 2018 to March 2019 and the role of sexual orientation in transmission

The increasing use of culture independent diagnostic testing for the diagnosis of Neisseria gonorrhoeae infection has led to gaps in surveillance of antimicrobial resistance (AMR) rates due to limited availability of cultures. Our study reports the findings of a second national survey of N. gonorrhoeae in New Zealand, utilizing whole-genome sequencing (WGS) to study the population structure, prevalence of AMR, epidemiology and transmission of gonorrhoea isolates. We analysed 314 isolates and found a strong correlation between carriage of acquired resistance genes or chromosomal point mutations and phenotypic susceptibility testing results. Overall, the New Zealand rates of azithromycin resistance and decreased susceptibility to ceftriaxone remain lower than in most countries, which are part of the World Health Organization (WHO) Global Gonococcal Antimicrobial Surveillance Programme (GASP). The phylogeny provides evidence of a diverse population significantly associated with sexual behaviour groups. Transmission clustering with a ten single nucleotide polymorphism (SNP) cut-off identified 49 clusters, of which ten were solely associated with men who have sex with men (MSM), whereas remaining clusters included heterosexual patients, as well as MSM, suggesting that bridging of sexual networks is occurring. Utilizing pairwise SNP differences between isolates of the same sequence types we determined genetic variation for the three typing schemes used in this study [Multi locus sequence typing (MLST), multi-antigen sequence typing (NG-MAST), and sequence typing for antimicrobial resistance (NG-STAR)]. A median of 0.0 to 52.5 pairwise SNP differences within a single NG-STAR sequence type underlines previous findings of the superiority of the NG-STAR typing scheme in terms of genomic inherency. With our analysis incorporating epidemiological and genomic data, we were able to show a comprehensive overview of the N. gonorrhoeae population circulating in New Zealand, focussing on AMR and transmission within sexual networks. Regular surveillance studies to understand the origin, evolution and spread of AMR for gonorrhoea remain necessary to make informed decisions about public health guidelines, as the internationally rising rates of ceftriaxone and azithromycin resistance have already led to adaptation of current treatment guidelines in the UK and the USA, highlighting the importance of regular surveillance in individual countries.

Therapeutic Response of Community Acquired Pneumonia in Geriatrics: A Case Series from Intensive Care Unit

Community acquired pneumonia (CAP) is a common major growing challenge to elderly populations. Several aging factors, including comorbidities, nutritional status and digestive dysfunctions have been associated with increasing CAP among older persons. Furthermore, Streptococcus pneumoniae remains the most predominant pathogen in geriatrics, although multiple drug resistance (MDR) species regularly occur, particularly in severe pneumonia. Broad-spectrum antibiotics or a combination of β-lactam and fluorokuinolones, or β-lactams and macrolides serve as a promising therapy mainly in critical CAP patients. This study describes two geriatric CAP cases representing two separate treatments with widely varied results. The combination of cefoperazone sulbactam-azithromycin did not generate suitable clinical response until 7 days. As a consequence, the macrolides were replaced with amikacin and continued for 3 days. Meanwhile, the cefoperazone sulbactam-levofloxacin samples significantly improved the clinical conditions under 9 days. The selection of antibiotics with sufficient lung penetration is important in providing the effective therapy. Conversely, azithromycin resistance potentially instigates ineffectiveness, but is also recommended due to its pleiotropic effects. The benefit of this case study shows that CAP treatment among older population requires a blend of antibiotics with either a fluorokuinolone or an aminoglycoside. In both instances, azitromisin is believed to demonstrate high resistance, therefore, it is incapable in functioning as a second antibiotic component.

The Accuracy of Molecular Detection Targeting the Mutation C2611T for Detecting Moderate-Level Azithromycin Resistance in Neisseria gonorrhoeae: A Systematic Review and Meta-Analysis

Background: Neisseria gonorrhoeae (N. gonorrhoeae) is now recognized as a commonly reported sexually transmitted pathogen, and the increasing drug resistance of N. gonorrhoeae has become a serious public health problem. The accuracy of molecular detection for detecting moderate-level azithromycin resistance is not well-established. We summarized the data from studies of the N. gonorrhoeae 23S rRNA mutation at position 2611 with azithromycin resistance to determine the relationship between the mutation and resistance. Methods and Findings: In this systematic review and meta-analysis, two researchers independently searched six databases for studies with data for the azithromycin minimum inhibitory concentrations (MICs) and the 23S rRNA mutation C2611T of each N. gonorrhoeae isolate. Since the breakpoint of moderate-level resistance to azithromycin (ML-AzmR) was not determined, we divided the moderate level into two groups according to the range of MICs (moderate resistance limited to 2–128 mg/L or 4–128 mg/L) for data extraction. A random-effects model was used to calculate the pooled sensitivity rate, the specificity rate, the pooled positive likelihood ratio (PLR), the negative likelihood ratio (NLR), and the diagnostic odds ratio (DOR). Meta-regression analyses by detection method, isolates sampling (a random sample or not), location, and sample size were performed to explore the possible causes of heterogeneity. The potential publication bias of the included studies was conducted by the Deeks’ test. We included 20 studies in our study: 20 studies have data of N. gonorrhoeae with MICs between 2 and 128 mg/L with mutation or without mutation at position 2611(4759 samples), and 14 studies have data of N. gonorrhoeae with MICs between 4 and 128 mg/L (3367 samples). In the group with the moderate level of 2–128 mg/L, the pooled sensitivity rate of the molecular assays was determined to be 71.9% (95% CI, 67.6–74%), the pooled specificity rate was 98.7% (95% CI, 98.2–99.0%), and the DOR ranged from 55.0 to 351.3 (mean, 139.1). In the 4–128 mg/L group, the pooled sensitivity rate was 91.9% (95% CI, 88.9–94.2%), the pooled specificity rate was 95.9% (95% CI, 95.1–96.6%), and the DOR ranged from 41.9 to 364.1 (mean, 123.6). Conclusion: Through this meta-analysis, we found that the C2611T mutation of 23S rRNA is valuable for the molecular diagnostic of moderate-level azithromycin resistance (ML-AzmR) in N. gonorrhoeae, especially when the moderate level is set at 4–128 mg/L. This rapid molecular detection method can be used for the rapid identification of ML-AzmR isolates in the clinic.

Mycoplasma genitalium in Primary Care: Prevalence and azithromycin resistance in Santiago de Compostela Health Care Area

Objectives. Mycoplasma genitalium is associated with persistent/recurrent sexually transmitted infections. The aim of this work was to estimate the prevalence and azithromycin resistance of M. genitalium in general population that was attended at Primary Care of Santiago de Compostela Health Care Area. Material and methods. The study was carried out in 2019 in general population of Santiago de Compostela Health Care Area. Real-time multiplex PCR was used for screening of sexually transmitted infections associated pathogens and detection of mutations in the 23S rRNA gene. Results. A total of 502 women and 532 men were studied. The prevalence of M. genitalium was 2,4% in men and 2,9% in women. Overall azithromycin resistance was 20% all of them detected in men. The mutations found were A2059G, A2058G and A2058T. Conclusions. Although the proportion of M. genitalium infection is low, the high percentage of azithromycin resistance detected supports the relevance of these data in order to the right management of the patients with sexually transmitted diseases and, so as, to avoid the emergence of resistance in other pathogens of the urogenital tract.

Retrospective analysis of infection and antimicrobial resistance patterns of Mycoplasma genitalium among pregnant women in the southwestern USA

BackgroundMycoplasma genitalium is a sexually transmitted infection (STI) pathogen. There have been no published studies concerning symptomatology, prevalence data, antibiotic resistance profiling or reports of co-infection with other STI in pregnant women.ObjectiveTo describe these characteristics among pregnant women attending prenatal clinics in a large tertiary care centre.DesignRemnant genital samples collected from pregnant women between August 2018 and November 2019 were tested for M. genitalium and Trichomonas vaginalis by the transcription-mediated amplification technique. Specimens with detectable M. genitalium RNA were sequenced for 23S rRNA mutations associated with azithromycin resistance and parC and gyrA mutations associated with resistance to moxifloxacin. Demographic, obstetric and STI co-infection data were recorded.ResultsOf the 719 samples, 41 (5.7 %) were positive for M. genitalium. M. genitalium infection was associated with black race, Hispanic ethnicity and young age (p=0.003, p=0.008 and p=0.004, respectively). M. genitalium infection was also associated with T. vaginalis co-infection and Streptococcus agalactiae (group B Streptococcus) colonisation (p≤0.001 and p=0.002, respectively). Of the 41 positive samples, 26 (63.4%) underwent successful sequencing. Eight (30.8%) had 23S rRNA mutations related to azithromycin resistance. One of 26 (3.8%) positive samples with sequencing results had the gyrA gene mutation and 1 of 18 sequenced samples (5.6%) had the parC gene mutation associated with moxifloxacin resistance.ConclusionsPrevalence rates of M. genitalium in pregnant women was 5.7%. M. genitalium infection disproportionately affects young black women co-infected with T. vaginalis. Pregnant women remain at risk for persistent infection with M. genitalium due to decreased azithromycin susceptibility.